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Excess mortality or excessive assumptions?

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Which country escaped the worst of the COVID pandemic?

A recent article by the Directors of the US National Institutes of Health gave a confident answer. It claimed that Sweden ‘was the best in the world at protecting human life during the Covid pandemic. It had the lowest level of age-adjusted, all-cause excess deaths in the world between March 2020 and December 2024.’

Excess mortality is commonly quoted when comparing the impact of COVID in different countries. The metric is often reported as if hard data, but it’s actually the output of a scenario model – and it can depend on some very strong assumptions.

Let’s start with the graph the above article links to1. In this plot, Sweden comes out with lowest cumulative excess mortality among the comparators considered, even above New Zealand by the end of 2024:

Notice anything unusual about the above plot? In particular, look at the sign of cumulative excess mortality: it is negative for both Sweden and New Zealand. It’s well established that New Zealand had a drop in mortality in 2020-21, given reduction in other seasonal infections. But is it really plausible that Sweden would have seen more mortality over the past six years had the COVID pandemic not happened?

‘The death-rate is a fact; anything beyond this is an inference.’ –William Farr (1807-1883)

Mortality is something that can be measured. But excess mortality is a hypothetical comparison. It asks: how many more deaths occurred than expected? Which requires that we come up with some model of what ‘expected’ looks like.

To illustrate the challenge, here is Sweden mortality from 2010-19. What would we have expected to happen in 2020-24 without the COVID pandemic?

The excess mortality plot earlier used the average mortality in 2017-19 as the baseline for what would have been ‘expected’. But you’ll notice that 2018 and especially 2019 were quite a lot lower than 2017, so taking the average fixes the ‘expected’ baseline at quite a high level. Hence post-2020, this assumption leads to Sweden having a substantially negative excess mortality.

But is a fixed baseline really that plausible if there’s a downward trend in mortality prior to 2020? What if we instead fit a linear trend to 2017-19 and use that as the expectation? Under this assumption, the actual mortality in Sweden ended up much higher than the expected trend:

This subtle difference in assumptions about the baseline matters. If we use the first assumption, with a fixed baseline, then Sweden has very low – and negative – excess mortality, lower than nearby countries and New Zealand.

If we instead use a linear trend as the post-2020 baseline for all countries, Sweden ends up with a much higher – and positive – excess, with all the others lower:

Because excess mortality calculations can be so sensitive to the baseline assumption we choose, and we are effectively extrapolating from a short time series (2017-19) to a longer time period (2020-24), it’s possible to cherry-pick baselines that can generate all sorts of different rankings.

For example, if we pick 2018-19 for the linear trend baseline, then Sweden comes out worse than even the US:

In contrast, if we pick a (totally arbitrary and unjustified) 2013-15 period for the linear trend to extrapolate from, we could even make New Zealand come out with the highest excess mortality of the three, and the US with the lowest:

This doesn’t mean it’s impossible to say anything at all about the impact of the pandemic, and we should all just cherry-pick our favourite baseline. Regardless of the assumption we use, Sweden was hit hard by COVID in 2020, like many other countries in Europe. It’s the extrapolation beyond this point that becomes very sensitive to assumptions.

We can use statistical models to identify which trend assumption might be more or less plausible given the data. For example, if we fit a generalised additive model (i.e. a flexible extension of a linear regression), it suggests there is evidence for a near-linear decline as the most reasonable expectation:

However, that low 2019 data point makes it difficult to be confident. If we focus only on data from 2015-19 instead, we get a steeper downward trend, which would produce a higher estimate of excess mortality:

It’s somewhat ironic that the country in Europe that was an outlier in its COVID response also had an outlier mortality data point immediately before the pandemic, making it near impossible to reliably compare it to other countries.

This is a useful reminder that excess mortality is not data. It is a scenario model for a reality that didn’t happen – and it depends a lot on the assumptions we make along the way.

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sarcozona
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Hiltzik: It's not too soon to talk about the post-Trump era - Los Angeles Times

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  • Scientists warn that federal agencies and research institutions affected by Trump’s systematic dismantling could take a generation or longer to rebuild.
  • Key agencies such as the Centers for Disease Control and Prevention have been so damaged that future administrations may need to start completely from scratch.
  • Economic warning signs are mounting as inflation rises and unemployment climbs to its highest level since the COVID-19 pandemic.

The all-purpose adage offering optimism — and sometimes pessimism — to those confronting a crisis head-on is: “This too shall pass.”

One gets the impression that this is a crutch favored by some major institutions that have capitulated to Donald Trump’s demands — such as universities that have committed to fines and payouts stretching out beyond the end of Trump’s current (and final) term, and law firms that have made nebulous commitments to represent Trump’s favored litigants in cases that may not even be brought until after the 2028 elections.

Some institutions and services that have suffered major cuts in government funding may be tempted to hunker down, covering what they think may be a temporary shortfall in the expectation that a subsequent administration will restore the withheld funding and cover their interim losses. Recovery, however, may be tougher than they think.

‘The best-case scenario is that we limp along for the next three and a half years. ... But that’s just a hope.’

— Jonathan Howard, New York University neurologist

I reached out to some of my most trusted contacts in science, medicine, labor and other fields, hoping to hear encouragement that the current situation will be fleeting and it isn’t too soon to look ahead; Trump’s presidential term, after all, is finite.

I ended up with a string of the gloomiest conversations in my long career — and I’ve covered two foreign civil wars and more stock market crashes and economic slumps than I can count. (Well, let’s say more than a dozen.)

“We’re still in free fall and people are still in a ‘shock and awe’ phase,” said vaccinologist Peter Hotez, who has written to defend sound science throughout Trump’s terms. “What’s happening right now is continuing to evolve, and we don’t really know where it’s going. It’s important not to take the attitude of ‘this too will pass,’ hunker down for a couple of years and then it will go back to the way it was.”

The administration’s cuts in biomedical research funding, the “continuing ascendance of the MAHA movement” — Robert F. Kennedy Jr.’s disdain for accepted science in favor of pseudoscience — betokens a dark period ahead, Hotez told me. “Even if these things stop tomorrow, you’ve got a pretty demoralized physician and scientific workforce. What this administration has done has given being a scientist an unsavory element — it’s no longer a noble profession.”

Of particular concern is the administration’s injection of partisan ideologies into the scientific grant-making process, shattering applicants’ confidence that their submissions are considered fairly. The scoring of grant applications by professional panels used to be the key element in the process.

“Now, even if you get a fundable score,” Hotez said, “there’s still somebody behind the curtain who still could nix it for ideological reasons. And even if your first year is funded, there’s no guarantee for out years.”

The uncertainty could hamstring scientific research for a generation, or longer.

“How easy is it to rebuild a lab that’s been hit by cuts?” said John P. Moore, a professor of microbiology and immunology at Weill Cornell Medical College, where labs have been hobbled by the administration’s toying with grants. “The answer is it’s very difficult, once you lose key members of a research group, who are often the senior technicians who have institutional memory and keep a program going day to day. At a certain point, a freeze or a termination is not reversible.”

Moore also pointed to the consequences of a loss of foreign-born scientists. “America is now not a welcoming country for immigrants, period. Scientists who are here on short-term visas are realizing that their future is not in this country. Other countries are seeking to suck up talent that otherwise would have come here. That’s going to have an impact over time, and it’s not going to be easy to reverse.”

In my conversations with scientists, one name kept coming up: Trofim Lysenko, the charlatan whose reign over Soviet science during Stalin’s regime from the 1930s to the 1960s and whose promotion of an anti-science ideology, especially a campaign against genetics research, encompassed repeated crop failures and famines costing some 7 million lives. I made the connection between Lysenkoism and Trump’s appointment of Robert F. Kennedy Jr. to head the Department of Health and Human Services in November.

“The Soviet Union did everything they could to invest back in science and genetics and molecular biology, but it was still stagnant,” said Angela Rasmussen, a leading American virologist now working in Canada. “But despite the attempts to rebuild what Lysenko had torn down, they were never able to compete with people everywhere else because they had lost so much by shutting down all genetics research during that time.”

Three factors could be lasting obstacles: Trump’s undermining of federal employment, of the law and of the economy.

Trump has systematically demoralized the workforce responsible for enforcing the regulations that remain. That’s the observation of David Weil, a labor expert at Brandeis University whose nomination by President Biden for a top-level post at the Department of Labor was sidelined by conservative opposition in 2022.

The law has been a thin reed to lean on, Weil observes. A key example is the attack by Elon Musk’s SpaceX on the National Labor Relations Board, which garnered an opinion from the notoriously right-wing 5th Circuit Court of Appeals last month finding that the NLRB’s structure “violates the separation of powers” established by the Constitution. That’s a remarkable finding, given that the NLRB was established 90 years ago, in 1935.

“If the Supreme Court upholds the 5th Circuit,” Weil told me, “that’s the end of the NLRA,” the act that established the board, “and we go back to a system where there’s no federal statutory method for protecting private sector workers.”

What Weil finds especially disquieting is the Supreme Court’s practice of allowing Trump to continue challenged policies while the underlying issues are litigated. “Instead of letting the status quo to prevail until we adjudicate the issues, they’re letting Trump prevail until they adjudicate. That, to me, is a formula for destruction. How do you rebuild then?”

The court has done this by lifting the stays on Trump policies imposed by lower courts, pending further rulings. That’s what happened as recently as Monday, when the court overturned a Los Angeles federal judge’s order that had barred “roving patrols” of immigration officers from snatching people off Southern California streets based on how they look, what language they speak, what work they do or where they happen to be.

One issue casting a shadow over all others is the future course of Trump’s economy. At this moment, the warning signs are all flashing red. Inflation is on the rise — core inflation as measured by the personal consumption index, the Federal Reserve’s preferred metric, rose in July to an annualized rate of 2.9%, the highest rate since February; economists expect the rate to keep rising as businesses pass through more of their tariff-related costs to consumers.

Meanwhile, new hiring has ground to a screeching halt, according to the latest government statistics. The unemployment rate notched up to 4.3% in July, not the direction Trump would like to see. The rate hasn’t been this high since the pandemic year of 2021.

Trump also has remade the government’s relationship with industry, extracting a fee from the AI chipmaker Nvidia of 15% of its revenue from selling chips to China and taking a 9.9% equity stake in the faltering chipmaker Intel. That’s not the first time the government has owned a piece of a public company — it owned most of GM during the Great Recession, but later sold its stake; Trump is talking about making a habit of these buy-ins through a sovereign wealth fund, an idea that’s far from universally favored by political leaders and economists.

Trump’s rampage through government agencies, especially those devoted to science, health and the economy, has left some so severely damaged that fixing what’s broken might require the establishment of a Cabinet-level post to oversee the repair job.

Consider the state of the Centers for Disease Control and Prevention, where five top officials resigned or were forced out late last month — including CDC Director Susan Monarez, who was fired after less than a month on the job after tangling with Kennedy. Anyone tasked by a future administration with rebuilding the CDC, which once set the global gold standard for public health, will have to be told: “You know you’ll be starting from scratch, right?”

It’s only fair to say that the GOP hasn’t had a monopoly on philistine attacks on scientific research. The pioneer of such cocksure philistinism was Sen. William Proxmire (D-Wis.), who started issuing his “Golden Fleece” awards in 1975. Proxmire became addicted to the fawning press attention he got from caricaturing serious scientific research as ludicrous. His know-nothing rabble-rousing appalled progressives who otherwise admired him for his principled stands against the Vietnam War and in favor of campaign finance reform.

But its more lasting and destructive effect was to render political attacks on scientific research acceptable. Proxmire’s goal was personal aggrandizement. The goal of the current attackers is more sinister — they’re engaged in an anti-science campaign for strictly ideological purposes.

“The best-case scenario is that we limp along for the next three and a half years,” said Jonathan Howard, a neurologist at New York University and a practiced debunker of the pseudoscience that contaminated efforts to fight the pandemic. “Good people stay on and do good work the best they can and we get a reprieve in three and a half years and the amount of damage they’re able to do is limited in that time. But that’s just a hope.”

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sarcozona
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How to bury your father • Buttondown

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rocketo
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“To live it in such a way that our life is filled with love, and to live it in such a way that we become intertwined with other lives that we can fill with love and they, in turn, replenish our own lives with love.”

jfc this essay
seattle, wa
sarcozona
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All of the betters

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After our 24-year-long marriage ended in divorce, barely three months later my Republican ex-husband brought his Singaporean girlfriend and her 14 year old son to his family’s Thanksgiving gathering.

These are, simply, facts.

I feel so settled in my house now. I feel so settled in my new LIFE now. A few weeks ago out at the barn I adjusted my stirrups so they are one notch shorter and I could not believe what a difference that made riding, like I was finally in the perfect alignment and felt so deep and confident on Little Joe’s back. I don’t know why that took me two whole years to figure out, but it’s so good now. I thought I was comfortable, but I wasn’t. I thought I was steady, but it’s so much better now.

I drink better coffee. I sleep better. I go on better walks. I have a better social life. I feel better about myself. I feel better about how I move through the world.

I will always remember and honor the good times because there were plenty, but I see now how I was living. How I did not realize just how much better my life could be. I was so afraid to leave the comfort I had, I didn’t know it was like riding wrong in the saddle. You think it’s fine until you feel something better, and then that just blows your whole world wide open.

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sarcozona
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Scientists Thought Parkinson’s Was in Our Genes. It Might Be in the Water | WIRED

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After a century of putting genetics on a pedestal, the geneticists have some surprising news for us: The vast majority of chronic disease isn’t caused by our genes. “The Human Genome Project was a $3 billion investment, and what did we find out?” says Thomas Hartung, a toxicologist at Johns Hopkins. “Five percent of all disease is purely genetic. Less than 40 percent of diseases even have a genetic component.”
Most of the conditions we worry about, instead, stem from a complex interaction between our genes and our environment.
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sarcozona
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Violence over water resources reaches record levels

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There is growing evidence that climate change is worsening the severity of extreme floods and droughts, contributing to the global increase in water violence. (Photo by Chamika Jayasri on Unsplash)

On November 28, 2024, Russian missile attacks cut water and electricity to 280,000 people in the Rivne region of Ukraine. On the same day, thousands of miles away, a mother and her daughter were assaulted by their neighbors in a dispute over access to water in Panvel, India. The following day, explosives planted in a canal in Kosovo destroyed critical water infrastructure and cut water and power to cities across the country in an attack Kosovo attributed to Serbia. On December 1, forces opposed to the Syrian government of Assad seized the main water pumping plant for Aleppo, the largest city in Syria, and cut off water to the city.

These events are just a few of the 420 violent events over water resources reported in 2024 in the newly updated Water Conflict Chronology, which tracks incidents where water has been a trigger, casualty, or weapon of conflict. That database now includes over 2,750 documented cases of water conflicts, spanning thousands of years. Violence over water has reached record levels, continuing the increase in such events over the past two decades. The number of incidents reported in 2024 was nearly 20 percent higher than 2023 and nearly 80 percent higher than 2022, reflecting a steep growth in such incidents.

Water conflicts reported in the Water Conflict Chronology, categorized as casualty, trigger, or weapon, showing the dramatic increase in the past 15 years. Some events are included in multiple categories.

Violence over water has been reported around the world, in every region, including events where access to or control of water resources triggers conflict and where water or water systems are used as weapons or targets of war and armed conflict. Almost a third of the events reported in 2024 occurred in the conflicts between the Israelis and Palestinians and in the Russia-Ukraine war, where civilian water systems, dams, treatment plants, and energy supplies critical for providing safe water have been repeatedly attacked. There has also been a substantial increase in conflicts between farmers and pastoralists in sub-Saharan Africa, between cities and rural areas over diversions of rivers and overpumping of groundwater, and between clans and even families over access to scarce water resources.

Cyberattacks on water utilities are also increasing, where hackers—often working for foreign governments—have sought to gain control over water treatment and delivery plants. In January 2024, a pro-Russia hacktivist group accessed control systems at two Texas water facilities and tampered with controls and alarms. In a survey of 350 US and UK water and electric utilities, more than three-fifths reported being targeted by cyberattacks, with a majority reporting serious disruption or corruption of data or systems.

There is also growing evidence that climate change is worsening the severity of extreme floods and droughts, contributing to growing water violence. As temperatures rise and as climate disruptions worsen, water resources are particularly vulnerable. In southern Asia, local protests over water scarcity and drought and fights over water access have been reported. Extreme drought in Iran, worsened by recent heatwaves, threatens to completely dry up Tehran’s water supply, while water diversions from rural areas to Iranian cities have repeatedly provoked protests and riots over the past several years, with many injuries and deaths reported. At the same time, tensions between Iran and Afghanistan are growing over the shared Helmand River, with several instances of armed conflicts along the border.

It is urgent that efforts be made to reduce the threat of water-related conflicts and to reverse the worsening trend of water violence. Accelerating efforts to meet basic human needs for safe water and sanitation universally, already an objective of the UN Sustainable Development Goals, will reduce conflicts triggered by water poverty and disputed water rights. International laws like the Geneva Convention and its Protocols, which are supposed to protect civilian water systems from attacks during wars, are being flouted. They should be aggressively enforced and violators prosecuted by the International Criminal Court in The Hague. Hundreds of rivers and aquifers cut across national borders, and countries that share these watersheds should negotiate treaties that allocate water equitably among the parties and include tools and approaches for peacefully resolving disputes. Even where treaties exist, such as between the United States and Mexico on the Rio Grande, climate change and drought are threatening both diplomatic disputes and violence over water deliveries. The nations of the world have just concluded another round of disappointing negotiations at COP30 in Brazil and must accelerate efforts to slow and reverse climate change and to improve the resilience of water systems against those climate impacts that can no longer be avoided.

Although water has increasingly become a source of violence and conflict, underscoring the need for international attention, water can also be a source of cooperation and peace if nations, communities, and water institutions acknowledge the problem and work to ensure access to safe, affordable water for all. But first, global leaders need to be willing to abide by and enforce international laws and principles protecting the world’s water.

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sarcozona
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