Lots of bad science still gets published. Here’s how we can change that.

Read the full story at Vox.

A new project aims to tackle the “replication crisis” by shifting incentives among scientists.

How a dangerous stew of air pollution is choking the United States

Read the full story in Nature.

Fires and droughts in the western states are getting worse — and they’re combining with industrial sources to threaten air quality and people’s health.

Why we need open-source science innovation — not patents and paywalls

A virology lab researcher works to develop a test that will detect the P.1 variant of the coronavirus, in São Paulo, Brazil, in March 2021. (AP Photo/Andre Penner)

by Joshua M. Pearce, Western University

As we prepare to invest money to prevent the next global pandemic and find solutions to many other problems, science funders have a large opportunity to move towards open science and more research collaboration by offering open-source endowed chairs.

In these research positions, professors agree to ensure all of their writing is distributed via open access — and they release all of their intellectual property in the public domain or under appropriate open-source licences.

The global scholarly publishing market has grown steadily and is now worth over US$28 billion. Researchers estimate universities are also able to capture billions through patent licensing, although most technology transfer offices at universities actually lose money.

But many academics want to see their research fully accessible — free for everyone. My research with colleagues has found the majority of American and Canadian academics want to see universities establish open-source endowed chairs.

How academics use intellectual property

Intellectual property (IP) refers to mind creations like patents and copyrights. Academics use all kind of IP. For example, professors publish their work as articles in peer-reviewed journals, the majority of which are under copyright.

If you have ever tried to read an academic paper, you probably couldn’t. Most academic papers are behind paywalls.

A red journal seen tipping off a shelf.
Most academic papers are behind paywalls. (Shutterstock)

To gain access through the paywalls costs an enormous amount of money for a library (even Harvard’s library balked at having to pay more than US$1 million per year to access articles from a single publisher).

At the beginning of the pandemic, when fast innovation was needed, most major publishers made their COVID-19 collections “open access,” which means everyone could read them for free. They did this to speed up innovation because it is obvious that paywalls slow science.

Accessible research in science matters because the more scientists that can read the relevant literature, the more scientists can help push innovations forward and the faster we are able to find solutions.

The open access movement is growing quickly. Authors must pay to make their work available in some open-access journals. Now, however, there are many respected peer-reviewed open-access journals that are free to publish in and free to read.

Patents hamper innovation

Many universities brag about the number of patents their professors write. Patents are supposed to encourage innovation because they give the inventor a 20-year monopoly to profit from an invention and this provides a financial incentive.

The basic idea is a professor would patent an invention that could be mass manufactured and then reap licence revenue for 20 years.

This does happen. However, a tidal wave of academic study after study, have shown that patents actively hamper innovation.

This is because most innovation builds on other ideas and there is no “fair use” for patents.

It is illegal to even experiment on a patented idea without a licence. If you need to wait 20 years to build on a good idea, it obviously takes a lot of time to innovate. Historically innovation moved rather slowly, now the rate of innovation is fast. Consider now how ancient a 20-year-old phone would be in your pocket.

Some academics like science and engineering professors do make money on patents for their universities. But the patent revenue they keep tends to be meager, because the costs to get the patent must first be recovered before the inventors get anything.

People stand next to fake coffins with signs that say 'drop the patents.'
Advocacy to drop patents grew in the pandemic, seen in the work of global justice campaigners standing by fake coffins to highlight COVID-19 deaths globally, in October 2021, in London. (AP Photo/Alastair Grant)

Open source is a better way

Open source is the answer to speeding up innovation. Open source originally was developed in the software industry as inventors would share the source code of computer programs to innovate faster.

Open source works amazingly well because having a lot of people work on a problem together tends to get a much better solution than a few.

Today open source is dominant in all supercomputers, 90 per cent of cloud servers, 82 per cent of smartphones and most artificial intelligence. Ninety per cent of the Fortune Global 500 use open-source software.

Study on university professors

The results of a survey study of university professors in Canada found 81.1 per cent of Canadian faculty would trade all IP for an open-source endowed chair and 34.4 per cent of these faculty would require no additional compensation. Surprisingly, even more American faculty (86.7 per cent) are willing to accept an open-source endowed professorship.

In both these studies, we presented participants with information about open-source endowed professorships to provide context and clarity for the subsequent multiple-choice and open-ended questions.

We looked at professors in every stage of their career (assistant to emeritus), tenured and non-tenured, at all types of universities (colleges to institutions with very high research activity), and in all disciplines including professional programs.

We analyzed results for three core disciplines of engineering/technology, natural sciences and social sciences to assess if there are differences in preferred compensation types among scholars of various disciplines.

The will to share was robust across all variables. Professors as a whole would be willing to make all of their IP freely available in exchange for the open-source endowed chair.

Accelerating innovation

I currently hold the John M. Thompson Chair in Information Technology and Innovation, and am one of the first endowed chairs to make an open-source commitment.

It is clear, even from my own work that has been sped along by many others freely contributing to my open-source projects, that science will move faster with open-source methods.

There is a clear willingness of academics to leave behind antiquated IP models for the good of science and society. It is time to provide incentives to accelerate innovation using open science to hasten scientific progress while also making science more just and inclusive.

All research funders — governments, foundations, private companies, donors and universities — should start funding open-source endowed chairs to maximize the impact of their resources.

Joshua M. Pearce, Department of Electrical and Computer Engineering, Western University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Bee study: Both habitat quality and biodiversity can impact bee health

Read the full story from the University of Michigan.

Efforts to promote the future health of both wild bees and managed honeybee colonies need to consider specific habitat needs, such as the density of wildflowers. At the same time, improving other habitat measures — such as the amount of natural habitat surrounding croplands — may increase bee diversity while having mixed effects on overall bee health.

Those are the key findings from a new analysis of several thousand Michigan bees from 60 species. The study looked at how the quality and quantity of bee habitat surrounding small farm fields affects the levels of common viral pathogens in bee communities.

Climate change in the forests of northern Germany

Read the full story from the University of Göttingen.

More and more trees are suffering the consequences of decades of human-made climate change. The growth of the European beech has so far suffered decline mainly in southern Europe. European beech is Germany’s most important native forest tree species and it is most commonly found in Central Europe.

A research team has now been able to show that the European beech is suffering from increasing drought stress in summer in northern Germany as well. This climate stress is particularly pronounced at warmer sites, when there is a higher density of these trees together, and on very sandy soils.

Post-lockdown auto emissions can’t hide in the grass

Read the full story from the University of California – Riverside.

University of California scientists have a new way to demonstrate which neighborhoods returned to pre-pandemic levels of air pollution after COVID restrictions ended.

Pandoravirus: the melting Arctic is releasing ancient germs – how worried should we be?

by Paul Hunter, University of East Anglia

Scientists have recently revived several large viruses that had been buried in the frozen Siberian ground (permafrost) for tens of thousands of years.

The youngest virus to be revived was a sprightly 27,000 years old. And the oldest – a Pandoravirus – was around 48,500 years old. This is the oldest virus ever to have been revived.

As the world continues to warm, the thawing permafrost is releasing organic matter that has been frozen for millennia, including bacteria and viruses – some that can still reproduce.

This latest work was by a group of scientists from France, Germany and Russia; they managed to reanimate 13 viruses – with such exotic names as Pandoravirus and Pacmanvirus – drawn from seven samples of Siberian permafrost.

Assuming that the samples were not contaminated during extraction (always difficult to guarantee) these would indeed represent viable viruses that had previously only replicated tens of thousands of years ago.

This is not the first time that a viable virus has been detected in permafrost samples. Earlier studies have reported the detection of a Pithovirus and a Mollivirus.

In their preprint (a study that is yet to be reviewed by other scientists), the authors state that it is “legitimate to ponder the risk of ancient viral particles remaining infectious and getting back into circulation by the thawing of ancient permafrost layers”. So what do we know so far about the risk of these so-called “zombie viruses”?

All the viruses cultured so far from such samples are giant DNA viruses that only affect amoebae. They are far from viruses that affect mammals, let alone, humans and would be very unlikely to pose a danger to humans.

However, one such large amoebae-infecting virus, called Acanthamoeba polyphaga mimivirus, has been linked to pneumonia in humans. But this association is still far from proven. So it does not appear that the viruses cultured from permafrost samples pose a threat to public health.

A more relevant area of concern is that as the permafrost thaws it could release the bodies of long-dead people who might have died of an infectious disease and so release that infection back into the world.

The only human infection that has been eradicated globally is smallpox and the reintroduction of smallpox, especially in hard-to-reach locations, could be a global disaster. Evidence of smallpox infection has been detected in bodies from permafrost burials but “only partial gene sequences” so broken bits of virus that could not infect anyone. The smallpox virus does, however, survive well when frozen at -20°C, but still only for a few decades and not centuries.

In the last couple of decades, scientists have exhumed the bodies of people who died from the Spanish flu and were buried in permafrost-affected ground in Alaska and Svalbard, Norway. The influenza virus was able to be sequenced but not cultured from the tissues of these deceased people. Influenza viruses can survive frozen for at least a year when frozen but probably not several decades.

Bacteria could be more of a problem

Other types of pathogen, such as bacteria, could be a problem, though. Over the years, there have been several outbreaks of anthrax (a bacterial disease that affects livestock and humans) affecting reindeer in Siberia.

There was a particularly large outbreak in 2016 that led to the deaths of 2,350 reindeer. This outbreak coincided with a particularly warm summer, which led to the suggestion that anthrax released from thawing permafrost may have triggered the outbreak.

Anthrax spores. Cultura Creative Ltd / Alamy Stock Photo

Identified outbreaks of anthrax affecting reindeer in Siberia date back to 1848. In these outbreaks, humans were also often affected from eating the dead reindeer. But others have highlighted alternative theories for these outbreaks that do not necessarily rely on thawing permafrost, such as stopping anthrax vaccination and overpopulation by reindeer.

Even if permafrost thawing was triggering anthrax outbreaks that had serious effects on the local population, anthrax infection of herbivores is widespread globally, and such local outbreaks are unlikely to trigger a pandemic.

Another concern is whether antimicrobial-resistant organisms could be released into the environment from thawing permafrost. There is good evidence from multiple studies that antimicrobial resistance genes can be detected in samples of permafrost. Resistance genes are the genetic material that enable bacteria to become resistant to antibiotics and can be spread from one bacterium to another. This should not be surprising as many antimicrobial resistance genes have evolved from soil organisms that predate the antimicrobial era.

However, the environment, especially rivers, is already heavily contaminated with antimicrobial-resistant organisms and resistance genes. So it is doubtful that antimicrobial resistance bacteria thawing from the permafrost would contribute greatly to the already great abundance of antimicrobial resistance genes already in our environment.

Paul Hunter, Professor of Medicine, University of East Anglia

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Dr. Veronica Mengqi Zhang: Gaining resourcess Support & opportunities through the GCC community

Read the full story from Beyond Benign.

Dr. Veronica Mengqi Zhang joined Michigan State University (MSU) as the Organic Chemistry Laboratory Coordinator and has been working on implementing and refining the reformed laboratory curriculum towards cooperative learning and green chemistry. As a Green Chemistry Commitment (GCC) signer, MSU has prioritized green chemistry education and knowledge sharing for several years.

In this Q&A, Dr. Zhang shares her story about being part of the GCC community.

Earth and Space Science Open Archive takes a big step forward

Read the full story from EOS.

Over the past four years, the Earth and Space Science (ESS) Open Archive has preserved over 10,000 early research outputs – preprints, posters, and presentations – contributed by nearly 37,000 authors across 25 subject areas. Now, ESS Open Archive is moving to a different platform supported by Authorea. Nick Violette, AGU Senior Program Manager for Publications and ESS Open Archive, spoke with the Editor in Chief, Jonathan Jiang, about how these new features will serve the community.

Expired foods get new life from budget shoppers as inflation soars, but are they safe?

Read the full story at USA Today.

Household budgets are being squeezed by the highest inflation in a generation. Food prices are a particular concern. That’s making people look for ways to save on food. One answer is finding stores that sell expired or nearly expired foods.