By Ted Smillie on Tuesday, July 28th, 2020
Features in QESP NewsletterVolume 32 , Issue 7 - ISSN 1325-2070
Stanford University. “Researchers develop a method for predicting unprecedented events.” ScienceDaily. ScienceDaily, 23 July 2020.
“Researchers combined avalanche physics with ecosystem data to create a computational method for predicting extreme ecological events. The method may also have applications in economics and politics”
(QESP Editor’s Note: The following is a reprint of a 23 July 2020 ScienceDaily article from Stanford University. The original, with links to related material, is available at www.sciencedaily.com/releases/2020/07/200723143755.htm)
A black swan event is a highly unlikely but massively consequential incident, such as the 2008 global recession and the loss of one-third of the world’s saiga antelope in a matter of days in 2015. Challenging the quintessentially unpredictable nature of black swan events, bioengineers at Stanford University are suggesting a method for forecasting these supposedly unforeseeable fluctuations.
“By analyzing long-term data from three ecosystems, we were able to show that fluctuations that happen in different biological species are statistically the same across different ecosystems,” said Samuel Bray, a research assistant in the lab of Bo Wang, assistant professor of bioengineering at Stanford. “That suggests there are certain underlying universal processes that we can take advantage of in order to forecast this kind of extreme behavior.”
The forecasting method the researchers have developed, which was detailed recently in PLOS Computational Biology, is based on natural systems and could find use in health care and environmental research. It also has potential applications in disciplines outside ecology that have their own black swan events, such as economics and politics.
“This work is exciting because it’s a chance to take the knowledge and the computational tools that we’re building in the lab and use those to better understand — even predict or forecast — what happens in the world surrounding us,” said Wang, who is senior author of the paper. “It connects us to the bigger world.”
From microbes to avalanches
Over years of studying microbial communities, Bray noticed several instances where one species would undergo an unanticipated population boom, overtaking its neighbors. Discussing these events with Wang, they wondered whether this phenomenon occurred outside the lab as well and, if so, whether it could be predicted.
In order to address this question, the researchers had to find other biological systems that experience black swan events. The researchers needed details, not only about the black swan events themselves but also the context in which they occurred. So, they specifically sought ecosystems that scientists have been closely monitoring for many years.
“These data have to capture long periods of time and that’s hard to collect,” said Bray, who is lead author of the paper. “It’s much more than a PhD-worth of information. But that’s the only way you can see the spectra of these fluctuations at large scales.”
Bray settled on three eclectic datasets: an eight-year study of plankton from the Baltic Sea with species levels measured twice weekly; net carbon measurements from a deciduous broadleaf forest at Harvard University, gathered every 30 minutes since 1991; and measurements of barnacles, algae and mussels on the coast of New Zealand, taken monthly for over 20 years.
The researchers then analyzed these three datasets using theory about avalanches — physical fluctuations that, like black swan events, exhibit short-term, sudden, extreme behavior. At its core, this theory attempts to explain the physics of systems like avalanches, earthquakes, fire embers, or even crumpling candy wrappers, which all respond to external forces with discrete events of various magnitudes or sizes — a phenomenon scientists call “crackling noise.”
Built on the analysis, the researchers developed a method for predicting black swan events, one that is designed to be flexible across species and timespans, and able to work with data that are far less detailed and more complex than those used to develop it.
“Existing methods rely on what we have seen to predict what might happen in the future, and that’s why they tend to miss black swan events,” said Wang. “But Sam’s method is different in that it assumes we are only seeing part of the world. It extrapolates a little about what we’re missing, and it turns out that helps tremendously in terms of prediction.”
Forecasting in the real world
The researchers tested their method using the three ecosystem datasets on which it was built. Using only fragments of each dataset — specifically fragments which contained the smallest fluctuations in the variable of interest — they were able to accurately predict extreme events that occurred in those systems.
They would like to expand the application of their method to other systems in which black swan events are also present, such as in economics, epidemiology, politics and physics. At present, the researchers are hoping to collaborate with field scientists and ecologists to apply their method to real-world situations where they could make a positive difference in the lives of other people and the planet.
This research was funded by the Volkswagen Foundation and Arnold and Mabel Beckman Foundation. Wang is also a member of Stanford Bio-X and the Wu Tsai Neurosciences Institute.
- Samuel R. Bray, Bo Wang. Forecasting unprecedented ecological fluctuations. PLOS Computational Biology, 2020; 16 (6): e1008021 DOI: 10.1371/journal.pcbi.1008021
Cite This Page:
Stanford University. “Researchers develop a method for predicting unprecedented events.” ScienceDaily. ScienceDaily, 23 July 2020. www.sciencedaily.com/releases/2020/07/200723143755.htm
As if space wasn’t dangerous enough, bacteria become more deadly in microgravity
July 24, 2020 by Vikrant Minhas, PhD candidate, University of Adelaide
Vikrant Minhas is a co-founder of the space research company ResearchSat
(QESP Editor’s Note: The full article, with photographs and links to related material, is available on The Conversation, see
China has launched its Tianwen-1 mission to Mars. A rocket holding an orbiter, lander and rover took flight from the country’s Hainan province yesterday, with hopes to deploy the rover on Mars’s surface by early next year.
Similarly, the launch of the Emirates Mars Mission on Sunday marked the Arab world’s foray into interplanetary space travel. And on July 30, we expect to see NASA’s Mars Perseverance rover finally take off from Florida.
For many nations and their people, space is becoming the ultimate frontier. But although we’re gaining the ability to travel smarter and faster into space, much remains unknown about its effects on biological substances, including us.
While the possibilities of space exploration seem endless, so are its dangers. And one particular danger comes from the smallest life forms on Earth: bacteria.
Bacteria live within us and all around us. So whether we like it or not, these microscopic organisms tag along wherever we go – including into space. Just as space’s unique environment has an impact on us, so too does it impact bacteria.
We don’t yet know the gravity of the problem
All life on Earth evolved with gravity as an ever-present force. Thus, Earth’s life has not adapted to spend time in space. When gravity is removed or greatly reduced, processes influenced by gravity behave differently as well.
In space, where there is minimal gravity, sedimentation (when solids in a liquid settle to the bottom), convection (the transfer of heat energy) and buoyancy (the force that makes certain objects float) are minimised.
It’s not yet fully understood how such changes impact lifeforms.
How bacteria become more deadly in space
Worryingly, research from space flight missions has shown bacteria become more deadly and resilient when exposed to microgravity (when only tiny gravitational forces are present).
More research is needed to examine whether such adaptations do, in fact, allow the bacteria to cause more disease.
Bacterial team work is bad news for space stations
Research has shown space’s microgravity promotes biofilm formation of bacteria.
Biofilms are densely-packed cell colonies that produce a matrix of polymeric substances allowing bacteria to stick to each other, and to stationary surfaces.
Biofilms increase bacteria’s resistance to antibiotics, promote their survival and improve their ability to cause infection. We have seen biofilms grow and attach to equipment on space stations, causing it to biodegrade.
For example, biofilms have affected the Mir space station’s navigation window, air conditioning, oxygen electrolysis block, water recycling unit and thermal control system. The prolonged exposure of such equipment to biofilms can lead to malfunction, which can have devastating effects.
Another affect of microgravity on bacteria involves their structural distortion. Certain bacteria have shown reductions in cell size and increases in cell numbers when grown in microgravity.
In the case of the former, bacterial cells with smaller surface area have fewer molecule-cell interactions, and this reduces the effectiveness of antibiotics against them.
Moreover, the absence of effects produced by gravity, such as sedimentation and buoyancy, could alter the way bacteria take in nutrients or drugs intended to attack them. This could result in the increased drug resistance and infectiousness of bacteria in space.
All of this has serious implications, especially when it comes to long-haul space flights where gravity would not be present. Experiencing a bacterial infection that cannot be treated in these circumstances would be catastrophic.
The benefits of performing research in space
On the other hand, the effects of space also result in a unique environment that can be positive for life on Earth.
For example, molecular crystals in space’s microgravity grow much larger and more symmetrically than on Earth. Having more uniform crystals allows the formulation of more effective drugs and treatments to combat various diseases including cancers and Parkinson’s disease.
Also, the crystallisation of molecules helps determine their precise structures. Many molecules that cannot be crystallised on Earth can be in space.
So, the structure of such molecules could be determined with the help of space research. This, too, would aid the development of higher quality drugs.
Optical fibre cables can also be made to a much better standard in space, due to the optimal formation of crystals. This greatly increases data transmission capacity, making networking and telecommunications faster.
As humans spend more time in space, an environment riddled with known and unknown dangers, further research will help us thoroughly examine the risks – and the potential benefits – of space’s unique environment.
Australian Government sued by 23-year-old Melbourne student over financial risks of climate change
By national science, technology and environment reporter Michael Slezak and the Specialist Reporting Team’s Rahni Sadler July 23 2020
(QESP Editor’s Note: The full article, with photographs and links to related material, is available at https://www.abc.net.au/news/2020-07-22/student-sues-australian-government-over-climate-change/12480612)
“A 23-year-old Melbourne law student is suing the Australian Government for failing to disclose the risk climate change poses to Australians’ super and other safe investments.
The world-first case filed on Wednesday in the Federal Court alleges the Government, as well as two government officials, failed in a duty to disclose how climate change would impact the value of government bonds.
Katta O’Donnell, the head litigant for the class action suit, said she hoped the case would change the way Australia handled climate change.
“I’m suing the Government because I’m 23 [and] I think I need to be aware of the risks to my money and to the whole of society and the Australian economy,” Ms O’Donnell said.”
“I think the Government needs to stop keeping us in the dark so we can be aware of the risks that we’re all faced with.”
Experts say it is the first where a national government has been sued for its lack of transparency on climate risks.
Government bonds are considered the safest form of investment, with most Australians invested in them through compulsory superannuation.
Bonds are similar to shares, but instead of investing in companies, the investor lends a government money to build infrastructure and fund critical services such as health, welfare and national security.
Ms O’Donnell, who has invested in bonds independently from her super, said she did it to “protect her future”.
However bonds, like shares, can lose value if they become less attractive to the market. This can occur if investors question a government’s ability to repay them due to rising government debt, ethical or reputational reasons.
Ms O’Donnell said watching the impact of bushfires in Australia made her worry about the value of her bonds.
Despite the Government not disclosing climate-related risks to its investment products, government regulators are increasingly forcing companies to disclose how climate change will impact their shareholders.
APRA — the Australian financial industry regulator — said in 2017 that climate change was not only a “foreseeable” risk, but also “material and actionable now”.
APRA is working with corporate regulator ASIC and the Reserve Bank of Australia to ensure public companies are examining climate risk, disclosing it to investors, and acting on it.
Ms O’Donnell’s lawyer, David Barnden from Equity Generation Lawyers, said the duty to be transparent extended to the Government.
“We allege that the Government is misleading and deceiving investors by not telling them about the risks,” Mr Barnden said.
“We don’t see any disclosure to investors about the risks that climate change poses to bonds and to society as a whole. So it certainly appears as though there is a double standard.”
No damages, just recognition
Ms O’Donnell’s case names the Commonwealth, as well as the secretary to the Department of Treasury and the chief executive of the Australian Office of Financial Management — both of whom are alleged to be responsible for promoting government bonds.
The case is a class action, with Ms O’Donnell representing all investors and potential investors in government bonds tradeable on the Australian Securities Exchange.
It does not seek damages, but instead a declaration that the Government and those two officials breached their duty.
It also seeks an injunction, forcing the Government to stop promoting bonds until it updates its disclosure information to include information about Australia’s climate change risks.
The case is backed by heavy-hitting silk and former Federal Court judge Ron Merkel and barrister Thomas Wood, who was previously the counsel assisting the solicitor-general of the Commonwealth.
A spokesman for the Australian Government Treasury said it did not comment on matters concerning current court proceedings.
Australia a climate litigation ‘hotspot’
According to University of Melbourne Professor Jaqueline Peel, Australia is a “hotspot” for climate litigation.
“We have around 90 or so cases so far, stretching back to the 1990s,” Professor Peel, who has published extensively on the topic, said.
“Only the US has more. But we’ve never seen a case like this brought forward in Australia, [or] the world.
“It could potentially be very significant because it ties climate change to real-world financial risk which might make those in the financial sector, investors, sit up and take notice.”
She said it could force the Government to take more action on climate change and spur on a new wave of climate litigation around the world by showing private-sector cases had the potential to be brought against governments.
“This has the potential to be big news around the world,” she said.
Australian government bonds ‘exposed’
Most super funds have a significant portion of the public’s money invested in them, with a fixed interest rate.
But they are often also tradeable and if demand drops it could lower the value of the bonds, impacting investors, including super funds here.
Former NAB chief economist Rob Henderson said Australians needed to consider the impact of climate change.
“Australian government bonds are significantly more exposed [to climate change] than some other countries,” Mr Henderson said.
Mr Henderson said Australian government bonds could be impacted by physical impacts of climate change, like bushfires, which forced governments to spend money.
Or they could be impacted by “reputational risks” of climate change, as investors around the world avoided bonds from polluting countries.
Sweden’s central bank has already divested from Western Australian government and Queensland government bonds because of climate change.
In November 2019, the deputy governor of the Swedish central bank, Martin Floden, said it was dumping those bonds, as well as bonds from the oil-rich Canadian province of Alberta.
“Australia and Canada are countries that are not known for good climate work,” he said.
The move was described by former Liberal MP Bronwyn Bishop as a form of “protectionism”.
Mr Henderson said he was surprised a case like this had not been brought before.
“It’s not clear to me why already the Government is not putting those risks on the table and telling us what they’re going to do about them.”
University of California – Davis. “Brain builds and uses maps of social networks, physical space, in the same way.” ScienceDaily. ScienceDaily, 22 July 2020.
(QESP Editor’s Note: The following is a reprint of a 22 July 2020 ScienceDaily article from University of California – Davis. The original, with photographs and links to related material, is available at www.sciencedaily.com/releases/2020/07/200722112657.htm )
Even in these social-distanced days, we keep in our heads a map of our relationships with other people: family, friends, coworkers and how they relate to each other. New research from the Center for Mind and Brain at the University of California, Davis shows that we put together this social map in much the same way that we assemble a map of physical places and things.
“When we’re learning to navigate the real world, we don’t start off by seeing a whole map,” said Erie Boorman, assistant professor at the Center for Mind and Brain and UC Davis Department of Psychology. “We sample the world and reconstruct it.” The work is published July 22 in the journal Neuron.
Research has shown that animals navigate using a representation of the outside world in their brain. Whether rats in a maze or people in a new city, they build this internal map in pieces then stitch them together. That work earned a Nobel Prize for Physiology or Medicine for John O’Keefe, May-Britt Moser and Edvard Moset in 2014.
Boorman and UC Davis colleagues Seongmin Park, Douglas Miller and Charan Ranganath, with Hamed Nili at the University of Oxford, wondered if our brains represent abstract relationships, such as social networks, in the same way.
To find out, they gave volunteers pieces of information about two groups of people ranked by perceived relative competence and popularity. The volunteers were only told about relations on one dimension between a pair of people who differed by one rank level at a time: for example, that Alice is more popular than Bob, but Bob is seen as more competent than Charles.
The true social hierarchy could be mapped as a two-dimensional grid defined by dimensions of competence and popularity, but this was not shown to the volunteers. They only could infer it by integrating piecemeal learned relationships between pairs of individuals in one dimension at a time.
They also learned about relative ranks of a few people between groups.
Assembling a map
They were later asked about relationships between new pairs of people in the grid while the researchers used functional magnetic resonance imaging to measure brain activity. Without being prompted, based only on pairwise comparisons, the volunteers organized the information into a two-dimensional grid in their brains. This two-dimensional map was present across three brain regions called the hippocampus, entorhinal cortex and ventromedial prefrontal cortex/medial orbitofrontal cortex.
Based on limited comparisons between the two groups, they were also able to generalize to the rest of the group. For example, if Cynthia from group 1 was more popular than David from group 2, that affected the rank of other members of group 2 compared to group 1.
The volunteers weren’t told to think about the data in that way, Boorman said. Given only pairwise comparisons, they inferred the remaining hierarchical arrangement of the whole set.
“If you know how two social networks are related to each other, you can make a good inference about the relationship between two individuals in different social networks before direct experiences,” Park said.
The study points to a general principle behind how we make decisions based on past experience. Whether we are remembering a route in the physical world, or learning about a set of friends and acquaintances, we start with a template, such as a 2-D topology, and a few landmarks, and fit new data around them.
“Our results show that our brain organizes knowledge learned from separate experiences in a structural form like a map, which allows us to use past experiences to make a novel decision,” Park said.
That allows us to quickly adapt to a new situation based on past experience. This may help to explain humans’ remarkable flexibility in generalizing experiences from one task to another, a key challenge in artificial intelligence research.
“We know a lot about how the neural codes for representing physical space,” Boorman said. “It looks like the human brain uses the same codes to organize abstract, non-spatial information as well.”
- Seongmin A. Park, Douglas S. Miller, Hamed Nili, Charan Ranganath, Erie D. Boorman. Map Making: Constructing, Combining, and Inferring on Abstract Cognitive Maps. Neuron, 2020; DOI: 10.1016/j.neuron.2020.06.030
Cite This Page:
University of California – Davis. “Brain builds and uses maps of social networks, physical space, in the same way.” ScienceDaily. ScienceDaily, 22 July 2020. <www.sciencedaily.com/releases/2020/07/200722112657.htm>.
Monash University. “Breakthrough blood test detects positive COVID-19 result in 20 minutes.” ScienceDaily. ScienceDaily, 17 July 2020.
“Researchers report a new method that detects positive COVID-19 cases using blood samples in about 20 minutes, and identifies whether someone has contracted the virus.”
(QESP Editor’s Note: The following is a reprint of a 17 July 2020 ScienceDaily article from Monash University. The original, with photographs and links to related material, is available at www.sciencedaily.com/releases/2020/07/200717101037.htm )
New research by Monash University in Australia has been able to detect positive COVID-19 cases using blood samples in about 20 minutes, and identify whether someone has contracted the virus.
In a discovery that could advance the worldwide effort to limit the community spread of COVID-19 through robust contact tracing, researchers were able to identify recent COVID-19 cases using 25 microlitres of plasma from blood samples.
The research team, led by BioPRIA and Monash University’s Chemical Engineering Department, including researchers from the ARC Centre of Excellence in Convergent BioNano Science and Technology (CBNS), developed a simple agglutination assay — an analysis to determine the presence and amount of a substance in blood — to detect the presence of antibodies raised in response to the SARS-CoV-2 infection.
Positive COVID-19 cases caused an agglutination or a clustering of red blood cells, which was easily identifiable to the naked eye. Researchers were able to retrieve positive or negative readings in about 20 minutes.
While the current swab / PCR tests are used to identify people who are currently positive with COVID-19, the agglutination assay can determine whether someone had been recently infected once the infection is resolved — and could potentially be used to detect antibodies raised in response to vaccination to aid clinical trials.
Using a simple lab setup, this discovery could see medical practitioners across the world testing up to 200 blood samples an hour. At some hospitals with high-grade diagnostic machines, more than 700 blood samples could be tested hourly — about 16,800 each day.
Study findings could help high-risk countries with population screening, case identification, contact tracing, confirming vaccine efficacy during clinical trials, and vaccine distribution.
This world-first research was published July 18, 2020, in the journal ACS Sensors.
A patent for the innovation has been filed and researchers are seeking commercial and government support to upscale production.
Dr Simon Corrie, Professor Gil Garnier and Professor Mark Banaszak Holl (BioPRIA and Chemical Engineering, Monash University), and Associate Professor Timothy Scott (BioPRIA, Chemical Engineering and Materials Science and Engineering, Monash University) led the study, with initial funding provided by the Chemical Engineering Department and the Monash Centre to Impact Anti-microbial Resistance.
Dr Corrie, Senior Lecturer in Chemical Engineering at Monash University and Chief Investigator in the CBNS, said the findings were exciting for governments and health care teams across the world in the race to stop the spread of COVID-19. He said this practice has the potential to become upscaled immediately for serological testing.
“Detection of antibodies in patient plasma or serum involves pipetting a mixture of reagent red blood cells (RRBCs) and antibody-containing serum/plasma onto a gel card containing separation media, incubating the card for 5-15 minutes, and using a centrifuge to separate agglutinated cells from free cells,” Dr Corrie said.
“This simple assay, based on commonly used blood typing infrastructure and already manufactured at scale, can be rolled out rapidly across Australia and beyond. This test can be used in any lab that has blood typing infrastructure, which is extremely common across the world.”
Researchers collaborated with clinicians at Monash Health to collect blood samples from people recently infected with COVID-19, as well as samples from healthy individuals sourced before the pandemic emerged.
Tests on 10 clinical blood samples involved incubating patient plasma or serum with red blood cells previously coated with short peptides representing pieces of the SARS-CoV-2 virus.
If the patient sample contained antibodies against SARS-CoV-2, these antibodies would bind to peptides and result in aggregation of the red blood cells. Researchers then used gel cards to separate aggregated cells from free cells, in order to see a line of aggregated cells indicating a positive response. In negative samples, no aggregates in the gel cards were observed.
“We found that by producing bioconjugates of anti-D-IgG and peptides from SARS-CoV-2 spike protein, and immobilising these to RRBCs, selective agglutination in gel cards was observed in the plasma collected from patients recently infected with SARS-CoV-2 in comparison to healthy plasma and negative controls,” Professor Gil Garnier, Director of BioPRIA, said.
“Importantly, negative control reactions involving either SARS-CoV-2-negative samples, or RRBCs and SARS-CoV-2-positive samples without bioconjugates, all revealed no agglutination behaviour.”
Professor Banaszak Holl, Head of Chemical Engineering at Monash University, commended the work of talented PhD students in BioPRIA and Chemical Engineering who paused their projects to help deliver this game changing COVID-19 test.
“This simple, rapid, and easily scalable approach has immediate application in SARS-CoV-2 serological testing, and is a useful platform for assay development beyond the COVID-19 pandemic. We are indebted to the work of our PhD students in bringing this to life,” Professor Banaszak Holl said.
“Funding is required in order to perform full clinical evaluation across many samples and sites. With commercial support, we can begin to manufacture and roll out this assay to the communities that need it. This can take as little as six months depending on the support we receive.”
COVID-19 has caused a worldwide viral pandemic, contributing to nearly 600,000 deaths and more than 13.9 million cases reported internationally (figures dated 17 July 2020).
- Diana Alves, Rodrigo Curvello, Edward Henderson, Vidhishri Kesarwani, Julia A. Walker, Samuel C. Leguizamon, Heather McLiesh, Vikram Singh Raghuwanshi, Hajar Samadian, Erica M. Wood, Zoe K. McQuilten, Maryza Graham, Megan Wieringa, Tony M. Korman, Timothy F. Scott, Mark M. Banaszak Holl, Gil Garnier, Simon R. Corrie. Rapid Gel Card Agglutination Assays for Serological Analysis Following SARS-CoV-2 Infection in Humans. ACS Sensors, 2020; DOI: 10.1021/acssensors.0c01050
Cite This Page:
Monash University. “Breakthrough blood test detects positive COVID-19 result in 20 minutes.” ScienceDaily. ScienceDaily, 17 July 2020. <www.sciencedaily.com/releases/2020/07/200717101037.htm>.
Neuroscientists Identify Brain Cells That Help Humans Adapt to Change
July 15, 2020
(QESP Editor’s Note: The following is a reprint of a 15 July 2020 ScienceDaily article from Vanderbilt University. The original, with photographs and links to related material, is available at
There are 86 billion neurons, or cells, in the human brain. Of these, an infinitely small portion of them handle cognitive flexibility – our ability to adjust to new environments and concepts.
A team of researchers with interdisciplinary expertise in psychology, informatics (the application of information science to solve problems with data) and engineering along with the Vanderbilt Brain Institute (VBI) gained critical insights into one of the biggest mysteries in neuroscience, identifying the location and critical nature of these neurons.
The article was published in the journal Proceedings of the National Academy of Science (PNAS) on July 13. The discovery presents an opportunity to enhance researchers’ understanding and treatment of mental illnesses rooted in cognitive flexibility.
Brain circuits created by these neurons have led to an evolutionary advantage in the ability of humans to adapt to changing environments. When these neurons are weakened, people may have trouble adjusting to changes in their environment including difficulty in overcoming traditions, biases and fears. Typically, people oscillate between repeating rewarding behavior and exploring newer and potentially better rewards. The cost-benefit ratio of repeating to exploring is an equation that the brain is constantly working to resolve, particularly when there are changes to a person’s environment. A lack of cognitive flexibility results in debilitating mental conditions.
The consequences of this research could be multifold. “These cells could be part of the switch that determines your best attentional strategy,” said Thilo Womelsdorf, associate professor of psychology and computer science, and the paper’s principal investigator. “Weakening these brain cells could make it difficult to switch attention strategies, which can ultimately result in obsessive-compulsive behaviors or a struggle to adjust to new situations. On the opposite end, if such a switch is ‘loose’ attention might become ‘loose’ and people will experience a continuously uncertain world and be unable to concentrate on important information for any amount of time.”
The researchers hypothesized that within the area of the brain that helps people learn fine motor skills like playing an instrument, there exists a subregion that could enable the same flexible processes for thoughts.
The group of brain cells, located below the outer cortical mantle in the basal ganglia, were identified by measuring the activity of brain cells during computer-simulated real-world tasks. To mimic many real-world situations the researchers, including scientists from the Centre for Vision Research at York University, developed a simulation to present more than one object at a time and changed what was rewarded. This created flexible learning as to which objects are linked to a reward through trial-and-error. By measuring the activity of brain cells, the team observed an interesting pattern: brain cell activity was heightened amid change and diminished when confidence in the outcome grew. “These neurons seem to help the brain circuits to reconfigure and transition from formerly relevant information, and a tenuous connection to attend to new, relevant information,” said Kianoush Banaie Boroujeni, the study’s first author and Ph.D. candidate in the Womelsdorf lab.
There is a technological revolution in neuroscience,” said Lisa Monteggia, Barlow Family Director of the Vanderbilt Brain Institute and professor of pharmacology. “The ability to use technology to control a single cell with molecular and genetic tools can only work when scientists know where to look. Dr. Womelsdorf and his collaborators have given us the ability to do such work and significantly move the field of neuroscience forward.”
This research was supported by grants from the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health (R01EB028161) and the Canadian Institutes of Health Research (MOP 102482).
Australia’s Digital Trust Report 2020 – Submitted on Mon, 13/07/2020
“Australia’s digital infrastructure and the data it carries are core to the value and growth of the nation’s economy. The growing economic dependency on the digital domain has an intrinsic relationship with the trust users and consumers have in it and therefore the security, privacy and resilience of the infrastructure and data.
Australia’s Digital Trust Report 2020 highlights the role ‘digital trust’ plays in attracting investment and driving jobs growth. It draws on data modelled by Synergy’s Advanced Modelling Group to quantify the value of digital activity to the Australian economy and model the impact of a major cyber security incident creating a digital interruption to the Australian economy.
Together with AustCyber’s other key advisories on cyber security sector growth in Australia – Australia’s Cyber Security Sector Competitiveness Plan and the Australian Cyber Security Industry Roadmap – this report demonstrates the role that cyber security plays as a ‘horizontal sector’ in enabling growth opportunities across other sectors of the economy.
The timing of the release of this report is both critical and deliberate. The COVID-19 pandemic caused a rapid move to remote working and education, renewed focus on online business delivery and fast adaptation of supply chains using digital technologies .”
Max Delbrück Center for Molecular Medicine in the Helmholtz Association. “Janggu makes deep learning a breeze.” ScienceDaily. ScienceDaily, 13 July 2020.
(QESP Editor’s Note: The following is a reprint of a 13 July 2020 ScienceDaily article from Max Delbrück Center for Molecular Medicine in the Helmholtz Association. The original, with photographs and links to related material, is available at
Researchers from the MDC have developed a new tool that makes it easier to maximize the power of deep learning for studying genomics. They describe the new approach, Janggu, in the journal Nature Communications.
Imagine that before you could make dinner, you first had to rebuild the kitchen, specifically designed for each recipe. You’d spend way more time on preparation, than actually cooking. For computational biologists, it’s been a similar time-consuming process for analyzing genomics data. Before they can even begin their analysis, they spend a lot of valuable time formatting and preparing huge data sets to feed into deep learning models.
To streamline this process, researchers from the Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC) developed a universal programming tool that converts a wide variety of genomics data into the required format for analysis by deep learning models. “Before, you ended up wasting a lot of time on the technical aspect, rather than focusing on the biological question you were trying to answer,” says Dr. Wolfgang Kopp, a scientist in the Bioinformatics and Omics Data Science research group at MDC’s Berlin Institute of Medical Systems Biology (BIMSB), and first author of the paper. “With Janggu, we are aiming to relieve some of that technical burden and make it accessible to as many people as possible.”
Unique name, universal solution
Janggu is named after a traditional Korean drum shaped like an hourglass turned on its side. The two large sections of the hourglass represent the areas Janggu is focused: pre-processing of genomics data, results visualization and model evaluation. The narrow connector in the middle represents a placeholder for any type of deep learning model researchers wish to use.
Deep learning models involve algorithms sorting through massive amounts data and finding relevant features or patterns. While deep learning is a very powerful tool, its use in genomics has been limited. Most published models tend to only work with fixed types of data, able to answer only one specific question. Swapping out or adding new data often requires starting over from scratch and extensive programming efforts.
Janggu converts different genomics data types into a universal format that can be plugged into any machine learning or deep learning model that uses python, a widely-used programming language.
“What makes our approach special is that you can easily use any genomic data set for your deep learning problem, anything goes in any format,” Dr. Altuna Akalin, who heads the Bioinformatics and Omics Data Science research group.
Separation is key
Akalin’s research group has a dual mission: developing new machine learning tools, and using them to investigate questions in biology and medicine. During their own research efforts, they were continually frustrated by how much time was spent formatting data. They realized part of the problem was each deep learning model included its own data pre-processing. By separating the data extraction and formatting from the analysis, it provides a much easier way to interchange, combine or reuse sections of data. It’s kind of like having all the kitchen tools and ingredients at your fingertips ready to try out a new recipe.
“The difficulty was finding the right balance between flexibility and usability,” Kopp says. “If it is too flexible, people will be drowned in different options and it will be difficult to get started.”
Kopp has prepared several tutorials to help others begin using Janggu, along with example datasets and case studies. The Nature Communications paper demonstrates Janggu’s versatility in handling very large volumes of data, combining data streams, and answering different types of questions, such as predicting binding sites from DNA sequences and/or chromatin accessibility, as well as for classification and regression tasks.
While most of Janggu’s benefit is on the front end, the researchers wanted to provide a complete solution for deep learning. Janggu also includes visualization of results after the deep learning analysis, and evaluates what the model has learned. Notably, the team incorporated “higher-order sequence encoding” into the package, which allows to capture correlations between neighboring nucleotides. This helped to increase accuracy of some analyses. By making deep learning easier and more user-friendly, Janggu helps throw open the door to answering all kinds of biological questions.
“One of the most interesting applications is predicting the effect of mutations on gene regulation,” Akalin says. “This is exciting because now we can start understanding individual genomes, for instance, we can pinpoint genetic variants that cause regulatory changes, or we can interpret regulatory mutations occurring in tumors.”
Materials provided by Max Delbrück Center for Molecular Medicine in the Helmholtz Association. Original written by Laura Petersen. Note: Content may be edited for style and length.
- Wolfgang Kopp, Remo Monti, Annalaura Tamburrini, Uwe Ohler, Altuna Akalin. Deep learning for genomics using Janggu. Nature Communications, 2020; 11 (1) DOI: 10.1038/s41467-020-17155-y
Cite This Page:
Max Delbrück Center for Molecular Medicine in the Helmholtz Association. “Janggu makes deep learning a breeze.” ScienceDaily. ScienceDaily, 13 July 2020. www.sciencedaily.com/releases/2020/07/200713104357.htm
Here’s how scientists know the coronavirus came from bats and wasn’t made in a lab
July 13, 2020 Polly Hayes
Lecturer in Parasitology and Medical Microbiology, University of Westminster
Polly Hayes does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.
(QESP Editor’s Note: The following is a reprint of a 13 July 2020 article [n The Conversation, from University of Westminster. The original, with photographs and links to related material, is available at
One of the conspiracy theories that have plagued attempts to keep people informed during the pandemic is the idea that the coronavirus was created in a laboratory. But the vast majority of scientists who have studied the virus agree that it evolved naturally and crossed into humans from an animal species, most likely a bat.
How exactly do we know that this virus, SARS-CoV-2, has a “zoonotic” animal origin and not an artificial one? The answers lie in the genetic material and evolutionary history of the virus, and understanding the ecology of the bats in question.
An estimated 60% of known infectious diseases and 75% of all new, emerging, or re-emerging diseases in humans have animal origins. SARS-CoV-2 is the newest of seven coronaviruses found in humans, all of which came from animals, either from bats, mice or domestic animals. Bats were also the source of the viruses causing Ebola, rabies, Nipah and Hendra virus infections, Marburg virus disease, and strains of Influenza A virus.
The genetic makeup or “genome” of SARS-CoV-2 has been sequenced and publicly shared thousands of times by scientists all over the world. If the virus had been genetically engineered in a lab there would be signs of manipulation in the genome data. This would include evidence of an existing viral sequence as the backbone for the new virus, and obvious, targeted inserted (or deleted) genetic elements.
The genome of SARS-CoV-2 is similar to that of other bat coronaviruses, as well as those of pangolins, all of which have a similar overall genomic architecture. Differences between the genomes of these coronaviruses show natural patterns typical of coronavirus evolution. This suggests that SARS-CoV-2 evolved from a previous wild coronavirus.
One of the key features that makes SARS-CoV-2 different from the other coronaviruses is a particular “spike” protein that binds well with another protein on the outside of human cells called ACE2. This enables the virus to hook into and infect a variety of human cells. However, other related coronaviruses do have similar features, providing evidence that they have evolved naturally rather than being artificially added in a lab.
Coronaviruses and bats are locked in an evolutionary arms race in which the viruses are constantly evolving to evade the bat immune system and bats are evolving to withstand infections from coronaviruses. A virus will evolve multiple variants, most of which will be destroyed by the bat’s immune system, but some will survive and pass to other bats.
Some scientists have suggested that SARS-CoV-2 may have come from another known bat virus (RaTG13) found by researchers at the Wuhan Institute of Virology. The genomes of these two viruses are 96% similar to one another.
This might sound very close but in evolutionary terms this actually makes them significantly different and the two have been shown to share a common ancestor. This shows that RaGT13 is not the ancestor of SARS-CoV-2.
In fact, SARS-CoV-2 most likely evolved from a viral variant that couldn’t survive for a long period of time or that persists at low levels in bats. Coincidentally, it evolved the ability to invade human cells and accidentally found its way into us, possibly by means of an intermediate animal host, where it then thrived. Or an initially harmless form of the virus might have jumped directly into humans and then evolved to become harmful as it passed between people.
The mixing or “recombination” of distinct coronavirus genomes in nature is one of the mechanisms that brings about novel coronaviruses. There is now further evidence that this process could be involved in the generation of SARS-CoV-2.
Since the pandemic started, the SARS-CoV-2 virus appears to have started evolving into two distinct strains, acquiring adaptations for more efficient invasion of human cells. This could have occurred through a mechanism known as a selective sweep, through which beneficial mutations help a virus to infect more hosts and so become more common in the viral population. This is a natural process that can ultimately reduce the genetic variation between individual viral genomes.
The same mechanism would account for the lack of diversity seen in the many SARs-CoV-2 genomes that have been sequenced. This indicates that the ancestor of SARS-CoV-2 could have been circulating in bat populations for a considerable amount of time. It then would have acquired the mutations that allowed it to spill over from bats into other animals, including humans.
It is also important to remember that around one in five of all mammal species on Earth are bats, with some found only in certain locations and others migrating across vast distances. This diversity and geographical spread makes it a challenge to identify which group of bats SARS-CoV-2 originally came from.
There is evidence that early cases of COVID-19 occurred outside of Wuhan in China and had no clear link to the city’s wet market where the pandemic is thought to have begun. But that isn’t evidence of a conspiracy.
It could simply be that infected people accidentally brought the virus into the city and then the wet market, where the enclosed, busy conditions increased the chances of the disease spreading rapidly. This includes the possibility of one of the scientists involved in bat coronavirus research in Wuhan unknowingly becoming infected and bringing the virus back from where their subject bats lived. This would still be considered natural infection, not a laboratory leak.
Only through robust science and the study of the natural world will we be able to truly understand the natural history and origins of zoonotic diseases like COVID-19. This is pertinent because our ever-changing relationship and increasing contact with wildlife is raising the risk of new deadly zoonotic diseases emerging in humans. SARS-CoV-2 is not the first virus that we have acquired from animals and certainly will not be the last.
Is the airborne route a major source of coronavirus transmission?
July 7, 2020 by Hassan Vally, Associate Professor, La Trobe University
Hassan Vally does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.
(QESP Editor’s Note: The following is a reprint of a 13 July 2020 article [n The Conversation, from La Trobe University. The original, with photographs and links to related material, is available at
As the world continues to grapple with the coronavirus pandemic, one question that keeps coming up is whether COVID-19 can be transmitted through the air.
In fact, 239 scientists in 32 countries have written an open letter to the World Health Organisation (WHO) arguing there is mounting evidence the airborne route plays a role in the transmission of COVID-19.
Like a lot of issues to do with the pandemic, what seems to be a relatively straightforward question is deceptively complex. We actually don’t know the answer for sure.
Why do we need to understand the modes of transmission?
Understanding how COVID-19 is transmitted from one person to the next enables us to design effective public health interventions to minimise the risk of transmission.
For instance, we’re advised to keep 1.5 metres away from others because there’s consensus one of the main ways the virus spreads is via large droplets.
These “large” droplets are usually greater than 5 micrometres in size and are propelled from an infected person’s nose or mouth in their mucus and saliva when they sneeze, cough or talk.
Thanks to gravity, these large droplets don’t generally travel far before landing. If you position yourself more than 1.5 metres from someone who is infected, the expectation is you’ll be clear of the droplets’ path.
Similarly, understanding these large droplets can land on surfaces and that the virus can survive on these surfaces means we know we need to wash our hands to avoid transferring the virus to our mouth, nose or eyes.
Until now, the WHO has maintained these large droplets are the major source of COVID-19 transmission. But the authors of the open letter suggest they are underplaying the role of airborne transmission.
Airborne transmission and COVID-19
In its simplest interpretation, airborne transmission refers to the ability of a virus to be spread by droplets small enough to be suspended in the air. These droplets are less than 5 micrometres in size and generally called aerosols.
Whereas large droplets can only travel short distances, these smaller droplets, in theory, can be spread further, or can linger in a room even after an infected person has left.
Evidence supporting the notion that transmission of COVID-19 can occur via the airborne route takes several forms.
First, laboratory studies have demonstrated that SARS-CoV-2, the coronavirus that causes COVID-19, can be aerosolised, and can survive for up to four hours in this form.
Second, genetic material from SARS-CoV-2 has been detected in aerosols sampled at hospitals, including two hospitals in Wuhan, the Chinese city from which the pandemic emerged. But it’s important to note the presence of this genetic material doesn’t necessarily mean the virus is infectious in this form.
Perhaps the strongest evidence, however, comes through the various case reports of superspreading events. These are situations in which many people appear to have been infected with coronavirus in the absence of close contact.
One notable early example was from a choir practice in the United States where almost 50 people were infected even though they maintained physical distance. Two died.
Another example is an outbreak in Guangzhou, China, where ten people from three families contracted COVID-19 after dining in a restaurant. Non-infected people were not in close contact with any infected person, but those who became infected were in the direct line of one air conditioning unit.
The study of this outbreak is not yet peer-reviewed but is part of the evidence the authors of the open letter draw on.
What are the implications of airborne transmission?
Airborne transmission of this novel coronavirus is potentially a worry, because if it occurs often, it means the virus may be commonly transmitted in the absence of close contact.
It also raises the possibility the virus may travel on air currents, and even be transmitted through air conditioning.
This means social distancing may not always be effective, and in particular, crowded indoor areas with poor ventilation pose a major threat.
So where does this leave us?
The key question is not whether airborne transmission is theoretically possible; it certainly is. But rather, how significant is its role in the transmission of COVID-19?
If, for example, most transmission of SARS-CoV-2 happens via large droplets and the airborne route plays a role only occasionally, this has very different implications to a scenario where the airborne route is a significant mode of transmission.
Reassuringly, the interventions that have been implemented to limit spread of the virus, such as social distancing, have been largely successful so far in most of Australia. This suggests even if the virus can be spread by the airborne route, it’s not likely to be a major route of transmission.
Given what we know, the dilemma is whether to employ the precautionary principle and assume the airborne route plays an important role in disease transmission — and adjust infection control measures accordingly. This may take the form of encouraging wider use of masks and looking at increasing ventilation in enclosed spaces.
The other approach is to wait for more definitive evidence before changing the public health advice.
We will await with interest the WHO’s response to the open letter.
A choir decided to go ahead with rehearsal. Now dozens of members have COVID-19 and two are dead
By Richard Read Seattle Bureau Chief
March 29, 2020