Strength is in engagement: The rise of an online scientific community during the COVID‐19 pandemic

Many scientists, confined to home office by COVID‐19, have been gathering in online communities, which could become viable alternatives to physical meetings and conferences. Subject Categories: S&S: Careers & Training, Methods & Resources, S&S: Ethics

As COVID‐19 has brought work and travel to a grinding halt, scientists explored new ways to connect with each other. For the gene regulation community, this started with a Tweet that quickly expanded into the “Fragile Nucleosome” online forum, a popular seminar series, and many intimate discussions connecting scientists all over the world. More than 2,500 people from over 45 countries have attended our seminars so far and our forum currently has ~ 1,000 members who have kick‐started discussion groups and mentorship opportunities. Here we discuss our experience with setting up the Fragile Nucleosome seminars and online discussion forum, and present the tools to enable others to do the same.Too often, we forget the importance of social interactions in science. Indeed, many creative ideas originated from impromptu and fortuitous encounters with peers, in passing, over lunch, or during a conference coffee break. Now, the ongoing COVID‐19 crisis means prolonged isolation, odd working hours, and less social interactions for most scientists confined to home. This motivated us to create the “Fragile Nucleosome” virtual community for our colleagues in the chromatin and gene regulation field.

… the ongoing COVID‐19 crisis means prolonged isolation, odd working hours and less social interactions for most scientists confined to home.

While the need to address the void created by the COVID‐19 pandemic triggered our actions, a large part of the international community already has had limited access to research networks in our field. Our initiative offered new opportunities though, in particular for those who have not benefited from extensive networks, showing how virtual communities can address disparities in accessibility. This should not be a stop‐gap measure during the pandemic: Once we come out from our isolation, we still need to address the drawbacks of in‐person scientific conferences/seminars, such as economic disparities, travel inaccessibility, and overlapping family responsibilities (Sarabipour, 2020). Our virtual community offers some solutions to the standing challenges (Levine & Rathmell, 2020), and we hope our commentary can help start conversations about the advantages of virtual communities in a post‐pandemic world.

… once we come out from our isolation we still need to address the drawbacks of in‐person scientific conferences/seminars, such as economic disparities, travel inaccessibility and overlapping family responsibilities…

     

Helpful amnesia: Neuroscience unravels the role of forgetting as a prerequisite for establishing new long‐term memories

As neuroscience has been analysing the mechanisms behind long‐term memory, it demonstrated that forgetting is crucial for being able to remember.

“To be able to forget means sanity,” explained American writer Jack London (The Star Rover) referring to our sometimes infuriating inability to recall past events. In fact, being able to remember everything ever said and done might drive even the strongest mind insane. It is through forgetting and letting go of memories that the brain is able to acquire fresh impressions and new experience to move on, instead of being mired in the past.The importance of forgetting also fits well into and has inspired research to understand the molecular and cognitive basis of long‐term memory and how all the components and processes fit together. This puzzle of what is being remembered and why has been a long‐standing challenge for neuroscience; while progress has been made identifying more of the mechanisms and some of the existential drivers of memory formation, it is only recently that work has begun analyzing how these interact in animal models, often focusing on how the brain “decides” which things to remember and which things to send into oblivion.

This puzzle of what is being remembered and why has been a long‐standing challenge for neuroscience…

As a result, the field now sees collaboration across disciplines, driven by the realization that different parts and processes all play a part in memory formation and long‐term consolidation. This has led to one tangible if still tentative conclusion about long‐term memory, namely that forgetting occurs through loss of retrieval capability rather than erasure. It would appear to confirm the observation attributed to German philosopher Friedrich Nietzsche that “the existence of forgetting has never been proved: we only know that some things do not come to our mind when we want them to.”

The existence of forgetting has never been proved: we only know that some things do not come to our mind when we want them to.

     

Biology lessons in times of COVID: The pandemic has forced educators to teach and instruct online with varying success and challenges

Since COVID‐19 hit last year, lecturers and professors have been exploring digital and other tools to teach and instruct their students. Subject Categories: S&S: Careers & Training, Methods & Resources

As Director of the Digital Pedagogy Lab at the University of Colorado in Denver, USA, Michael Sean Morris’ work took on new significance as the COVID‐19 pandemic hit campuses around the world. “What happened with the pandemic was a lot of people who weren''t accustomed to teaching online, or dealing with distance learning, or remote learning in any way, shape, or form, really tried to create a live classroom situation on their screen, mostly using Zoom or other similar technologies”, Morris said. “With technology now, we can do things which make us feel closer. So, we can do a Zoom; there can be synchronous chat in technologies like Slack, or discussion forums or what‐have‐you to make you feel like you''re closer, to make you feel like you''re sort of together at the same time. But the majority of online learning actually has been asynchronous, it''s been everyone coming in when they can and doing their work when they can”.Educators have been divided over the use of online learning. But this changed when a deadly pandemic forced everyone from kindergarten to university into digital spaces. Luckily, many digital tools, such as Zoom, Slack, Blackboard Collaborate, or WhatsApp, were available to enable the migration. Nonetheless, teachers, lecturers, and professors struggle to educate their students with knowledge and the hands‐on training that is paramount for teaching biology.

… teachers, lecturers and professors struggle to educate their students with knowledge and the hands‐on training that is paramount for teaching biology.

     

A CRISPR response to pandemics?: Exploring the ethics of genetically engineering the human immune system

Ethical challenges should be addressed before gene editing is made available to improve the immune response against emerging viruses. Subject Categories: S&S: Economics & Business, Genetics, Gene Therapy & Genetic Disease, Immunology

In 1881, Louis Pasteur proved the “germ theory of disease”, namely that microorganisms are responsible for causing a range of diseases. Following Pasteur’s and Robert Koch’s groundbreaking work on pathogens, further research during the 20^th century elucidated how the immune system fends off disease‐causing microorganisms from a molecular perspective.The COVID‐19 pandemic has again focused scientific and public attention on immunology not the least owing to the race of employing vaccines to halt the spread of the virus. Although most countries have now started vaccination programs to immunize a large part of the world''s population, the process will take time, vaccines may not be available to everyone, and a number of unresolved issues remain including the potential contagiousness of vaccinated individuals and the duration of protection (Polack et al, 2020).It would therefore be extremely helpful from a public health perspective—and indeed lifesaving for those with elevated risk of developing severe course of the disease—if we could boost the human immune system by other means to better fight off SARS‐CoV‐2 and possibly other viruses. Recent studies showing that some individuals may be less susceptible to contract severe COVID‐19 depending on their genetic status support such visions (COVID‐19 Host Genetics Initiative, 2020). This could eventually inspire research projects on gene therapy with the aim of generally enhancing immunity against viral infections.

It would therefore be extremely helpful from a public health perspective […] if we could boost the human immune system by other means to better fight off SARS‐CoV‐2 …

The idea of genetically enhancing the human immune response is not new and spread from academic circles to policymakers and the general public even before the pandemic, when He Jiankui announced in November 2018 the birth of genetically edited twins who, he claimed, were resistant to HIV. The public outcry was massive, not only because He violated standards of methodological rigor and research ethics, but also because of fundamental doubts about the wisdom and legitimacy of human germline manipulation (Schleidgen et al, 2020).Somatic gene therapy has been met with a less categorical rejection, but it has also been confronted with skepticism when major setbacks or untoward events occurred, such as the death of Jesse Gelsinger during an early clinical trial for gene therapy in 1999. Nonetheless, given the drastic impact the current pandemic has on so many lives, there may be a motivation to put concerns aside. In fact, even if we managed to get rid of COVID‐19 owing to vaccines—or at least to keep its infectiousness and mortality low—another virus will appear sooner or later; an improved resistance to viral pathogens—including coronaviruses—would be an important asset.Interventions to boost the immune system could in fact make use of either germline gene editing, as has been the case of the Chinese twins, or through somatic gene editing. The first requires time and only the next generation would potentially benefit while the latter could be immediately applied and theoretically used to deal with the ongoing COVID‐19 pandemic.

Interventions to boost the immune system could in fact make use of either germline gene editing, as has been the case of the Chinese twins, or through somatic gene editing.

     

The role of fear in modern societies: Our ancient fear response to new situations is not always helpful in a civilised society

The COVID‐19 pandemic highlights how our ancient fear response can be exploited for nefarious purposes with social media lending a helping hand. Subject Categories: S&S: Economics & Business, Ecology, Microbiology, Virology & Host Pathogen Interaction

The COVID‐19 pandemic has underscored more than any previous crisis how fear can be exploited by multiple actors from outright conspiracy theorists with pernicious agendas to governments seeking to maximise public compliance with lockdowns and social distancing. The crisis has also given new urgency to the debate over how to handle fake news and its rapid propagation over social media, as well as the part science should play in leading and supporting governments'' decisions.At a fundamental level, the pandemic has highlighted the balance evolution has struck between fear and its aversion, between risk taking and risk avoidance. Indeed, for many animals, fear is necessary to avoid predation or accidental death, but it must be kept in check to avoid starvation by never setting out to search for food.

At a fundamental level, the pandemic has highlighted the balance evolution has struck between fear and its aversion, between risk taking and risk avoidance.

     

Context matters: On the road to responsible biosafety technologies in synthetic biology

Biosafety is a major challenge for developing for synthetic organisms. An early focus on application and their context could assist with the design of appropriate genetic safeguards. Subject Categories: Synthetic Biology & Biotechnology, S&S: Economics & Business

One of the goals of synthetic biology is the development of robust chassis cells for their application in medicine, agriculture, and the food, chemical and environmental industries. These cells can be streamlined by removing undesirable features and can be augmented with desirable functionalities to design an optimized organism. In a direct analogy with a car chassis, they provide the frame for different modules or “plug‐in” regulatory networks, metabolic pathways, or safety elements. In an effort to ensure a safe microbial chassis upfront, safety measures are implemented as genetic safeguards to limit risks such as unwanted cellular proliferation or horizontal gene transfer. Examples of this technology include complex genetic circuits, sophisticated metabolic dependencies (auxotrophies), and altered genomes (Schmidt & de Lorenzo, 2016; Asin‐Garcia et al, 2020). Much like seat belts or airbags in cars, these built‐in measures increase the safety of the chassis and of any organisms derived from it. Indeed, when it comes to safety, synthetic biology can still learn from a century‐old technology such as cars about the significance of context for the development of biosafety technologies.Every car today has seat belts installed by default. Yet, seat belts were not always a standard component; in fact, they were not even designed for cars to begin with. The original 2‐point belts were first used in aviation and only slowly introduced for motorized vehicles. Only after some redesign, the now‐common 3‐point car seat belts would become the life‐saving equipment that they are today. A proper understanding of the context of their application was therefore one of the crucial factors for their success and wide adoption. Context matters: It provides meaning for and defines what a technological application is best suited for. What was true for seat belts may be also true for biosafety technologies such as genetic safeguards.

… when it comes to safety, synthetic biology can still learn from a century‐old technology such as cars about the significance of context for the development of biosafety technologies.

Society has a much higher awareness of technology’s risks compared to the early days of cars. Society today requires that technological risks are anticipated and assessed before an innovation or its applications are widely deployed. In addition, society increasingly demands that research and innovation take into account societal needs and values. This has led to, among others, the Responsible Research and Innovation (RRI; von Schomberg, 2013) concept that has become prominent in European science policy. In a nutshell, RRI requires that innovative products and processes align with societal needs, expectations, and values in consultation with stakeholders. RRI and similar frameworks suggest that synthetic biology must anticipate and respond not only to risks, but also to societal views that frame its evaluation and risk assessment.     

Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users

Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.

Core facilities and research infrastructures have become an essential part of the scientific ecosystem. In the field of proteomics, national and international networks and research platforms have been established during the past decade that are supposed to set standards for high‐quality services, promote an exchange of professional information, and enable access to cutting‐edge, specialized proteomics technologies. Either centralized or distributed, these national and international proteomics infrastructures and technology platforms are generating massive amounts of data for the research community, and support a broad range of translational, computational and multi‐omics initiatives and basic research projects.By delegating part of their work to these services, researchers expect that the core facility adjusts their analytical protocols appropriately for their project to acquire data conforming best research practice of the scientific community. The implementation of quality assessment measures and commonly accepted quality controls in data generation is therefore crucially important for proteomics research infrastructures and the scientists who rely on them.However, current quality control and quality assessment procedures in proteomics core facilities and research infrastructures are a motley collection of protocols, standards, reference compounds and software tools. Proteomics relies on a customized multi‐step workflow typically consisting of sample preparation, data acquisition and data processing, and the implementation of each step differs among facilities. For example, sample preparation involves enzymatic digestion of the proteins, which can be performed in‐solution, in‐gel, or on‐beads, with often different proteolytic enzymes, chemicals, and conditions among laboratories. Data acquisition protocols are often customized to the particular instrument set up, and the acquired spectra and chromatograms are processed by different software tools provided by equipment vendors, third parties or developed in‐house.

…current quality control and quality assessment procedures in proteomics core facilities and research infrastructures are a motley collection of protocols, standards, reference compounds and software tools.

Moreover, core facilities implement their own guidelines to monitor the performance and quality of the entire workflow, typically utilizing different commercially available standards such as pre‐digested cell lysates, recombinant proteins, protein mixtures, or isotopically labeled peptides. Currently, there is no clear consensus on if, when and how to perform quality control checks. There is even less quality control in walk‐in facilities, where the staff is only responsible for correct usage of the instruments and users select and execute the analytical workflow themselves. It is not surprising therefore that instrument stability and robustness of the applied analytical approach are often unclear, which compromises analytical rigor.     

Fermentation for future food systems: Precision fermentation can complement the scope and applications of traditional fermentation

Modern biotechnology holds great potential for expanding the scope of fermentation to create novel foods and improve the sustainability of food production.

The growing human population and global warming pose an impending threat for global food security (Linder, 2019). This has prompted a critical re‐examination of the food supply chain from producers to consumers in order to increase the overall efficiency of food production, storage and transport. Much research in plant science consequently aims to increase production with new, high‐yield crop, fruit and vegetable varieties better adapted to changing climatic conditions. Yet, there is also much room for improving food safety by minimising food losses and recycling waste, valorising by‐products, improving nutritional value and increasing storage time. This is where fermentation comes in as a cost‐efficient, versatile and proven technology that extends the shelf life of food products and enhances their nutritional content. Moreover, there is enormous potential in fermentation to further increase efficiency and product range and even create new food products from non‐food biomass.

… there is enormous potential in fermentation to further increase efficiency and product range and even create new food products from non‐food biomass.

In a broader sense, fermentation can be defined as the cultivation of microorganisms such as bacteria, yeasts and fungi to break down complex molecules into simpler ones, notably organic acids, alcohols or esters. In a practical sense, it is one of the oldest food processing technologies to increase storage life along with cooking, smoking or air‐drying: fermentation was already fully industrialised for producing beer and bread millennia ago in ancient Mesopotamia and Egypt. It is also an elegant and simple technology as these microorganisms do most of the work without much human involvement.Louis Pasteur’s discovery that microorganisms cause fermentation laid the basis for further improvement of the technology from traditional spontaneous fermentation to the use of defined starter cultures. Fermentation is now widely used to produce alcoholic beverages, bread and pastry, dairy products, pickled vegetables, soy sauce and so on. More recent advances based on genomics and synthetic biology include precision and biomass fermentation to produce specific compounds for the food and chemical industry or medicinal use. This is not the limit though: when combined with genomics, fermentation has even greater potential for creating novel foods and other products.     

Biosafety in DIY‐bio laboratories: from hype to policy: Discussions about regulating DIY biology tend to ignore the extent of self‐regulation and oversight of DIY laboratories

Policymakers should treat DIY‐biology laboratories as legitimate parts of the scientific enterprise and pay attention to the role of community norms. Subject Categories: Synthetic Biology & Biotechnology, S&S: Economics & Business, S&S: Ethics

DIY biology – very broadly construed as the practice of biological experiments outside of traditional research environments such as universities, research institutes or companies – has, during the past decade, gained much prominence. This increased attention has raised a number of questions about biosafety and biosecurity, both in the media and by policy makers who are concerned about safety and security lapses in “garage biology”. There are a number of challenges here though when it comes to policies to regulate DIY biology. For a start, the term itself escapes easy definition: synonyms or related terms abound, including garage biotechnology, bio‐hacking, self‐modification/grinding, citizen science, bio‐tinkering, bio‐punk, even transhumanism. Some accounts even use ‘DIY‐bio’ interchangeably with synthetic biology, even though these terms refer to different emerging trends in biology. Some of these terms are more charged than others but each carries its own connotations with regard to practice, norms and legality. As such, conversations about the risk, safety and regulation of DIY‐bio can be fraught.

Synonyms or related terms abound, including garage biotechnology, bio‐hacking, self‐modification/grinding, citizen science, bio‐tinkering, bio‐punk, even transhumanism.

Given the increasing policy discussions about DIY‐bio, it is crucial to consider prevailing practice thoughtfully, and accurately. Key questions that researchers, policy makers and the public need to contemplate include the following: “How do different DIY‐bio spaces exist within regulatory frameworks, and enact cultures of (bio)safety?”, “How are these influenced by norms and governance structures?”, “If something is unregulated, must it follow that it is unsafe?” and “What about the reverse: does regulatory oversight necessarily lead to safer practice?”.The DIY‐bio movement emerged from the convergence of two trends in science and technology. The first one is synthetic biology, which can broadly be defined as a conception of genetic engineering as systematic, modular and programmable. While engineering living organisms is obviously a complex endeavour, synthetic biology has sought to re‐frame it by treating genetic components as inherently modular pieces to be assembled, through rational design processes, into complex but predictable systems. This has prompted many “LEGO” metaphors and a widespread sense of democratisation, making genetic engineering accessible not only to trained geneticists, but also to anyone with an “engineering mindset”.The second, much older, trend stems from hacker‐ and makerspaces, which are – usually not‐for‐profit – community organisations that enable groups of enthusiasts to share expensive or technically complex infrastructure, such as 3D printers or woodworking tools, for their projects. These provide a model of community‐led initiatives based on the sharing of infrastructure, equipment and knowledge. Underpinning these two trends is an economic aspect. Many of the tools of synthetic biology – notably DNA sequencing and synthesis – have seen a dramatic drop in cost, and much of the necessary physical apparatus is available for purchase, often second‐hand, through auction sites.DIY‐bio labs are often set‐up under widely varying management schemes. While some present themselves as community outreach labs focusing on amateur users, others cater specifically to semi‐ or professional members with advanced degrees in the biosciences. Other such spaces act as incubators for biotech startups with an explicitly entrepreneurial culture. Membership agreements, IP arrangements, fees, access and the types of project that are encouraged in each of these spaces can have a profound effect on the science being done.     

COVID‐19 and the opportunities for research: The lockdowns’ impacts on wildlife,ecology and conservation biology,and the humanities

The ongoing lockdowns provide ideal conditions to study the relationship between wildlife and humans but among humans themselves. Subject Categories: Ecology, S&S: History & Philosophy of Science

Almost all research has been affected in some way or another by the COVID‐19 pandemic, at the very least by challenging collaboration and interaction. But some areas have been affected more than others. Ecology and conservation biology experience a real boon as ongoing lockdowns have presented unique opportunities to study the impact of human activities on animals and ecosystems. This has not just galvanised research but also promises to leave a legacy of networks and collaborations to explore means to reduce negative human impacts on biodiversity long after the pandemic has subsided. In the social sciences and humanities, however, the pandemic is raising fundamental questions about their ability to contribute meaningfully to inform policy and public health responses.

In the social sciences and humanities […] the pandemic is raising fundamental questions about their ability to contribute meaningfully to inform policy and public health responses.

     

The COVID‐19 pandemic: agile versus blundering communication during a worldwide crisis: Important lessons for efficient communication to maintain public trust and ensure public safety

Governments’ measures to control the COVID‐19 pandemic and public reaction hold important lessons for science and risk communication in times of crisis.

The world is in the grips of a global pandemic, the end of which is not yet in sight. Nations struggle to deal with the severe health, economic and social impacts of COVID‐19 with varying success. Their ability to handle this crisis depends on many factors, some of which, such as the availability of vaccines, are variable, while others – geographical location or population density – are determined. More importantly though, public health infrastructures, political will and action, and clear communication have so far proved to be the most successful levers for coping with the pandemic. This article examines how political will and communication in particular have helped to alleviate the impact of the virus in some countries.

… public health infrastructures, political will and action, and clear communication have so far proved to be the most successful levers for coping with the pandemic.

News that a new virus had emerged in Wuhan, China, was just of fleeting interest for most people in December 2019. This changed rapidly: by March 2020, large parts of the world had gone into lockdown to curtail the rapid spread of SARS‐CoV‐2. Many governments issued more or less harsh restrictions on private contacts, travel and other freedoms, followed by easing these regulations during the summer, which precipitated new outbreaks in the fall along with mutations of the virus that triggered new restrictions; it is likely that this pattern will continue until a sufficient number of people are vaccinated to achieve herd immunity.COVID‐19 came “out of the blue”, hit a largely unprepared human population and has therefore affected human civilisation in an unprecedented manner (Fig 1). People are not only concerned about their health: as the pandemic continues, citizens also worry about the social, economic and psychological impacts. Even though vaccination programmes are under way, only a few countries will be able to achieve herd immunity by the summer; in the meantime, public acceptance for the ongoing restrictions of freedom are waning as the negative social and economic effects become more urgent. Thus, political action and planning along with efficient communication in particular are crucially important to ensure the public’s understanding of the situation and maintain acceptance for restrictive measure until enough vaccines become available. The antipodes in communication strategies were a mixture of evidence‐based messages, transparency, building confidence and open discussion of scientific uncertainty to gain and maintain public trust versus the unfettered spread of alternative facts, targeted disinformation and omission of important information that eventually eroded said trust.Open in a separate windowFigure 1Fear in times of COVID‐19An elderly pedestrian wearing a face mask due to the COVID‐19 pandemic, walks past graffiti depicting the subjects within famous artworks, in Glasgow on 2 September 2020 after the Scottish government imposed fresh restrictions on the city after a rise in cases of the novel coronavirus (© Andy Buchanan/AFP via Getty Images)

… political action and planning along with efficient communication in particular are crucially important to ensure the public’s understanding of the situation and maintain acceptance for restrictive measure…

     

Pond Acoustic Sampling Scheme: A draft protocol for rapid acoustic data collection in small waterbodies

1. Freshwater conservation is vital to the maintenance of global biodiversity. Ponds are a critical, yet often under‐recognized, part of this, contributing to overall ecosystem functioning and diversity. They provide habitats for a range of aquatic, terrestrial, and amphibious life, often including rare and declining species.
2. Effective, rapid, and accessible survey methods are needed to enable evidence‐based conservation action, but freshwater taxa are often viewed as “difficult”—and few specialist surveyors are available. Datasets on ponds are therefore limited in their spatiotemporal coverage.
3. With the advent of new recording technologies, acoustic survey methods are becoming increasingly available to researchers, citizen scientists, and conservation practitioners. They can be an effective and noninvasive approach for gathering data on target species, assemblages, and environmental variables. However, freshwater applications are lagging behind those in terrestrial and marine spheres, and as an emergent method, research studies have employed a multitude of different sampling protocols.
4. We propose the Pond Acoustic Sampling Scheme (PASS), a simple protocol to allow a standardized minimal sample to be collected rapidly from small waterbodies, alongside environmental and methodological metadata. This sampling scheme can be incorporated into a variety of survey designs and is intended to allow access to a wide range of participants, without requiring complicated or prohibitively expensive equipment.
5. Adoption of this sampling protocol would enable consistent sound recordings to be gathered by researchers and conservation organizations, and allow the development of landscape‐scale surveys, data sharing, and collaboration within an expanding freshwater ecoacoustic community—rather than individual approaches that produce incompatible datasets. The compilation of standardized data would improve the prospects for effective research into the soundscapes of small waterbodies and aid freshwater conservation efforts.

     

Underwater photogrammetry for close‐range 3D imaging of dry‐sensitive objects: The case study of cephalopod beaks

• Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry‐sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro‐CT scanning. Here, we use cephalopod beaks as an example as their size, thickness, transparency, and dry‐sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.
• We used a camera with a macrophotography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D model. These models were compared with others obtained with micro‐CT scanning to verify their accuracy.
• The models can be obtained quickly and cheaply compared with micro‐CT scanning and have sufficient precision for quantitative interspecific morphological analyses. Our work shows that underwater photogrammetry is a fast, noninvasive, efficient, and accurate way to reconstruct 3D models of dry‐sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro‐CT scanning. The mean difference between both methods is very small (10⁻⁵ to 10⁻⁴ mm) and is significantly lower than differences between meshes of different individuals.
• This photogrammetry protocol is portable, easy‐to‐use, fast, and reproducible. Micro‐CT scanning, in contrast, is time‐consuming, expensive, and nonportable. This protocol can be applied to reconstruct the 3D shape of many other dry‐sensitive objects such as shells of shellfish, cartilage, plants, and other chitinous materials.

     

Understanding the human language processor: Neurobiology’s insights into the human brain’s semantic processing of information could inform education and therapies for language disorders

Brain imaging and research on bilinguals and patients with speech disorders is helping to unravel semantic processing – the way how the brain interprets and stores sentences and stories. Subject Categories: Neuroscience

The human brain is a powerful biological computer capable of using information to construct elaborate virtual scenarios. This is in effect what happens when people read or listen to stories: the information is both stored and used by the brain’s virtuality engine, along with other knowledge and experience, to simulate the story. This so‐called lexical and semantical knowledge is represented across distributed and flexible spatial maps in the brain that can be reconfigured to any task in hand. For decades, neurobiologists have been trying to understand how this process works and where the knowledge from reading or listening is stored and processed, but these higher brain functions have so far been elusive. It was only the application of advanced imaging techniques, especially fMRI (functional magnetic resonance imaging) during the past decade, that allowed scientists to observe in real time what happens in the brain while reading or listening. These advances could benefit various fields, including therapies for speaking or language disorders and, more generally, education.

It was only the application of advanced imaging techniques […] that allowed scientists to observe in real time what happens in the brain while reading or listening.

Progress has come in slow steps. At first, fMRI analysis was confined to analysing the brain’s reaction to single words. During the past year or two, scientists have been able to map study participants’ reaction to whole sentences or even complete narratives to the spatial representation of more complex semantic knowledge. Further advances will depend on analysing differences between individuals and between bilingual and monolingual people. This will help to separate purely semantic aspects from those that rely on language or even culture. Progress is also expected to come from patients with neurological defects, such as brain lesions, epilepsy or ill‐defined conditions associated with learning difficulties such as dyslexia.     

Biodiversity 2030: a road paved with good intentions: The new EU Commission's biodiversity Strategy risks to remain an empty husk without proper implementation

The EU''s Biodiversity Strategy for 2030 makes great promises about halting the decline of biodiversity but it offers little in terms of implementation. Subject Categories: S&S: Economics & Business, Ecology, S&S: Ethics

Earth is teeming with a stunning variety of life forms. Despite hundreds of years of exploration and taxonomic research, and with 1.2 million species classified, we still have no clear picture of the real extent of global biodiversity, with estimates ranging from 3 to 100 million species. A highly quoted—although not universally accepted—study predicted some 8.7 million species, of which about 2.2 million are marine (Mora et al, 2011). Although nearly any niche on the surface of Earth has been colonized by life, species richness is all but evenly distributed. A large share of the known species is concentrated in relatively small areas, especially in the tropics (Fig 1). Ultimately, it is the network of the interactions among life forms and the physical environment that make up the global ecosystem we call biosphere and that supports life itself.Open in a separate windowFigure 1Biological hotspots of the worldA total of 36 currently recognized hotspots make up < 3% of the planet''s land area but harbor half of the world''s endemic plant species and 42% of all terrestrial vertebrates. Overall, hotspots have lost more than 80% of their original extension. Credit: Richard J. Weller, Claire Hoch, and Chieh Huang, 2017, Atlas for the End of the World, http://atlas‐for‐the‐end‐of‐the‐world.com/. Reproduced with permission.Driven by a range of complex and interwoven causes–such as changes in land and sea use, habitat destruction, overexploitation of organisms, climate change, pollution, and invasive species–biodiversity is declining at an alarming pace. A report by the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services (IPBES) issued a clear warning: “An average of around 25 per cent of species in assessed animal and plant groups are threatened, suggesting that around 1 million species already face extinction, many within decades, unless action is taken to reduce the intensity of drivers of biodiversity loss. Without such action, there will be a further acceleration in the global rate of species extinction, which is already at least tens to hundreds of times higher than it has averaged over the past 10 million years” (IPBES, 2019) (Fig 2). Although focused on a smaller set of organisms, a more recent assessment by WWF has reached similar conclusions. Their Living Planet Index, that tracks the abundance of thousands of populations of mammals, birds, fish, reptiles, and amphibians around the world, shows a stark decline in monitored populations (WWF, 2020). As expected, the trend of biodiversity decline is not homogeneous with tropical areas paying a disproportionately high price, mostly because of unrestrained deforestation and exploitation of natural resources.Open in a separate windowFigure 2The global, rapid decline of biodiversity(A) Percentage of species threatened with extinction in taxonomic groups that have been assessed comprehensively, or through a “sampled” approach, or for which selected subsets have been assessed by the IUCN Red List of Threatened Species. Groups are ordered according to the best estimate, assuming that data‐deficient species are as threatened as non‐data deficient species. (B) Extinctions since 1500 for vertebrate groups. (C) Red List Index of species survival for taxonomic groups that have been assessed for the IUCN Red List at least twice. A value of 1 is equivalent to all species being categorized as Least Concern; a value of zero is equivalent to all species being classified as Extinct. Data for all panels from www.iucnredlist.org. Reproduced from (IPBES, 2019), with permission.

Driven by a range of complex and interwoven causes […] biodiversity is declining at an alarming pace.

Against this dire background, the EU has drafted a Biodiversity Strategy 2030, an ambitious framework aimed to tackling the key reasons behind biodiversity loss. The plan hinges around a few main elements, such as the establishment of protected areas for at least 30% of Europe''s lands and seas (Fig 3); a significant increase of biodiversity‐rich landscape features on agricultural land by establishing buffer zones like hedges and fallow fields; halting and reversing the decline of pollinators; and planting 3 billion trees by 2030 (https://ec.europa.eu/info/strategy/priorities‐2019‐2024/european‐green‐deal/actions‐being‐taken‐eu/eu‐biodiversity‐strategy‐2030_en). The budget for implementing these measures was set at €20 billion per year.Open in a separate windowFigure 3Natura 2000, the EU''s network of protected areasIn 2019, 18% of land in the EU was protected as Natura 2000, with the lowest share of protected land in Denmark (8%) and the highest in Slovenia (38%). In 2019, the largest national network of terrestrial Natura 2000 sites was located in Spain, covering 138,111 km², followed by France (70,875 km²) and Poland (61,168 km²). Reproduced from Eurostat: https://ec.europa.eu/eurostat/statistics‐explained/index.php?title=Main_Page “Nature is vital for our physical and mental wellbeing, it filters our air and water, it regulates the climate and it pollinates our crops. But we are acting as if it didn''t matter, and losing it at an unprecedented rate”, said Virginijus Sinkevičius, Commissioner for the Environment, Oceans and Fisheries, at the press launch of the new EU action (https://ec.europa.eu/commission/presscorner/detail/en/ip_20_884). “This new Biodiversity Strategy builds on what has worked in the past, and adds new tools that will set us on a path to true sustainability, with benefits for all. The EU''s aim is to protect and restore nature, to contribute to economic recovery from the current crisis, and to lead the way for an ambitious global framework to protect biodiversity around the planet”.Environmental groups and other stakeholders have welcomed the EU''s pledge in principle. “This is a unique opportunity to shape a new society in harmony with nature”, applauded Wetlands International. “We must not forget that the biodiversity and climate crisis is a much bigger and persistent challenge for humanity than COVID‐19”, (https://europe.wetlands.org/news/welcoming‐the‐eu‐biodiversity‐strategy‐for‐2030/). EuroNatur, a foundation focused on conservation, stated that the goals set out by the new strategy provide a strong basis for improving the state of nature in the EU (www.euronatur.org).Alongside the voices of praise, however, many have expressed concerns that the strategy could turn into a little more than a wish list. “The big issue of the strategy is that while setting a goal for financial funds, the EU does not specify where the money is supposed to come from. It only says it should include ‘EU funds and national and private funding’”, commented the European Wilderness Society, an environmental advocacy non‐profit organization headquartered in Tamsweg, Austria. “Goals are important, but do not create change without an organized and sustainable implementation. It''s a good and ambitious document, but what is also obvious is the lack of strategy of how to implement it, and a lack of discussion of why previous documents of this type failed” (https://wilderness‐society.org/ambitious‐eu‐biodiversity‐strategy‐2030/).

Alongside the voices of praise, however, many have expressed concerns that the strategy could turn into a little more than a wish list.

The Institute for European Environmental Policy (IEEP) is on the same page. The sustainability think‐tank based in Brussels and London noted that the outgoing EU 2020 biodiversity strategy showed major implementation problems, especially because of lack of engagement at national level and of ad hoc legislation supporting the meeting of key targets. Therefore, “[it] can be argued that a legally binding approach to the biodiversity governance framework is urgently needed unless Member States and other key stakeholders can show greater intrinsic ownership to deliver on agreed objectives”, (https://ieep.eu/news/first‐impressions‐of‐the‐eu‐biodiversity‐strategy‐to‐2030). In addition, IEEP remarked that money is an issue, since the €20 billion figure appears more as an estimate than a certified obligation.“The intentions of the Commission are good and the strategy contains a number of measures and targets that can really make a difference. However, implementation depends critically on the member states and experiences with the Common Agricultural Policy the past decade or so have taught us that many of them are more interested in short‐term economic objectives than in safeguarding the natural wealth of their country for future generations”, commented David Kleijn, an ecologist and nature conservation expert at the Wageningen University, the Netherlands. “I think it is important that we now have an ambitious Biodiversity Strategy but at the same time I have little hope that we will be able to achieve its objectives”.

I think it is important that we now have an ambitious Biodiversity Strategy but at the same time I have little hope that we will be able to achieve its objectives.

There is further criticism against specific measures, such as the proposal of planting 3 billion trees. “To have lots of trees planted in an area does not necessarily translate into an increase of biodiversity. Biodiverse ecosystems are the result of million years of complex multi‐species interactions and evolutionary processes, which are not as easy to restore”, explained plant ecologist Susana Gómez‐González, from the University of Cádiz, Spain. Planting a large number of trees is a too simplistic approach for saving European forests from the combined effects of excessive anthropic pressure and climate change, and could even have detrimental effects (see Box 1). More emphasis should be placed instead in reducing tree harvesting in sensitive areas and in promoting natural forest renewal processes (Gómez‐González et al, 2020). “For a biodiversity strategy, increasing the number of trees, or even increasing the forest area, should not be an objective; priority should be given to the conservation and restoration of natural ecosystems, forests and non‐forests”, Gómez‐González said.In other cases, it could be difficult, if not impossible, to reach some of the goals because of lack of information. For example, one of the roadmap''s targets is to restore at least 25,000 km of Europe''s rivers back to free‐flowing state. However, the number of barriers dispersed along European rivers will probably prevent even getting close to the mark. An international research team has collected detailed information on existing instream barriers for 147 rivers in 36 European countries, coming up with the impressive figure of over 1.2 million obstacles that inevitably impact on river ecosystems, affecting the transport and dispersion of aquatic organisms, nutrients, and sediments (Belletti et al, 2020). Existing inventories mainly focused on dams and other large barriers, while, in fact, a large number of artificial structures are much smaller, such like weirs, locks, ramps, and fords. As a result, river fragmentation has been largely underestimated, and the models used to plan flow restoration might be seriously flawed. “To avoid ‘death by a thousand cuts’, a paradigm shift is necessary: to recognize that although large dams may draw most of the attention, it is the small barriers that collectively do most of the damage. Small is not beautiful”, concluded the authors (Belletti et al, 2020).

Box 1: Why many trees don''t (always) make a forestForests are cathedrals of biodiversity. They host by far the largest number of species on land, which provide food and essential resources for hundreds of millions of people worldwide. However, forests are disappearing and degrading at an alarming pace. The loss of these crucial ecosystems has given new impulses to a variety of projects aimed at stopping this devastation and possibly reversing the trend.Once it is gone, can you rebuild a forest? Many believe the answer is yes, and the obvious solution is to plant trees. Several countries have thus launched massive tree‐planting programs, notably India and Ethiopia, where 350 million trees have been planted in single day (https://www.unenvironment.org/news‐and‐stories/story/ethiopia‐plants‐over‐350‐million‐trees‐day‐setting‐new‐world‐record). The World Economic Forum has set up its own One Trillion Tree initiative (https://www.1t.org/) “to conserve, restore, and grow one trillion trees by 2030”. Launched in January last year at Davos, 1t.org was conceived as a platform for governments, companies and NGOs/civil society groups to support the UN Decade on Ecosystem Restoration (2021–2030). The initiative has been christened by renowned naturalist Jane Goodall, who commented: “1t.org offers innovative technologies which will serve to connect tens of thousands of small and large groups around the world that are engaged in tree planting and forest restoration”, (https://www.weforum.org/agenda/2020/01/one‐trillion‐trees‐world‐economic‐forum‐launches‐plan‐to‐help‐nature‐and‐the‐climate/).However, things are way more complicated than they appear: large‐scale tree planting schemes are rarely a viable solution and can even be harmful. “[A] large body of literature shows that even the best planned restoration projects rarely fully recover the biodiversity of intact forests, owing to a lack of sources of forest‐dependent flora and fauna in deforested landscapes, as well as degraded abiotic conditions resulting from anthropogenic activities”, commented Karen Holl from the University of Caliornia, Santa Cruz, and Pedro Brancalion from the University of São Paulo (Holl & Brancalion, 2020). A common problem of tree plantations, for example, is the low survival rate of seedlings, mostly because the wrong tree species are selected and due to poor maintenance after planting. Moreover, grasslands and savannas, which are often targeted for establishing new forests, are themselves treasure troves of biodiversity. Ending indiscriminate deforestation, improving the protection of existing forests, and promoting their restoration would therefore be a more efficient strategy to preserve biodiversity in the shorter term. If tree planting is indeed necessary, it should be well planned by selecting the right areas for reforestation, using suitable tree species that can maximize biodiversity, and involving local populations to maintain the plantations, Holl and Brancalion argue (Holl & Brancalion, 2020).

…even the best planned restoration projects rarely fully recover the biodiversity of intact forests, owing to a lack of sources of forest‐dependent flora and fauna in deforested landscapes…

The health of soil, where a high proportion of biodiversity is hosted, is another problem the new strategy should address in a more focused manner. “In my opinion, the EU Biodiversity Strategy is already a leap forward in terms of policy interest in soils in general and in soil biodiversity in particular. Compared with other nations/regions of the world, Europe is by far in the forefront regarding this issue”, commented Carlos António Guerra at the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, Germany, and Co‐leader of the Global Soil Biodiversity Observation Network (https://geobon.org/bons/thematic‐bon/soil‐bon/). “Nevertheless, the connection between soil biodiversity and ecological functions needs further commitments. Soils allow for horizontal integration of several policy agendas, from climate to agriculture and, very importantly, nature conservation. This is not explicit in the EU Biodiversity Strategy in regard to soils”. It remains to be seen if EU restoration plan will emphasize soil biodiversity, or consider it as a mere side effect of other initiatives, Guerra added. “A soil nature conservation plan should be proposed”, he said. “Only such a plan, that implies that current and future protected areas have to consider, describe and protect their soil biodiversity would make a significant push to help protect such a valuable resource”.More generally, research shows that the current paradigm of protection must be shifted to prevent further losses to biodiversity. In fact, an analysis of LIFE projects—a cornerstone of EU nature protection—found that conservation efforts are extremely polarized and strongly taxonomically biased (Mammola et al, 2020). From 1992 to 2018, investment in vertebrates was sixfold higher than that for invertebrates, with birds and mammals alone accounting for 72% of the targeted species and 75% of the total budget. In relative terms, investment per species for vertebrates has been 468 times higher than for invertebrates (Fig 4). There is no sound scientific reasoning behind this uneven conservation attention, but just popularity. “[T]he species covered by a greater number of LIFE projects were also those which attracted the most interest online, suggesting that conservation in the EU is largely driven by species charisma, rather than objective features”, the researchers wrote (Mammola et al, 2020).Open in a separate windowFigure 4Taxonomic bias in EU fauna protection effortsBreakdown of the number of projects (A) and budget allocation (B) across main animal groups covered by the LIFE projects (n = 835). (C) The most covered 30 species of vertebrates (out of 410) and invertebrates (out of 78) in the LIFE projects analyzed (n = 835). The vertical bar represents monetary investment and the blue scatter line the number of LIFE projects devoted to each species. Reproduced from (Mammola et al, 2020), with permission.     

The Data Governance Act and the EU's move towards facilitating data sharing

The implementation of the EU General Data Protection Regulation (GDPR) has had significant impacts on biomedical research, often complicating data sharing among researchers. The recently announced proposal for a new EU Data Governance Act is a promising step towards facilitating data sharing, if it can interplay well with the GDPR.Subject Categories: S&S: Ethics

The EU General Data Protection Regulation (GDPR) has affected biomedical research, often complicating data sharing. The recently announced proposal for a new EU Data Governance Act, is a promising step towards facilitating data sharing.

In an attempt to improve and increase data sharing in the EU and to optimize the re‐use of personal and non‐personal data, the European Commission has recently announced the proposal for a new EU Data Governance Act (https://ec.europa.eu/digital‐single‐market/en/news/proposal‐regulation‐european‐data‐governance‐data‐governance‐act). If approved, it will enable the creation and regulation of “secure spaces” where various types of data, including health data, can be shared and re‐used for both commercial and altruistic purposes, including scientific research. The Data Governance Act, within the framework of a European Strategy for Data, (https://ec.europa.eu/info/sites/info/files/communication‐european‐strategy‐dat‐19feb2020_en.pdf), would address some of the shortcomings and drawbacks of the current regulatory framework which holds back sharing and re‐using data for biomedical research purposes.While the proposed Act would apply to all types of personal and non‐personal data, the increasing demand for sharing health data has most likely been a major rationale for this new legislation of data governance. Notably, sharing health and genetic data for scientific research entails an extra layer of complexity, owing to concerns over data protection and privacy when sharing sensitive personal data. Vice versa, there are also concerns in the scientific community over the negative impact of regulatory restrictions on sharing health data in data‐driven biomedical research. The pressing question here is how far the EU’s proposed legislative and policy framework can offset either concerns?     

A method to the madness: Disentangling the individual forces that shape the rumen microbiome

The rumen microbiome ‐ a remarkable example of obligatory symbiosis with high ecological and social relevance Subject Categories: Digestive System, Ecology, Microbiology, Virology & Host Pathogen Interaction

Ruminants are intimately linked to mankind since their domestication some 8,000 years ago, and their close relationship may have well been one of the main drivers of human civilization (Diamond, 1997). Ruminants—cattle, sheep, goats, deer, gazelles, and so on—also embody the close link between solar energy transformed via photosynthesis and digestion into consumable products, such as meat, milk, leather, or wool, that have sustained humanity for millennia. Throughout this shared history, constant improvements through breeding, husbandry, and industrial livestock farming have greatly increased the production of milk, meat, and other animal‐based products.Ruminants, more so than any other mammalian group also represent the epitome of mammalian‐microbe symbiosis, as they rely completely on microbial fermentation to sustain their lives. In the rumen, the fermentative organ situated in the upper gastrointestinal tract resides a vast microbial community from all domains of life—bacteria, archaea, and eukarya—that turn indigestible plant feed into food for the animal. The rumen microbiome produces up to 70% of the energy the animal needs for growth and maintenance, and, from mankind''s perspective, for the production of food and other consumables.

Ruminants, more so than any other mammalian group, also represent the epitome of mammalian‐microbe symbiosis, as they rely completely on microbial fermentation to sustain their lives.

With growing understanding that these microorganisms are responsible for degrading plant material and supplying nutrients for the animals, a new research discipline emerged along with aspirations to improve the yield of livestock farming. While most research had understandably focused on production efficiency, it also showed that the rumen microbiome is intricately linked to many other phenotypes of the animal. This understanding comes at a time when we increasingly realize that mankind''s actions have a detrimental effect on the environment. The microbial fermentation in the rumen produces large amounts of methane, a potent greenhouse gas that has been demonstrated to contribute to global climate change. We therefore need to consider both our increased demand for meat and milk products and aim to mitigate the negative environmental impact of intensive livestock farming. Modulating the microbial community to sustain or further increase productivity while decreasing methane emissions has indeed become a major goal for microbial ecologists studying the rumen microbiome and its interactions with the host animal. In this article, we discuss the driving forces that affect the establishment and composition of the rumen microbiome and its plasticity, and potential avenues for harnessing these forces for a more sustainable production of animal products.     

N‐glycosylation of PD‐1 promotes binding of camrelizumab

PD‐1 is a highly glycosylated inhibitory receptor expressed mainly on T cells. Targeting of PD‐1 with monoclonal antibodies (MAbs) to block the interaction with its ligand PD‐L1 has been successful for the treatment of multiple tumors. However, polymorphisms at N‐glycosylation sites of PD‐1 exist in the human population that might affect antibody binding, and dysregulated glycosylation has been observed in the tumor microenvironment. Here, we demonstrate varied N‐glycan composition in PD‐1, and show that the binding affinity of camrelizumab, a recently approved PD‐1‐specific MAb, to non‐glycosylated PD‐1 proteins from E. coli is substantially decreased compared with glycosylated PD‐1. The structure of the camrelizumab/PD‐1 complex reveals that camrelizumab mainly utilizes its heavy chain to bind to PD‐1, while the light chain sterically inhibits the binding of PD‐L1 to PD‐1. Glycosylation of asparagine 58 (N58) promotes the interaction with camrelizumab, while the efficiency of camrelizumab to inhibit the binding of PD‐L1 is substantially reduced for glycosylation‐deficient PD‐1. These results increase our understanding of how glycosylation affects the activity of PD‐1‐specific MAbs during immune checkpoint therapy.