Swiss Academy of Sciences

Abstract. Computational models play an increasingly vital role in scientific research by enabling the numerical simulation of complex processes. Such models are also fundamental in geosciences. For instance, they offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of models, coupled with their integration into broader workflows, also often makes it challenging to reproduce results, evaluate processes, and build upon them. In this paper, we review the state and current practices of the development processes of the state-of-the-art land surface models used by the Global Carbon Budget. We combine the experience of modelers from the respective research groups with the expertise of software engineers from tech companies to outline key principles and tools for improving software quality in research. We explore four main areas: (1) model testing and validation, (2) scientific, technical, and user documentation, (3) version control, continuous integration, and code review, and (4) the portability and reproducibility of workflows. Our review reveals that while modeling communities are incorporating many best practices, significant room for improvement remains in areas such as automated testing, automated documentation, and reproducibility. Therefore, we here identify and promote essential software engineering practices, including numerous examples of practices from within the community that can serve as guidelines for other models and could help streamline processes across the entire community. We conclude with an open-source example implementation of these principles, demonstrating portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

Land use management can help address the human-induced climate and biodiversity crises. However, substantial transformations in land systems are needed to meet internationally agreed targets concerning nature conservation, restoration, sustainable agriculture, and tree cover. Such transformations influence land-atmosphere exchanges of energy, water, and carbon, and could have particularly strong effects on local to regional climate through changes in albedo and evapotranspiration. Here, we explore how land use management in Europe, consistent with the Kunming-Montreal Global Biodiversity Framework, the Nature Futures Framework, and a sustainable low-emissions scenario, would affect the European climate mid-century. Using Earth System Modelling and detailed land use, habitat, and species projections, we show that policy implementation guided by relational values (Nature as Culture) could lead to additional warming and drying further threatening biodiversity and human well-being. Conversely, promoting intrinsic values (Nature for Nature) or ecosystem services (Nature for Society) would not add major challenges for climate adaptation and mitigation. These different outcomes highlight the need to develop integrative land use scenarios that enhance biodiversity and stabilise the climate, while considering feedbacks from land to the atmosphere. Such scenarios could help navigate trade-offs and inform policy implementation in Europe.

Dynamic Global Vegetations Models (DGVM) are essential for understanding terrestrial carbon and nitrogen cycling, yet uncertainties remain high due to challenges in accurately representing complex biogeochemical processes in the models and limited ava

<strong class="journal-contentHeaderColor">Abstract.</strong> Soil carbon sequestration is an important strategy for climate change mitigation with several co-benefits, including increased water holding capacity and infiltration. However, a global-scale quantification of hydrological co-benefits for water availability to plants is still lacking. In this study, we investigate the effect of soil carbon sequestration on hydrology and water resources by conducting experiments with the Community Terrestrial Systems Model (CTSM). Using global experiments with spatially explicit soil organic carbon (SOC), we apply various carbon sequestration scenarios, including one aligned with the '4 per 1000' initiative, to investigate the effect on soil moisture and soil water balance variables with a focus on cropland regions. Our results show that soil organic carbon redistributes water within the soil profile, retaining moisture in the rooting zone and limiting percolation into deeper layers, which is particularly pronounced in arid regions with sandy soils. Under a scenario with a uniform SOC increase of gC kg^-1 soil, globally averaged total global soil liquid water content increases by 4 mm in the first 30 cm. Carbon sequestration also redistributes the soil water balance, with global mean reductions in surface runoff (&ndash;1 mm), subsurface runoff (&ndash;0.6 mm), and an increase in evapotranspiration (+2 mm), contributing to improved vegetation productivity. Water stress is modestly reduced across most regions, though effects vary spatially. Although the hydrological impacts of soil carbon sequestration are generally small in magnitude, they are consistent and systematic. The relative changes following realistic and policy-relevant SOC enhancement scenarios, such as those under the 4 per 1000 initiative, are limited due to the modest carbon additions involved. Nevertheless, these changes offer measurable eco-hydrological co-benefits that may support both climate mitigation and ecosystem resilience, particularly in water-limited environments.

This brief response to reviews of the Ascona Charter asks how it resonates with and connects diverse realities, concerns, and experiences of transformation. The Charter responds to a collective call from students and engaged scholars for adopting collective action that prioritizes transformation and positive change in the world, rather than remaining caught in neoliberal metrics and individualized trajectories. By operationalizing the Charter’s values, anthropology can reclaim its relevance and contribute meaningfully to addressing the triple planetary crisis. Through embracing multimodal approaches, fostering ethical partnerships, and advocating for systemic change, anthropologists can play a pivotal role in addressing the pressing challenges of our time.

ABSTRACT Understanding how actors perceive and anticipate future states of the world is gaining traction in climate change governance scholarship and related calls for sustainability transformations. However, smallholder farmers, indigenous groups, and local communities, who are expected to bear disproportionate burdens of loss and damage from climate change, remain underrepresented in future‐oriented research. In this paper, we outline key barriers to integrating bottom‐up perspectives on visions of the future in sustainability transformation research and develop a framework to support transdisciplinary research to more productively engage with diverse perspectives on agrarian‐climate futures. The framework is derived from (a) literature on climate change, loss and damage, anticipatory climate governance, and critical agrarian studies; (b) interviews, focus group discussions, and a stakeholder workshop in Ratanakiri province, Cambodia; and (c) an analysis of Cambodian climate change policies. It consists of five dimensions: (i) desirability; (ii) viability; (iii) agency; (iv) heuristics; and (v) responsibility. The framework aims to support researchers in better accounting for complex rural‐agrarian realities and reorienting future framingsfield from loss towards nurturing a “brighter” side of transformation. Integrating diverse rural‐agrarian perspectives on climate futures is critical for fostering and co‐creating more just and locally contingent pathways.

<strong class="journal-contentHeaderColor">Abstract.</strong> Computational models play an increasingly vital role in scientific research, by numerically simulating processes that cannot be solved analytically. Such models are fundamental in geosciences and offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of these models, coupled with their integration into broader workflows, also often makes reproducing results, evaluating processes, and building upon them highly challenging. In this paper, we review the current practices within the development processes of the state-of-the-art land surface models used by the Global Carbon Project. By combining the experience of modelers from the respective research groups with the expertise of professional software engineers, we bridge the gap between software development and scientific modeling to outline key principles and tools for improving software quality in research. We explore four main areas: 1) model testing and validation, 2) scientific, technical, and user documentation, 3) version control, continuous integration, and code review, and 4) the portability and reproducibility of workflows. Our review of current models reveals that while modeling communities are incorporating many of the suggested practices, significant room for improvement remains in areas such as automated testing, documentation, and reproducible workflows. For instance, there is limited adoption of automated documentation and testing, and provision of reproducible workflow pipelines remains an exception. This highlights the need to identify and promote essential software engineering practices within the scientific community. Nonetheless, we also discuss numerous examples of practices within the community that can serve as guidelines for other models and could even help streamline processes within the entire community. We conclude with an open-source example implementation of these principles built around the LPJ-GUESS model, showcasing portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

This special issue is dedicated to exploring some of the evolving landscapes of biomanufacturing in Switzerland, highlighting some of the key innovations, challenges, and opportunities shaping the sector.Switzerland's strong academic institutions, world-class research facilities and a robust regulatory framework have made it an attractive hub for both established pharmaceutical giants and innovative biotech startups.Switzerland has been an important contributor to innovation in the chemical, pharmaceutical and life sciences, building on the foundations of this success, which was laid in the 18 th century.Michael Altorfer et al. 'Biomanufacturing in Switzerland -Past, Present and Future' describe the development of the Swiss biotechnology sector from the early beginnings in the 1930s with a biocatalytic step in the vitamin C production to today's multifaceted application of biotechnology in Switzerland.As a matter of fact biotechnology has become a key asset to the contemporary Swiss economy, and the article outlines early steps, the current state of biomanufacturing, and key factors required to stay on a successful track.The Swiss Industrial Biocatalysis Consortium (SIBC) was founded in 2004 to promote biocatalysis as a technology across various industries within Switzerland for fine-or agro-chemicals, flavors and fragrances, or pharmaceuticals, where there are plenty of common denominators when discussing biocatalysis.Serena Bisagni et al. 'The Swiss Industrial Biocatalysis Consortium (SIBC) turns 20!' share examples of using biocatalysis to solve (stereo)chemical challenges and highlighting the innovative approaches and successful implementations in various industries.The beginnings of single-use technologies (SUT) dates back to the early 1950s with the polyethylene bags for blood.For readers who are not familiar with single use technology (SUT), the paper of Diego Schmidhalter et al. 'Single-Use Technology Today -A Cornucopia of Applications' is rich in technical and other information, gives an insight to SUT, applied today to the production of biopharmaceuticals ranging from cell cultures to products containing highly active compounds such as drug conjugates.Human and animal food and feed products today come from either plant or animal production systems.The huge potential of single cell-based nutrient production, based on the natural available microbial biodiversity, is not leveraged yet.Fabian Wahl et al. 'Microalgae as Key to a Land-free Circular On-farm Feed Production System' addresses the options of using microalgae as nutritious biomass with excellent bioavailability using atmospheric CO 2 as a carbon source.For this purpose, the Swiss microalgae collection AlgoScope was launched to identify, catalog, characterize, and conserve native Swiss microalgae with biotechnological potential.The perfusion mode for the production of biopharmaceuticals goes back to the 1990s.It has become increasingly important in biopharmaceutical production in recent years, and Vivianne Ott et al. 'Perfusion-Based Antibody Production in the Ambr 250 Modular' discuss a bioreactor system for the production of a mAb with Chinese Hamster Ovary (CHO) cells with ultra-high cell densities of more than 150 10 6 cells mL -1 for the inoculation and continuous mAb production over 23 days in a proof-of-concept experiment, achieving a volumetric productivity of 0.65 g L -1 d -1 .The paper of Andrew Gomm et al. from Syngenta 'Biotransformations at Syngenta: A Focused Perspective on Metabolites and Natural Products' concentrates on the use of biocatalysis for the production of metabolites and the importance of fermentation for natural products.The authors point to the fact that the structural complexity of agrochemicals is steadily increasing and resembles more and more that of pharmaceuticals.As in pharmaceuticals, it is important for market registration to know and profile the possible metabolites generated by the degradation of agrochemicals.However, this is actually more complicated than with pharmaceuticals, as many different degradation pathways of fungi or bacteria must be considered to assess the environmental fate and potential noxiousness of an agrochemical.Biomanufacturing can offer significant economic and environmental benefits compared to chemical production.Ulla Letinois et al. describe the biomanufacturing of vitamin B 1 (riboflavin), the antioxidant canthaxanthin and the fat-soluble vitamin A in their contribution 'Way Forward For Biomanufacturing and Biotechnology in Europe'.Global warming, loss of biodiversity, hunger and malnutrition requires immediate private-public commitments and investments, where biocatalysis, biotransformation and biosynthesis can contribute significantly to sustainable alternatives.Precision and efficiency are key aspects of biomanufacturing, advantages which ultimately lead to more sustainable processes.The strategic importance of biomanufacturing is the topic of Roland Wohlgemuth in 'Biomanufacturing as Key Technology for a Sustainable Bioeconomy'.The author describes why industrial biomanufacturing has been considered as the future of chemical production.The biomanufacturing initiatives which are ongoing and planned worldwide by several governments are an indication of its strategic importance.The challenges for sustainable solutions remain, and the search and innovation for future-proof solutions must be maintained.Switzerland, with its strong foundation and forwardthinking approach, is poised to play an important role in this rapidly evolving domain.We invite you to explore the articles in this issue and join the conversation on the future of biomanufacturing.

Abstract Aspergillus fungi are opportunistic pathogens that affect millions of people worldwide. Aspergilli produce organic acids to optimize the environmental pH and match the needs of their enzymatic machinery. In this study, we tested the hypothesis that this also occurs during infection. By producing oxalic acid (OA), Aspergillus would manipulate pH during lung infection and thus, interfering with this process could control the pathogen. To test this hypothesis, we assessed in silico the potential for OA production in a wide range of Aspergilli. A genetic marker for AO production was detected in most of the species including prevalent human pathogens. We tested OA production in vitro in four strains of A. niger and A. fumigatus , but only one of the A. niger strains produced OA consistently. For this fungal strain, oxalotrophic bacteria were able to control fungal growth via OA consumption. To translate this observation into a pre-clinical system, increasingly complex experiments were performed. In 3D-cell cultures, A. niger also secreted OA and modified pH and free Ca 2+ . Co-inoculation of the oxalotrophic bacterium inhibited the development of the fungus. However, biocontrol could not be replicated in Galleria mellonella , which is often used as an infection model. In contrast, the bacterium improved disease score and the absence of oxalate crystals in the lungs in the mouse model. This biocontrol interaction between oxalotrophic bacteria and A. niger represents a paradigm shift in the fight against opportunistic fungal pathogens, where the goal is to render the host environment less permissive to pathogen development One Sentence Summary Demonstration of biocontrol as a therapeutic concept to combat Aspergillus niger with oxalotrophic bacteria in an animal infection model