Max Planck Institute for the History of Science

In this unit, we approach soil as an active material that contributes to compos- ing (and decomposing!) our lifeworlds. Doing so asks us to consider how the composition of soil is linked to flows of energy and materials and dynamically intertwined with perception and response of various living and non-living processes. We borrow Tim Ingold’s notion of the ‘ecology of material’ to help us think through soil as ‘matter that is always already historical’ and how its mate- rial properties become a matter of concern for present communities and future generations. This unit seeks to answer these questions through 1) introductory overview to the material composition of soil and its relation to use; 2) a review of the ‘metabolic’ turn in soil studies; and 3) an exercise to think through the composition of soil as a form of material memory that shapes future growth. See the source list at the end of the syllabus for full details of suggested reading and viewing materials.

Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SP) score, and relatively little attention has been paid to whether this objective function accurately reflects alignment accuracy. Here, we evaluate the performance of the SP score using simulated and empirical benchmark alignments. For each dataset, we compare alternative MSAs derived from the same unaligned sequences and quantify the relationship between their SP scores and their distances from a reference alignment. We show that the alignment with the optimal SP score often does not correspond to the most accurate alignment. To address this limitation, we develop deep-learning-based scoring functions that integrate a collection of MSA features. We first introduce Model 1, a regression model that predicts the distance of a given MSA from the reference alignment. Across simulated and empirical datasets, this learned score correlates more strongly with true alignment accuracy than the SP score. However, Model 1 is less effective at identifying the best alignment among alternatives. We therefore develop Model 2, which takes as input a set of alternative MSAs generated from the same sequences and predicts their relative ranking. Model 2 more accurately identifies the top-ranking MSA than the SP score, Model 1, and several widely used alignment programs. Using simulations, we show that selecting MSAs based on our approach leads to more accurate phylogenetic reconstructions.

Abstract Stable acquisitions of metabolism, such as the endosymbiotic incorporation of eukaryotic chloroplasts, are thought to proceed through mechanisms that increase the genetic repertoire of the host and allow for vertical integration of new metabolism. Here we test these predictions using the chloroplast-stealing marine ciliate genus Mesodinium by comparing transcriptomes from species that represent a spectrum from full heterotrophy to nearly full phototrophy. In contrast to theory, we find a striking divestment in metabolic autonomy with increased reliance on acquired photosynthesis. Indeed, the highly photosynthetic, red tide-forming Mesodinium rubrum appears to have lost the capacity to synthesize amino acids, metabolize fatty acids, and produce peroxisomes. Our results portray a metabolic parasite, masquerading as a free-living ciliate, yet incapable of satisfying most of its basic anabolic needs.

Abstract The selection and availability bias concerning digital archives can be a problem for empirical studies. In the context of historical correspondence networks, we still have limited information about how missing data can affect and hinder the variables of our interest. Along these lines, we introduce an agent-based model to reconstruct historical communication using letters. We use this model to simulate the letter-sending process and its subsequent archival. We use it to build counterfactual networks and learn how the missing data caused by the archival of the letters might bias the network statistics.

Abstract In the previous paper, we have outlined the systematic interconnections that, between the 1950s and 1960s, Iron Curtain notwithstanding, prepared a unitary framework for the exploration of the “violent universe”, thanks to the emergence of new astronomies (radio, gamma, X-ray) and the rise of relativistic astrophysics. In this paper, we will zoom-in on a Soviet event, the nature of which is not entirely clear, that took place in Tartu in the summer of 1962. Calling attention to it will not only allow us to fill a historiographical gap (since the premonitions of relativistic and neutrino astrophysics that were discussed have eluded the historians’ attention), but also to highlight important elements of its broader context and focus on some significant personalities who were present there. In this way, we will further show how the conceptual links that we have previously traced were indeed embedded in the technological scenario of the Cold War, shaped by the arms race and the space race. Once these aspects are clarified, we will expand on three versatile personalities who, in different ways, embodied the flowing together of new physical, astronomical, and cosmological developments: I.S. Shklovsky, B.M. Pontecorvo and, perhaps more than anyone else, one of the former leaders of the Soviet H-bomb project, Ya.B. Zel’dovich. Starting from the period of the Tartu event, Zel’dovich put his military work to the side (but exapting new technological possibilities from that) and led one of the world’s most important groups in the newly born relativistic astrophysics, with all its implications and interconnections with fundamental physics. By sketching the outcomes of the research of these scientists around the year of the Tartu event and then throughout the 1960s, we will also be able to outline the transition from the early “shared culture” (1950s-beginning of the 1960s) that we have been emphasizing to the unified perspectives that emerged in the following decades, up to multimessenger astronomy.

The International Geophysical Year (1957–58), a collaboration of sixty-seven countries across fourteen disciplines to study the Earth, provides a compelling case study for examining the complex interplay between the Cold War’s geopolitical alliances and scientific practice. This article focuses on Mexico, with its rich seismological tradition and geographical proximity to the United States, as a unique vantage point to explore this intersection. By analyzing the collaborations, research planning, and data-sharing efforts of Mexican seismologists and their international counterparts, the article investigates how Cold War geopolitical tensions influenced scientific practice during the International Geophysical Year and how scientific practices, in turn, offered new language for geopolitics. As scientists organized hemispheric geophysical practices and data management, science emerged as both a manifestation of US hegemony over the Americas and a tool for negotiating this hegemony. This article delves into how Mexican geophysicists diplomatically navigated a global scientific endeavor in the multipolar Cold War, drawing on documents from the Comité Spécial of the International Geophysical Year, the Pan-American Committee for the International Geophysical Year, and the Mexican Committee for the International Geophysical Year. We argue that the International Geophysical Year served as a platform for global diplomacy, enabling Latin American scientists to assert their countries’ sovereignty and challenge the United States’ dominant geophysical data management system in the Western Hemisphere. This article highlights the underlying tensions surrounding data sovereignty and scientific collaboration amid the Inter-American Cold War, shedding light on the International Geophysical Year’s significance in shaping international relations.

Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include thePhotorhabdus asymbioticavirulence cassettes and the antifeeding prophage fromSerratia entomophila, which have been engineered for heterologous cargo delivery. Recent genomic analyses identified previously uncharacterized eCIS gene clusters in the opportunistic human pathogenSalmonella entericasubspeciessalamae, but their structure, function, and biotechnological potential remain unexplored. Here, we report a high-resolution cryo-electron microscopy structure of theS. entericaeCIS. Our atomic models reveal a unique sheath architecture, an expansive cage-like shell around a central spike, and an associated transmembrane hydrolase. We identify a putative effector encoded within the operon exhibiting periplasmic toxicity and provide evidence that theS. entericaeCIS deviates from canonical eCISs by interacting with the inner membrane. Guided by these structural features, we uncover a previously unannotated cluster of contractile injection systems (CISs). Together, our findings expand the known diversity of CIS structures and functions and lay the groundwork for engineering customizable protein delivery platforms.

Abstract Cancer-associated fibroblasts remain poorly understood, with some of them originating from the bone marrow. We therefore took advantage of the diversity of bone marrow stromal cells to shed light on how fibroblasts modulate cancer growth. In two murine cancer models, adding these fibroblasts to tumor cells resulted in smaller lesions. Suppression was enhanced by pretreatment with fibronectin, while genetic deletion of fibronectin in a small subpopulation of stromal cells expressing osterix/ sp7 restored growth. The suppressive stromal population showed two more characteristics: the absence of CD31/ pecam1 and CD105/ endoglin . However, only a decrease in CD105/ ENDOGLIN in melanoma patients translated in improved survival. Mechanistically, fibronectin or fibronectin fragments activate integrin α5β1 and TLR4 and increase chemokine production by stromal cells ultimately leading to enhanced recruitment and activity of Ly6G + myeloid cells without T-cell involvement. This work thus characterizes a beneficial interaction between stromal cells and neutrophils enhancing the immune response against early cancer. Highlights Stromal cells can be divided into two populations, a tumor supportive one with the potential to stimulate angiogenesis and an inhibitory one with the potential to enhance the immune response Stromal fibronectin expressing the transduction factor osterix/ sp7 produce fibronectin that acts on α5β1 integrin and/or TLR4 on neighboring fibroblasts to modulate Ly6G + immune cells and suppress tumor growth One sentence summary Tumor inhibitory fibroblasts have three characteristics and through production of fibronectin act on neighboring cells inducing signaling cascades that ultimately lead to a stronger immune response against early cancer.

In South Korea, the nation with the world's highest density of nuclear power plants, the disposal of high-level radioactive waste has become a pressing sociotechnical concern. Faced with local residents’ refusal of disposal facilities, scientists at the national research institutes have been making their case that the nation's underground is a safe and trustworthy site for radioactive waste disposal. This paper examines three strategies used by government scientists to turn the underground into a reliable container of radioactive waste. First, their practice of mapping mitigates uncertainties about underground irregularities and produces a widely acceptable representation of strata. Second, scientists utilize simulations to contain long-term changes and extend their epistemological power into the far future. Third, scientists propagate their subterranean visions to a broader audience by using underground laboratories as a site of demonstration and persuasion. These spatial, temporal, and cultural strategies let scientists and the Korean government consolidate the strata into physically durable and politically governable territory. The analysis of geological disposal in South Korea asks us to move beyond the technopolitics of extraction to explore that burial as an increasingly important site for STS research.