Hasil untuk "Human evolution"

G. Roth, U. Dicke

David C. Geary

S. Rakoff-Nahoum, K. Foster, L. Comstock

Cooperative phenotypes are considered central to the functioning of microbial communities in many contexts, including communication via quorum sensing, biofilm formation, antibiotic resistance, and pathogenesis. The human intestine houses a dense and diverse microbial community critical to health, yet we know little about cooperation within this important ecosystem. Here we test experimentally for evolved cooperation within the Bacteroidales, the dominant Gram-negative bacteria of the human intestine. We show that during growth on certain dietary polysaccharides, the model member Bacteroides thetaiotaomicron exhibits only limited cooperation. Although this organism digests these polysaccharides extracellularly, mutants lacking this ability are outcompeted. In contrast, we discovered a dedicated cross-feeding enzyme system in the prominent gut symbiont Bacteroides ovatus, which digests polysaccharide at a cost to itself but at a benefit to another species. Using in vitro systems and gnotobiotic mouse colonization models, we find that extracellular digestion of inulin increases the fitness of B. ovatus owing to reciprocal benefits when it feeds other gut species such as Bacteroides vulgatus. This is a rare example of naturally-evolved cooperation between microbial species. Our study reveals both the complexity and importance of cooperative phenotypes within the mammalian intestinal microbiota.

D. Graur, Yichen Zheng, Nicholas Price et al.

A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as “affirming the consequent,” by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

Jordan Aiko Deja, Isidro Butaslac, Nicko Reginio Caluya et al.

Robots are moving beyond industrial settings into creative, educational, and public environments where interaction is open-ended and improvisational. Yet much of human-AI-robot interaction remains framed around performance and efficiency, positioning humans as supervisors rather than collaborators. We propose a re-framing of AI interaction with robots as scaffolding: infrastructure that enables humans to shape robotic behaviour over time while remaining meaningfully in control. Through scenarios from creative practice, learning-by-teaching, and embodied interaction, we illustrate how humans can act as executive directors, defining intent and steering revisions, while AI mediates between human expression and robotic execution. We outline design and evaluation implications that foreground creativity, agency, and flow. Finally, we discuss open challenges in social, scalable, and mission-critical contexts. We invite the community to rethink interacting with Robots and AI not as autonomy, but as sustained support for human creativity.

Shuo Niu, Dylan Clements, Marina Margalit Nemanov et al.

GenAI's ability to produce text and images is increasingly incorporated into human-AI co-creation tasks such as storytelling and video editing. However, integrating GenAI into these tasks requires enabling users to retain control over editing individual story elements while ensuring that generated visuals remain coherent with the storyline and consistent across multiple AI-generated outputs. This work examines a paradigm of creative decomposition and linking, which allows creators to clearly communicate creative intent by prompting GenAI to tailor specific story elements, such as storylines, personas, locations, and scenes, while maintaining coherence among them. We implement and evaluate StoryComposerAI, a system that exemplifies this paradigm for enhancing users' sense of control and content consistency in human-AI co-creation of digital stories.

Kevin Neis, Laia Civit, Kathrine Pedersen et al.

RNA therapeutics are powerful tools for gene modulation and targeted therapies, but their clinical application is hindered by nuclease degradation and immunogenicity. Incorporating chemical modifications, like locked nucleic acids (LNAs), can enhance nuclease resistance, targeting properties, and thermal stability. Traditionally, LNA incorporation has relied on solid‐phase synthesis of short RNAs. Engineered polymerases capable of incorporating xenonucleic acids (XNAs), including LNA, into longer RNAs have been described. However, their XNA yield is limited by primer and template copy numbers, and the generated DNA‐XNA duplexes can be difficult to purify. We present a novel approach for incorporating LNA‐ATP and LNA‐TTP alongside 2′fluoro (2′F)‐modified pyrimidines via in vitro transcription using a mutant T7 RNA polymerase. This method enables efficient, primer‐independent synthesis and amplification of LNA‐modified RNA with low error rates. To demonstrate its utility, we performed systematic evolution of ligands by exponential enrichment (SELEX) to select LNA‐ and 2′F‐modified aptamers targeting influenza hemagglutinin and human CD40 ligand, two therapeutically relevant proteins. Iterative SELEX cycles yielded aptamers with low‐nanomolar affinities, high specificity, increased thermal stability, and high nuclease resistance. Overall, this approach provides a scalable and versatile platform for generating chemically stabilized RNAs, fully compatible with SELEX, and holds potential for developing next‐generation RNA‐based therapeutics with improved pharmacokinetics.

Benedict Paten, Adam M. Novak, Jordan M. Eizenga et al.

The human reference genome is part of the foundation of modern human biology, and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph based models. Here, we survey various projects underway to build and apply these graph based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.

Asmita Pathak, A. Agrawal

C-reactive protein (CRP) is an evolutionarily conserved protein. From arthropods to humans, CRP has been found in every organism where the presence of CRP has been sought. Human CRP is a pentamer made up of five identical subunits which binds to phosphocholine (PCh) in a Ca2+-dependent manner. In various species, we define a protein as CRP if it has any two of the following three characteristics: First, it is a cyclic oligomer of almost identical subunits of molecular weight 20–30 kDa. Second, it binds to PCh in a Ca2+-dependent manner. Third, it exhibits immunological cross-reactivity with human CRP. In the arthropod horseshoe crab, CRP is a constitutively expressed protein, while in humans, CRP is an acute phase plasma protein and a component of the acute phase response. As the nature of CRP gene expression evolved from a constitutively expressed protein in arthropods to an acute phase protein in humans, the definition of CRP became distinctive. In humans, CRP can be distinguished from other homologous proteins such as serum amyloid P, but this is not the case for most other vertebrates and invertebrates. Literature indicates that the binding ability of CRP to PCh is less relevant than its binding to other ligands. Human CRP displays structure-based ligand-binding specificities, but it is not known if that is true for invertebrate CRP. During evolution, changes in the intrachain disulfide and interchain disulfide bonds and changes in the glycosylation status of CRP may be responsible for different structure-function relationships of CRP in various species. More studies of invertebrate CRP are needed to understand the reasons behind such evolution of CRP. Also, CRP evolved as a component of and along with the development of the immune system. It is important to understand the biology of ancient CRP molecules because the knowledge could be useful for immunodeficient individuals.

Steve Benford, Eike Schneiders, Juan Pablo Martinez Avila et al.

As robots enter the messy human world so the vital matter of safety takes on a fresh complexion with physical contact becoming inevitable and even desirable. We report on an artistic-exploration of how dancers, working as part of a multidisciplinary team, engaged in contact improvisation exercises to explore the opportunities and challenges of dancing with cobots. We reveal how they employed their honed bodily senses and physical skills to engage with the robots aesthetically and yet safely, interleaving improvised physical manipulations with reflections to grow their knowledge of how the robots behaved and felt. We introduce somatic safety, a holistic mind-body approach in which safety is learned, felt and enacted through bodily contact with robots in addition to being reasoned about. We conclude that robots need to be better designed for people to hold them and might recognise tacit safety cues among people.We propose that safety should be learned through iterative bodily experience interleaved with reflection.

Ri-Zhao Qiu, Shiqi Yang, Xuxin Cheng et al.

Training manipulation policies for humanoid robots with diverse data enhances their robustness and generalization across tasks and platforms. However, learning solely from robot demonstrations is labor-intensive, requiring expensive tele-operated data collection which is difficult to scale. This paper investigates a more scalable data source, egocentric human demonstrations, to serve as cross-embodiment training data for robot learning. We mitigate the embodiment gap between humanoids and humans from both the data and modeling perspectives. We collect an egocentric task-oriented dataset (PH2D) that is directly aligned with humanoid manipulation demonstrations. We then train a human-humanoid behavior policy, which we term Human Action Transformer (HAT). The state-action space of HAT is unified for both humans and humanoid robots and can be differentiably retargeted to robot actions. Co-trained with smaller-scale robot data, HAT directly models humanoid robots and humans as different embodiments without additional supervision. We show that human data improves both generalization and robustness of HAT with significantly better data collection efficiency. Code and data: https://human-as-robot.github.io/

Thomas Versosky, Dilshodbek Nishonov, Li- Tu

Proper genome organization is essential for genome function and stability. Disruptions to this organization can lead to detrimental effects and the transformation of cells into diseased states. Individual chromosomes and their subregions can move or rearrange during transcriptional activation, in response to DNA damage, and during terminal differentiation. Techniques such as fluorescence in situ hybridization (FISH) and chromosome conformation capture (e.g., 3C and Hi-C) have provided valuable insights into genome architecture. However, these techniques require cell fixation, limiting studies of the temporal evolution of chromatin organization in detail. Our understanding of the heterogeneity and dynamics of chromatin organization at the single-cell level is still emerging. To address this, clustered regularly interspaced short palindromic repeats (CRISPR)/dead Cas9 (dCas9) systems have been repurposed for precise live-cell imaging of genome dynamics. This protocol uses a system called CRISPRainbow, a powerful tool that allows simultaneous targeting of up to seven genomic loci and tracks their locations over time using spectrally distinct fluorescent markers to study real-time chromatin organization. Multiple single-guide RNA (sgRNA), carrying specific RNA aptamers for labeling, can be cloned into a single vector to improve transfection efficiency in human cells. The precise targeting of CRISPRainbow offers distinct advantages over previous techniques while also complementing them by validating findings in live cells.

Zhixin Guo, Tao Wang, Chaoyang Wang et al.

Abstract The rare earth elements Sm and Nd significantly address fundamental questions about crustal growth, such as its spatiotemporal evolution and the interplay between orogenesis and crustal accretion. Their relative immobility during high-grade metamorphism makes the Sm-Nd isotopic system crucial for inferring crustal formation times. Historically, data have been disseminated sporadically in the scientific literature due to complicated and costly sampling procedures, resulting in a fragmented knowledge base. However, the scattering of critical geoscience data across multiple publications poses significant challenges regarding human capital and time. In response, we present an automated tabular extraction method for harvesting tabular geoscience data. We collect 10,624 Sm-Nd data entries from 9,138 tables in over 20,000 geoscience publications using this method. We manually selected 2,118 data points from it to supplement the previously constructed global Sm-Nd dataset, increasing its sample count by over 20%. Our automatic data collection methodology enhances the efficiency of data acquisition processes spanning various scientific domains.

Cinthya Soledad Manjarrez-Rangel, Silvana Raquel Halac, Luciana Del Valle Mengo et al.

Eutrophication has intensified in lacustrine systems across the American continent, which has been primarily driven by human activities such as intensive agriculture, wastewater discharge, and land-use change. This phenomenon adversely affects water quality, biodiversity, and ecosystem functioning. However, studies addressing the historical evolution of trophic states in lakes and reservoirs remain limited—particularly in tropical and subtropical regions. In this context, sedimentary records serve as invaluable archives for reconstructing the environmental history of water bodies. Paleolimnological approaches enable the development of robust chronologies to further analyze physical, geochemical, and biological proxies to infer long-term changes in primary productivity and trophic status. This review synthesizes the main methodologies used in paleolimnological research focused on trophic state reconstruction with particular attention to the utility of proxies such as fossil pigments, diatoms, chironomids, and elemental geochemistry. It further underscores the need to broaden spatial research coverage, fostering interdisciplinary integration and the use of emerging tools such as sedimentary DNA among others. High-resolution temporal records are critical for disentangling natural variability from anthropogenically induced changes, providing essential evidence to inform science-based lake management and restoration strategies under anthropogenic and climate pressures.

Doris Esenarro, Jimena Ccalla, Guisela Yabar et al.

The objective of this research is to conduct a spatial analysis of the functional Andean worldview of the Ankasmarka Archaeological Site, located in Calca, Peru. The preservation of cultural heritage in Latin America faces significant challenges that threaten the integrity of key sites such as Ankasmarka. Despite its historical relevance, this site lacks available open access information and data, collected in accessible reports, which hinders the attraction of attention and funding necessary for its conservation. Furthermore, urbanization and uncontrolled tourism negatively impact both cultural traditions and the connection of local communities with their past. The methodology employed is based on a systematic review of primary information, supplemented by excavation reports and official sources. Specialized software such as AutoCAD Architecture and Revit were used to carry out the topographic and architectural survey of the site, enabling the precise and rigorous interpretation of the data. This article focuses on the spatial and functional description of the site, with the aim of paving the way for future research in specific areas such as formal and structural analysis, as well as social and political dynamics. The results reveal a complex organizational structure at Ankasmarka, with enclosures designated for various functions, particularly storage and agricultural activities. The site is divided into three sectors: Sector A, which includes housing, storage areas, and tombs; and Sector B and C, with the highest concentration of housing and agricultural zones with storage areas, respectively. The findings underscore the interrelationship between agriculture, funerary practices, and architecture, highlighting the importance of Ankasmarka in the lives of its ancient inhabitants and the need for continued future research.

Daniel B. Mills, Jennifer L. Macalady, Adam Frank et al.

According to the "hard-steps" model, the origin of humanity required "successful passage through a number of intermediate steps" (so-called "hard" or "critical" steps) that were intrinsically improbable with respect to the total time available for biological evolution on Earth. This model similarly predicts that technological life analogous to human life on Earth is "exceedingly rare" in the universe. Here, we critically reevaluate the core assumptions of the hard-steps model in light of recent advances in the Earth and life sciences. Specifically, we advance a potential alternative model where there are no hard steps, and evolutionary novelties (or singularities) required for human origins can be explained via mechanisms outside of intrinsic improbability. Furthermore, if Earth's surface environment was initially inhospitable not only to human life, but also to certain key intermediate steps in human evolution (e.g., the origin of eukaryotic cells, multicellular animals), then the "delay" in the appearance of humans can be best explained through the sequential opening of new global environmental windows of habitability over Earth history, with humanity arising relatively quickly once the right conditions were established. In this co-evolutionary (or geobiological) scenario, humans did not evolve "early" or "late" with respect to the total lifespan of the biosphere, but "on time."

Sergio. Martín Serrano, Rubén Izquierdo, Iván García Daza et al.

In the field of autonomous driving research, the use of immersive virtual reality (VR) techniques is widespread to enable a variety of studies under safe and controlled conditions. However, this methodology is only valid and consistent if the conduct of participants in the simulated setting mirrors their actions in an actual environment. In this paper, we present a first and innovative approach to evaluating what we term the behavioural gap, a concept that captures the disparity in a participant's conduct when engaging in a VR experiment compared to an equivalent real-world situation. To this end, we developed a digital twin of a pre-existed crosswalk and carried out a field experiment (N=18) to investigate pedestrian-autonomous vehicle interaction in both real and simulated driving conditions. In the experiment, the pedestrian attempts to cross the road in the presence of different driving styles and an external Human-Machine Interface (eHMI). By combining survey-based and behavioural analysis methodologies, we develop a quantitative approach to empirically assess the behavioural gap, as a mechanism to validate data obtained from real subjects interacting in a simulated VR-based environment. Results show that participants are more cautious and curious in VR, affecting their speed and decisions, and that VR interfaces significantly influence their actions.

Laura Stegner, David Porfirio, Laura M. Hiatt et al.

End-user development (EUD) represents a key step towards making robotics accessible for experts and nonexperts alike. Within academia, researchers investigate novel ways that EUD tools can capture, represent, visualize, analyze, and test developer intent. At the same time, industry researchers increasingly build and ship programming tools that enable customers to interact with their robots. However, despite this growing interest, the role of EUD within HRI is not well defined. EUD struggles to situate itself within a growing array of alternative approaches to application development, such as robot learning and teleoperation. EUD further struggles due to the wide range of individuals who can be considered end users, such as independent third-party application developers, consumers, hobbyists, or even employees of the robot manufacturer. Key questions remain such as how EUD is justified over alternate approaches to application development, which contexts EUD is most suited for, who the target users of an EUD system are, and where interaction between a human and a robot takes place, amongst many other questions. We seek to address these challenges and questions by organizing the first End-User Development for Human-Robot Interaction (EUD4HRI) workshop at the 2024 International Conference of Human-Robot Interaction. The workshop will bring together researchers with a wide range of expertise across academia and industry, spanning perspectives from multiple subfields of robotics, with the primary goal being a consensus of perspectives about the role that EUD must play within human-robot interaction.

Alessia Morittu

Prison culture encompasses the unwritten rules, values, behaviors, and power structures within correctional institutions, emerges from interactions among inmates, staff, and the broader societal context. This culture encompasses social hierarchies, unwritten behavioral codes, survival mechanisms, and attitudes towards correctional systems. Its influence extends to inmates’ behavior, perceptions, psychological well-being, and the dynamics of prison management. Studying prison culture is vital for identifying institutional gaps, enhancing safety and efficiency, supporting inmate rehabilitation, safeguarding human rights, and informing evidence-based criminal justice policies. This chapter examines the historical evolution of prison culture from the 1800s to today, exploring its elements, effects, and the challenges it poses. By analyzing these aspects, the chapter aims to foster a comprehensive understanding to guide humane and effective corrections practices.   Inside-out: esplorare la cultura carceraria. La cultura carceraria comprende le regole non scritte, i valori, i comportamenti e le strutture di potere all’interno delle istituzioni correttive, e nasce dalle interazioni tra detenuti, personale e il contesto sociale più ampio. Questa cultura include gerarchie sociali, codici comportamentali non scritti, meccanismi di sopravvivenza e atteggiamenti nei confronti dei sistemi correttivi. La sua influenza si estende al comportamento dei detenuti, alle loro percezioni, al benessere psicologico e alle dinamiche della gestione carceraria. Studiare la cultura carceraria è fondamentale per identificare lacune istituzionali, migliorare la sicurezza e l’efficienza, supportare la riabilitazione dei detenuti, tutelare i diritti umani e informare politiche di giustizia penale basate su dati concreti. Questo capitolo esamina l’evoluzione storica della cultura carceraria dal 1800 a oggi, esplorandone gli elementi, gli effetti e le sfide che pone. Analizzando questi aspetti, il capitolo mira a promuovere una comprensione approfondita per guidare pratiche correttive umane ed efficaci.

Parag Khanna, Elmira Yadollahi, Mårten Björkman et al.

Despite great advances in what robots can do, they still experience failures in human-robot collaborative tasks due to high randomness in unstructured human environments. Moreover, a human's unfamiliarity with a robot and its abilities can cause such failures to repeat. This makes the ability to failure explanation very important for a robot. In this work, we describe a user study that incorporated different robotic failures in a human-robot collaboration (HRC) task aimed at filling a shelf. We included different types of failures and repeated occurrences of such failures in a prolonged interaction between humans and robots. The failure resolution involved human intervention in form of human-robot bidirectional handovers. Through such studies, we aim to test different explanation types and explanation progression in the interaction and record humans.