Pluralism in Evolutionary Theory

The review by Waxman and Gavrilets (Waxman and Gavrilets 2005) illustrates the collision of different mindsets in evolutionary theory. These differences originate from the awe-inspiring complexity of the evolutionary process itself: evolutionary understanding critically depends on processes at many biological levels. Starting out with base pairs and their sequences, scholars of evolution have to consider -- in the order of biological complexity -- alleles, quantitative allelic traits, physiological and morphological traits, life-history traits, demographic rates, fitness, changes in genotype frequencies, population population dynamics, trait substitution sequences, and population bifurcations, to eventually arrive at the levels of ecological communities and the biosphere. It would appear that no other field of contemporary science sports comparable ambitions

Long-Range Transformer Architectures for Document Understanding

Since their release, Transformers have revolutionized many fields from Natural Language Understanding to Computer Vision. Document Understanding (DU) was not left behind with first Transformer based models for DU dating from late 2019. However, the computational complexity of the self-attention operation limits their capabilities to small sequences. In this paper we explore multiple strategies to apply Transformer based models to long multi-page documents. We introduce 2 new multi-modal (text + layout) long-range models for DU. They are based on efficient implementations of Transformers for long sequences. Long-range models can process whole documents at once effectively and are less impaired by the document's length. We compare them to LayoutLM, a classical Transformer adapted for DU and pre-trained on millions of documents. We further propose 2D relative attention bias to guide self-attention towards relevant tokens without harming model efficiency. We observe improvements on multi-page business documents on Information Retrieval for a small performance cost on smaller sequences. Relative 2D attention revealed to be effective on dense text for both normal and long-range models.Comment: Conference: ICDAR 2023 Workshops on Document Analysis and Recognitio

Transport of proteins across mitochondrial membranes

The vast majority of proteins comprising the mitochondrion are encoded by nuclear genes, synthesized on ribosomes in the cytosol, and translocated into the various mitochondrial subcompartments. During this process proteins must cross the lipid membranes of the mitochondrion without interfering with the integrity or functions of the organelle. In recent years an approach combining biochemical, molecular, genetic, and morphological methodology has provided insights into various aspects of this complex process of intracellular protein sorting. In particular, a greater understanding of the molecular specificity and mechanism of targeting of mitochondrial preproteins has been reached, as a protein complex of the outer membrane which facilitates recognition and initial membrane insertion has been identified and characterized. Furthermore, pathways and components involved in the translocation of preproteins across the two mitochondrial membranes are being dissected and defined. The energetics of translocation and the processes of unfolding and folding of proteins during transmembrane transfer are closely linked to the function of a host of proteins known as heat-shock proteins or molecular chaperones, present both outside and inside the mitochondrion. In addition, the analysis of the process of folding of polypeptides in the mitochondrial matrix has allowed novel and unexpected insights into general pathways of protein folding assisted by folding factors. Pathways of sorting of proteins to the four different mitochondrial subcompartments — the outer membrane (OM), intermembrane space, inner membrane (IM) and matrix — are only partly understood and reveal an amazing complexity and variation. Many additional protein factors are involved in these latter processes, a few of which have been analyzed, such as cytochrome c heme lyase and cytochrome c 1 heme lyase, enzymes that catalyze the covalent addition of the heme group to cytochrome c and c 1 preproteins, and the mitochondrial processing peptidase which cleaves signal sequence after import of preproteins into the matrix. Thus, the study of transport of polypeptides through the mitochondrial membranes does not only contribute to the understanding of how biological membranes facilitate the penetration of macromolecules but also provides novel insights into the structure and function of this organelle. are being dissected and defined. The energetics of translocation and the processes of unfolding and folding of proteins during transmembrane transfer are closely linked to the function of a host of proteins known as heat-shock proteins or molecular chaperones, present both outside and inside the mitochondrion. In addition, the analysis of the process of folding of polypeptides in the mitochondrial matrix has allowed novel and unexpected insights into general pathways of protein folding assisted by folding factors. Pathways of sorting of proteins to the four different mitochondrial subcompartments — the outer membrane (OM), intermembrane space, inner membrane (IM) and matrix — are only partly understood and reveal an amazing complexity and variation. Many additional protein factors are involved in these latter processes, a few of which have been analyzed, such as cytochrome c heme lyase and cytochrome c 1 heme lyase, enzymes that catalyze the covalent addition of the heme group to cytochrome c and c 1 preproteins, and the mitochondrial processing peptidase which cleaves signal sequences after import of preproteins into the matrix. Thus, the study of transport of polypeptides through the mitochondrial membranes does not only contribute to the understanding of how biological membranes facilitate the penetration of macromolecules but also provides novel insights into the structure and function of this organelle

Achieving shared understanding in chronic care interactions: the role of caregivers

Purpose: Within the context of a research program on the most relevant discourse types in chronic care medical encounters, this contribution reports on a qualitative study on the role caregivers play within the process of shared understanding occurring between health-care professionals and elderly patients. The purpose of the paper is to highlight one dimension of such complexity, by bringing to light the challenges connected to the achievement of shared understanding between health-care professionals and elderly patients when caregivers are involved in the conversation. Design/methodology/approach: The paper reports on a two-step analysis of a corpus of transcripts of interactions in diabetes and hypertension settings. In the first step, caregivers’ contributions to deliberative sequences have been analyzed. In the second step, the analysis was extended to caregivers’ contributions to the whole encounter. Findings: The results show that professionals’ ability to engage caregivers in deliberations during the encounter and, more generally, to assign a role to caregivers as legitimate participants in the consultation may favor the smooth development of the interaction and an effective process of shared understanding among all participants. Originality/value: The paper further develops original research about the functions of the argumentative component in dialogues occurring in clinical settings

The Proceduralization of Hominin Knapping Skill: Memorizing Different Lithic Technologies

Reconstructing the technical and cognitive abilities of past hominins requires an understanding of how skills like stone toolmaking were learned and transmitted. We ask how much of the variability in the uptake of knapping skill is due to the characteristics of the knapping sequences themselves? Fundamental to skill acquisition is proceduralization, the process whereby skilful tasks are converted from declarative memories (consciously memorized facts and events) into procedural memories (sub-consciously memorized actions) via repetitive practice. From knapping footage, we time and encode each action involved in discoidal, handaxe, Levallois and prismatic blade production. The structure and complexity of these reduction sequences were quantified using k-mer analysis and Markov chains. The amount of time spent on tasks and the pattern of core rotations revealed portions of these reduction sequences that are predisposed to being converted into procedural memories. We observed two major pathways to achieve this proceduralization: either a repetitive or a predictable sequence of core rotations. Later Acheulean handaxes and Levallois knapping involved a predictable platform selection sequence, while prismatic blade knapping involved a repetitive exploitation of platforms. Technologies and the portions of their reduction sequence that lend themselves to proceduralization probably facilitated the more rapid uptake of stone toolmaking skill

Sedimentation, re-sedimentation and chronologies in archaeologically-important caves: problems and prospects

Excavations in the photic zones of caves have provided cornerstone archaeological sequences in many parts of the world. Before the appearance of modern dating techniques, cave deposits provided clear evidence for the antiquity, relative ages and co-occurrence of ancient human remains, material culture and fauna. Earlier generations of archaeologists had generally rather limited understanding of taphonomic and depositional processes, but the twentieth century saw considerable improvement in excavation and analytical techniques. The advent of modern dating and chronological methodologies offers very powerful tools for the analysis of cave fill deposits and this has resulted in the recognition of chronological incoherence in parts of some sites, with consequent re-evaluation of previous archaeological disputes. Obtaining multiple dates per context provides a means to assess the integrity and coherence of the archaeological and environmental records from cave fills. In the case of the Haua Fteah (Libya), this technique allowed the recognition of chronological coherence in low-energy depositional environments and limited recycling in high-energy contexts. We provide a conceptual model of the relationship between recycling, sedimentation rate and process energy. High-resolution investigation enables recognition of the complexity of the formation of cave sequences, thus an increasingly sophisticated understanding of human behaviour and environmental relationships in the past, and potentially gives a new life to old data

Earthquake Size Distribution: Power-Law with Exponent Beta = 1/2?

We propose that the widely observed and universal Gutenberg-Richter relation is a mathematical consequence of the critical branching nature of earthquake process in a brittle fracture environment. These arguments, though preliminary, are confirmed by recent investigations of the seismic moment distribution in global earthquake catalogs and by the results on the distribution in crystals of dislocation avalanche sizes. We consider possible systematic and random errors in determining earthquake size, especially its seismic moment. These effects increase the estimate of the parameter beta of the power-law distribution of earthquake sizes. In particular, we find that estimated beta-values may be inflated by 1-3% because relative moment uncertainties decrease with increasing earthquake size. Moreover, earthquake clustering greatly influences the beta-parameter. If clusters (aftershock sequences) are taken as the entity to be studied, then the exponent value for their size distribution would decrease by 5-10%. The complexity of any earthquake source also inflates the estimated beta-value by at least 3-7%. The centroid depth distribution also should influence the beta-value, an approximate calculation suggests that the exponent value may be increased by 2-6%. Taking all these effects into account, we propose that the recently obtained beta-value of 0.63 could be reduced to about 0.52--0.56: near the universal constant value (1/2) predicted by theoretical arguments. We also consider possible consequences of the universal beta-value and its relevance for theoretical and practical understanding of earthquake occurrence in various tectonic and Earth structure environments. Using comparative crystal deformation results may help us understand the generation of seismic tremors and slow earthquakes and illuminate the transition from brittle fracture to plastic flow.Comment: 46 pages, 2 tables, 11 figures 53 pages, 2 tables, 12 figure