scholarly journals Rooting the tree of life: the phylogenetic jury is still out

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140329 ◽  
Author(s):  
Richard Gouy ◽  
Denis Baurain ◽  
Hervé Philippe
Keyword(s):  
Evolutionary Process ◽  
Phylogenetic Inference ◽  
Life Forms ◽  
Tree Of Life ◽  
Fundamental Issue ◽  
Long Branch Attraction ◽  
Substitution Process ◽  
Phylogenetic Framework ◽  
New Evidence ◽  
Shed Light

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.

Aleksey Peshkov as an editor of Samarskaya Gazeta

2020 ◽  
pp. 128-138
Author(s):  
A. S. Bik-Bulatov
Keyword(s):  
Local History ◽  
Organizational Skills ◽  
First Time ◽  
New Evidence ◽  
Insight Into ◽  
Shed Light

The article uses little known letters of M. Gorky, many of which were published for the first time in 1997, as well as findings of Samara-based experts in local history to shed light on the writer’s work as editor-in-chief of the Samarskaya Gazeta newspaper in 1895. The researcher introduces hitherto unstudied reminiscences of the journalist D. Linyov (Dalin) about this period, which reference a letter by Gorky, now lost. The paper details a newly discovered episode of Gorky’s professional biography as a journalist: it concerns his campaign against a Samara ‘she-wolf,’ the madam of a local brothel A. Neucheva. Linyov’s reminiscences turn out to be an important and interesting source, offering an insight into the daily grind of the young editor Gorky, providing new evidence of his excellent organizational skills, and describing his moral and social stance. The author presents his work in the context of a recently initiated broader discussion about the need to map out all Russian periodicals for the period until 1917, as well as all research devoted to individual publications.

scholarly journals Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST

2020 ◽  
Vol 70 (1) ◽  
pp. 181-189
Author(s):  
Guy Baele ◽  
Mandev S Gill ◽  
Paul Bastide ◽  
Philippe Lemey ◽  
Marc A Suchard
Keyword(s):  
High Performance ◽  
Markov Models ◽  
Marginal Likelihood ◽  
Likelihood Estimation ◽  
Phylogenetic Inference ◽  
Time Variability ◽  
Substitution Process ◽  
Wide Range ◽  
Markov Modulated ◽  
Over Time

Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.]

scholarly journals Application of Biomimetics to Architectural and Urban Design: A Review across Scales

2020 ◽  
Vol 12 (23) ◽  
pp. 9813 ◽  
Author(s):  
Yuta Uchiyama ◽  
Eduardo Blanco ◽  
Ryo Kohsaka
Keyword(s):  
Urban Design ◽  
Architectural Design ◽  
Evolutionary Process ◽  
Future Research ◽  
Conceptual Level ◽  
Sustainable Society ◽  
Types Of Knowledge ◽  
The Social ◽  
Different Types ◽  
Shed Light

Application of biomimetics has expanded progressively to other fields in recent years, including urban and architectural design, scaling up from materials to a larger scale. Besides its contribution to design and functionality through a long evolutionary process, the philosophy of biomimetics contributes to a sustainable society at the conceptual level. The aim of this review is to shed light on trends in the application of biomimetics to architectural and urban design, in order to identify potential issues and successes resulting from implementation. In the application of biomimetics to architectural design, parts of individual “organisms”, including their form and surface structure, are frequently mimicked, whereas in urban design, on a larger scale, biomimetics is applied to mimic whole ecosystems. The overall trends of the reviewed research indicate future research necessity in the field of on biomimetic application in architectural and urban design, including Biophilia and Material. As for the scale of the applications, the urban-scale research is limited and it is a promising research which can facilitate the social implementation of biomimetics. As for facilitating methods of applications, it is instrumental to utilize different types of knowledge, such as traditional knowledge, and providing scientific clarification of functions and systems based on reviews. Thus, interdisciplinary research is required additionally to reach such goals.

scholarly journals Where the action could be: Speakers look at graspable objects and meaningful scene regions when describing potential actions

2019 ◽  
Author(s):  
Gwendolyn L Rehrig ◽  
Candace Elise Peacock ◽  
Taylor Hayes ◽  
Fernanda Ferreira ◽  
John M. Henderson
Keyword(s):  
Visual Attention ◽  
Real World ◽  
Language Production ◽  
Native English Speakers ◽  
English Speakers ◽  
Linguistic Processing ◽  
General Meaning ◽  
New Evidence ◽  
Shed Light ◽  
Better Than

The world is visually complex, yet we can efficiently describe it by extracting the information that is most relevant to convey. How do the properties of real-world scenes help us decide where to look and what to say? Image salience has been the dominant explanation for what drives visual attention and production as we describe displays, but new evidence shows scene meaning predicts attention better than image salience. Here we investigated the relevance of one aspect of meaning, graspability (the grasping interactions objects in the scene afford), given that affordances have been implicated in both visual and linguistic processing. We quantified image salience, meaning, and graspability for real-world scenes. In three eyetracking experiments, native English speakers described possible actions that could be carried out in a scene. We hypothesized that graspability would preferentially guide attention due to its task-relevance. In two experiments using stimuli from a previous study, meaning explained visual attention better than graspability or salience did, and graspability explained attention better than salience. In a third experiment we quantified image salience, meaning, graspability, and reach-weighted graspability for scenes that depicted reachable spaces containing graspable objects. Graspability and meaning explained attention equally well in the third experiment, and both explained attention better than salience. We conclude that speakers use object graspability to allocate attention to plan descriptions when scenes depict graspable objects within reach, and otherwise rely more on general meaning. The results shed light on what aspects of meaning guide attention during scene viewing in language production tasks.

From Capital to Colony: Five New Inscriptions from Roman Crete

2006 ◽  
Vol 101 ◽  
pp. 385-426
Author(s):  
M. W. Baldwin Bowsky
Keyword(s):  
Southern Italy ◽  
Religious Practice ◽  
Geographical Mobility ◽  
New Evidence ◽  
Shed Light

This article present and contextualises five new inscriptions from central Crete: one from the hinterland of Gortyn, two from Knossos, and two more in all likelihood from Knossos. Internal geographical mobility from Gortyn to Knossos is illustrated by a Greek inscription from the hinterland of Gortyn. The Knossian inscriptions add new evidence for the local affairs of the Roman colony. A funerary or honorary inscription and two religious dedications – all three in Latin – give rise to new points concerning the well-attested link between Knossos and Campania. The colony's population included people, many of Campanian origin, who were already established in Crete, as well as families displaced from southern Italy in the great post-Actium settlement. The two religious dedications shed light on the city's religious practice, including a newly revealed cult of Castor, and further evidence for worship of the Egyptian gods. Oddest of all, a Greek inscription on a Doric epistyle names Trajan or Hadrian. These four inscriptions are then set into the context of linguistic choice at the colony. Epigraphic and numismatic evidence for the use of Latin and Greek in the life of the colony is analyzed on the basis of the available inscriptions, listed by category and date in an appendix.

Tymieniecka’s phenomenology of life

2001 ◽  
Vol 2 (1) ◽  
pp. 103-134
Author(s):  
Gary Backhaus
Keyword(s):  
Phenomenological Study ◽  
Evolutionary Process ◽  
Life Forms ◽  
Moral Sense ◽  
Constitutive Function ◽  
Passive Synthesis ◽  
Evolution Of Life ◽  
The Aesthetic ◽  
The Mind ◽  
Transformative Function

Anna-Teresa Tymieniecka expands the phenomenological study of meanings (sense-bestowal) into an onto-genetic inquiry by grounding it in a phenomenology of life, including the emotional dimension. This phenomenology of life is informed by the empirical sciences and its doctrines parallel the new scientific paradigm of open dynamic systems. Embedded in the dynamics of the real individuation of life forms, human consciousness emerges at a unique station in the evolutionary process. Tymieniecka treats the constitution of sense as a function of life, and thus the transcendental constitutive function of the cognitive, objectifying intentionality of consciousness, the purview of classical phenomenology, is viewed as a project that is limited in its scope. According to the phenomenology of life, meaning-genesis is exhibited throughout the various stages of structurization in the evolution of life. This paper highlights the transformative function of the “Imaginatio Creatrix,” which is the dynamic process at the human station of evolution that accounts for humanity’s inventive capacities necessary for the construction of a human world. The Imaginatio Creatrix transforms the more primitive stirrings of the human “soul” into subliminal passions of human existential significance. The enactive theory of the mind corroborates Tymieniecka’s rejection of Husserl’s doctrine of passive synthesis. However, Tymieniecka’s study of the creative function offers a key for further advancement in enactive theory. Three sense-bestowing functions of the Imaginatio Creatrix account for the human expansion of life: the Aesthetic/Poetic sense, the Objectifying Sense, and the Moral Sense. The Moral Sense, for Tymieniecka, is not the product of reasoning powers, but rather the fruit of subliminal passions that acquire their moral aspect through trans-actions guided by the “benevolent sentiment.”

An Evolutionary Approach to Synthetic Biology: Zen and the Art of Creating Life

1993 ◽  
Vol 1 (1_2) ◽  
pp. 179-209 ◽  
Author(s):  
Thomas S. Ray
Keyword(s):  
Natural Selection ◽  
Synthetic Biology ◽  
Evolutionary Biology ◽  
Evolutionary Process ◽  
Life Forms ◽  
Evolutionary Approach ◽  
Artificial Medium ◽  
Natural Form ◽  
Evolution By Natural Selection ◽  
Physical Laws

Our concepts of biology, evolution, and complexity are constrained by having observed only a single instance of life, life on earth. A truly comparative biology is needed to extend these concepts. Because we cannot observe life on other planets, we are left with the alternative of creating Artificial Life forms on earth. I will discuss the approach of inoculating evolution by natural selection into the medium of the digital computer. This is not a physical/chemical medium; it is a logical/informational medium. Thus, these new instances of evolution are not subject to the same physical laws as organic evolution (e.g., the laws of thermodynamics) and exist in what amounts to another universe, governed by the “physical laws” of the logic of the computer. This exercise gives us a broader perspective on what evolution is and what it does. An evolutionary approach to synthetic biology consists of inoculating the process of evolution by natural selection into an artificial medium. Evolution is then allowed to find the natural forms of living organisms in the artificial medium. These are not models of life, but independent instances of life. This essay is intended to communicate a way of thinking about synthetic biology that leads to a particular approach: to understand and respect the natural form of the artificial medium, to facilitate the process of evolution in generating forms that are adapted to the medium, and to let evolution find forms and processes that naturally exploit the possibilities inherent in the medium. Examples are cited of synthetic biology embedded in the computational medium, where in addition to being an exercise in experimental comparative evolutionary biology, it is also a possible means of harnessing the evolutionary process for the production of complex computer software.

scholarly journals Comparative phylogeography of oceanic archipelagos: Hotspots for inferences of evolutionary process

2016 ◽  
Vol 113 (29) ◽  
pp. 7986-7993 ◽  
Author(s):  
Kerry L. Shaw ◽  
Rosemary G. Gillespie
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Community Dynamics ◽  
Evolutionary Process ◽  
Comparative Phylogeography ◽  
Origin And Evolution ◽  
Species Radiation ◽  
Remote Island ◽  
Oceanic Archipelagos ◽  
Shed Light

Remote island archipelagos offer superb opportunities to study the evolution of community assembly because of their relatively young and simple communities where speciation contributes to the origin and evolution of community structure. There is great potential for common phylogeographic patterns among remote archipelagos that originate through hotspot volcanism, particularly when the islands formed are spatially isolated and linearly arranged. The progression rule is characterized by a phylogeographic concordance between island age and lineage age in a species radiation. Progression is most likely to arise when a species radiation begins on an older island before the emergence of younger islands of a hotspot archipelago. In the simplest form of progression, colonization of younger islands as they emerge and offer appropriate habitat, is coincident with cladogenesis. In this paper, we review recent discoveries of the progression rule on seven hotspot archipelagos. We then discuss advantages that progression offers to the study of community assembly, and insights that community dynamics may offer toward understanding the evolution of progression. We describe results from two compelling cases of progression where the mosaic genome may offer insights into contrasting demographic histories that shed light on mechanisms of speciation and progression on remote archipelagos.

scholarly journals Institutional Ownership and Corporate Tax Avoidance: New Evidence

2016 ◽  
Vol 92 (2) ◽  
pp. 101-122 ◽  
Author(s):  
Mozaffar Khan ◽  
Suraj Srinivasan ◽  
Liang Tan
Keyword(s):  
Tax Avoidance ◽  
Institutional Ownership ◽  
Regression Discontinuity Design ◽  
Corporate Tax ◽  
Profit Margins ◽  
Exogenous Shocks ◽  
Analyst Expectations ◽  
Tax Shelters ◽  
New Evidence ◽  
Shed Light

ABSTRACT We provide new evidence on the agency theory of corporate tax avoidance (Slemrod 2004; Crocker and Slemrod 2005; Chen and Chu 2005) by showing that increases in institutional ownership are associated with increases in tax avoidance. Using the Russell index reconstitution setting to isolate exogenous shocks to institutional ownership, and a regression discontinuity design that facilitates sharper identification of treatment effects, we find a significant and discontinuous increase in tax avoidance following Russell 2000 inclusion. The tax avoidance involves the use of tax shelters, and immediate benefits include higher profit margins and likelihood of meeting or beating analyst expectations. Collectively, the results shed light on the effect of increased ownership concentration on tax avoidance.

scholarly journals The Pathological Mechanism and Potential Application of IL-38 in Autoimmune Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Miao-miao Han ◽  
Xin-rong Yuan ◽  
Xiang Shi ◽  
Xing-Yu Zhu ◽  
Yue Su ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Immune Cells ◽  
Human Heart ◽  
New Technologies ◽  
Regulatory Mechanism ◽  
Interleukin 1 ◽  
Future Prospects ◽  
Pathological Mechanism ◽  
New Evidence ◽  
Shed Light

Interleukin-38 (IL-38), a new cytokine of interleukin-1 family (IL-1F), is expressed in the human heart, kidney, skin, etc. Recently, new evidence indicated that IL-38 is involved in the process of different autoimmune diseases. Autoimmune diseases are a cluster of diseases accompanied with tissue damage caused by autoimmune reactions, including rheumatoid arthritis (RA), psoriasis, etc. This review summarized the links between IL-38 and autoimmune diseases, as well as the latest knowledge about the function and regulatory mechanism of IL-38 in autoimmune diseases. Especially, this review focused on the differentiation of immune cells and explore future prospects, such as the application of IL-38 in new technologies. Understanding the function of IL-38 is helpful to shed light on the progress of autoimmune diseases.

Sign in / Sign up

Export Citation Format

Share Document