scholarly journals From computer operating systems to biodiversity: co-emergence of ecological and evolutionary patterns

2016 ◽  
Author(s):  
Petr Keil ◽  
Joanne M Bennett ◽  
Bérenger Burgeois ◽  
Gabriel E García-Peña ◽  
Andrew M MacDonald ◽  
...  
Keyword(s):  
Operating Systems ◽  
Phylogenetic Signal ◽  
Biological Species ◽  
System Level ◽  
Evolutionary Patterns ◽  
Data Accessibility ◽  
Software Packages ◽  
Empirical Argument ◽  
Phylogenetic Lineages ◽  
Mean Variance

Comparisons between biodiversity and other complex systems can facilitate cross-disciplinary exchange of theories and the identification of key system processes and constraints. For example, due to qualitative structural and functional analogies to biological systems, coupled with good data accessibility, computer operating systems offer opportunities for comparison with biodiversity. However, it remains largely untested if the two systems also share quantitative patterns. Here, we employ analogies between GNU/Linux operating systems (distros) and biological species, and look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe match the macroecological patterns: Linux distro commonness and rarity (popularity of a distro) follow a lognormal distribution, power law mean-variance scaling of temporal fluctuation, and there is a significant relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: The number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that is unobservable in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. Our study provides foundations for using Linux as a model system for eco-evolutionary studies, as well as insights into patterns and dynamics of computer operating systems, which may be used to inform their future development and maintenance. The co-emergence of patterns across systems suggests that some patterns might be produced by system-level properties, independently of system identity, which offers an empirical argument for non-biological explanations of fundamental biodiversity patterns.

scholarly journals From computer operating systems to biodiversity: co-emergence of ecological and evolutionary patterns

2016 ◽  
Author(s):  
Petr Keil ◽  
Joanne M Bennett ◽  
Bérenger Burgeois ◽  
Gabriel E García-Peña ◽  
Andrew M MacDonald ◽  
...  
Keyword(s):  
Operating Systems ◽  
Phylogenetic Signal ◽  
Biological Species ◽  
System Level ◽  
Evolutionary Patterns ◽  
Data Accessibility ◽  
Software Packages ◽  
Empirical Argument ◽  
Phylogenetic Lineages ◽  
Mean Variance

Comparisons between biodiversity and other complex systems can facilitate cross-disciplinary exchange of theories and the identification of key system processes and constraints. For example, due to qualitative structural and functional analogies to biological systems, coupled with good data accessibility, computer operating systems offer opportunities for comparison with biodiversity. However, it remains largely untested if the two systems also share quantitative patterns. Here, we employ analogies between GNU/Linux operating systems (distros) and biological species, and look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe match the macroecological patterns: Linux distro commonness and rarity (popularity of a distro) follow a lognormal distribution, power law mean-variance scaling of temporal fluctuation, and there is a significant relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: The number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that is unobservable in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. Our study provides foundations for using Linux as a model system for eco-evolutionary studies, as well as insights into patterns and dynamics of computer operating systems, which may be used to inform their future development and maintenance. The co-emergence of patterns across systems suggests that some patterns might be produced by system-level properties, independently of system identity, which offers an empirical argument for non-biological explanations of fundamental biodiversity patterns.

scholarly journals From computer operating systems to biodiversity: co-emergence of ecological and evolutionary patterns

2016 ◽  
Author(s):  
Petr Keil ◽  
Joanne M Bennett ◽  
Bérenger Burgeois ◽  
Gabriel E García-Peña ◽  
Andrew M MacDonald ◽  
...  
Keyword(s):  
Operating Systems ◽  
Phylogenetic Signal ◽  
Biological Species ◽  
System Level ◽  
Evolutionary Patterns ◽  
Data Accessibility ◽  
Software Packages ◽  
Empirical Argument ◽  
Phylogenetic Lineages ◽  
Mean Variance

Comparisons between biodiversity and other complex systems can facilitate cross-disciplinary exchange of theories and the identification of key system processes and constraints. For example, due to qualitative structural and functional analogies to biological systems, coupled with good data accessibility, computer operating systems offer opportunities for comparison with biodiversity. However, it remains largely untested if the two systems also share quantitative patterns. Here, we employ analogies between GNU/Linux operating systems (distros) and biological species, and look for a number of well-established ecological and evolutionary patterns in the Linux universe. We demonstrate that patterns of the Linux universe match the macroecological patterns: Linux distro commonness and rarity (popularity of a distro) follow a lognormal distribution, power law mean-variance scaling of temporal fluctuation, and there is a significant relationship between niche breadth (number of software packages) and commonness. The diversity in the Linux universe also follows general macroevolutionary patterns: The number of phylogenetic lineages increases linearly through time, with clear per-species diversification and extinction slowdowns, something that is unobservable in biology. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. Our study provides foundations for using Linux as a model system for eco-evolutionary studies, as well as insights into patterns and dynamics of computer operating systems, which may be used to inform their future development and maintenance. The co-emergence of patterns across systems suggests that some patterns might be produced by system-level properties, independently of system identity, which offers an empirical argument for non-biological explanations of fundamental biodiversity patterns.

Security Gaps in Databases

2011 ◽  
Vol 2 (3) ◽  
pp. 42-62
Author(s):  
Afonso Araújo Neto ◽  
Marco Vieira
Keyword(s):  
Best Practices ◽  
Operating Systems ◽  
Software Package ◽  
Web Applications ◽  
Gap Analysis ◽  
Database Security ◽  
Security Requirements ◽  
Management Systems ◽  
Software Products ◽  
Software Packages

When deploying database-centric web applications, administrators should pay special attention to database security requirements. Acknowledging this, Database Management Systems (DBMS) implement several security mechanisms that help Database Administrators (DBAs) making their installations secure. However, different software products offer different sets of mechanisms, making the task of selecting the adequate package for a given installation quite hard. This paper proposes a methodology for detecting database security gaps. This methodology is based on a comprehensive list of security mechanisms (derived from widely accepted security best practices), which was used to perform a gap analysis of the security features of seven software packages composed by widely used products, including four DBMS engines and two Operating Systems (OS). The goal is to understand how much each software package helps developers and administrators to actually accomplish the security tasks that are expected from them. Results show that while there is a common set of security mechanisms that is implemented by most packages, there is another set of security tasks that have no support at all in any of the packages.

scholarly journals An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns

2017 ◽  
Author(s):  
Thomas Denk ◽  
Guido W. Grimm ◽  
Paul S. Manos ◽  
Min Deng ◽  
Andrew Hipp
Keyword(s):  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Traditional Concept ◽  
Infrageneric Classification ◽  
Systematic Scheme ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Phylogenetic Lineages

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl Anton Schwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.

scholarly journals Provides a New Way to Enhance Security in the Linux Operating System

2018 ◽  
Vol 2 (5) ◽  
pp. 295
Author(s):  
Hamid Reza Ganji ◽  
Kiarash Aghakhani
Keyword(s):  
Operating System ◽  
Performance Analysis ◽  
Operating Systems ◽  
System Level ◽  
Important Thing ◽  
Evaluation Parameters ◽  
Or Applications ◽  
Cyber Criminals

The security of the configuration of files in the Linux operating system depends on many factors that can be referenced to the system level and the applicable level. The most important thing about the security of Linux operating systems is its dynamism, for example, when you secure your Linux system, it will not stay safe forever, because applications and cyber criminals through new threats and/or new exploits that are packaged Systems or applications that cause the operating system to become unsafe, for this reason, we need a secure operating system. The main purpose of this article is to provide a new way to enhance the security of the Linux operating system. For this purpose, how can simple, continuous, and practical Linux environment be secured, solutions are presented, also based on performance analysis of the proposed method and evaluation parameters for existing systems against the proposed system, the superiority of this method is introduced.

scholarly journals Evolutionary patterns of range size, abundance and species richness in Amazonian trees

2016 ◽  
Author(s):  
Kyle Dexter ◽  
Jérôme Chave
Keyword(s):  
Species Richness ◽  
Phylogenetic Signal ◽  
Negative Relationship ◽  
Range Size ◽  
Biological Traits ◽  
Evolutionary Patterns ◽  
Phylogenetically Independent Contrasts ◽  
Significant Negative Relationship ◽  
The Mean ◽  
Amazonian Trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to analyse evolutionary patterns of range size, abundance, and species richness. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics, i.e. closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species, while mean range size and abundance are significantly, positively correlated. These correlations are stronger in the raw data, but still significant when using phylogenetically independent contrasts. We suggest that tree stature and/or other phylogenetically related biological traits underlie these results. Lineages comprised of small-statured trees show greater species richness and smaller range sizes and abundances. Lastly, the phylogenetic signal that we evidence for range size suggests that should many small ranged species go extinct, greater phylogenetic diversity may be lost than expected if range size were distributed randomly across the phylogeny.

scholarly journals Much more than a clasp: evolutionary patterns of amplexus diversity in anurans

2020 ◽  
Vol 129 (3) ◽  
pp. 652-663 ◽  
Author(s):  
Juan D Carvajal-Castro ◽  
Yelenny López-Aguirre ◽  
Ana María Ospina-L ◽  
Juan C Santos ◽  
Bibiana Rojas ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Sexual Size Dimorphism ◽  
Phylogenetic Signal ◽  
Evolutionary Relationships ◽  
Behavioural Ecology ◽  
Ancestral State ◽  
Evolutionary Patterns ◽  
Evolutionary Transitions ◽  
Size Dimorphism ◽  
Reproductive Modes

Abstract The evolution and diversification of animal reproductive modes have been pivotal questions in behavioural ecology. Amphibians present the highest diversity of reproductive modes among vertebrates, involving various behavioural, physiological and morphological traits. One such feature is the amplexus, which is the clasp or embrace of males on females during reproduction and is found almost universally in anurans. Hypotheses about the origin of amplexus are limited and have not been tested thoroughly, nor have they taken into account evolutionary relationships in most comparative studies. However, these considerations are crucial to an understanding of the evolution of reproductive modes. Here, using an evolutionary framework, we reconstruct the ancestral state of amplexus in 685 anuran species. We investigate whether the type of amplexus has a strong phylogenetic signal and test whether sexual size dimorphism could have influenced amplexus type or male performance while clasping females. Overall, we found evidence of ≥34 evolutionary transitions in amplexus type across anurans. We found that amplexus type exhibits a high phylogenetic signal and that amplexus type does not evolve in association with sexual size dimorphism. We discuss the implications of our findings for the diversity of amplexus types across anurans.

scholarly journals The timing mega-study: comparing a range of experiment generators, both lab-based and online

2020 ◽  
Author(s):  
David Bridges ◽  
Alain Pitiot ◽  
Michael R. MacAskill ◽  
Jonathan Westley Peirce
Keyword(s):  
Operating Systems ◽  
High Performance ◽  
Response Times ◽  
Research Software ◽  
Software Packages ◽  
Psychophysics Toolbox ◽  
Wide Range ◽  
Stimulus Timing ◽  
Behavioural Experiments ◽  
And Performance

Many researchers in the behavioral sciences depend on research software that presents stimuli, and records response times, with sub-millisecond precision. There are a large number of software packages with which to conduct these behavioural experiments and measure response times and performance of participants. Very little information is available, however, on what timing performance they achieve in practice. Here we report a wide-ranging study looking at the precision and accuracy of visual and auditory stimulus timing and response times, measured with a Black Box Toolkit. We compared a range of popular packages: PsychoPy, E-Prime®, NBS Presentation®, Psychophysics Toolbox, OpenSesame, Expyriment, Gorilla, jsPsych, Lab.js and Testable. Where possible, the packages were tested on Windows, MacOS, and Ubuntu, and in a range of browsers for the online studies, to try to identify common patterns in performance. Among the lab-based experiments, Psychtoolbox, PsychoPy, Presentation and E-Prime provided the best timing, all with mean precision under 1 millisecond across the visual, audio and response measures. OpenSesame had slightly less precision across the board, but most notably in audio stimuli and Expyriment had rather poor precision. Across operating systems, the pattern was that precision was generally very slightly better under Ubuntu than Windows, and that Mac OS was the worst, at least for visual stimuli, for all packages. Online studies did not deliver the same level of precision as lab-based systems, with slightly more variability in all measurements. That said, PsychoPy and Gorilla, broadly the best performers, were achieving very close to millisecond precision on a number of browser configurations. For response times (using a high-performance button box), most of the packages achieved precision at least under 10 ms in all browsers, with PsychoPy achieving a precision under 3.5 ms in all. There was considerable variability between operating systems and browsers, especially in audio-visual synchrony which is the least precise aspect of the browser-based experiments. Nonetheless, the data indicate that online methods can be suitable for a wide range of studies, with due thought about the sources of variability that result.The results, from over 110,000 trials, highlight the wide range of timing qualities that can occur even in these dedicated software packages for the task. We stress the importance of scientists making their own timing validation measurements for their own stimuli and computer configuration.

scholarly journals Reconstructed evolutionary patterns for crocodile-line archosaurs demonstrate impact of failure to log-transform body size data

2021 ◽  
Author(s):  
Roger Benson ◽  
Pedro L Godoy ◽  
Mario Bronzati ◽  
Richard Butler ◽  
William Gearty
Keyword(s):  
Body Size ◽  
Measurement Data ◽  
Methodological Error ◽  
Evolutionary Patterns ◽  
Aquatic Life ◽  
Rates Of Evolution ◽  
Size Evolution ◽  
Main Driver ◽  
Body Size Evolution ◽  
Phylogenetic Lineages

Pseudosuchia includes crocodylians, plus all extinct species more closely related to them than to birds. They appeared around 250 million years ago and have a rich fossil history, showing extinct diversity that exceeds that of their living members1-4. Recently, Stockdale & Benton5 presented analyses of a new dataset of body size estimates spanning the entire evolutionary history of this group. They quantified patterns of average body size, body size disparity through time, and rates of evolution along phylogenetic lineages. Their results suggest that pseudosuchians exhibited considerable variation in rates of body size evolution, for which they provided various group-specific explanations and asserted the importance of climatic drivers. This differs from two recent studies that analysed a substantial portion of pseudosuchian body size evolution and proposed that adaptation to aquatic life, a biological innovation of some subgroups, was the main driver of body size evolution, with patterns of disparity also being influenced by size-dependent extinction risk6,7. Here we show that the analytical results of Stockdale & Benton5 are strongly influenced by a methodological error in their body size index. Specifically, that they chose not to log-transform measurement data prior to analyses.

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