bluuebunny/crossref_metadata_2025 huggingface dataset:
OLHAR HUMANIZADO COMO CONDIÇÃO NECESSÁRIA PARA CONCRETIZAÇÃO DOS DIREITOS HUMANOS
Authors: Miranda Vasconcellos Cunha Mércia
Published: September 2023

O presente estudo versa sobre a necessidade de humanização do ser humano e do olhar sobre a proteção dos direitos humanos. Não se teoriza a vida humana, vive-se. As origens históricas, culturais, sociais devem estruturar a elaboração de instrumentos jurídicos de proteção da humanidade, sob pena de, em assim não sendo, haver ameaça à própria humanidade. Fundamentos teóricos não se sustentam e não são suficientes para o arcabouço formal de proteção aos direitos humanos. Nesse viés, a problematização sobre a concretização dos direitos humanos, na ótica apresentada, está estritamente vinculada à nova ordem de valores éticos contidos na Ética da Libertação de Enrique Dussel. O autor, embora se utilize de categorias teóricas, rompe com o formalismo técnico e abstracionista, revelando-se como expressão autêntica dos valores culturais, das condições materiais e da historicidade dos seres humanos em sociedade. Para se alcançar a efetiva proteção aos direitos humanos, com respeito à humanidade e, não somente, à formalidade, é preciso compreender a vida como complexa, heterogênea, plural e buscar-se a reprodução e desenvolvimento da vida.
TRANSFILOSOFÍA SENTIPENSANTE
Authors: Rodriguez Milagros Elena
Published: September 2023

¡Oh Espíritu Santo, gracias por tocar mi puerta, entrar en mi vida y rebozarla de gozo. Resguarda nuestro andar, caminar y preserva con cuidado lo que ha inspirado Dios! Isagoge Journal of Humanities and Social Sciences, en nuestro amado Brasil, con sus magníficos editores seres excepcionales; con el don de la persona nos han unido en una invitación de dossier, he aceptado de forma responsable y muy gratificante, por ello, les reitero las !Gracias! El compromiso que se presenta a la humanidad está centrado en esencias decoloniales planetaria - complejas de la filosofía. Es vital responder: ¿la filosofía colonizada? Si. Sin duda. Planetariamente la decolonialidad se refiere al proceso encaminado a trascender históricamente la modernidad-postmodernidad-colonialidad; esto es: el proyecto libertario para conciliar la filosofía con la liberación, pensando en las victimas soterradas aún en el siglo de las tecnologías, en nuestro sentipensar y en filosofías latinoamericanas; pero también las africanas; y así las planetaria; con la necesidad de que la diada decolonialidad planetaria – complejidad incite a ser liberadora, que coadyuve a la Tierra como patria. Ciencia-filosofía-teología transcienden el pensamiento disyuntivo. Es un ejercicio que va en escala y transcendencia en mis líneas de investigación. Con gran regocijo dando el honor, gloria, honra y poder a mi Padre Dios, se presenta el dossier titulado: Transfilosofía Sentipensante: Re-ligajes ecosóficos en tiempos de colonialidad global; para provecho de la humanidad. La convocatoria ha resultado excepcional, los textos científicos se vinculan y arman un tejido epistémico de real valor que sobre pasan los ejes temáticos. Los investigadores, con extraordinaria elocuencia han dado fe de la máxima: liberación de la filosofía a la luz de la decolonialidad planetaria-complejidad.
Variações gastronômicas do mungunzá ao percorrer o Brasil: estudo bibliográfico
Authors: Costa Fládia Carneiro da , Neto Pedro Abreu da Silva , Carvalho Diana Valesca , Gouveia Sandro Thomaz , Lima Francisca Elisângela Teixeira , Sousa Paulo Henrique Machado
Published: September 2023

Com o milho é possível criar vários preparos, podendo servi-lo de diversas formas e satisfazer todos os gostos. Dentre os preparos, figura o mungunzá, alimento que é consumido nas festividades juninas, variando suas terminologias ligadas ao regionalismo. Este estudo teve como objetivo descrever as transformações que ocorreram na produção do mungunzá no Brasil ao longo dos tempos. Foi formulada uma pergunta de investigação: quais transformações ocorreram na produção do mungunzá no Brasil? Foram encontrados 958 trabalhos a partir da busca dos descritores nas bases de dados: CAPES, Science Direct, ScieELO e Repositório Institucional da Universidade Federal do Ceará. Somente 14 foram selecionados com base na avaliação do conteúdo e na pesquisa bibliográfica. Diante da leitura dos trabalhos, pode-se perceber que canjica, curau, mungunzá, servem para designar preparações diferentes à base de milho e estão presentes de norte a sul do Brasil, se diversificando na alimentação e no campo linguístico com funções semelhantes. A nomenclatura “munguzá” tem influência africana e seu consumo está ligado às festividades juninas e julhinas. As diferentes trajetórias alimentares, baseadas em matérias-primas comuns, mostram que os estudos gastronômicos precisam levar em consideração as culturas e a história dos processos de produção dos pratos. O mungunzá em sua versão salgada é servido no sertão nordestino como refeição, preparações salgadas representam o alimento energético, que provoca saciedade. Considera-se assim que diversas transformações ocorrem na produção e denominação do mungunzá no Brasil, sendo elas no campo linguístico, histórico, cultural, social, geográfico e gastronômico.
EOL, the BBC, and Wikipedia
Authors: Page Roderic
Published: September 2023

Last month EOL took the brave step of including Wikipedia content in its pages. I say "brave" because early on EOL was pretty reluctant to embrace Wikipedia on this scale (see the report of the Informatics Advisory Group that I chaired back in 2008), and also because not all of EOL's curators have been thrilled with this development.
Why 3D phylogeny viewers don't work
Authors: Page Roderic
Published: September 2023

Matt Yoder (@mjyoder had a Twitter conversation yesterday about phylogeny viewers, prompted by my tweeting about my latest displacement activity, a 2D tree browser using the tiling approach made popular by Google Maps.As part of that conversation, Matt tweeted:Well, Matt's imagination has gone into overdrive, and he's blogged about his ideas. This issue deserves more exploration, but here are some quick thoughts.
Linking the NCBI taxonomy to BBC Wildlife Finder
Authors: Page Roderic
Published: September 2023

A few weeks ago I spent some time mapping pages from the BBC Wildlife Finder to the equivalent taxa in the NCBI taxonomy. This seemed a useful exercise because the Wildlife Finder pages have some wonderful picture, video, and audio content, as well as other nice features, such as reusing Wikipedia page titles as "slugs" in the BBC page URLs.
Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library
Authors: Page Roderic
Published: September 2023

Yesterday I uploaded a manuscript to Nature Precedings that describes the inner workings of BioStor.
Web Hooks and OpenURL: making databases editable
Authors: Page Roderic
Published: September 2023

For me one of the most frustrating things about online databases is that they often can't be edited. For example, I've recently created a version of the Australian Faunal Directory on CouchDB, which contains a list of all animals in Australia, and a fairly comprehensive bibliography of taxonomic publication on those animals. What I'd like to do is locate those publications online.
Scripting Life
Authors: Page Roderic
Published: September 2023

Not really a blog post, more a note to self. If I ever did get around to writing a book again, I think   Scripting Life   would be a great title.
Linking NCBI to Wikipedia
Authors: Page Roderic
Published: September 2023

In an earlier post I discussed linking NCBI taxonomy to Wikipedia. One way to tackle this is to add NCBI Taxonomy ID to Wikipedia pages. I reopened the case for adding the Taxonomy IDs to the Taxobox on each taxon page, but this met with substantial resistance.
Replicating and forking data in 2010: Catalogue of Life and CouchDB
Authors: Page Roderic
Published: September 2023

Time (just) for a Friday folly. A couple of days ago the latest edition of the Catalogue of Life (CoL) arrived in my mailbox in the form of a DVD and booklet:While in some ways it's wonderful that the Catalogue of Life provides a complete data dump of its contents, this strikes me as a rather old-fashioned way to distribute it. So I began to wonder how this could be done differently, and started to think of CouchDB.
An open letter to Stephen Meyer
Authors: Matheson Stephen
Published: September 2023

Dear Steve: It was good to meet you last month at Biola.
Bread and circus: Signature in the Cell at Biola (Part II)
Authors: Matheson Stephen
Published: September 2023

Here are some further observations on the Stephen Meyer book-signing appearance. Part I dealt with Meyer's talk and the other festivities. Here I'll describe the last third of the event, in which Art Hunt and I (the "powerful group of credentialed critics") spent a short time questioning Meyer. 1. Our time was short.
NCBI Taxonomy IDs and Wikipedia
Authors: Page Roderic
Published: September 2023

I've written a note on the Wikipedia Taxobox page making the case for adding NCBI taxonomy IDs to the standard Taxobox used to summarise information about a taxon. Here is what I wrote:Some discussion has ensued on the Taxobox page, all positive. I'm blogging this here to encourage anyone who as any more thoughts on the matter to contribute to the discussion.
It's just a stage. A phylotypic stage. Part II: The flies
Authors: Matheson Stephen
Published: September 2023

The controversy about the existence of the phylotypic stage is more than some bickering about whether one blobby, slimy fish-thing looks more like a Roswell alien than another one does. It's about whether the phylotypic stage means something, whether it tells us something important about development and how developmental changes contribute to evolution.
Signature in the Cell: Chapters 4 and 5 - major themes
Authors: Matheson Stephen
Published: September 2023

Chapter 4 is called "Signature in the Cell." It's an important chapter for two reasons. First, along with chapter 5 ("The Molecular Labyrinth") it lays out Meyer's central question by pointing to the specific features of cellular information systems in need of explanation. Second, it exemplifies an aspect of ID thought that I want to highlight. I'll discuss these two themes here, then add some further critiques in a second post.
Mendeley Connect
Authors: Page Roderic
Published: September 2023

When I first launched BioStor (an article finding tool built on the top of the (Biodiversity heritage Library) I wanted people to be able to edit metadata and add references, but also minimise the chances that junk would get added.
Why won't The Plant List won't let me do this?
Authors: Page Roderic
Published: September 2023

In my last post I discussed why I thought the decision of The Plant List to use a restrictive license (CC-BY-NC-ND) was such a poor choice. CC-BY-NC-ND states that To make this point more concrete, I've created this site:Experiments with The Plant Listto show the kinds of things that The Plant List's choice of license prevents the taxonomic community from doing.
Social citations: using Mendeley API to measure citation readership
Authors: Page Roderic
Published: September 2023

Quick note on an app I threw together using the Mendeley API that I discussed in the previous post. This app is crude, and given that the Mendeley API is rate-limited and in flux it might not work for you.The basic idea is to embellish make the list of literature cited in an article with information that might help a reader decide whether a given citation is worth reading. One clue might be how many people on Mendeley are reading that article.
ZooKeys publishes articles of the future
Authors: Page Roderic
Published: September 2023

The open access taxonomic journal ZooKeys has published a special issue with four papers, each available in HTML, PDF, and XML, the later being extensively marked up. Penev et al. ("Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples", doi:10.3897/zookeys.50.538) describes the process involved in creating these XML files.
GeoCouch
Authors: Page Roderic
Published: September 2023

.bbpBox25151382818 {background:url(http://a1.twimg.com/profile_background_images/2527748/tiling.gif) #000000;padding:20px;} p.bbpTweet{background:#fff;padding:10px 12px 10px 12px;margin:0;min-height:48px;color:#000;font-size:18px !important;line-height:22px;-moz-border-radius:5px;-webkit-border-radius:5px} p.bbpTweet span.metadata{display:block;width:100%;clear:both;margin-top:8px;padding-top:12px;height:40px;border-top:1px solid
Biodiversity informatics = #fail (and what to do about it)
Authors: Page Roderic
Published: September 2023

The context for this post is the PLos markup meeting held at the California Academy of Sciences over the weekend (many thanks to Brian Fisher for the invitation). PLoS are launching a "biodiversity hub" and were looking for ideas on how to implement this.
Data matters but do data sets?
Authors: Page Roderic
Published: September 2023

Interest in archiving data and data publication is growing, as evidenced by projects such as Dryad, and earlier tools such as TreeBASE. But I can't help wondering whether this is a little misguided. I think the issues are granularity and reuse.Taking the second issue first, how much re-use do data sets get? I suspect the answer is "not much". I think there are two clear use cases, repeatability of a study, and benchmarks.
Viewing scientific articles on the iPad: cloning the Nature.com iPhone app using jQuery Mobile
Authors: Page Roderic
Published: September 2023

Over the last few months I've been exploring different ways to view scientific articles on the iPad, summarised here. I've also made a few prototypes, either from scratch (such as my response to the PLoS iPad app) or using Sencha Touch (see Touching citations on the iPad).Today, it's time for something a little different. The Sencha Touch framework I used earlier is huge and wasn't easy to get my head around.
Viewing scientific articles on the iPad: browsing articles
Authors: Page Roderic
Published: September 2023

In previous articles I've looked at how various apps display scientific articles. The apps I looked at were:PLoS ReaderNaturePapersMendeleySo, where next? As Ian Mulvany noted in a comment on an earlier post, I haven't attempted to summarise the best user interface metaphors for navigation. Rather than try and do that in the abstract, I'd like to create some prototypes to play with various ideas.
Love. Peace. Unity. Or?
Authors: Matheson Stephen
Published: September 2023

Last month, I read that Biologos (a Christian "think tank" that advances evolutionary creation) and Reasons To Believe (a Christian "think tank" that advances old-earth creationism) were reporting on a dialogue between their two organizations that was intended "to discuss areas of agreement and disagreement" with a particular focus on "the biological record of the past 700 million years." This is very interesting to me. My position is very close
Navigating the Encyclopedia of Life tree on the desktop and the iPhone
Authors: Page Roderic
Published: September 2023

This week seems to be API week. The Encyclopedia of Life API Beta Test has been out since August 12th.
Mendeley mangles my references: phantom documents and the problem of duplicate references
Authors: Page Roderic
Published: September 2023

One issue I'm running into with Mendeley is that it can create spurious documents, mangling my references in the process. This appears to be due to some over-zealous attempts to de-duplicate documents.
Mendeley API: we'll bring the awesome if you bring the documentation
Authors: Page Roderic
Published: September 2023

Menedeley's API has been publicly launched at http://dev.mendeley.com/, accompanied by various announcements such as:All good fun to be sure, but it's a pity more effort has been spent on Easter eggs than on documenting and testing the API. If you visit the API development site there's precious little in the way of documentation, and few examples.
PLoS Biodiversity Hub launches
Authors: Page Roderic
Published: September 2023

The PLoS Biodiversity Hub has launched today. There's a PLoS blog post explaining the background to the project, as well as a summary on the Hub itself:Readers of iPhylo may recall my account of one of the meetings involved in setting up this hub, in which I began to despair about the lack of readiness of biodiversity informatics to provide much of the information needed for projects such as hubs.
Bread and circus: Signature in the Cell at Biola (Part I)
Authors: Matheson Stephen
Published: September 2023

So last week was the big book-signing shindig and Discovery Institute Annual Convention at Biola University. I knew the DI spin machine would move quickly, and sure enough I've already been quotemined and utterly misconstrued. But my real weakness is research, lab meetings and new papers to present in lab meeting, so some of you had to wait. I'm okay with that.
Introns. Let's think about this, people. Part IV.
Authors: Matheson Stephen
Published: September 2023

So why is it that I and many other biologists hypothesize that introns are mostly non-functional? (I'll assume that you've read the previous posts, and that you understand what it is that I mean when I challenge claims that introns are functional elements in an information-rich genome.
Referring to a one-degree square in RDF using c-squares
Authors: Page Roderic
Published: September 2023

I'm in the midst of rebuilding iSpecies (my mash-up of Wikipedia, NCBI, GBIF, Yahoo, and Google search results) with the aim of outputting the results in RDF. The goal is to convert iSpecies from a pretty crude "on-the-fly" mash-up to a triple store where results are cached and can be queried in interesting ways. Why?
Zooming a large tree, now with thumbnails
Authors: Page Roderic
Published: September 2023

Continuing experiments with a zoom viewer for large trees (see previous post), I've now made a demo where the labels are clickable. If the NCBI taxon has an equivalent page in Wikipedia the demo displays and link to that page (and, if present, a thumbnail image). Give it a try athttp://iphylo.org/~rpage/deeptree/3.htmlor watch the short video clip below: Zoomable viewer with Wikipedia thumbnails from Roderic Page on Vimeo.
Viewing scientific articles on the iPad: Papers
Authors: Page Roderic
Published: September 2023

Continuing the series of posts about reading scientific articles on the iPad, here are some quick notes on perhaps the most polished app I've seen, Papers for iPad. As with earlier posts on the Nature and PLoS apps, I'm not writing an in-depth review - rather I'm interested in the basic interface design.Papers is available for the Mac, as well as the iPhone and iPad.
Signature in the Cell: Chapter 7
Authors: Matheson Stephen
Published: September 2023

The chapter is called "Of Clues to Causes" and it's about scientific explanation. That's an interesting and important topic, one that opponents of evolutionary theory rarely understand. Meyer's summary is predictably fluffy but not inaccurate. Those seeking an introduction to philosophical questions pertaining to scientific explanation should look elsewhere, since Meyer says little in the 22-page chapter.
Microcitations: linking nomenclators to BHL
Authors: Page Roderic
Published: September 2023

One of the challenges of linking databases of taxonomic names to the primary literature is the minimal citation style used by nomenclators (see my earlier post Nomenclators + digitised literature = fail).For example, consider Nomenclator Zoologicus.
TreeBASE, again
Authors: Page Roderic
Published: September 2023

My views on TreeBASE are pretty well known. Lately I've been thinking a lot about how to "fix" TreeBASE, or indeed, move beyond it. I've made a couple of baby steps in this direction.The first step is that I've created a group for TreeBASE papers on Mendeley.
Why we need wikis
Authors: Page Roderic
Published: September 2023

I've just spent a frustrating few minutes trying to find a reference in BioStor. The reference in question isand comes from the Reptile Database page for the gecko Phyllodactylus gilberti HELLER, 1903. This is primary database for reptile taxonomy, and supplies the Catalogue of Life, which repeats this reference verbatim.Thing is, this reference doesn't exist! Page 39 of  Proc. Biol. Soc. 
Viewing scientific articles on the iPad: towards a universal article reader
Authors: Page Roderic
Published: September 2023

There are a growing number of applications for viewing scientific articles coming out for the iPhone and iPad. I'm toying with extending the experiments described in an earlier post when I took the PLoS iPad app to task for being essentially a PDF page-turner, so I thought I should take a more detailed look at the currently available apps.
First thoughts on CiteBank and BHL-Europe
Authors: Page Roderic
Published: September 2023

This week saw the release of two tools from the Biodiversity Heritage Library, CiteBank and the BHL-Europe portal. Both have actually been quietly around for a while, but were only publicly announced last week.In developing a new tool there are several questions to ask. Does something already exist that meets my needs? If it doesn't exist, can I build it using an existing framework, or do I need to start from scratch?
Introns and design
Authors: Matheson Stephen
Published: September 2023

Mike Gene has posted an interesting series on introns that's worthy of a few comments. His thesis is that "introns facilitated the evolution of multicellular life." A. The idea is interesting and rational but not novel.
Live demo of zooming a large tree
Authors: Page Roderic
Published: September 2023

After the teaser on Friday (see Deep zooming a large 2D tree) I've put a live demo of my experiments with viewing a large tree online at:http://iphylo.org/~rpage/deeptree/The first example (Experiment 1) is the NCBI classification for frogs: Simple deep tree viewer from Roderic Page on Vimeo.This version displays internal node labels, leaf labels (as many as can be displayed at a given zoom level), and works in Safari, Firefox, and Internet
Biologos and Christian unity: mission accomplished?
Authors: Matheson Stephen
Published: September 2023

And so, last week, some of my friends from BioLogos and Calvin College participated in this Vibrant Dance thing. These are people I hold in very high regard, people pursuing goals that I consider to be among the most important projects a Christian scientist can tackle.
Extracting semantic goodness from Zootaxa articles
Authors: Page Roderic
Published: September 2023

I've just come back from a holiday in New Zealand, during which time I spent a morning chatting with Zhi-Qiang Zhang (@Zootaxa, editor of  Zootaxa  ) and Stephen Thorpe (stho002, a major contributor to Wikispecies).Fresh from playing with PLoS XML to explore ways of redisplaying articles (described in my commentary on the PLoS iPad app), I was extolling the virtues of the XML mark-up that underlies PLoS (and other Open Access journals, such
Viewing a BioStor reference in Cooliris
Authors: Page Roderic
Published: September 2023

Cooliris is a web browser plugin that can display a large number of images as a moving "infinite" wall. It's Friday, so for fun I added a media RSS feed to BioStor to make the BHL page scans available to Cooliris.
Towards an interactive DjVu file viewer for the BHL
Authors: Page Roderic
Published: September 2023

The bulk of the Biodiversity Heritage Library's content is available as DjVu files, which package together scanned page images and OCR text. Websites such as BHL or my own BioStor display page images, but there's no way to interact with the page content itself.
Signature in the Cell: Chapter 3
Authors: Matheson Stephen
Published: September 2023

The chapter is called "The Double Helix," and there's not much to say about it. Meyer provides a fairly standard narrative of the discoveries that led to Watson and Crick and molecular biology. Anyone who's read The Eighth Day of Creation, along with a decent genetics textbook and/or a memoir by one of the principals (What Mad Pursuit by Francis Crick is a personal favorite) will already know everything here. Two observations.
NCBI to Wikipedia links are now live...
Authors: Page Roderic
Published: September 2023

The 52,956 links from NCBI to Wikipedia that I've been busy creating are now "live." If you go to a NCBI taxon such as Sphaerius you'll see something like this:Clicking the "Wikipedia" link takes you to the Wikipedia page for this taxon.
Browsing a digital library using a map
Authors: Page Roderic
Published: September 2023

Every so often I revisit the idea of browsing a collection of documents (or specimens, or phylogenies) geographically.
Mendeley, OpenURL, BioStor, and BHL
Authors: Page Roderic
Published: September 2023

Mendeley has added a feature which makes it easier to use Mendeley with repositories such as BioStor and BHL.
Why is the Atlas of Living Australia is invisible to Google?
Authors: Page Roderic
Published: September 2023

Jeff Atwood, one of the co-founders of Stack Overflow recently wrote a blog post Trouble In the House of Google, where he noted that several sites that scrape Stack Overflow content (which Stack Overflow's CC-BY-SA license permits) appear  higher in Google's search rankings than the original Stack Overflow pages  . When Stack Overflow chose the CC-BY-SA license they made the assumption that:Jeff Atwood's post goes on to argue that something
ReaderMeter: what's in a name?
Authors: Page Roderic
Published: September 2023

Dario Taraborelli has released ReaderMeter, an elegant app built on top of the Mendeley API. You enter an author's name and it summarises that authorship's readership in Mendeley.
TreeView X now on Google Code
Authors: Page Roderic
Published: September 2023

TreeView X, the open source version of TreeView, has been slowly suffering bit rot as C++ compilers and operating systems change. Every so often I'd tweak the code to build on some Linux version or other, but this isn't something I've a lot of time for. Moreover, because of the hassle of rebuilding binaries and source tar balls the updated versions weren't uploaded to the TreeView X web site.
Deep zooming a large 2D tree
Authors: Page Roderic
Published: September 2023

Here's a quick demo of a 2D large tree viewer that I'm working on. The aim is to provide a simple way to view and navigate very large trees (such as the NCBI classification) in a web browser using just HTML and Javascript. At the moment this is simply a viewer, but the goal is to add the ability to show "tracks" like a genome browser.
Time for some decent service
Authors: Page Roderic
Published: September 2023

The BBC web site has an article entitled Giant deep sea jellyfish filmed in Gulf of Mexico which has footage of  Stygiomedusa gigantea  , and mentions an associated fish,  Thalassobathia pelagica  .One thing that frustrates me beyond belief is how hard it is to get more information about these organisms. Put another way, the biodiversity informatics community is missing a huge opportunity here.
Nomenclator Zoologicus meets Biodiversity Heritage Library: linking names directly to literature
Authors: Page Roderic
Published: September 2023

Following on from my previous post on microcitations I've blasted all the citations in Nomenclator Zoologicus through my microcitation service and created a simple web site where these results can be browsed.The web site is here: http://iphylo.org/~rpage/nz/.To create it I've taken a file dump of Nomenclator Zoologicus provided by Dave Remsen and run all the citations through the microcitation service, storing the results in a simple database.
PLoS doesn't "get" the iPad (or the web)
Authors: Page Roderic
Published: September 2023

PLoS recently announced a dedicated iPad app, that covers all the PLoS Journals, and which is available from the App Store. Given the statement that "PLoS is committed to continue pushing the boundaries of scientific communication" I was expecting something special.
BioStor updates on Twitter
Authors: Page Roderic
Published: September 2023

BioStor has had a Twitter account @biostor_org for a while, but it's not been active.
BHL and OCR
Authors: Page Roderic
Published: September 2023

Some quick notes on OCR. Revisiting my DjVu viewer experiments it really struck me how "dirty" the OCR text is. It's readable, but if we were to display the OCR text rather than the images, it would be a little offputting.
Mendeley, BHL, and the "Bibliography of Life"
Authors: Page Roderic
Published: September 2023

One of my hobby horses is the disservice taxonomic databases do their users by not linking to original scientific literature.
Mapping fitness: protein display, fitness, and Seattle
Authors: Matheson Stephen
Published: September 2023

A couple of months ago we started looking at the concept of fitness landscapes and at some new papers that have significantly expanded our knowledge of the maps of these hypothetical spaces. Recall that a fitness landscape, basically speaking, is a representation of the relative fitness of a biological entity, mapped with respect to some measure of genetic change or diversity.
BHL, DjVu, and reading the f*cking manual
Authors: Page Roderic
Published: September 2023

One of the many biggest challenges I've faced with the BioStor project, apart from dealing with messy metadata, has been handling page images. At present I get these from the Biodiversity Heritage Library. They are big (typically 1 Mb in size), and have the caramel colour of old paper.
How Wikipedia can help scope a project
Authors: Page Roderic
Published: September 2023

I'm revisiting the idea of building a wiki of phylogenies using Semantic Mediawiki. One problem with a project like this is that it can rapidly explode.
Geography and genes: zoomable view of frog NCBI classification with linked map
Authors: Page Roderic
Published: September 2023

More zoom viewer experiments (see previous post), this time with a linked map that updates as you browse the tree (SVG-capable browser required). As you browse the frog classification the map updates to show the location of georeferenced sequences in GenBank from the taxa in the part of the tree you are looking at. The map is limited to not more than 200 localities, and many frog sequences aren't georeferenced, but it's a fun way to combine
Mapping fitness: landscapes, topographic maps, and Seattle
Authors: Matheson Stephen
Published: September 2023

The concept of a "fitness landscape" is a fundamental idea in evolutionary biology, first introduced and established during the so-called "evolutionary synthesis" in the early 20th century.
Signature in the Cell: Chapters 9 and 10
Authors: Matheson Stephen
Published: September 2023

"He..strikes at randome at a man of straw." – Richard Saunders, A Balm to heal Religious Wounds, 1652.
DjVu XML to HTML
Authors: Page Roderic
Published: September 2023

This post is simply a quick note on some experiments with DjVu that I haven't finished. Much of BHL's content is available as DjVu files, which contain both the scanned images and OCR text, complete with co-ordinates of each piece of text. This means that it would, in principle, be trivial to lay out the bounding boxes of each text element on a web page.
It's just a stage. A phylotypic stage. Part I.
Authors: Matheson Stephen
Published: September 2023

Disputes and controversies in science are always a good thing. They're fun to read about (and to write about), and they're bellwethers of the health of the enterprise. Moreover, they tend to stimulate thought and experimentation. Whether scientists are bickering about evo-devo, or about stem cells in cancer, or about prebiotic chemistry, and whether or not the climate is genial or hostile, the result is valuable.
Signature in the Cell: Chapter 1
Authors: Matheson Stephen
Published: September 2023

The chapter is called "DNA, Darwin, and the Appearance of Design." It's a poor start. Meyer sketches some key themes of the rest of the book in this sloppy chapter. Here are those themes (in my words) and some comments. 1. DNA stores information, using a code that is similar to that of a computer. We know a lot about how that works. 2. Life gives the appearance of design. No one disputes that.
Viewing scientific articles on the iPad: Mendeley
Authors: Page Roderic
Published: September 2023

Previously I've looked at the Nature, PLoS, and Papers apps, now it's the turn of the Mendeley iPad app.
It's okay, Bono. I'm on it.
Authors: Matheson Stephen
Published: September 2023

U2 can't make it to Michigan this year, due to Bono's back injury. (Me: "Ouch. He'll be fine." My girlfriend Susan: "What do you expect? He's old. He should pack it in.") So here are my attempts to fill the void. 1. I was a guest on the Skeptics Guide to the Universe podcast about a week and a half ago. The subject was "junk DNA" and boy was it fun to talk to people who actually understand.
Elsevier Grand Challenge paper out
Authors: Page Roderic
Published: September 2023

At long last the peer-reviewed version of the paper "Enhanced display of scientific articles using extended metadata" (doi:10.1016/j.websem.2010.03.004), in which I describe my entry in the Elsevier Grand Challenge, has finally appeared in the journal  Web Semantics: Science, Services and Agents on the World Wide Web  . The pre-print version of this paper has been online (hdl:10101/npre.2009.3173.1) for a year prior to appearance of the
Viewing scientific articles on the iPad: iBooks
Authors: Page Roderic
Published: September 2023

Apple's iBooks app is an ePub and PDF reader, and one could write a lengthy article about its interface. However, in the context of these posts on visualising the scientific article there's one feature that has particularly struck me. When reading a book that cited other literature the citations are hyper-links: click on one and iBooks forwards you (via the page turning effect) to the reference in the book's bibliography.
BioStor gets PDFs with XMP metadata - bibliographies made easy with Mendeley and Papers
Authors: Page Roderic
Published: September 2023

The ability to create PDFs for the articles BioStor extracts from the Biodiversity Heritage Library has been the single most requested feature for BioStor. I've taken a while to get around to this -- for a bunch of reasons -- but I've finally added it today.
CouchDB and Lucene
Authors: Page Roderic
Published: September 2023

Quick notes to self on fulltext search and CouchDB. Note that links to CouchDB are local to my machine(s),and won't work unless you are me, or have a copy of the same database running on your machine). CouchDB and Lucene adds fulltext indexing to CouchDB. After a few false starts I now have this working.
Mapping fitness: bacteria, mutations, and Seattle
Authors: Matheson Stephen
Published: September 2023

Thinking about fitness landscapes can stimulate detailed discussion and consideration of the meanings and limitations of such metaphors, and my introductory comments at The Panda's Thumb did just that. Most notably, Joe Felsenstein pointed us to the various ways these depictions can be employed, and urged everyone to use caution in interpreting them.
The Mendeley API Binary Battle - win $US 10,001
Authors: Page Roderic
Published: September 2023

Now we'll bring the awesome. Mendeley have announced The Mendeley API Binary Battle, with a first prize of $US 10,0001, and some very high-profile judges (Juan Enriquez, Tim O'Reilly, James Powell, Werner Vogels, and John Wilbanks). Deadline for submission is August 31st 2011, with the results announced in October. The criterion for judging are:How active is your application? We’ll look at your API key usage.How viral is the app?
Signature in the Cell: Chapter 2
Authors: Matheson Stephen
Published: September 2023

The chapter is called "The Evolution of a Mystery and Why It Matters." It's interesting and engaging, and I enjoyed reading it. The "mystery" in question is first described on page 35: ...most philosophers and scientists have long thought that Darwin's theory of evolution by natural selection destroyed the design argument. Yet I also discovered that Darwin himself admitted that his theory did not explain the origin of life itself.
The demise of phthiraptera.org and the perils of using Internet domain names as identifiers
Authors: Page Roderic
Published: September 2023

Geoffery Bilder's comments about the unsuitability of URLs as long term identifiers (as opposed, say, to DOIs) came to mind when I discovered that the domain phthiraptera.org is up for sale: This domain used to be home to a wealth of resources on lice (order Phthiraptera). I discovered that ownership of the domain had expired when a bunch of links to PDFs returned by an iSpecies search for  Collodennyus  all bounced to the holding page
Quantum treemaps meet BHL and the Australian Faunal Directory
Authors: Page Roderic
Published: September 2023

One of the things I'm enjoying about the Australian Faunal Directory on CouchDB is the chance to play with some ideas without worrying about breaking lots of code or, indeed, upsetting any users ('cos, let's face it, there aren't any). As a result, I can start to play with ideas that may one day find their way into other projects.One of these ideas is to use quantum treemaps to display an author's publications.
34th Carnival of Evolution
Authors: Matheson Stephen
Published: September 2023

Welcome to the 34th Edition (1 April 2011) of the Carnival of Evolution, and welcome to Quintessence of Dust. It's nice to be hosting this fine carnival, and to see that it's still going strong. I've organized the carnival under some chapter and section headings that I got from some old Victorian's magnum opus, but I think you'll find the topics require no further creative embellishment.
It's just a stage. A phylotypic stage. Part III: Fish and more
Authors: Matheson Stephen
Published: September 2023

Given that disputes over the existence and meaning of the phylotypic stage and the hourglass model have simmered in various forms for a century and a half, the remarkable correspondence between the hourglass model and gene expression divergence discovered by Kalinka and Varga and colleagues would be big news all by itself. But amazingly, that issue of Nature included two distinct reports on the underpinnings of the phylotypic stage.
Touching citations on the iPad
Authors: Page Roderic
Published: September 2023

Quick demo of the mockup I alluded to in the previous post. Here's a screen shot of the article "PhyloExplorer: a web server to validate, explore and query phylogenetic trees" (doi:10.1186/1471-2148-9-108) as displayed as a web-app on the iPad.
Introns. Let's think about this, people. Part III.
Authors: Matheson Stephen
Published: September 2023

What does it mean to claim that an intron has a function? The question is obviously important, at least as long as there are disputes about whether introns have "functions" and whether science ignored them for decades. Now, I can't help the ID people with their propensity for repeating falsehoods about the history of "junk DNA" and the role of "Darwinism" in its characterization.
Fun things about crustaceans
Authors: Page Roderic
Published: September 2023

One side effect of playing with ways to visualise and integrate biology databases is that you stumble across the weird and wonderful stuff that living organisms get up to. My earliest papers were on crustacean taxonomy, so I thought I'd try my latest toy on them.  What lives on crustaceans?  The "symbiome" graph for crustacea shows a range of associations, including marine bacteria (  Vibrio  ), fungi (microsporidians), and other
Behe and probability: one more try
Authors: Matheson Stephen
Published: September 2023

Almost two years ago, I reviewed Michael Behe's latest book, The Edge of Evolution, here on the blog. I was unimpressed, to say the least, and remain of the opinion that Behe should not be considered a serious scientific thinker given his failure in that ludicrous book.
Introns. Let's think about this, people. Part II.
Authors: Matheson Stephen
Published: September 2023

Before we explore what introns are and how they work, let me correct the misuse of my words by one of the ID attack kittens.
Dark taxa: GenBank in a post-taxonomic world
Authors: Page Roderic
Published: September 2023

In an earlier post (Are names really the key to the big new biology?, I questioned Patterson et al.'s assertion in a recent TREE article (doi:10.1016/j.tree.2010.09.004) that names are key to the new biology.In this post I'm going to revisit this idea by doing a quick analysis of how many species in GenBank have "proper" scientific names, and whether the number of named species has changed over time.
Alu need to know about parasitic DNA: Introduction to Alu elements
Authors: Matheson Stephen
Published: September 2023

Defenders of intelligent design theory often dwell on the topic of "junk DNA," which has been molded into a masterpiece of folk science. The ID approach to "junk DNA" involves a fictional story about "Darwinism" discouraging its study, and a contorted and simplistic picture of a "debate" about whether "junk DNA" has "function." The fictional story is ubiquitous despite being repeatedly debunked.
Are names really the key to the big new biology?
Authors: Page Roderic
Published: September 2023

David ("Paddy") Patterson, Jerry Cooper, Paul Kirk, Rich Pyle, and David Remsen have published an article in TREE entitled "Names are key to the big new biology" (doi:10.1016/j.tree.2010.09.004). The abstract states:  Do we need names?  Reading this (full disclosure, I was a reviewer) I can't wondering whether the assumption that names are key really needs to be challenged.
How do I know if an article is Open Access?
Authors: Page Roderic
Published: September 2023

One of my pet projects is to build a "Universal Article Reader" for the iPad (or similar mobile device), so that a reader can seemlessly move between articles from different publishers, follow up citations, and get more information on entities mentioned in those articles (e.g., species, molecules, localities, etc.). I've made various toys towards this, the latest being a HTML5 clone of Nature's iPhone app.One impediment to this is knowing
Progress on a phylogeny wiki
Authors: Page Roderic
Published: September 2023

I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do.First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021:In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.
Incrementos dasométricos en plantaciones de Tectona grandis L. f. (Teca) en la provincia del Guayas: influencia en el entorno paisajístico de la zona
Authors: López Tobar Rolando , Montilla López Yomber , Solano Apuntes Edison , Belezaca Pinargote Carlos , Núñez Castro Marlon
Published: September 2023

La investigación se la realizó con la finalidad de determinar el incremento en las variables diámetro y altura de plantaciones de la especie forestal Tectona grandis L. f. (Teca), y su influencia en el entorno paisajístico de la zona que afectaría a la flora y fauna existente en las plantaciones evaluadas; estos datos proporcionan una proyección del tiempo que le tomará a las plantaciones de esta especie para ser aprovechadas, además para determinar el impacto que estas generan al paisaje de la zona. La proyección se la realizó con el software matemático Maple 18 aplicado a una base de datos elaborada en el programa Excel la cual fue registrada en plantaciones de teca establecidas en el cantón Balzar de la provincia del Guayas. Se encontró que con el transcurso de los años la especie forestal provee de muchos beneficios al paisaje por su incidencia en la aportación al hábitat de especímenes de flora y fauna, además que la sucesión ecológica observada fue interesante en lo que respecta a regeneración de especies florísticas en especial en los lugares donde se realizó manejo silvicultural. Los sitios analizados son aptos para el cultivo de la teca, analizando las proyecciones realizadas en base a los datos obtenidos en las parcelas establecidas en cada uno de ellos. Las proyecciones de crecimiento realizadas a la especie en estudio, reflejaron que el incremento en diámetro y altura son prácticamente homogéneos; los datos reflejan que para alcanzar un diámetro comercial la plantación necesita 21 años, presentando DAP de 33,64 centímetros (1,646 cm/año) y 31,70 metros de altura, (1,55 m/año); la relación de altura respecto al diámetro es de 94, esto significa que los crecimientos se mantienen constantes y la relación es que por cada centímetro que incrementa en diámetro, el árbol incrementa su altura aproximadamente un metro.
Trazabilidad de la madera y destino final: lecciones aprendidas de un proceso de gobernanza forestal en la Amazonía Ecuatoriana
Authors: Reyes Morán Héctor Fernando , Zambrano Erika , Villacrés Damián , Luna Murillo Marcelo Vicente , Torres Navarrete Segundo Bolier
Published: September 2023

Con la implementación de la Estrategia Nacional de Desarrollo Forestal Sustentable del año 2000 y sobre todo con la normativa de MFS del bosque húmedo, se iniciaron las prácticas en el Manejo Forestal Sustentables (MFS) en Ecuador. En la Amazonía ecuatoriana, varios autores han estimado que el aprovechamiento de madera contribuye en promedio entre 14 y 21% del total de los ingresos monetarios en los hogares rurales. En este contexto, se desarrolló un proceso de gobernanza forestal en la provincia de Napo, que comenzó en el año 2009 cuando se constituyó la Mesa Forestal de Napo y promovió un proceso de gobernanza participativa. El propósito principal de este estudio fue comprender en qué medida las normas existentes, acompañadas del control y trazabilidad de madera en destino final, repercuten en la forma en que los actores interactúan entre sí durante el aprovechamiento y la comercialización de los Productor Forestales.
La gastronomía como recurso de la identidad ancestral: el caso de la Parroquia Chuquiribamba, Loja, Ecuador
Authors: Montalván Fernández Anabell Stefania , Cabrero Miret Ferrán
Published: September 2023

El presente artículo plantea que la identificación de elementos gastronómicos desde la perspectiva de patrimonio cultural inmaterial es un paso previo que permitirá fortalecer la identidad cultural y el desarrollar el turismo rural en el sector, tomando en cuenta el origen antropológico, la identidad cultural, la transmisión de conocimientos ancestrales, aportando con la elaboración de una guía gastronómica. Aplicando de manera oportuna la metodología más apropiada para trabajar en la comunidad sin interferir en su cotidianeidad a diferencia una investigación aislada y apática.