The French breast implant scandal

zarq — Sat, 18 Feb 2012 19:19:30 -0800

In March 2010, a pair of health inspectors responding to multiple tips paid a three-day visit to the factory headquarters of the Poly Implant Prothese (PIP) company, a leading international maker of breast implants. On their second day, the inspectors found something odd: six discarded plastic containers of Silopren, a liquid silicone designed for industrial, not medical use, lined up along the outside wall of the production site. The lead inspector estimated they had contained nearly 9 tons of liquid silicone. It now appears as if between 300,000 and 400,000 women throughout the world may have received potentially toxic, faulty breast implants containing ingredients never clinically tested on humans, manufactured and distributed by a company that knowingly deceived regulators, suppliers, distributors, medical professionals and ultimately, patients. Reuters photographer's Blog: Operating on an implant scandal. (Last link NSFW, graphic images that contain nudity.) PIP also sold chest and testicle implants for men which used the same non-medical, industrial grade silicone. Coverage from CNN, The Guardian. On February 7, 2012, BBC's Newsnight program featured a Q&A between 25 women who had been implanted with PIP breast implants and Anne Milton, a health minister for the UK coalition government. Evidence had apparently been available that PIP implants were likely defective for several years, yet the NHS had chosen not to inform patients of potential warnings. Milton stated, "The evidence to date is that they [PIP implants] are not [dangerous]." Response editorial by Naomi Wolf. There have been multiple demonstrations in London. Wikipedia's page on the company has a decent breakdown of the continuing aftermath of the scandal.

iBOL iWish there were an app for that already

infinite intimation — Wed, 14 Jul 2010 20:40:44 -0800

What is dna barcoding?

tl;Linnaeus
tl;Edward Norton Barcode of Life: Global Biodiversity Challenge Earth is home to an estimated 10 to 100 million species but 250 years of study has formally described fewer than two million of them. The International Barcode of Life (iBOL) project includes biodiversity scientists from 26 countries working to identify every species on the planet using short snippets of DNA. Over the next 5 years, they are hoping to process 5 million specimens and they need your help! Students and youth from around the world, along with local scientists at colleges and universities, will participate in a collaborative social networking educational game in a race to identify and assign unique DNA barcodes to as many species as possible. Student Sleuths Using DNA Reveal Zoo of 95 Species in NYC Homes -- And New Evidence of Food Fraud Tan and Cost plan to pursue biology and music respectively at university next fall. What is DNA barcoding?

In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Barcoding uses a very short genetic sequence from a standard part of the genome the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC). Two items may look very similar to the untrained eye, but in both cases the barcodes are distinct. Until now, biological specimens were identified using morphological features like the shape, size and color of body parts. In some cases a trained technician could make routine identifications using morphological “keys” (step-by-step instructions of what to look for), but in most cases an experienced professional taxonomist is needed. If a specimen is damaged or is in an immature stage of development, even specialists may be unable to make identifications. Barcoding solves these problems because even non-specialists can obtain barcodes from tiny amounts of tissue. This is not to say that traditional taxonomy has become less important. Rather, DNA barcoding can serve a dual purpose as a new tool in the taxonomists toolbox supplementing their knowledge as well as being an innovative device for non-experts who need to make a quick identification. The gene region that is being used as the standard barcode for almost all animal groups is a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene (“CO1”). COI is proving highly effective in identifying birds, butterflies, fish, flies and many other animal groups. COI is not an effective barcode region in plants because it evolves too slowly, but two gene regions in the chloroplast, matK and rbcL, have been approved as the barcode regions for land plants. Barcoding projects have four components: 1 The Specimens: Natural history museums, herbaria, zoos, aquaria, frozen tissue collections, seed banks, type culture collections and other repositories of biological materials are treasure troves of identified specimens. 2 The Laboratory Analysis: Barcoding protocols can be followed to obtain DNA barcode sequences from these specimens. The best equipped molecular biology labs can produce a DNA barcode sequence in a few hours. The data are then placed in a database for subsequent analysis. 3 The Database: One of the most important components of the Barcode Initiative is the construction of a public reference library of species identifiers which could be used to assign unknown specimens to known species. There are currently two main barcode databases that fill this role: a) The International Nucleotide Sequence Database Collaborative is a partnership among GenBank in the U.S., the Nucleotide Sequence Database of the European Molecular Biology Lab in Europe, and the DNA Data Bank of Japan. They have agreed to CBOL's data standards (pdf; 30Kb) for barcode records. b) Barcode of Life Database (BOLD) was created and is maintained by University of Guelph in Ontario. It offers researchers a way to collect, manage, and analyze DNA barcode data. 4 The Data Analysis: Specimens are identified by finding the closest matching reference record in the database. CBOL's Data Analysis Working Group has created the Barcode of Life Data Portal which offers researchers new and more flexible ways to store, manage, analyze and display their barcode data.

Welcome to ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian, and Mexican agencies (ITIS-North America); other organizations; and taxonomic specialists. ITIS is also a partner of Species 2000 and the Global Biodiversity Information Facility (GBIF). The ITIS and Species 2000 Catalogue of Life (CoL) partnership is proud to provide the taxonomic backbone to the Encyclopedia of Life (EOL). Why?

Species identifications underpin all of biological research. Existing morphologically-based diagnostic approaches are often both cumbersome to use and are effective only for certain life stages. DNA-based systems promise to revolutionize the task of identification by providing reliable, inexpensive and rapid diagnosis of species identity. Imagine a day when any living thing can be identified accurately and rapidly to the species level using a hand-held device the size of a cellular phone. A day when the biodiversity of an entire nation can be inventoried and monitored, and thereby better protected. When invasive species, disease agents and their vectors, and agricultural pests can all be identified and tracked with ease, thus saving millions of dollars and improving both human health and that of the natural environment. When pollen grains at a crime scene can be linked to those on a suspect’s shoes, the quality of water analyzed in terms of its living inhabitants as well as its chemical constituents, and endangered or dangerous species crossing national borders immediately recognized – not just by highly trained professional taxonomists, but by anyone. A day when bio-prospectors will be able to collect and rapidly identify thousands of species that may yield new lifesaving drugs, and when the plant and animal ingredients in food products can be assessed with certainty even after processing. Imagine a day when every curious mind, from professional biologists to schoolchildren, will have immediate access to the names and biological attributes of any species on the planet. To be sure, this still rings of science fiction. But thanks to an ambitious effort by a growing consortium of scientists, it is poised to become reality. The method that will enable this advance is "DNA barcoding", an approach that employs a small fragment of DNA, a portion of a single gene, to provide a unique identifier – a "DNA barcode" – for each living species on Earth. Using these DNA barcodes, it will be possible to identify any organism, be it juvenile or adult, male or female, large or small, from only a tiny piece of tissue. This is vastly more efficient than traditional approaches which are often based on the detailed examination of specific body parts and which typically require interpretation by trained experts. In addition, because DNA barcoding quickly distinguishes new species, it will greatly accelerate the rate of their discovery. Given that it has taken 250 years to describe roughly 15% of life’s estimated diversity and that this diversity is now being lost at an alarming rate, the taxonomic revolution incited by DNA barcoding arrives at a critical time.

international Barcode Of Life iBOL: About How DNA Barcoding Works and What it Will Do? How does iBOL work? Massive partnership The Core Partners of DNA barcoding are: • iBOL, the largest consortium of projects, labs, and networks, • CBOL, the global initiative to promote barcoding, • BOLD, the global workbench for assembly, analysis and curation of barcode data, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community. GenBank, the public archival repository for barcode data. These Core Partners work with the wide range of Featured Partners shown below. Together the Core and Featured Partners make up the Barcoding Landscape. Project Site Canadian Barcode of Life Network The Canadian Barcode of Life Network, made up of nearly 50 researchers from across the country, represents the first national network dedicated to large-scale DNA barcoding. The goal of this network is to make important contributions to biodiversity research, and to maintain Canada's place as a leader in the development of DNA barcoding. Project Site Catalogue of Life (CoL) The Catalogue of Life (CoL) is a joint effort between the Species 2000 and IT IS organizations aimed at completing coverage for all 1.75 million known species by 2011. Project Site Encyclopedia of Life (EOL) The Encyclopedia of Life (EOL) is an online reference and database for all 1.9 million species currently known to science, and will stay current by capturing information on newly discovered and formally described species. EOL aims to help all of us better understand life on our planet. Project Site EOL Previously More previously (check out EOL’s Photosynth library) Bee Barcode of Life Initiative (Bee-BOL) Bee-BOL, the Bee Barcode of Life Initiative, is a global effort to coordinate the assembly of a standardized reference sequence library for all ~20,000 bee species. Bee-BOL is creating a valuable public resource in the form of an electronic database containing DNA barcodes, images, and geospatial coordinates of examined specimens. The database contains linkages to voucher specimens, information on species distributions, nomenclature, authoritative taxonomic information, collateral natural history information and literature citations. Coral Reef Barcode of Life The Coral Reef Barcode of Life campaign is a detailed barcode study of fishes at one site in the Great Barrier Reef to generate a barcode library that will aid taxonomic work by clarifying species boundaries and by revealing cryptic taxa. European Consortium for the Barcode of Life (ECBOL) ECBOL is an information and coordination hub on DNA barcoding in Europe organized within EDIT, the European Institute of Taxonomy and maintained by CBS, the Centraalbureau voor Schimmelcultures in Utrecth. The ECBOL initiative (Calibrating European Biodiversity using DNA Barcodes) is a network of European researchers and is seeking to obtain funding fro the coordination and maintenance of a Network of European Leading Labs. Fish Barcode of Life Campaign (FISH-BOL) FISH-BOL, the Fish Barcode of Life campaign, is collecting barcodes from at least five specimens representing the 30,000+ species of marine, freshwater and estuarine fish of the world. Like ABBI, FISH-BOL has a central Steering Committee and Regional Working Groups. HealthBOL HealthBOL coordinates initiatives to barcode vectors, pathogens, and parasites for the betterment of human health around the world. Lepidoptera Barcode of Life The aim of the Lepidoptera Barcode of Life campaign is to build a COI barcode library for all butterfly and moth species. This library will permit the rapid, reliable identification of Lepidoptera at any stage of their development (egg, caterpillar, pupa or adult) and will facilitate the discovery and description of new species. Such barcode libraries, in combination with the ones built for other groups of terrestrial animals, will make possible the detailed biodiversity maps required to guide the positioning of protected areas and to monitor the status of terrestrial life. Mammalia Barcode of Life Campaign The Mammalia Barcode of Life campaign is a part of the larger effort encompassing all vertebrates, and aims to build a comprehensive reference library of DNA barcodes for the global mammal fauna. The campaign seeks to assemble a broad global coalition of leading researchers, museums, and other institutions with interest in mammal taxonomy and biodiversity Marine Barcode of Life (MarBOL) MarBOL is an international campaign to obtain at least 50,000 barcode records of marine species by October 2010. MarBOL is led by an international Steering Committee and an affiliated project of the Census of Marine Life (CoML). Mosquito Barcode Initiative (MBI) MBI, the Mosquito Barcode Initiative is another "demonstration project" aimed at producing a global operational system for identifying mosquitoes in two years. MBI plans to barcode at least five specimens from 80% of the 3200 known mosquito species. Disease-bearing species and their closest relatives will be the highest priority. Polar Barcode of Life (PolarBOL) The Polar Barcode of Life campaign coordinates barcoding efforts in ongoing bioinventory projects in Arctic and Antarctic marine, freshwater and terrestrial ecosystems. Quarantine Barcode of Life (QBOL) QBOL is a project financed by the 7th Framework Program of the European Union that makes collections harboring plantpathogenic quarantine organisms available. Informative genes from selected species on the EU Directive and EPPO lists are DNA barcoded from vouchered specimens. In the next 3 year the sequences, together with taxonomic features, will be included in an internet-based database system. Shark Barcode of Life (SharkBOL) The Shark Barcode of Life project aims to barcode the 1,000 marine and 100 freshwater shark species. Sponge Barcoding Project (SpongeBOL) The Sponge Barcoding Project is the first global barcoding project on any diploblast taxon and covers the complete taxonomic range of Porifera. Tephritid Barcode Initiative (TBI) TBI, the Tephritid Barcode Initiative is a two-year "demonstration project" that will create an operational system for identifying fruit flies around the world. TBI will barcode at least five representatives of all tephritid fruit flies that are either (1) agricultural pests, (2) beneficial species used for biological control of other pests, (3) closely related to pests or beneficial species; and (4) representative species from other families of tephritids. TBI plans to obtain barcodes from approximately 2000 species of the estimated 4500 known tephritid species. Trichoptera Barcode of Life (TrichopteraBOL) Trichoptera Barcode of Life is a long-term project to barcode the world’s approximately 13,000 species of caddisflies. The All Birds Barcoding Initiative (ABBI), launched in September 2005, aims to collect standardized genetic data in the form of DNA barcodes from the approximately 10,000 known species of world birds. Despite several hundred years of careful study, genetic surveys including those with DNA barcoding suggest there are hundreds of as yet undescribed avian species. ABBI aims to help speed discovery of new species, provide a practical tool for specimen identification, and open new avenues for scientific investigation. National GEO focus on Paul Hebert's 'big idea'; barcoding life.

If you turn on a light at night in the mountains of Papua New Guinea, says Paul Hebert, you will collect some 2,000 species of moth. Moving up the mountain a bit will net you a different but equally daunting crowd. As a young postdoc in the 1970s, Hebert, now an evolutionary biologist at the University of Guelph in Ontario, spent five years trying to make sense of that fluttering confusion, before finally deciding it was beyond his or any human’s capacity. For two decades after that he retreated to water fleas, of which there are only 200 species. Then in 2003 he did something new. In a paper that year he began by describing the diversity of life as a “harsh burden” for biologists, and proceeded to suggest some relief: Every species on Earth could be assigned a simple DNA bar code, Hebert wrote, so it would be easy to tell them apart. The bar code Hebert suggested is part of a gene called CO1, which helps produce the energy-carrying molecule ATP. CO1 is so essential that every multicellular organism has it. But there is enough variation in its sequence—each of the 600-odd spots in the bar code region can be filled by any of four different DNA bases—that two species rarely have the exact same one. Such differences in a gene are readily scanned by machine even when the animals themselves might confound an expert; Hebert’s group is now sequencing a thousand specimens a day. They’ve bar coded nearly 40,000 species of moth and butterfly already. The technique has commercial as well as scientific promise. Mislabeling of fish on menus is rampant, it turns out.

Welcome to the Biodiversity Institute of Ontario, here Paul Hebert D.N. is Director of the Biodiversity Institute of Ontario, Canada Research Chair, Scientific Director

(News/Archives) Biodiversity measures the variation of life shaped through ecology and evolution from genes to species and ecosystems. Genetic variation plays a critical role in the ability of individuals and species to respond and adapt to environmental change while the diversity of species within and between ecosystems provides significant advantages to ecosystem function and resilience. One of the ironies of biological research is that after more than 250 years of dedicated biological science, the total number of species within any country or region remains unknown. While we often have a good idea of the identities and ecological roles of the larger, more charismatic animals (birds, mammals) the truth of the matter is that most of life is small (insects, bacteria, fungi) and currently undescribed. Shedding light onto these lesser known groups is important because all of the larger groups, including ourselves, depend on these smaller organisms for some part of their daily natural history. In order to protect and understand the diversity of life in Ontario, we must be able to know the species and ecosystems upon which humans, and our industry and lifestyle, depend.

Google Tech Talks: Current Issues in Computational Biology and Bioinformatics Gary Bader is Assistant Professor at the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) at the University of Toronto. Jonathan Rosenberg introduces, Drs. Paul Hebert and Dan Janzen discuss their transformative (and very Googley) International Barcode of Life project (www.dnabarcoding.org)
iBOL's goal is to capture, using a handheld device, the unique "DNA barcode" of each and every species on earth, and organize that information to be accessible and useful for everyone (sound familiar?). A DNA barcode is a gene sequence that uniquely identifies any species, and iBOL has already barcoded 35,000 of them. There are approximately 10M species on the planet (half of which have yet to be discovered), so there's a long way to go, but the components for success are in place. During my recent family vacation to Costa Rica I hiked the rain forest, and by the end of the trip could easily identify a toucan, eyelash viper, and three types of monkeys (howling, spider, and Rosenberg offspring). Pretty impressive, right? Then Dr. Janzen showed me a photo of that same rain forest and told me that there were approximately 400 species of animals and plants in that picture, and not a toucan or monkey among them. So it turns out that I'm just as bio-illiterate as everyone else, but Google can do something about this. When we talk about organizing all the world's information, a blueprint of the world's natural biodiversity should be part of it.
Is IT ready for the Dreaded DNA Data Deluge? -Dr. Andras Pellionisz

In 18 months full human genome sequences will be available under $100 - and in minutes. The $5,000 full human genome was announced to come in 9 months. Is "Big IT" ready for the avalanche of data, to be obtained and processed e.g. while the patient is still on the operating table, to be diagnosed, and how the genomics glitch, that caused a benign or malign tumor, could be compensated for? Algorithmic approaches are needed to better understand genome regulation, even for the simple reason to deploy most effective data retrieval, data storage and computational means, via both parallel hardware and software, but more importantly for opening entirely new perspectives. In the 100+ year old Genomics, for over half a Century had us to resign to the fatalistic gloom that we are stuck with any glitches in our inherited genome. Is it true that genomic glitches doom one to "incurable" hereditary diseases? No longer. Genomics now considers the DNA-RNA-Protein chain not as a thermodynamically closed system, where entropy increases, but as an open system that can be interfered with. There is theoretically sound hope that you are not stuck with your genomic glitches. After half a Century of sticking to two mistaken axioms of Genomics, the paradigm of recursive genome function must quickly make up for lost time for those (potentially) inflicted with formerly "incurable" diseases. "The Genome baby is left on the doorsteps of Information Technology". Doctors sent those inflicted with fleece for "debugging". Debugging genome information (by Genome Computers) would be much harder without understanding the algorithms that our natural genome computing operates with.

Third International Barcode of Life Conference, Mexico City: dnabarcodes Past Meetings and Conferences... Third International Barcode of Life Conference Conference program overview To review all the files in one place, try downloading a copy of the hyperlinked Table of Contents in PDF format (this is really the best way to see how many talks, papers, and videos [Many Videos] are available from this conference [PDF]). Poster Presentations Barcode of life publications Introduction Session 1 (Tuesday, 10-November) - Welcome and Introduction Session 2 (Tuesday, 10-November) - Lessons learned from 2004-2009 Parallel Technical Session A (Tuesday, 10-November) - Plant Working Group Parallel Technical Session A (Tuesday, 10-November) - Pathogens, Disease Vectors & Parasites Parallel Technical Session A (Tuesday, 10-November) - FISH-BOL Parallel Technical Session A (Tuesday, 10-November) - Barcoding Species for Quarantine/Plant Protection Parallel Technical Session A (Tuesday, 10-November) - Marine Barcoding Parallel Technical Session A (Tuesday, 10-November) - All Bird Barcoding initiative & Vertebrates Parallel Technical Session B (Tuesday, 10-November) - Plant Working Group Parallel Technical Session B (Tuesday, 10-November) - Pathogens, Disease Vectors & Parasites Parallel Technical Session B (Tuesday, 10-November) - FISH-BOL Parallel Technical Session B (Tuesday, 10-November) - Barcoding Species for Quarantine/Plant Protection Parallel Technical Session B (Tuesday, 10-November) - Marine Barcoding Parallel Technical Session B (Tuesday, 10-November) - All Bird Barcoding Initiative & Vertebrates Session 3 (Wednesday, 11-November) - Case Studies: Impact of barcode data in research areas beyond taxonomy Session 4 (Wednesday, 11-November) - Informatics and Data Analysis Parallel Technical Session C (Wednesday, 11-November) - Plant Working Group Parallel Technical Session C (Wednesday, 11-November) - Insects/Terrestrial Arthropods: Utility & Alternative Approaches Parallel Technical Session C (Wednesday, 11-November) - Fish-BOL Parallel Technical Session C (Wednesday, 11-November) - Large-Scale Initiatives Parallel Technical Session C (Wednesday, 11-November) - Fungi, Algae, Protists & New Groups Parallel Technical Session C (Wednesday, 11-November) - Data Analysis Working Group (DAWG) Parallel Technical Session C (Wednesday, 11-November) - BeeBOL Symposium Parallel Technical Session D (Wednesday, 11-November) - Barcoding the Trees of Africa Parallel Technical Session D (Wednesday, 11-November) - Insects/Terrestrial Arthropods: Biodiversity Studies Parallel Technical Session D (Wednesday, 11-November) - FISH-BOL Parallel Technical Session D (Wednesday, 11-November) - Barcoding Databases, Protocols, and Education Parallel Technical Session D (Wednesday, 11-November) - Fungi, Algae, Protists & New Groups Parallel Technical Session D (Wednesday, 11-November) - Data Analysis Working Group (DAWG) Parallel Technical Session D (Wednesday, 11-November) - BeeBOL Symposium Session 5 (Thursday, 12-November) - Case Studies of Applications Session 6 (Thursday, 12-November) - Barcoding and Next Generation Sequencing Technologies Parallel Technical Session E (Thursday, 12-November) - Meso-American Symposium Parallel Technical Session F (Thursday, 12-November) - Meso-American Symposium Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates Pre-Conference Workshop, Botanical Garden Auditorium:Dr. Paul Hebert Professor Hebert is Canada Research Chair in Molecular Biodiversity at the University of Guelph and directs the Biodiversity Institute of Ontario. Previously, he was Chair of the Department of Zoology, Board Chair at the Huntsman Marine Science Centre at Guelph, and Director of the Great Lakes Institute at the University of Windsor. Professor Hebert is best known for founding the concept of DNA barcoding, and has published more than 270 papers employing molecules to probe biological diversity. Over the past triennium, he has raised more than $30M to construct the world's first barcode 'factory' and the informatics platform needed to support the barcode registration of all multi-cellular life. Together with a few colleagues, Professor Hebert is now leading efforts to establish the $150M International Barcode of Life Project that will barcode 500K species within 5 years. He is a Fellow of the Royal Society of Canada and has received several national and international scientific awards. Professor Hebert completed a BSc at Queen's University, a PhD in genetics at Cambridge University and postdoctoral fellowships at the University of Sydney and the Natural History Museum (London). Garden Auditorium: Junko Shimura Pre-Conference Workshop, Botanical Garden Auditorium: Planning and Funding DNA Barcoding Projects Global Taxonomy Initiative and Implementation of the CBD The Convention on Biological Diversity (CBD) entered into force on 29 December 1993. It has 3 main objectives: 1. The conservation of biological diversity 2. The sustainable use of the components of biological diversity 3. The fair and equitable sharing of the benefits arising out of the utilization of genetic resources These countries are involved in the CBD (very interesting) CBD Fact Sheets; .... But tougher regulation could come with a cost[PDF], warns David Schindel, an invertebrate palaeontologist and executive secretary of the Consortium for the Barcode of Life, an international initiative to identify species using short genetic sequences, based at the Smithsonian Institution in Washington DC. “We are very concerned that it will become more restrictive,” he says. In some cases, it can already take at least two years and reams of paperwork to agree the terms on which research can be conducted, specimens exported and profits shared. “You could go through a field season collecting specimens and then the government says they are going to hold on to them because you don’t have the right permission,” he says.

MetaFilter posts tagged with Mas

The French breast implant scandal

iBOL iWish there were an app for that already

Wind it up, wine up, wine up, jump up.

interference in bolivian elections by usa (why if he is unlikely to win?)