The title of this posting refers to the excellent article from David Dobbs I bookmarked very recently. I’d like to present you a very interesting initiative from French bioscience research program for high-school students called “Tous chercheurs”. The Community Page of the very last PLoS Biology is dedicated to this project and I find it really great. Because, indeed, publishing your science paper is only half of the job.
Shadows on the wall: “Truth never triumphs, but its opponents eventually die”Standard
Gregory Petsko wrote a small comment in the very last Genome Biology titled Shadows on the wall. A very angry but still contained one, nicely written and important to think about. Here is some of my thoughts about.
Bookmark: Indicators of the interdisciplinarity of journals: diversity, centrality, and citationsStandard
Loet Leydesdorff and Ismael Rafols have written a paper aiming at introducing citation-based indicators for interdisciplinarity. Here is the abstract, the whole publication is available for download at arXiv:
The cocoa genome has been released last week, by Mars (you know, the company producing M&M’s and suchlikes). They announced it as data released in the public domain. This sounds great! Well, it only sounds…
Bookmark: “It’s brutal, the funding situation has ended lots of careers”Standard
A very interesting insight into funding procedures comes in the latest Nature. This 3-page testimonial by Kendall Powell describes a decisionary session at the American Cancer Society (ACS), the largest private non-profit funding agency for cancer research in the US. Recommended reading and lots of food for the brain…
How to perform responsible researchStandard
Whereas professionals from medical care have the Hippocratic oath and researchers on human have the Nuremberg code for ethics to subscribe to, there are no such guidelines for people in sciences. The 2nd World Conference on Research Integrity in Singapore took place at the end of July this year. The output of this meeting gathering more than 300 individuals from 51 countries is the Singapore Statement on Research Integrity released on September 22.
Bookmark: Publishing your science paper is only half the jobStandard
An excellent posting from David Dobbs and the importance of bringing your research to non scientists. I particularly liked the conclusion:
Getting your research out there and taking time out from the lab is a pain, no doubt. But if you’re a scientist, surely you don’t expect the rest of us to just assume your work is important. No. If you want the world to believe that your work is important and that modern life and a free society depend on a rigorous, evidence-based approach to things, you wouldn’t ask us to take it on faith. You’d want to show us the evidence.
Get involved: Making metrics that measure what mattersStandard
Cameron Neylon is inviting today everybody to join and take actively part in a poject to redefine bibliographic metrics. Creating this kind of system is essential for sharing knowledge and “there is an opportunity to connect technical expertise and data with the needs of funders, researchers, and perhaps even the mainstream media and government.”. The current proposal stands for a Barcamp day in UK followed by two-day hackfest. The proposal is available to view and edit as a GoogleDoc.
Bookmark: BMJ Open, accessible medical researchStandard
This is an open access journal launched very recently and focused on medical research. It aims at publishing not only full-text reports, but also pilot studies and pre-protocols. Moreover, all data will be published online and reviewers’ comments will figure alongside the main text. This initiative emphasizes the importance of transparency and data sharing in science. Support BMJ Open, submit your results there!
Brevia: A new link between art and science, or towards hackerspaces’ fundingStandard
Alt. Art-Sci is the phrase coming frequently in mind when some people talk about establishing a link between art and science. A recent joint workshop gathering representatives from the National Science Foundation (NSF) and the National Endowment for the Arts (NEA) but also researchers, faculty members and artists discussed about this indispensable link between art and science.
Bookmark: The horniest dino species discovered in UtahStandard
National Science Foundation announced today that a novel dinosaur species was discovered in Utah. It is a close relative to Triceratops and is called Kosmoceratops richardsoni; it lived at about 76 millions of years ago. It was 5 meters long from snout to tail and its weight is estimated at 2.5 tonnes. His head measures 2 meters and is disproportional compared to the total body size.
How to handle the paper glutStandard
In a Letter to Science, Donald Siegel and Philippe Baveye discuss what they call “the paper glut” we face and address suggestions to improve the reviewing system.
Bookmark: Videos from the Conference on Open Access Publishing are availableStandard
Just a quick link to the videos of the COASP (Conference on Open Access Scholarly Publishing) held from August 22 to August 24, 2010 in Prague (Czech Republic). Enjoy!
Bookmark: Conference on Open Access in AfricaStandard
BioMed Central announced last week they will be hosting a 2-day conference on Open Access publishing at Kenyatta University (Nairobi, Kenia). It will take place from November 10 to November 11, 2010.
In the mood: French minister of education and research on Shanghai rankingStandard
The French version of this posting is available here.
The French newspaper Libération organizes regular chatrooms where questions are adressed to various politicians. On September 15, the guest was Mrs Valérie Pécresse, the French minister of Education and Research. She answered several interesting questions and, among them, the one on the Shanghai ranking published a little ago. I prefer laughing than crying from despair when I read this…
Brevia: Open Knowledge, Open data and moreStandard
Some exciting events and pieces of news on Open data and Open knowledge are summarized below, don’t hesitate to spread the word!
Journal Club: Three great PLoS Biology papersStandard
PLoS Biology is definitely one of my favorite journals 🙂 Here are 3 papers I find really great, for various reasons:
Bookmark: DIYbio and quick thoughts after the bioethics commissionStandard
Here is a small and quite encouraging summary of the bioethics commission, by Matt Feltz. More to come at the end of the week.
Bookmark: After Google instant, here comes PubMed instantStandard
Just a bookmark post to tell that a search engine called PubMed Instant is now available 🙂 Here is the link: https://web.archive.org/web/20220525094927/http://pminstant.com/ Have a nice PubMed crawling!
Brevia: Getting dumb and dumber while software improves?Standard
Today’s BBC News has an article about how ever improving software could damage our ability to think innovatively.
Bookmark: On good study habitsStandard
A nice posting from Daniel Lende on his Neuroanthropology blog @PLoS titled From Good Study Habits to Better Teaching. Some extracts below:
Bookmark: Bioinformatics education should start in High schoolStandard
Xconomy|Seattle publishes opinion from Jodie Spitze where the question about the crossroad between biology and computer science is addressed:
In this digital age, one of the areas that should be most exciting to students is the intersection between technology and biology. Public databases store an abundance of biological data and a variety of programs enable this data to be searched, compared, and visualized. Termed bioinformatics, researchers use these capabilities to understand and treat genetic conditions, discern evolutionary relationships, and learn about how cancer cells differ from normal cells. What is especially exciting is that this technology is available to all, including high school students.
So why is bioinformatics rarely included in biology courses?
Nice analysis, recommended reading!
Improving biofuel production thanks to yeastStandard
Everybody knows humankind produces beer and wine since ever. In this case, we put a bug – yeast, from the same family as the one helping to produce the pastries – in presence of sugar and absence of oxygen which concludes in the production of bioethanol.
What is biofuel?
Biofuels are a wide range of fuels which are in some way derived from biomass. When people think of producing some liquid biofuel, it is generally alcohol-based, namely bioethanol. People like it because it is renewable energy. It can be made from agricultural feedstocks (sugar cane, maize, potato).
The problem is that if we use these crops, the food prices will increase and moreover, a lot of arable lands is needed; but most of all, the concerns went to the energy required to keep the pollution balance of the whole cycle of ethanol production (especially when it comes from corn).Continue reading
Brevia: Teaching the zombie condition at the universityStandard
The Baltimore Sun announced the other day that a class on the undead will be held at the Baltimore University. It is called Zombies 101 and will be taught by Arnold Blumberg, the author of Zombiemania (a book on zombie movies) and the curator of Geppi’s Entertainment Museum, which focuses on American pop culture. This class will be part of English 333. The students will watch 16 movies on zombies. If they want, as an alternative to a final research paper, they may write scripts or draw storyboards for their ideal zombie flicks.
Definitely, a class to die for!
P.S. If you want to know more on other fancy courses provided in the academia, check out the catalogue Laura Davis from Belfast Telegraph presents.
The futur of biotech patents – part 1Standard
What is the futur (if any) of biotech patents? What did the Bilski ruling change? Did it change something at all? I’m not a specialist, but I’ll give it a try. First, this posting will adress the question about the definition of what patenting the living means. In another one, I’ll try to go more into some historical details and their importance for the futur of biotech patents.
Journal club: Papers to read from BMC Bioinfo, PNAS, ScienceStandard
After several airport adventures because of French air controllers’ strike on Tuesday, September 7, I’m back. Here are a bunch of papers which just came out:
EMBO meeting special session: The intelligent brain – does sexe matter?Standard
This is a summary of the talk Prof. Richard Haier gave on September 6 titled The new science of intelligence: men, women and brains. There are various things I do not agree with. However, I will not comment on them in this posting to let everybody read what Prof. Haier said and not what I think about what he said.
Contrary to myth, intelligence can be defined and measured. Intelligence tests scores are related to brain features. Genetic and epigenetic influence on intelligence can be assessed: intelligence is thus 100% biological. The talk was organized as follows:
- Examples of people with extraordinary intelligence;
- Measuring intelligence;
- Brain localisation of intelligence;
- Gender-specific intelligence.
EMBO meeting day 2: Plenary lectures on human enhancers discovery and synthetic biologyStandard
Today begins with the session Systems biology & functional genomics. Here are some notes from those I was really interested into. The abstracts for all the talks can be found on the EMBO meeting dedicated page.
EMBO meeting day 1: Innovation forum and mobility for scientistsStandard
Today was the first day of the EMBO meeting. I already told a bit about the opening session; some words below go to the Innovation forum held in the very beginning of this first interesting – and quite exhausting – day.
Exclusive: opening of the EMBO meeting in Barcelona, SpainStandard
I haven’t said it yet, but I’m at the EMBO meeting in Barcelona (Spain) at the moment. I’ll attend some exciting workshops and lectures, but – last but not least – I’ll present a poster at the session dedicated to Genomics and Computational Biology on Tuesday. The satellite session is finished now and the opening talks and lectures took place after 6 pm in the Auditorium of the Palau des Congressos. Some impressions below 🙂
Bookmark: BioMed Central launches a new initiative to promote data sharingStandard
BMC Researcher Notes’ latest editorial titles A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. It announces a new initiative aiming at promoting best practice in sharing and publishing data, with a focus on standardized, re-useable formats. Thus, data from original research project described by precised Data Notes will be made publicly accessible and, along with, an example dataset will be included.
This great initiative is a new step towards open data and research reproducibility!
Read the original announcement from BMC.
Brevia: Welcome to PLoS Blogs!Standard
Liz Allen announced the official PLoS Blogs today:
The launch of this network is a natural extension of the support that PLoS has always offered to bloggers in recognition of the excellent work that they do in bridging the gap between scientific and medical articles and mainstream media headlines.
Bookmark: Hackers blind quantum cryptographersStandard
Nature News reports a nice crack: a team from the Norwegian University of Science and Technology in Trondheim succeeded in cracking commercial encryption systems by intercepting photons of light to create a security leak; the whole procedure leaves no trace.
Bookmark: “We come in peace” – the Chaos Communication Congress announcedStandard
We come in peace, said the conquerers of the New World.
We come in peace, says the government, when it comes to colonise, regulate, and militarise the new digital world.
We come in peace, say the nation-state sized companies that have set out to monetise the net and chain the users to their shiny new devices.
We come in peace, we say as hackers, geeks and nerds, when we set out towards the real world and try to change it, because it has intruded into our natural habitat, the cyberspace. Let us explore each other’s truly peaceful intentions at this year’s Chaos Communication Congress 27C3 to be held from Monday December 27 to Thursday December 30, 2010 in Berlin, Germany.
27C3 calls for participation! The following areas are of particular interest this year:
Gender equality and diversity summit at the Open World Forum (Paris)Standard
The Open World Forum is an annual event held in Paris in the fall and bringing together actors from the Free/Libre and Open Source Software (FLOSS) world. This year, a special satellite session will be dedicated to women’s participation in communities and business activities in relationship with FLOSS. Panel discussions and workshops will be organized and many questions will be addressed. To assess women’s participation, a questionnaire has been prepared: I invite you to fill it in order to provide more depth in the vision of the subject.
Journal Club: PNAS, Science, PLoS papers to readStandard
Here are some papers with interesting titles and abstracts:
Bug 626593 – Gnome ate my boyfriend! Help!Standard
A bug… or a feature? Awesome!
Bookmark: Foldit, biology for gamersStandard
In the very latest Nature issue (August 5), a paper presents Foldit which is a program for predicting protein structures. But it’s kinda special program: better say, it’s a multiplayer online game. Thus, its leitmotiv is “Solve puzzles for science”.
Scientopia is presented as “a collective of people who write about science because they love to do so”. Sounds nice. Participation seems a bit restrictive, though. Haven’t had a closer look yet, but I read this on Pharyngula’s blog (and it is not that far from my first impression):
Although, I do have to say that I’m not a fan of their published code. It throws around the word “respect” way too much, which happens to be one of those words that annoys me, because it is too easily assumed when it should be earned. I don’t respect everyone who blogs on science, and not everyone respects me (nor should they)…but it does put me on edge when a group announces a demand for mutual respect and also lays out a protocol for eviction, when I know that several of the people in the collective had little respect for some others on the Sb network. I have no respect for the pretense of respect.
Read and see.
Call for participation: GMOD Tools for Evolutionary Biology HackathonStandard
Here is an announcement I received through a mailing-list in evolutionary biology. I paste is such as below, it may interest people 🙂
Bookmark: Women’s Caucus internship opportunityStandard
The Women’s Caucus at the FSF (Free Software Foundation) is seeking an intern to assist with its work to increase the number of women involved in free software. Please check the offer online.
Le Caucus est une initiative de la FSF (Fondation pour le Logiciel Libre) visant à augmenter la participation féminine dans les communautés libristes. Vous pouvez lire la traduction des recommandations en français (faite par votre humble serviteure qui est intéressée par toute suggestion d’amélioration). Ils proposent donc un poste de stage pour une personne intéressée par la thématique. L’offre (en anglais) est sur le site de la FSF.
Bookmark: Bethesda statement on Open Access publishingStandard
It can be read here. A translation in French is also available.
Bookmark: The third reviewerStandard
Il s’agit d’un forum pour scientifiques où ils peuvent commenter des papiers récemment publiés. Un peu comme un Journal club. Pour l’instant, le thème ayant le plus d’articles est Neurosciences, mais la Microbiologie commence à arriver aussi.
Le (très) mauvais point : les articles non open access ne présentent que les abstracts (résumés). Donc, si on n’a pas accès au journal, c’est loupé pour lire le tout.
Journal club: Tracking marsupial evolution with archaic genomic retroposon insertionsStandard
The phylogenetic relationships between two orders of marsupials have been intesively debated. Authors benefited from recent sequencing projects which provided two marsupial genomes: this of the South American opossum (Monodelphis domestica)and the one of a kangaroo, the Australian tammar wallaby (Macropus eugenii).Continue reading
Bookmark: Microarray analysisStandard
Nice and short article in PLoS Biology about microarray analysis: Genome-scale hypothesis scanning, Gibson G (2003) Microarray Analysis. PLoS Biol 1(1): e15.
Usually, people say “Hello world!” when they begin a blog. They often discuss why they wanted to begin writing and sharing their thougts and personal stuff with everybody having access to the web. I’m not inspired about doing this, so I won’t do it. Read ahead, you’ll find by yourselves 🙂
P.S. It’ll be a mixture of French and English posts. Don’t accuse your browser of being crap because of French and English words messed around.