O'Really?

May 31, 2010

Martin Rees on Science and the Citizen

This years Reith Lectures by Martin Rees are being broadcast on BBC Radio 4 during June. An important theme in the lectures this year is scientists relationship with society. Rees argues that science is part of our culture, crucial for dealing with pressing international issues like population growth, food security and energy development. He also argues that science is not just for scientists, everyone has have a feel for it, not just the specialists. Here is the blurb from the first lecture: “Science and the Citizen”

“In the first of this year’s Reith Lectures, entitled Scientific Horizons, Martin Rees, President of the Royal Society, Master of Trinity College and Astronomer Royal, explores the challenges facing science in the 21st century. We are increasingly turning to government and the media to explain the risks we face. But in the wake of public confusion over issues like climate change, the swine ‘flu vaccine and, more recently, Iceland’s volcanic ash cloud, Martin Rees calls on scientists to come forward and play a greater role in helping us understand the science that affects us all.”

Lectures are available below and via the iPlayer.

Lecture Topic File Play in Browser
1/4: The Scientific Citizen Who should we should trust to explain the risks we face? mp3
2/4: Surviving the Century Does science have the answers to help us save our planet? mp3
3/4: What We Will Never Know What are the limits of Scientific knowledge? mp3
4/4: The Runaway World How can countries stay scientifically competitive? mp3

[Creative Commons licensed picture of Martin Rees above by The Reith Lectures on Flickr, see also introductory clip on the lectures.]

May 28, 2010

The University of Twitter, UK: A Quick Survey

Twitter icon for a fluid app by Miha  FilejMany people are still trying to work out exactly what twitter is good for [1] but with more than 100 million users worldwide making around 50 million tweets per day, the website is clearly popular with those who like to communicate via short “sound bites” of 140 characters or less.

Communication is an important part of what Universities are all about, so how many UK universities are on twitter? Knowing this could help us assess the use of the latest web technology in research where adoption has been rather limited so far, especially in Science  [2]. Rather than survey all the @UniversitiesUK, for a quick overview, let’s pick the twenty Russell Group Universities. According to their website, the Russell Group:

“represents the 20 leading UK universities which are committed to maintaining the very best research, an outstanding teaching and learning experience and unrivalled links with business and the public sector.”

So they are exactly the kind of places you would expect to be embracing and experimenting with new technology. The table below shows which of these institutions are on twitter:

@RussellGroup University @Twitter?
University of Birmingham @unibirmingham
University of Bristol @bristoluni
University of Cambridge @cambridge_uni
Cardiff University @cardiffuni
University of Edinburgh @uniofedinburgh
University of Glasgow @glasgowuni
Imperial College London @imperialcollege
King’s College London None as of May 2010*
University of Leeds @universityleeds
University of Liverpool @liverpoolfirst
London School of Economics None as of May 2010*
University of Manchester None as of May 2010*
Newcastle University None as of May 2010*
University of Nottingham @uniofnottingham
University of Oxford @uniofoxford
Queen’s University Belfast @queensubelfast
University of Sheffield @sheffielduni
University of Southampton @southamptonnews
University College London @uclnews
University of Warwick @warwickuni

There are plenty of important UK universities (@1994group, @UniAlliance@million_plus etc) excluded from this quick-and-dirty survey but it gives us an idea of what is going on. As of May 2010, 16 out of 20 Russell Group Universities are on twitter – perhaps this is another reason to love Higher Education because it is full of twittering twits?

But the last words on the United Kingdom of Twitter should go to the @number10gov Prime Minister David Cameron who has enlightening views on twitter including this quote below:

“We complain about the sound bite culture [3] but if you think about it and go back in history sound bites have always been used. Do to others as you would be done by, that is a fantastic sound bite … If you can’t convey what you’re trying to convey in a few short sentences you’ve got a problem and you have a particular problem in the media age. You have to work at communicating something complicated in a simple way or you’re not going to take people with you.”

References

  1. Haewoon Kwak, Changhyun Lee, Hosung Park, & Sue Moon (2010). What is Twitter, a social network or a news media? WWW ’10: Proceedings of the 19th international conference on World Wide Web, New York, NY, USA, 591-600 DOI: 10.1145/1772690.1772751
  2. Amy Maxmen (2010). Science Networking Gets Serious Cell, 141 (3), 387-389 DOI: 10.1016/j.cell.2010.04.019
  3. David Slayden and Rita Kirk Whillock (1998). Soundbite Culture: The Death of Discourse in a Wired World. Sage Publications, Inc. ISBN:0761908722

* These Universities had no central account that I could find in May 2010 but some have departmental accounts like  @kingsbiomed, @kingsmedicine, @lsepublicevents, @lse_recruitment, @mcrmuseum and @manunicareers etc which are not counted here because they don’t represent the whole University in question. The University of Manchester has an account @UoMRSSFeed but it isn’t official and hasn’t been updated recently. Dear beloved Alma mater, sort it out!

[Creative commons licensed picture of Twitter icon for a fluid app via Miha Filej.]

May 27, 2010

The 2nd ChEBI workshop: Call for Participation

The NanoPutians:  Synthesis of Anthropomorphic MoleculesThe second Chemical Entities of Biological Interest (ChEBI) workshop will be held at the European Bioinformatics Institute (EBI) in Hinxton, Cambridgeshire, UK on the 23rd and 24th June 2010. The full provisional schedule (including registration page) for this workshop is now available. Speakers at the workshop include:

There will also be several discussion sessions on the future evolution of the ChEBI project. Training will be provided including using ChEBI for research purposes and submitting your chemicals to ChEBI for annotation. We (the ChEBI team) hope to welcome you to Hinxton in June.

References

  1. Image of The NanoPutians taken from: Chanteau, S., & Tour, J. (2003). Synthesis of Anthropomorphic Molecules: The NanoPutians The Journal of Organic Chemistry, 68 (23), 8750-8766 DOI: 10.1021/jo0349227

May 21, 2010

myExperiment: The Videos

myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole Goble at the Universities of Southampton and Manchester in the UK.

Last year, JISC made some professional videos describing the project. Needless to say, the videos were much more fun to make than the accompanying papers [1,2,3] and a probably more informative too. The best way of linking the research papers to the videos on youtube is to blog about them, so here they are. The first video (below) talks about the project generally:

The second video (below) discusses the data used in tackling African trypanosomiasis (sleeping sickness) in cattle.

The videos include interviews with Carole Goble, Dave De Roure, Paul Fisher, Andy Brass and yours truly.

References

  1. David De Roure, Carole Goble, & Robert Stevens (2007). Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows IEEE International Conference on e-Science and Grid Computing, 603-610 DOI: 10.1109/E-SCIENCE.2007.29
  2. David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman (2008). myExperiment: Defining the Social Virtual Research Environment IEEE Fourth International Conference on eScience, 2008. eScience ’08., 182-189 DOI: 10.1109/eScience.2008.86
  3. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., & De Roure, D. (2010). myExperiment: a repository and social network for the sharing of bioinformatics workflows Nucleic Acids Research DOI: 10.1093/nar/gkq429

May 6, 2010

Mephedrone: Entity of the Month

Overdosed by Elad R, on FlickrRelease 68 of Chemical Entities of Biological Interest (ChEBI) is now available, with 549,319 total entities, of which 21,075 are fully annotated. This month’s entity of the month is Mephedrone, a substance which has been in the news headlines lately and as wikipedia points out is “not to be confused with Methedrine, Methedrone, Methadone, or Methylone“. Don’t you just love chemical names?! Text below reproduced from the ChEBI website:

“Mephedrone (CHEBI:59331) is a synthetic central nervous system stimulant and entactogen drug chemically related to cathinone, the psychoactive alkaloid present in the khat plant (Catha edulis, family Celastraceae).

It can be synthesised from 4-methylpropiophenone by an initial bromination at the β-carbon followed by replacement of the bromine by a methylamino group derived from methylamine hydrochloride. Although it was probably not available until 2007, by 2009 mephedrone had become the fourth most popular street drug in the UK, behind cannabis, cocaine and ecstasy. Little is currently known regarding its pharmacology or toxicology, although one recent report suggests the likelihood that it stimulates the release of, and then inhibits the reuptake of, monoamine neurotransmitters [1].

Although already listed as a prohibited substance in many countries, in others it has varying degrees of legality (notably the USA where it is currently unscheduled under the Controlled Substances Act). In the UK, a decision by the Home Secretary to classify mephedrone as illegal caused the resignation of two members of the Advisory Council on the Misuse of Drugs (ACMD) which has led in turn to a general questioning of UK drugs policy. Mephedrone finally became classified as a Class B drug in the UK on April 16, 2010 – prior to this time it was often sold openly under the guise of a ‘plant food’ (although having no known use as such).”

References

  1. Winstock, A., Marsden, J., & Mitcheson, L. (2010). What should be done about mephedrone? BMJ, 340:c1605 DOI: 10.1136/bmj.c1605

[Creative Commons licensed picture ‘Overdosed’ by Elad Rahmin on flickr]

May 4, 2010

Ian Wilmut on the World after Dolly the Sheep

Bicolor sheep by Tambako the Jaguar, on FlickrAs part of the Gates Distinguished Lecture Series, Ian Wilmut will be giving a public lecture today in Cambridge titled Cloning, Stem Cells and Regenerative Medicine: The World After Dolly. More details below from talks.cam.ac.uk:

“Ian Wilmut soared to international prominence when Dolly, a baby lamb created from the cells of an adult sheep [1,2], was revealed to the world. Dolly was the first genetic replica of a living creature created from cells from an adult animal. The accomplishment sparked amazement and controversy as scientists, philosophers, ethicists and religious leaders perceived the potential to extend such work to humans.”

All are encouraged to attend, lecture starts at 6pm today the Cambridge Union Society see press release from the University. [Update: Note last minute change from previously advertised venue at Emmanuel College, Cambridge. See also the accompanying podcast page].
Audio of talk available

References

  1. Campbell, K., McWhir, J., Ritchie, W., & Wilmut, I. (1996). Sheep cloned by nuclear transfer from a cultured cell line Nature, 380 (6569), 64-66 DOI: 10.1038/380064a0
  2. Wilmut, I., Schnieke, A., McWhir, J., Kind, A., & Campbell, K. (1997). Viable offspring derived from fetal and adult mammalian cells Nature, 385 (6619), 810-813 DOI: 10.1038/385810a0

April 30, 2010

Daniel Cohen on The Social Life of Digital Libraries

Day 106 - I am a librarian by cindiann, on FlickrDaniel Cohen is giving a talk in Cambridge today on The Social Life of Digital Libraries, abstract below:

The digitization of libraries had a clear initial goal: to permit anyone to read the contents of collections anywhere and anytime. But universal access is only the beginning of what may happen to libraries and researchers in the digital age. Because machines as well as humans have access to the same online collections, a complex web of interactions is emerging. Digital libraries are now engaging in online relationships with other libraries, with scholars, and with software, often without the knowledge of those who maintain the libraries, and in unexpected ways. These digital relationships open new avenues for discovery, analysis, and collaboration.

Daniel J. Cohen is an Associate Professor at George Mason University and has been involved in the development of the Zotero extension for the Firefox browser that enables users to manage bibliographic data while doing online research. Zotero [1] is one of many new tools [2] that are attempting to add a social dimension to scholarly information on the Web, so this should be an interesting talk.

If you’d like to come, the talk starts at 6pm in Clare College, Cambridge and you need to RSVP by email via the talks.cam.ac.uk page

References

  1. Cohen, D.J. (2008). Creating scholarly tools and resources for the digital ecosystem: Building connections in the Zotero project. First Monday 13 (8)
  2. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204

April 28, 2010

Philip Campbell on Science Facts and Frictions

Philip Campbell: Will you pay for good online stuff, Dammit? (Libraries do, thankfully)As part of the Gates Distinguished Lecture Series editor Philip Campbell is giving a public lecture at 6.30pm tonight titled Science – facts and frictions at Emmanuel College, Cambridge. The abstract and text below is reproduced from talks.cam.ac.uk:

Climategate’, MMR vaccine, GM crops, stem cells – these are examples of public debates in which science and scientists have come under attack. And yet the processes of science were no different in kind from those in calmer territories, such as cancer research, where the public not only trusts researchers but directly donates half a billion pounds every year in their support. Why are there such contrasts? And what can scientists and others do in response to such attacks? The talk will offer some suggestions.

As Editor-in-Chief of Nature, Philip Campbell heads a team of about 90 editorial staff around the world. Dr. Campbell takes direct editorial responsibility for the content of Nature editorials, writing some of them. He is the seventh [1] Editor-in-Chief since the journal was launched in 1869.

Dr. Campbell’s role as Editor-in-Chief of Nature publications (of which there are many editorially independent journals and several websites) is to ensure that the quality and integrity appropriate to the Nature name are maintained, and that appropriate individuals are appointed as chief editors. He sits on the executive board of Nature’s parent company, Nature Publishing Group.

According to the accompanying press release from the University, Campbell:

“is particularly interested in groups of scientists who regularly produce blogs in order to help the public and journalists gain access to their perspectives on scientific developments and controversies.”

So, if you’re in or near Cambridge tonight, this talk is open the public and looks like it will be enlightening.

[Update, some interesting things mentioned in this talk in no particular order:

Refererences

  1. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
  2. Daniel Sarewitz (2004). How science makes environmental controversies worse Environmental Science & Policy, 7 (5), 385-403 DOI: 10.1016/j.envsci.2004.06.001

April 8, 2010

Embracing Open Science

Open Push (Oklahoma, Manchester)There’s an interesting article [1] by Chelsea Wald in Science magazine published today, about Open Science including Open Source Code, Open Notebook Science, Open Data and Open Access Publishing.

It interviews some of the advocates and sceptics of a more open approach to doing Science, including:

It’s well worth a read, despite being a bit US-centric, and looks like it’s freely available via Open Access Publishing [2] too.

[Update: There is some follow-up commentary on the original article here and here]

References

  1. Chelsea Wald (2010). Scientists Embrace Openness Science (2010-04-09) DOI: 10.1126/science.caredit.a1000036
  2. Declan Butler (2010). US seeks to make science free for all Nature, 464 (7290), 822-823 DOI: 10.1038/464822a

8-OHdG: Entity of the Month

DNA Origami by Alex BatemanChemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool. New in this release, the ChEBI ontology is now available in the Web Ontology Language (OWL), which is part of an ongoing research project to automate the classification of small molecules in ChEBI. If you’re using this data, we’d like to hear from you! This month’s entity of the month is 8-OHdG. Text below reproduced from ChEBI website:

8-Hydroxy-2′-deoxyguanosine (8-OHdG, ChEBI:40304) is an important molecule in oxidative stress used as a biomarker of many processes involving reactive oxygen species. Also known as 8-oxo-dG (this abbreviation derived from its tautomeric name 8-oxo-7,8-dihydro-2′-deoxyguanosine) and as HMDB03333 in the Human Metabolome Database [1], it has been used especially as a sensitive marker of the DNA damage caused by hydroxyl radical attack at C-8 of guanine. This damage, if left unrepaired, has been proposed to contribute to mutagenicity and cancer promotion [2]. This use of 8-OHdG as a biomarker for DNA damage extends over a wide range of scenarios [3,4,5,6], because it is one of the major products of DNA oxidation.

More recent work by Junko Fujihara and his colleagues at Shimane University in Japan has demonstrated how 8-OHdG can be used as a possible marker for arsenic poisoning, since antiquity a method of dispatch frequent in homicide and suicide cases [7]. Fujihara’s study however focuses principally on the use of arsenic in medicine, and specifically in demonstrating a relationship between concentrations of 8-OHdG and various arsenic compounds in the urine of a patient with acute promyelocytic leukaemia being treated with arsenic trioxide. Their conclusions that 8-OHdG in urine can be used therapeutically as a key biomarker for arsenic compounds may also find application in the diagnosis of arsenic poisoning when arising from the consumption of seafood such as fish, shrimp, oysters and seaweeds, organisms known to contain appreciable amounts of arsenic compounds.

[Picture of Alex Bateman‘s DNA origami in action from The Wellcome Trust Sanger Institute.]

References

  1. Wishart, D., Knox, C., Guo, A., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J., Lim, E., Sobsey, C., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H., & Forsythe, I. (2009). HMDB: a knowledgebase for the human metabolome Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn810
  2. Kuchino, Y., Mori, F., Kasai, H., Inoue, H., Iwai, S., Miura, K., Ohtsuka, E., & Nishimura, S. (1987). Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues Nature, 327 (6117), 77-79 DOI: 10.1038/327077a0
  3. Wu LL, Chiou CC, Chang PY, & Wu JT (2004). Urinary 8-OHdG: a marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. Clinica chimica acta; international journal of clinical chemistry, 339 (1-2), 1-9 PMID: 14687888
  4. Schriner, S. (2005). Extension of Murine Life Span by Overexpression of Catalase Targeted to Mitochondria Science, 308 (5730), 1909-1911 DOI: 10.1126/science.1106653
  5. Sumida S, Doi T, Sakurai M, Yoshioka Y, & Okamura K (1997). Effect of a single bout of exercise and beta-carotene supplementation on the urinary excretion of 8-hydroxy-deoxyguanosine in humans. Free radical research, 27 (6), 607-18 PMID: 9455696
  6. Tarng DC, Huang TP, Wei YH, Liu TY, Chen HW, Wen Chen T, & Yang WC (2000). 8-hydroxy-2′-deoxyguanosine of leukocyte DNA as a marker of oxidative stress in chronic hemodialysis patients. American journal of kidney diseases : the official journal of the National Kidney Foundation, 36 (5), 934-44 PMID: 11054349
  7. Fujihara, J., Agusa, T., Tanaka, J., Fujii, Y., Moritani, T., Hasegawa, M., Iwata, H., Tanabe, S., & Takeshita, H. (2009). 8-Hydroxy-2′-deoxyguanosine (8-OHdG) as a possible marker of arsenic poisoning: a clinical case study on the relationship between concentrations of 8-OHdG and each arsenic compound in urine of an acute promyelocytic leukemia patient being treated with a Forensic Toxicology, 27 (1), 41-44 DOI: 10.1007/s11419-008-0062-x
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