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Bar-Ilan University graduate student.
Information Culture
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- May 2, 2013
- 05:30 PM
- 74 views
Elite journals: to hell in a handbasket?
by Hadas Shema in Information Culture
Once upon a time, journals were made of paper and ink. However, we left the dark ages of dead woods behind us and moved forward to an age in which authors don’t need to publish in journals (but still want to). There’s an increasing decoupling between the individual article and its publishing journal, created by [...]
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Vincent Lariviere, George A. Lozano, & Yves Gingras. (2013) Are elite journals declining?. ArXiv. arXiv: 1304.6460v1
George A. Lozano, Vincent Lariviere, & Yves Gingras. (2012) The weakening relationship between the Impact Factor and papers' citations in the digital age. ArXiv. arXiv: 1205.4328v1
- April 22, 2013
- 03:26 PM
- 83 views
The Leiden University Ranking
by Hadas Shema in Information Culture
The new Leiden Ranking (LR) has just been published, and I would like to talk a bit about its indicators, what it represents and equally important – what it doesn’t represent. The LR is a purely bibliometrical ranking, based on data from Thomson-Reuters’ Web of Science database (there’s another bibliometrical ranking, Scimago, but it’s based [...]
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Ludo Waltman, Clara Calero-Medina, Joost Kosten, Ed C. M. Noyons, Robert J. W. Tijssen, Nees Jan van Eck, Thed N. van Leeuwen, Anthony F. J. van Raan, Martijn S. Visser, & Paul Wouters. (2012) The Leiden Ranking 2011/2012: Data collection, indicators, and interpretation. ArXiv. arXiv: 1202.3941v1
- April 11, 2013
- 08:54 AM
- 89 views
May the odds be ever in your favor: academic tenure
by Hadas Shema in Information Culture
“Excuse me; the whole tenure system is ridiculous. A guaranteed job for life only encourages the faculty to become complacent. If we really want science to advance, people should have chips implanted in their skulls that explode when they say something stupid.” Sheldon Cooper, The Big Bang Theory Between the recent ACUMEN (academic careers understood [...]
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Abbott, A., Cyranoski, D., Jones, N., Maher, B., Schiermeier, Q., & Van Noorden, R. (2010) Metrics: Do metrics matter?. Nature, 465(7300), 860-862. DOI: 10.1038/465860a
Clawson, D. (2009) Tenure and the Future of the University. Science, 324(5931), 1147-1148. DOI: 10.1126/science.1172995
- February 12, 2013
- 10:45 AM
- 111 views
Your theory is rubbish (but I won’t say it out loud)
by Hadas Shema in Information Culture
Science seems to be full of controversies and conflicts; famous scientists willing to kill and be killed for their pet theories, former students challenging the views of their academic “parents” and so on. My favorite biology professor used to tell about the time when his post-doc advisor, after a lecture given by his former post-doc [...]
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Brooks, T. A. (1986) Evidence of Complex Citer Motivations. JASIS. info:/
Hyland, K. (1999) Academic attribution: citation and the construction of disciplinary knowledge. Applied Linguistics, 20(3), 341-367. DOI: 10.1093/applin/20.3.341
MacRoberts, M., & MacRoberts, B. (1984) The Negational Reference: or the Art of Dissembling. Social Studies of Science, 14(1), 91-94. DOI: 10.1177/030631284014001006
- January 1, 2013
- 05:28 AM
- 215 views
What’s wrong with citation analysis?
by Hadas Shema in Information Culture
What’s wrong with citation analysis? Other than your papers not being cited enough, what’s wrong with measuring scientific influence based on citation count? Citation analysis-based decisions concerning grants, promotions, etc. have become popular because, among other things, they’re considered “unbiased.” After all, such analysis gives numbers even non-professionals can understand, helping them make the best [...]
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MacRoberts, M., & MacRoberts, B. (1996) Problems of citation analysis. Scientometrics, 36(3), 435-444. DOI: 10.1007/BF02129604
MacRoberts, M., & MacRoberts, B. (2010) Problems of citation analysis: A study of uncited and seldom-cited influences. Journal of the American Society for Information Science and Technology, 61(1), 1-12. DOI: 10.1002/asi.21228
Priem, J., Taraborelli, D., Groth, P., & Neylon, C. (2010) altmetrics: a manifesto. http://altmetrics.org/manifesto/. info:/
- September 21, 2012
- 03:11 PM
- 272 views
On Authorship, Part I
by Hadas Shema in Information Culture
Most articles today are results of teamwork, whether it’s only two authors working together or thousands, (think CERN). As science keeps getting bigger, authorship no longer equals actual writing, but one way or another of contribution to team effort. Authorship of massive scale, or “Hyperauthorship” (Cronin, 2001) is very common in high-energy physics and certain [...]
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Costas, R., & Bordons, M. (2011) Do age and professional rank influence the order of authorship in scientific publications? Some evidence a micro-level perspective. Scientometrics, 145-161. info:/
Cronin, B. (2001) Hyperauthorship: A postmodern perversion or evidence of a structural shift in scholarly communication practices? . JASIST, 52(7), 558-569. DOI: 10.1002/asi.1097
Wren, J.D., & et al. (2007) The write position. A survey of perceived contributions to papers based on byline position and number of authors. EMBO Rep, 8(11), 988-991. DOI: 10.1038/sj.embor.7401095
Solomon J. (2009) Programmers, professors, and parasites: credit and co-authorship in computer science. Science and engineering ethics, 15(4), 467-89. PMID: 19247811
Wuchty S, Jones BF, & Uzzi B. (2007) The increasing dominance of teams in production of knowledge. Science (New York, N.Y.), 316(5827), 1036-9. PMID: 17431139
- July 28, 2012
- 09:56 PM
- 295 views
Self-citing bloggers: my research is the coolest thing ever (let me tell you all about it!)
by Hadas Shema in Information Culture
Every enthusiastic scientist knows that once you reach a certain level of specialization, there are very few people in your immediate surroundings that actually understand what you say. Eyes of family and friends get a bit glassy when you tell them about the SIR2 homologs, and nobody wants to look at your C. elegans’ baby [...]
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Shema, H., Bar-Ilan, J., & Thelwall, M. (2012) Self- Citation of Bloggers in the Science Blogosphere. To be presented at COSCI12, Dusseldorf, August 1-5. info:/
Shema H, Bar-Ilan J, & Thelwall M. (2012) Research blogs and the discussion of scholarly information. PloS one, 7(5). PMID: 22606239
- July 24, 2012
- 04:27 PM
- 292 views
On Self-Citation
by Hadas Shema in Information Culture
Self-citing is often frowned upon, being considered (and sometimes is) vanity, egotism or an attempt in self-advertising. However, everyone self-cite because sooner or later, everyone builds upon previous findings “Given the cumulative nature of the production of new knowledge, self-citations constitute a natural part of the communication process.” (Costas et al., 2010). The argument whether [...]
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Costas, R., van Leeuwen, T.N., & Bordons, M. (2010) Self-citations at the meso and individual levels: effects of different calculation methods. Scientometrics, 517-537. DOI: 10.1007/s11192-010-0187-7
Aksnes, D. W. (2003) A macro study of self-citation. Scientometrics, 56(2), 235-246. info:/
Fowler, J. H., & Aksnes, D. W. (2007) Does self-citation pay? . Scientometrics, 72(3), 427-437. DOI: 10.1007/s11192-007-1777-2
- June 24, 2012
- 07:57 PM
- 330 views
Understanding the Journal Impact Factor – Part Two
by Hadas Shema in Information Culture
Despite its many faults (see part I), the Journal Impact Factor (JIF) is considered an influential index to a journal’s quality, and publishing in high-impact journals is essential to a researcher’s academic career. Reminder: to calculate, for example, the 2010 JIF for a journal - JIF= (2010 citations to 2009+2008 articles)/(no. of “citable” articles published in [...]
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Amin, M, & Mabe, M. (2007) Impact factors: use and abuse. Perspectives in Publishing. info:/
Archambault, E., & Lariviere, V. (2009) History of the journal impact factor: Contingencies and consequences . Scientometrics, 635-649. DOI: 10.1007/s11192-007-2036-x
Seglen, P. O. (1997) Why the impact factor of journals should not be used for evaluating research. BMJ. DOI: 10.1136/bmj.314.7079.497
Kostoff, R. N. (2007) The difference between highly and poorly cited medical articles in the journal Lancet. Scientometrics, 513-520. DOI: 10.1007/s11192-007-1573-7
Campanario, J. M. (2011) Empirical study of journal impact factors obtained using the classical two-year citation window versus a five-year citation window. Scientometrics. DOI: 10.1007/s11192-010-0334-1
Vanclay, J.K. (2012) Impact factor: outdated artefact or stepping-stone to journal certification?. Scientometrics. DOI: 10.1007/s11192-011-0561-0
- May 21, 2012
- 08:37 PM
- 288 views
Discussion of scholarly information in research blogs
by Hadas Shema in Information Culture
Discussion of scholarly information in research blogs As some of you know, Mike Thelwall, Judit Bar-Ilan (both are my dissertation advisors) and myself published an article called “Research Blogs and the Discussion of Scholarly Information” in PLoS One. Many people showed interest in the article, and I thought I’d write a “director’s commentary” post. Naturally, [...]
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Shema H, Bar-Ilan J, & Thelwall M. (2012) Research Blogs and the Discussion of Scholarly Information. PloS one, 7(5). PMID: 22606239
Groth, P., & Gurney, T. (2010) Studying Scientific Discourse on the Web Using Bibliometrics: A Chemistry Blogging Case Study. Proceedings of the WEbSci10: Extending the Frontiers of Society On-Line. info:/
- May 7, 2012
- 11:31 AM
- 453 views
Understanding the Journal Impact Factor – Part One
by Hadas Shema in Information Culture
The journals in which scientists publish can make or break their career. A scientist must publish in “leading” journals, with high Journal Impact Factor (JIF), (you can see it presented proudly on high-impact journals’ websites). The JIF has gone popular partly because it gives an “objective” measure of a journal’s quality and partly because it’s [...]
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Bar-Ilan, J. (2012) Journal report card. Scientometrics. DOI: 10.1007/s11192-012-0671-3
- April 24, 2012
- 07:42 PM
- 667 views
The post-journal era
by Hadas Shema in Information Culture
Most of the scholarly publication today goes more or less like this: a scientist writes a manuscript about research funded by her university and/or the grant fairy (usually a government agency) then submits it to a commercial peer-review journal. An editor (either working for free or for "honorarium") reads her manuscript and sends it to appropriate peer reviewers (payment? what payment?). Then, if her manuscript is accepted, her institute's library gets the privilege of buying access to the published manuscript. This state of things is very profitable for the commercial publishers' stock owners, but less so for scientists, libraries and the general public, who rarely get to read research they paid for. While many people agree this system is, shall we say, less than optimal, attempts to remedy the situation have been less than successful, and the commercial publishers might be targeting our research budgets next.The latest attempt to renovate the system is by Priem & Hemminger (2012). At the beginning of their paper, they suggest that previous attempts in reinventing scholarly publishing have failed due to two reasons:1.Change to peer review are just patches on a fundamentally broken scholarly journal system2.Proposals offer no smooth transition from the present system.Today, the journal fills four main functions: It archives scholarly material and time-stamp the researchers' contributions, if disseminates scholarly products and it certifies contributions (if it's published in a high-impact journal it must be of value). Priem and Hemminger want to make each of these functions independent from the others.Their first suggestion is to "refactor" the system. This means locating "parts which are confusing, inefficient or redundant" and improving them without hurting the rest of the system. Their second suggestion is the "decoupled journal" (DcJ) (more about this later).Overlay journalsThese journals were suggested by Ginsparg (1997) and only provide the "stamp of approval" to an already published-archived-registered material. Despite the promise the overlay model represents, it hasn't been successful so far, and almost every journal which tried it went back to the traditional coupled model.The PLoS One modelPLoS One is an open access journal which publishes work not according to what the editors and reviewers consider significant, but consider only the paper's methodological quality. They decoupled the significant approval from the methodological approval. PLoS One also decoupled copy-editing: they warn in advance that they don't copy-edit in details, and instead provide a list of services which do just that. This model has proven to be profitable: PLoS One published more than 5,000 papers in 2010 at 1350$ each (and the other PLoS journals charge even more). The flaws here, beyond the price, are the exclusivity: authors publish only in one journal, and the danger of a future with only a few mega-journals.Post-publication review servicesThere are a few existing post-publication peer review services, the best-known of them are Faculty of 1000 (F1000) and Mathematical Reviews. F1000 "...identifies and evaluates the most important articles in biology and medical research publication." F1000 is supposed to function as additional help for researchers in managing their reading. It has actually been shown to identify quality papers which were overlooked by leading journals (Allen et al., 2009).Mathematical Reviews is and abstracting service, but as Priem & Hemminger say, it is "occasionally called into service as a post-publication peer review venue when the traditional journal fail in their role as certifiers. In this case, abstracters may abandon objectivity and attack papers and their reviewers directly."These services have one major problem: they aren't brand names, and can't replace the certification of well-established journals, no matter how much their peer review is sound.The Deconstructed JournalSmith (1999) had three insights about the Deconstructed Journal (DJ):1. The means (journal) and the functions are not the same.2. Any system that will be implanted instead of the journal has to be at least as good.3. Several cooperating agencies could successfully replace the central publisher.Priem and Hemminger cite van de Sompei et al. (2004) and Smith (2003) as those who pointed out the advantages of a deconstructed system:"...encourages innovation, adapts well to changing scholarly practices, and democratizes the largely monopolized scholarly communication market" However, van de Sompeis' and Smith' proposals are a bit outdated, because they hadn't taken into account the social media.The functions of the decoupled journalThe Decoupled journal (DcJ, rather than DJ) is the updated version of the DJ. This is a universal, or meta, journal, where everything scholars produce and share is stored long-term, added to other projects, linked to, commented about...etc. etc.With the DcJ, publication is the first step in the process of revisions, reviewes, etc. Scholarly items will need persistent IDs, storage, and mirror backup in order to survive long-term. This can be done with persistent identifiers such as the DOI and institutional or subject-area repositories (ArXiv, Pubmed).After the publication of a draft, it's time for preparation. Preparation is defined by the authors as "Changing the format of a work to make it more suitable for a given (human or electronic) audience". Today, many companies sell authors services (like copy-editing), but preparation is still mostly left to the journal. The DcJ will allow authors the freedom to choose the preparation they prefer (say, PDF or HTML format). PLoS One, as mentioned before, already leaves copy-editing to authors, perhaps showing the beginning of a trend.After the preparation comes the assessment. Defined as "Attaching an assessment of quality to a scholarly object". Today's method of assessment, peer review, is usually anonymous, unpublished to the general public, and done by invited reviewers. The reviewers give their opinion in free text first, then a final assessment whether the material should be published.In the Priem & Hemminger model, reviewers don't decide whether the material is publishable or not (it's already published!) but certificate it. In the future, Nature could become "Nature stamping agency" and give papers its "seal of approval". It will even be able to do so by giving grades, rather than just accept or reject the paper. There will be agencies that will only review the soundness of the work (like PLoS One does today), agencies who will certify only certain parts, open peer reviews and blind peer reviews. Other forms of assessments - blog posts, number of downloads, and even tweets - will be stored as well. The authors see the DcJ as a way to allow peer-review to evolve freely, without its tight coupling with the other functions of the journal.With libraries' budgets tighter than ever (even Harvard decided that commercial journals are just too expensive ) I expect more and more authors will choose the DcJ route. However, it could be that a certification bottle-neck will be created, with the prestigious journals of today becoming the prestigious stamping agencies of tomorrow. The number of expert peer-reviewers in each field could become a limitation as well. Will our grandchildren complain about the amount of money they have to pay for a Science certification? Only time will tell.Allen L, Jones C, Dolby K, Lynn D, & Walport M (2009). Looking for landmarks: the role of expert review and bibliometric analysis in evaluating scientific publication outputs. PloS one, 4 (6) PMID: 19536339Ginsparg, P. (1997). Winners and Losers in the Global Research Village The Serials Librarian, 30 (3-4), 83-95 DOI: 10.1300/J123v30n03_13... Read more »
Priem, J., & Hemminger, B. (2012) Decoupling the scholarly journal. Frontiers in Computational Neuroscience. DOI: 10.3389/fncom.2012.00019
Smith, J. (1999) The deconstructed journal – a new model for academic publishing. Learned Publishing, 12(2), 79-91. DOI: 10.1087/09531519950145896
Smith, J. W. T. (2003) The deconstructed journal revisited: a review of developments. ICCC/IFIP Conference on Electronic Publishing-ElPub03: From information to knowledge. (Minho, Portugal). info:/
- March 30, 2012
- 10:46 PM
- 656 views
When prince charming kissed Mendel: delayed recognition in science.
by Hadas Shema in Information Culture
Monk Gregor Mendel hadn't lived to see his peas become famous; his paper has been asleep, waiting for prince charming to cite it awake. Of course, not all "delay recognition" papers sleep as long as Mendel's, but "sleeping beauty" or "Mendel's syndrome" papers do exist in science. A "sleeping beauty" paper can go uncited for years, until suddenly it's awakened. Costas, van Leeuwen and van Raan (2010) classify published scientific papers according to three general types: Normal-type: these have the normal distribution of published papers, usually reaching the peak of their citation 3-4 years after publication and then decay. Flash in the pans-type: these get cited very often when they first come out, but are forgotten in the long run, kind of like a teenager pop star. Delayed-type: those who start drawing interest later than the normal-type papers. Costas et al. prefer not to call them all "sleeping beauties" because real sleeping beauties (never cited and then suddenly rise to fame) are very rare. Source: Costas, van Leeuwen and van Raan (2010) Looking at all the documents from Web of Science between the years 1980 and 2008 (over 30 million), Costas et al. found that the "flash in the pans" type of papers tend more to be editorial, notes, reviews and so forth, rather than research articles. Delayed documents tended to be more prominent in the "articles" category. When they checked Nature and Science, two 'letter' journals, Costas et al. found that they cover 10.9% and 10.5% of "flash in the pans" documents respectively, which is higher than average (9.8%) in the database. The castle of the sleeping beauty is the availability of information. The information has to be accessible, and it has to be visible. The Web, of course, has improved the accessibility of papers a great deal, especially when said papers are open-sourced. When a paper is digitalized or becomes open-accessed, its visibility and availability increase. But being available is not enough: researchers must have use for the information despite the passage of time. The prince kisses the sleeping beauty awake Source: Wang, Ma, Chen & Rao, 2012In 1995, Polchinski's paper on supergravity in string theory “Dirichlet branes and Ramond-Ramond charges” came out and cited an early work by Romans (1986) about the same subject. Romans' paper has not been cited from 1986 to 1995(!), but according to Google Scholar (which admittedly could be inflated) count, it has been cited 424 times since then. Why? One reason is that Romans' paper was simply ahead of its time, published in a "sleeping beauty" field. In the nine years until Polchinski's paper, interest in supergravity has considerably increased. Another reason is that Polchinski is a high-classed prince, with great academic authority. An unknown scholar probably wouldn't have been as successful in waking up Romans' paper.Source: Wang, Ma, Chen & Rao, 2012 An extension of the "Mendel Syndrome" is "Mendelism", when researchers "develop lines of research and have a profile of publications (‘oeuvres’) 'ahead of their time'’’ (recent Nobel Laureate Dan Shechtman comes to... Read more »
Costas, van Leeuwen, & van Raan. (2011) The ‘‘Mendel syndrome’’ in science: durability of scientific literature and its effects on bibliometric analysis of individual scientists. Scientometrics, 177-205. info:/
van Raan, A. (2004) Sleeping Beauties in science. Scientometrics, 59(3), 467-472. DOI: 10.1023/B:SCIE.0000018543.82441.f1
Rodrigo Costas, Thed N. van Leeuwen, & Anthony F. J. van Raan. (2009) Is scientific literature subject to a sell-by-date? A general methodology to analyze the durability of scientific documents. Journal of the American Society for Information Science and Technology. arXiv: 0907.1455v1
Wang, Chen, & Rao. (2012) Why and how can "sleeping beauties" be awakened?. The Electronic Library, 30(1), 5-18. info:/http://dx.doi.org/10.1108/02640471211204033
- December 31, 2011
- 02:54 AM
- 895 views
Correlation between reference managers and the WoS
by Hadas Shema in Information Culture
Even though web citations have been a part of our lives for several years now, the correlation between "traditional" citations and web resources like Mendeley, CiteULike, blog networks, etc. hasn't been thoroughly studied yet, and any new research in the field is very interesting (to me, anyway). The new paper was published at Scientometrics by Li, Thelwall (still one of my dissertation advisors) and Giustini. They focused on the correlation between user count - the number of users who save a particular paper - and WoS and Google Scholar citations. The researchers extracted from WoS all the Nature and Science research articles that were published in 2007 and their references. They ended up with 793 Nature and 820 Science articles, or 1,613 articles overall (not including references, of course). Then, they searched CiteULike for those articles' titles and number of citations, as well as for their user count in Mendeley. They also collected the same data from Google Scholar. It's important to note that Mendeley had 32.9 million articles indexed while CiteULike had only 3.5 at the time of the study.Google Scholar's mean and median number of citations were higher than in WoS (not surprising; If you want better citation numbers, always use GS). They found that despite Mendeley being "younger" than CiteULike (launched in 2004 and 2008 respectively), CiteULike had only about two-thirds of the sample articles saved, while Mendeley had about 92%.Spearman correlations between citations in GS and WoS were high in this research (0.957 for Nature and 0.931 for Science). The correlations between Mendeley's user count and the citations in GS and WoS were also rather good (0.559 and o.592 for WoS and GS respectively for Nature, 0.540 and 0.603 for Science). CiteULike had far weaker correlations: 0.366 with WoS and 0.396 with GS for Nature, 0.304 with WoS and 0.381 with GS for Science.LimitationsThe authors remind us that correlation isn't causation, saying they can't conclude a casual relationship based on correlations between two data sources. Therefore, it can't be determined for sure whether there is a connection between a high user count and a high number of citations. Only Nature and Science were studied, so it can very well be that the results aren't true for other journals. Also, group-saved and single-user saved references were given the same weight. The number of saved references in Mendeley and CiteULike is much smaller than in the WoS counts and therefore the results might be less reliable.The authors speculate that user count may represent a more accurate scientific impact of articles, and take note that one can measure the impact of all sorts of resources in online reference managers, unlike in the limited bibliographic indexes. I think it could be reference managers don't always reflect readership: one could save a reference and forget about it all together later (so many articles, so little time...). On the other hand, citation counts might suffer from the same problem, as many scientists use a "rolling citation" from other articles citing an earlier article, without actually having read the article themselves.Priem et al. also presented lately a study about web citations and WoS citations, based on data from the seven PLoS journals, but I think I'll wait for the journal article to cover it in the blog.Li, X., Thelwall, M., & Giustini, D. (2011). Validating online reference managers for scholarly impact measurement Scientometrics DOI: 10.1007/s11192-011-0580-x... Read more »
Li, X., Thelwall, M., & Giustini, D. (2011) Validating online reference managers for scholarly impact measurement. Scientometrics. DOI: 10.1007/s11192-011-0580-x
- December 14, 2011
- 09:08 PM
- 3,395 views
Reinventing Discovery, Part II
by Hadas Shema in Information Culture
This is the second part of my review of Michael Nielsen's book "Reinventing Discovery - The New Era of Networked Science" (first part is here). Last time we talked about Galaxy Zoo, the Polymath Project, and why scientists don't (usually) do Wikis. This time I'd like to focus on the book parts which talk about ArXiv. First of all, I have to say I've been using ArXiv extensively lately as part of the ACUMEN project, trying to figure out who and what can be found there. The place is a bit of a mess - it's not Pubmed - but it still left me in awe, because not only that most of the astronomers I've searched had papers there, most of them contributed at least one of the papers themselves (you can see who submitted the paper). ArXiv comes with a service called SPIRES (now inSPIRE) which can tell you how many times a paper was cited, who's citing who, and so forth. This way, it's possible to measure at least some of the impact of preprints (if you're a high-energy physicist). So, not only ArXiv makes the scientific communication faster, it also helps evaluate the impact of this kind of communication more accurately. Unfortunately, not everybody gives ArXiv the honor it deserves. Nielsen tells how when he was writing the book, a physicist told him that Paul Ginsparg, ArXiv's creator, was wasting his talent on "collecting garbage", reflecting a disregard certain scientists have for "mere" tool builders. I don't know if this attitude is common in the scientific community, but it's discouraging nonetheless. Open Access can be problematic Citizen science isn't always all that - in the Polymath Project, there were people with good intentions but not much knowledge, their contributions didn't have much value to the project and had to essentially filtered out. Misinformation - premature publications , especially in fields the mainstream media takes interest in, can spread far and wide, confuse the general public and discredit research projects in the eyes of the public. How we can be more open (if you're reading this, you probably don't need these suggestions). In the last few pages of the book, Nielsen suggests practical steps toward open science. A scientist can upload old data, code, etc. online for reuse (be sure to tell people how to cite it!); He/she can open a blog, contribute to other people's open science projects, or try to create a new one. Nielsen advises to "be generous in giving other scientists credit when they share their scientific knowledge in new ways" which I think is an excellent advice, even though the formatting and style guides are a bit behind the times when it comes to social media. All in all, Reinventing discovery is a great book, however, I was a little disappointed to find only a small section dedicated to science blogs. The author explains that he had enough of the hype around blogging and that he doesn't want "to cover that well-trodden ground again", but I think the book could have benefited from a few more pages about the subject (yes, I know I'm not very objective here...). Also, though the book deals with - and recommends - open access, it isn't under Creative Commons licence (you can read why here). Nielsen, Michael (2011). Reinventing Discovery Princeton University Press Other: 9780691148908... Read more »
Nielsen, Michael. (2011) Reinventing Discovery. Princeton University Press. info:other/9780691148908
- December 7, 2011
- 06:25 PM
- 973 views
Reinventing Discovery: Book Review, Part I
by Hadas Shema in Information Culture
In Arthur C. Clarke's story "Into the Comet" he describes a spaceship with a computer malfunction that dooms all abroad to eventual death by starvation/oxygen deprivation, whichever comes first. The solution is a device older than the computer: the abacus. The entire crew run calculations on acabi, and they make their way out of the comet's nucleus successfully. That is an extreme example of citizen science (or oh-my-God-we're-all-going-to-die science) but it shows the principle, that collaboration by a large number of people can solve very complicated problems. Michael Nielsen's excellent book, 'Reinventing Discovery' tells us about many such examples, though in most of them participants have to do a lot more than just calculate without thinking.Source Take 'Galaxy Zoo': volunteers can help classify galaxies (it turns out people do it faster and more accurately than a computer). It all began when one overworked grad student, Kevin Schawinski, wanted to prove that elliptical galaxies aren't always old, but had simply too many galaxies to go through in order to prove his theory. He and a post-doc, Chris Lintott, joined forces and opened a website which allowed anyone to come and classify galaxy photos. The project is an enormous success, with 22 scientific papers so far and the spin-offs Galaxy Zoo 2 and Galaxy Zoo:Hubble.Another story Nielsen recounts is the story of the Polymath Project: Fields Medal recipient Tim Gowers posted a mathematical problem in his blog and asked for a collaborative efforts. Twenty-seven people wrote 800 comments and solved the problem within 37 days. Now there is a Polymath blog which keeps up the good work.These projects were a success, but Nielsen also studies failed projects and the reasons for their failure. He argues (which I wholly agree!) that scientists are rewarded by writing as many good scientific papers as possible. Contributing to, say, Wikipedia, essentially takes away time from research and gives nothing in terms of academic reputation. Galaxy Zoo is a success because it gives astronomers something to write about, and it's possible the Polymath project succeeds because it A. involves people with tenure and B. involves people who want to be noticed by people with tenure. Personally, I think the solution to scientists' reluctance to cooperate in collaborative projects is simple: put them in a spaceship and tell them they won't be able to make it home until they collaborate. However, it is possible the oxygen run out while they'd argue about whose name gets to be first in the authors' list. Also, spaceships are very costly. Next part: what Nielsen has to say about Arxiv and the future of open science. Bora's ReviewJoerg Heber's ReviewMichael Nielsen talks Open Science in a TED event:Nielsen, Michael (2011). Reinventing Discovery Princeton University Press Other: 9780691148908... Read more »
Nielsen, Michael. (2011) Reinventing Discovery. Princeton University Press. info:other/9780691148908
- August 19, 2011
- 10:00 PM
- 1,368 views
Generic drug trials: more transparency needed
by Hadas Shema in Information Culture
The New York Times reported a couple of days ago that "Federal regulators and the generic drug industry are putting the final touches on an agreement that would help speed the approval of generic drugs in this country and increase inspections at foreign plants that export generic drugs and drug ingredients to the United States." The generic drug manufactures will pay an annual fee of 299$ million dollars, so that the FDA will be able to hire more reviewers and speed up approval of applications for marketing of generic drugs. The question is: what do we know about the generic drugs marketed today?
Van der Meesch et al. (2011) published in PLoS One a methodological systematic review about Bioequivalence trials which compared generic to brand-name drugs published between 2005 and 2008. They searched Medline for appropriate papers, as well as journals which regularly publish bioequivalence trials. Out of 134 papers that reported bioequivalence trials between brand-name drug and generic drug, 55 didn't include the reference drug name and were excluded. The final sample consisted of 79 papers which dealt with assessment of the bioequivalence of generic and brand-name drugs.
What do the FDA and the EuropeanMedicine Agency (EMA) demand from a generic drug?The FDA wants to know three things:
Cmax - maximum plasma drug concentrationTmax - time required to achieve a maximal concentrationAUC - total area under the plasma drug concentration-time curve
The 90% confidence intervals for the ratios (test:reference) have to be between 80% and 125%. The EMA wants to know only the Cmax and the AUC.
Source: Generics – equal or not? (Birkett, 2003)
Experiments of bioequivalence are usually randomized crossover trials. They are conducted on healthy volunteers by administrating one dose of the drug. Seventy-three (92%) of the trials were indeed single-dose trials (6 (8%) were multiple-dose) and 89% of the single-dose trials reported bioequivalence. About a third didn't report CIs for all the FDA criteria, and 20% didn't report the required EMA criteria. Only 41% of the papers reported funding, 25% had private funding.
As always, the study has limitations: it included only papers from the years 2005-2008 and relied on FDA guidelines from 2003 and EMA guidelines from 2001 (updated 2008). It's also possible that they researchers' search in Pubmed didn't retrieved all the relevant papers.
In conclusion, there is a serious lack of available data about generic drugs. The authors point out that while 1,661 generic drugs were approved by the FDA during the study period, there weren't any data available about trials assessing generic drugs on the FDA and/or EMA sites. The authors also hypothesize that such a small percent (10%) of failed bioequivalence trials seem unlikely and suggested a possibility of publication bias.
van der Meersch, A., Dechartres, A., & Ravaud, P. (2011). Quality of Reporting of Bioequivalence Trials Comparing
Generic to Brand Name Drugs: A Methodological
Systematic Review PLoS One : 10.1371/journal.pone.0023611
... Read more »
van der Meersch, A., Dechartres, A., & Ravaud, P. (2011) Quality of Reporting of Bioequivalence Trials Comparing Generic to Brand Name Drugs: A Methodological Systematic Review. PLoS One. info:/10.1371/journal.pone.0023611
- August 14, 2011
- 05:50 PM
- 940 views
The Wikipedia Gender Gap, Part III
by Hadas Shema in Information Culture
In part I and part II, we discussed several of the gender gaps in Wikipedia. In this part, we'll talk about reverted edits, blocking, and their association with female and male editors. .
Blocking The hypothesis here was that "Female editors are less likely to be blocked." However, there wasn't a statistically significant difference in the percentage of females blocked (4.39%) and males blocked (4.52%). Surprisingly, females were significantly more likely to be blocked indefinitely (3.85% and 3.32% respectively). Females were also significantly more likely to be reverted for vandalizing Wikipedia’s articles (3.26% and 2.11% respectively). This should be taken with a grain of salt, because the proportion of users who self-reported their gender and were blocked or reverted for vandalism was even smaller than the baseline.
Reverted EditsAre female editors more likely to have their early edits reverted? To find out, the editors first "cleaned" the data from the reverted edits that were vandalism damage repair and took into account only reverts that were made within one week of an edit (more than 95% of the edits in the data set). For the seven first edits, the average reverting percent for women was significantly higher than that of men. Beyond those first edits, men and women's chances of having their edits reverted are similar.
Are women more likely to leave Wikipedia after their early edits were reverted? The authors answered this question by building a Cox regression model, to find out which factors are associated with changes in activity life span. The model included gender, the number of edits made in the first 24 hours of editing Wikipedia, the proportion of edits made in the first 24 hoursthat were reverted for vandalism-related reasons, the proportion of edits made in the first 24hours that were reverted, but not for vandalism-related reasons, and %RvNV×Gen, an interaction term between %RvNonVandal (the non-vandalism reverted edits) and gender, which was used to study the interaction between gender and reverts for non-vandalism reasons.
All the variables except for %RvNV×Gen were significantly associated with activity lifespan. The more edits an editor made during her/his first 24 hours, the longer her/his lifespan was likely to be. Shorter life span was associated with having early edits reverted. Even after taking said factors into account, being female still had a strong association with shorter lifespan.
While early reverts tend to make a lifespan shorter for both men and women, the likelihood of their departure wasn't gender-related. Female editor was just as likely to leave after being reverted as a male editor. In short, it's not that women "give up" more often than men when being reverted, it's that they were more likely to be reverted.
In ConclusionWhy doesn't Wikipedia have more women editors? This isn't the first time this question has been widely discussed. Last year, after a survey that found that only 13% of the Wikipedia's editors were women, the NYT published an article about the subject, which lead to some serious discussions and blog posts. Sue Gardner, Executive Editor of the Wikimedia Foundation, wrote a blog post including several of the reasons women supplied when asked why they hadn't edit Wikipedia. Answers varied and included reasons like the less-than-friendly interface, lack of time, lack of self-confidence, and an overall atmosphere of misogyny.
Now, since we know women *do* edit Wikis and *do* deal with less than friendly interfaces (have you ever, for example, tried to convince a Live Journal post to behave?) one must wonder if the main problem is, indeed, a culture that isn't women-friendly enough for most women to make the effort to fit in.
Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011). WP:Clubhouse? An Exploration of Wikipedia’s GenderImbalance WikiSym’11, October 3–5, Mountain View, California
... Read more »
Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011) WP:Clubhouse? An Exploration of Wikipedia’s Gender Imbalance. WikiSym’11, October 3–5, Mountain View, California. info:/
- August 10, 2011
- 03:17 AM
- 957 views
The Wikipedia Gender Gap, Part II
by Hadas Shema in Information Culture
In part I we talked about the small percentage of female editors in Wikipedia and their shorter editing life span. In this part we'll talk about content areas female and male editor focus on, coverage of female and male-related topics and involvement in editing controversial entries.
Content areas The authors divided the data from the January 2008 data dump into 8 main areas: Arts, Geography, Health, History, Science, People, Philosophy and Religion. Then, they checked the focus areas of each editor's activity. The authors found that men focused more on Geography and Science, while women focused more on People and Arts.
January 2008 Gender distribution of editors in eight interest areas. Editors can be categorized into more than one area
The reason these data look different than those presented earlier is that they are taken from a different data pool (2008 as opposed to the more recent data used earlier).
Topics CoverageAre female-related topics covered in Wikipedia as well as male-related topics? The authors used their gender data to determine whether an article is of more interest to women or to men. Since there are so few female editors, the metrics were "subject to high relative variance and noise" so they had to use only high-activity articles where gender was known for at least 30 editors. Articles shorter than 100 bytes were exclude because they usually redirected to other articles. The authors ended up with a sample of 59,579 articles.
Articles were declared "male" if they were in the bottom quintile (lowest 20%) of female editing activity, "neutral" if they were in the third (center) quintile, and "female" if they were in the top quintile.
Male articles are significantly longer than female articles (33,301 and 28,434 bytes respectively, t-Test, p < 0.001). Neutral articles are the longest at 36,511 bytes. Since the authors used the articles' length as a crude measurement of quality, they concluded that coverage of female topics is indeed lacking. They hypothesized that neutral articles are longer because they appeal to editors of both genders and therefore receive more overall attention.
For an additional analysis, the authors used the movie recommender web site MovieLens, which has self-reported gender information from over 80% of users who started using MovieLens before May 2003 (when they stopped asking about gender). 32% of the site's users were females. The authors mapped each movie to its Wikipedia article and excluded movies with less than 10 known-gender raters or movies which had no article. The remaining data set included 5,850 movies. The Article Length was the dependent variable, "Movie Gender" the independent variable and Movie Popularity, Movie Quality and Movie Age were the control variables. Articles about "male" movies were longer than those about "female" movies.
However, when articles about Nobel Prize winners and recipients of the Academy Award for Best Actor/Actress were analysed, it was found that they are about of equal length. So, the length gender gap isn't noticeable for very popular and/or important articles.
Controversial TopicsThe authors hypothesized that "Females tend to avoid controversial or contentious articles." They determined controversial articles according to whether the articles were protected or not, reasoning that Wikipedia tend to lock articles which are often vandalized or subject to content disputes. 5.20% of the “female” articles were protected, compared with 2.39% of the “male” articles. Female editors are actually more likely to be involved in controversial articles.
Next time: are women less likely to be blocked? Are edits by women more likely to be reverted?
Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011). WP:Clubhouse? An Exploration of Wikipedia’s Gender
Imbalance WikiSym’11, October 3–5, Mountain View, California
... Read more »
Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011) WP:Clubhouse? An Exploration of Wikipedia’s Gender Imbalance. WikiSym’11, October 3–5, Mountain View, California. info:/
- August 7, 2011
- 11:25 PM
- 1,295 views
The Wikipedia Gender Gap, Part I
by Hadas Shema in Information Culture
Wikipedia editing is a men's club. We already talked here about the lack of Wikipedia female editors (barely 13% of the editors are women). However, that survey was self-selecting and most of the participants (75%) used Wikipedia in non-English languages. Now, Lam et al. (2011) present their analysis of the gender imbalance in English Wikipedia. They took most of their data out of the January 2011 data dump, as well as from the Wikipedia API and the January 2008 and 2010 data dumps.In Wikipedia, editors can specify their gender in their accounts' settings, place a gender user box in their User page, or mention their gender in their User page description and discussion. The authors collected data from the accounts' settings and from the gender user boxes through the Wikipedia's API. They didn't check whether the editors refer to their gender somewhere else as that would have been too progressed for the techniques they used. The final sample included 113,848 users. Only 2.8% of the Wikipedia editors report their gender, but the authors found that dedicated editors tend to state their gender more often: while only 6.5% of the editors who had at least ten edits stated their gender, 14.1% of those who had over a hundred edits and 34.7% of those with at least 1,000 edits did so.The overall gender gap is still in placeOut of the 38,497 editors who started edited in 2009 and specified their gender, only 16.1% were women. To add to this, 16.1% of those accounts may have belonged to women, but they only did 9.0% of the edits. Male editors make almost double the edits female editors do. Women are only 6% of the editors with over 500 edits. Life and death of editorsAn editors begins her or his life in the first edit date and "dies" after more than six months of inactivity. Women "die" sooner, while men tend to live on. The gender gap is consistentThe gender identification methods described earlier were introduced to Wikipedia in different times (gender user boxes in December 2005 and gender preference settings in January 2009). Since men usually "live" longer in Wikipedia, the authors could only compare the users who have joined Wikipedia after a gender identification method was introduced (otherwise they would have just carried the survival rate bias on and on in the analysis). The gap has remained more-or-less the same since December 2005.That's it for this part. Next time: Is there a difference in content areas between women and men? Do women editors tend to avoid confrontations, and they less likely to be blocked?Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011). WP:Clubhouse? An Exploration of Wikipedia’s GenderImbalance WikiSym’11, October 3–5, Mountain View, California... Read more »
Lam, S., Uduwage, A., Dong, Z., Sen, S., Musicant, D. R., Terveen, L., & Terveen, J. (2011) WP:Clubhouse? An Exploration of Wikipedia’s Gender Imbalance. WikiSym’11, October 3–5, Mountain View, California. info:/
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