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  • August 24, 2011
  • 08:00 AM

Taxonomy in decline or growth?

by Zen Faulkes in NeuroDojo

Earlier this year, Craig McClain from Deep Sea News wrote an editorial at Wired arguing that taxonomy as a scientific discipline was “going extinct.”

A short new paper challenges that view.

Joppa and colleagues looked at taxonomic research on cone snails (pictured), spiders, amphibians, birds, reptiles, and mammals. The number of taxonomists studying each group has gone up in every case, not down.

The number of species being described is also going up, but it is actually not keeping up with the growth of taxnomists: the average number of new species described by each taxonomist is getting smaller. It’s also noteworthy that taxonomists are not working alone, contrary to popular conceptions of expertise for whole groups being locked in the head of single individuals.

Can the perception of taxonomy as a discipline in decline be reconciled with the data? First, the data only goes to 2000. A lot has changed in ten years, though I don’t know if it has changed that much. Second, the authors suggest that taxonomy in North America and Europe might be running counter to a global trend: declining here while growing in the rest of the world.

Another idea I have that might explain the discrepancy is that there is no control group. The number of taxonomists may be increasing, but how does it compare to other disciplines in biology? I suspect that there has been healthy growth of biological sciences as a whole, and that while the number of taxonomists may have increased “exponentially” (as described by Joppa and colleagues), other fields, like cell and molecular biology, have increased even more exponentially. (Mathematicians, don’t bug me if that is a meaningless phrase.)


Joppa L, Roberts D, & Pimm S (2011). The population ecology and social behaviour of taxonomists Trends in Ecology & Evolution DOI: 10.1016/j.tree.2011.07.010

Photo by richard ling on Flickr; used under Creative Commons license.... Read more »

  • August 23, 2011
  • 10:43 PM

Microfluidics Education

by Hector Munoz in Microfluidic Future

The extent to which someone develops their passion and calling for is affected by when they are exposed to it, if it all. It wasn't until 2009 (the summer before my junior year) that I was first exposed to microfluidics when Dr. John T McDevitt came to Rice University. I wish I had met him earlier, because I was hooked from then on, and knew that I wanted to enter the field. Although I had been somewhat familiar with nanotechnology and MEMS since high school, I had never heard anything about microfluidics. I can only imagine what would have happened if I had started learning about the field when I was in high school. With the increasing presence of the microfluidics, it only makes sense to have people learn about it before they're working on it for their Master's or PhD, or seeing it in the news. That's the goal of Dr. Michelle Khine et al. of University of California Irvine. In case you're not familiar with Dr. Khine, you may remember her as one of the 2009 TR35 recipients. It's an award by MIT's Technology Review that recognizes young innovators under 35.In the paper "Shrink-film microfluidic education modules: Complete devices within minutes," which was published in Biomicrofluidics in June 2011, they outline a plan to introduce the field to middle schools, high schools and undergraduate programs. When compared to standard techniques, microfluidic systems can boast faster reaction times, portability and lower sample usage. Despite these advantages, they are still traditionally expensive to produce, which has limited their accessibility outside high-tech companies and universities. The authors of the paper note that thermoplastics (among other materials) are a low cost alternative fabrication technique that can also be used for education.Thermoplastics are essentially Shrinky Dinks you might have played with as a kid. You can draw on them, and they'll shrink when heated. The authors developed experiments using this material for middle school, high school and college classes, in which each level draws from and expands on the one before it. Using computer-aided design (CAD), the students are able to design their devices, and print them onto the plastic using a printer. After heating the plastic to shrink it to 95% its original size, it's used as a mold to create the device.H filterThe basic module for the middle school students is comprised of an H-filter. An H-filter is a simple microfluidic structure that is able to sort particles by their size without a membrane. The students replicate the filtration of blood using different sized microbeads. The results of the filtration can readily be seen.In addition to the previous module, high school students can build a microfluidic device that creates a gradient. A lot of biological processes are driven by gradients, making it a key environment to reproduce. The gradient generator design features branching and mixing channels that take inputs of plain water and dyed water to produce a gradient of concentrations at the end. Gradient GeneratorIn order to add a level of complexity for the gradient generator in a college classroom, it has been combined with an immunoassay. The channels of the structure are first coated with a primary antibody. A secondary fluorescent antibody is then fed through one inlet, as a serum is fed through the other. The resulting fluorescence indicates the same gradient occurs as was seen with the food dye previously.I think that this paper not only illustrates something cool to teach students, but takes it two steps further. It first illustrates some of the interesting characteristics of microfluidics such as diffusion mixing and laminar flow. It then illustrates possible applications of the technology in diagnostics or point-of-care devices. As microfluidics education grows, I think we'll eventually see grad students who started learning the same year as their mentors!Reference:Nguyen, D., McLane, J., Lew, V., Pegan, J., & Khine, M. (2011). Shrink-film microfluidic education modules: Complete devices within minutes Biomicrofluidics, 5 (2) DOI: 10.1063/1.3576930Claim token: blog4e48131515be7... Read more »

  • August 23, 2011
  • 11:54 AM

The Dubious Science of Teacher Coaching: "An Interaction-Based Approach to Enhancing Secondary School Instruction and Student Achievement"

by Chad Orzel in Uncertain Principles

A while back, I Links Dumped Josh Rosenau's Post Firing Bad Teachers Doesn't Create good Teachers, arguing that rather than just firing teachers who need some improvement, schools should look at, well, helping them improve. This produced a bunch of scoffing in a place I can't link to, basically taking the view that people are either good at what they do, or they're not, and if they're not, you just fire them and hire somebody else. I was too busy to respond at the time, but marked that doen as something to come back to. So I was psyched when I saw this paper in Science about a scientific trial of a teacher coaching service, which claims that:

The intervention produced substantial gains in measured student achievement in the year following its completion, equivalent to moving the average student from the 50th to the 59th percentile in achievement test scores.

"Ah-hah!" I said, "Scientific proof that teachers can, in fact, be improved with some extra instruction." So I sat down to go through the paper for ResearchBlogging purposes. Which is when I hit a problem, because the paper is kind of awful.

The awfulness isn't primarily on the scientific side, which is reasonably sound. They ran a controlled trial in Virigina with 78 teachers and more than 2000 students, randomly assigning teachers to the control and intervention groups. Teachers in the intervention group received coaching in making their classes more interactive, and regularly recorded themselves teaching then sent the recordings off for review. Experts at the coaching service being tested reviewed the recordings, then sent pointers to the teachers on what they could do better. They also followed up with a phone conversation.

The result wasn't all that dramatic, but in the year after the coaching, the teachers from the intervention group did substantially better than those from the control group. They measured performance by comparing student scores on the state-mandated end-of-year test the previous year to their performance on the state-mandated end-of-year test for the class being studied. The year after the trial, the intervention group's students improved from a raw score of 479 the previous year to a raw score of 488 for the year being studied, while the control group went from a raw score of 495 the previous year to 482 for the year being studied. This difference is statistically significant, and that's the origin of the 50th to 59th percentile claim.

So what's awful?

Read the rest of this post... | Read the comments on this post...... Read more »

  • August 22, 2011
  • 01:22 PM

Stoichiometric IR pulsed laser deposition of Yttrium doped Bi-2212 thin film

by nath in Imprints of Philippine Science

Yttrium-doped Bismuth Strontium Calcium Copper Oxide (BSCCO) films, specifically Bi 2212, were succesfully deposited with preserved sample concentration using Infrared Pulsed Laser Deposition (IR PLD) as written in a recent publication from the National Institute of Physics, University of the Philippines Diliman [1]. It was also shown that by using appropriate annealing, desired qualities for electronic applications can be obtained.... Read more »

  • August 21, 2011
  • 03:21 PM

PubMed’s Higher Sensitivity than OVID MEDLINE… & other Published Clichés.

by Laika in Laika's Medliblog

Is it just me, or are biomedical papers about searching for a systematic review often of low quality or just too damn obvious? I’m seldom excited about papers dealing with optimal search strategies or peculiarities of PubMed, even though it is my specialty. It is my impression, that many of the lower quality and/or less relevant papers are [...]... Read more »

Leclercq E, Kramer B, & Schats W. (2011) Limitations of the MEDLINE database in constructing meta-analyses. Annals of internal medicine, 154(5), 371. PMID: 21357916  

  • August 21, 2011
  • 02:09 PM

Get to know Jack & the story behind the paper by @gilbertjacka "Defining seasonal marine microbial community dynamics"

by Jonathan Eisen in The Tree of Life

A few days ago I became aware of the publication of a cool new paper: "Defining seasonal marine microbial community dynamics" by Jack A. Gilbert, Joshua A Steele, J Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Alice C McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A Fuhrman and Dawn Field.  The paper was published in the ISME Journal and is freely available using the ISME Open option.

If you want to know more about Jack (in case you don't know Jack, or don't know jack about Jack) check out some of his rantings material on the web like his Google Scholar page, and his twitter feed, his LinkedIn page, his U. Chicago page.

But rather than tell you about Jack or the paper, I thought I would send some questions to the first author, Jack Gilbert and see if I could get some of the "story behind the paper" out of him.  Since Jack likes to talk (and email and do things on the web), I figured it was highly likely I could get some good answers.  And indeed I was right.

Here are his answers to my quickly written up questions (been out of the office due to family illness)

...... READ MORE .......
This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.


... Read more »

Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I.... (2011) Defining seasonal marine microbial community dynamics. The ISME journal. PMID: 21850055  

  • August 20, 2011
  • 06:32 AM

Is being Self-Employed good for your Health?

by Stuart Farrimond in Dr Stu's Science Blog

Working for yourself will make you happier, more satisfied and more productive. These are the surprising conclusions of over two decades of life-satisfaction research – Which is rather odd; considering that being your own boss means no health insurance, no pension and no end of the month office party (!!) With increasing pressure on salaried … Continue reading »... Read more »

  • August 19, 2011
  • 10:00 PM

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 19, 2011
  • 03:36 PM

Racial Disparity in NIH Grants: Priority Scores

by DrugMonkey in DrugMonkey

Unless you have been hiding under a rock, my NIH-focused Reader, you will have heard of the explosive findings of Ginther et al (2011) who reported on an analysis of racial and ethnic disparity in the review and funding of NIH grant applications.

There is a lot to discuss about these findings. A LOT. Well beyond the scope of one or even six blog posts. Commentary from the Office of Extramural Research, the NIMH and the Chronicle of Higher Education are worthwhile reads and there is a bit on National Public Radio as well. Blogger Bashir suggests* that these data prove that if you are African-American you have to be twice as good to succeed.

I'm going to jump right into some grant review geekery. I'm sure you are shocked.
These data are graphed from Table S1 and represented as percentages. I was interested in this Table, and motivated to re-graph the raw number, because of a curiosity about qualitative outcome. In my view the qualitative breakdown for scores is "likely fundable", "could be picked up by Program" and "triaged". These are moving targets across fiscal years, different study sections (the paper did not evaluate the percentile ranks used for funding decisions) and different Institutes or Centers of the NIH (which could have different score/pay relationships). Nevertheless, 100-150 maps reasonably well onto "fundable" and 151-200 onto the grey zone in which Program could possibly make a funding exception.

As a reminder, the old scoring system of the NIH (in place during the 2000-2006 interval used for the paper) went from 100 (best possible score) to 500 (worst possible score). Streamlining ("triage") procedures that were in place meant that approximately half of the applications were not discussed at the study section meeting (based on the preliminary evaluation of the three assigned reviewers) and did not receive a panel-voted score ("Unscored" on the graph). In theory this meant that scores above about 250 should be rare. However, any proposal could be pulled up for discussion if any member of the panel wanted to do so, therefore there might be some initially poor-scoring proposals that received a correspondingly poor voted score. In addition, proposals that seemed initially promising might have flaws revealed during the discussion that drove their score down well past the putative line for initial streamlining.

Black applications are more likely to be triaged and less likely to be placed in the first two best-scoring bins. The disparity even continues into the "no way fundable" zone of 201-250. I'm interested in this because one hypothesis might be that when it comes to that last little push into the obviously-fundable territory, black applicants are not being favored. That might predict a boost in the just-missed-score bins. Not so. There really is a disproportionate triage burden here.

Supplementary Figure S1 provides pretty decent evidence that there is no disparity in funding outcome for a given priority score- so the decisions Program staff make to pick up a gray zone application (or, rarely, to pass over a highly scoring application) do not appear to play a role in the overall disparity effect.

I am also struck by this summary of the findings on grant submitting behavior:
On average, investigators had three to four Type 1 R01 grant applications each. We found that blacks and Asians resubmitted more times before being awarded an R01 (2.01, P

Together, these data indicate that black and Asian investigators are less likely to be awarded an R01 on the first or second attempt, blacks and Hispanics are less likely to resubmit a revised application, and black investigators that do resubmit have to do so more often to receive an award.

Emphasis added. You will recognize these as topics dear to my default advice to submit a lot of proposals, to revise and resubmit and generally to make friends with the process. I've occasionally had to smack down old school outdated advice to not revise triaged or even fairly poorly-scoring apps that were discussed.

You will also recall that at the same time I advise people to make use of the process as it stands, I complain that this default get-in-line-noob stuff puts a higher burden on the younger investigators. Maybe it places a similar burden on African-American applicants in some systematic way. Perhaps because of their job places and a lack of local support for spending a lot of time on a low-percentage behavior like grant submitting. Or maybe because there is a linear function of how much revising you have to do and your eventual learned-helplessness response of stopping swimming.

Perhaps this just points at the grantsmithing parts of how to effectively respond to criticism. Maybe African-American scientists are less likely to have good grant mentoring effectively available to them (no matter the type of employment location, remember they controlled for that).

Well, those are my thoughts for the day. This is a big issue that should be a big wake up to the NIH. I do hope this is not a mere flash in the pan that gets ignored. Likewise, I do hope we are not discussing the same disparity 5 or 10 years in the future and similarly wringing our hands.
Ginther, D., Schaffer, W., Schnell, J., Masimore, B., Liu, F., Haak, L., & Kington, R. (2011). Race, Ethnicity, and NIH Research Awards Science, 333 (6045), 1015-1019 DOI: 10.1126/science.1196783

*I hope the NIH is listening. If I am not mistaken this is coming from a postdoc who identifies on blog as African-American. Regardless of the outcome of upcoming analyses and pilot investigations mentioned by Tabak and Collins, there is going to be a HUGE perception problem. The NIH needs to take this just as seriously as resolving whatever obstacles and biases have resulted in the grant award disparity. ... Read more »

Ginther, D., Schaffer, W., Schnell, J., Masimore, B., Liu, F., Haak, L., & Kington, R. (2011) Race, Ethnicity, and NIH Research Awards. Science, 333(6045), 1015-1019. DOI: 10.1126/science.1196783  

  • August 18, 2011
  • 03:59 AM

Retractions correlate better with 'Impact Factor' than citations

by Björn Brembs in

Thomson Reuters' Impact Factor (IF) is supposed to provide a measure for how often the average publication in a scientific journal is cited and thus a quantitative basis for ranking journals. However, there are (at least) three major problems with the IF:The IF is negotiable and doesn't reflect actual citation counts (source)The IF cannot be reproduced, even if it reflected actual citations (source)The IF is not statistically sound, even if it were reproducible and reflected actual citations (source)Thus, it is not surprising that there is very little correlation between the IF and what it is supposed to measure: actual citations to scientific articles:Fig. 1: Four examples of publications from individual researchers. Plotted are the actual citations of the publications against the Impact Factor of the journals they were published in (image source.)Compare these correlations to the recently published correlation between retractions and Impact Factor (in Infection and Immunity, Infect. Immun. doi:10.1128/IAI.05661-11):Now, one would need to do some thorough quantification and testing of this, but at a first glance, it appears pretty obvious to me that Retractions are a much better predictor for Impact Factor than citations. Can anyone do such a test of this hypothesis?Fang, F., & Casadevall, A. (2011). RETRACTED SCIENCE AND THE RETRACTION INDEX Infection and Immunity DOI: 10.1128/IAI.05661-11Seglen PO (1997). Why the impact factor of journals should not be used for evaluating research. BMJ (Clinical research ed.), 314 (7079), 498-502 PMID: 9056804... Read more »

  • August 17, 2011
  • 03:29 AM

Pharmaceutical Company Threatens Blogger

by Neuroskeptic in Neuroskeptic

Boiron, a multinational pharmaceutical company, have threatened an Italian blogger with legal action, the BMJ reports.

Many people are concerned when big pharmaceutical companies do this kind of thing. So I don't think we should make any exception merely because Boiron's pharmaceuticals happen to be homeopathic ones.

Samuel Riva, who blogs (in Italian) at, put up some articles critical of homeopathy
which included pictures of Boiron’s blockbuster homoeopathic product Oscillococcinum, marketed as a remedy against flu symptoms. The pictures were accompanied by captions, which joked about the total absence of any active molecules in homoeopathic preparationsBoiron wrote to Riva's internet provider threatening legal action, if the offending references to Boiron weren't taken down. They also wanted them to lock Riva out of his blog, the BMJ says. In response Riva removed the references to Boiron, including the pictures and captions, but kept the posts on homeopathy in general.


Above you can see a new picture I made of a Boiron product, with some captions you may find interesting. I've made sure to limit these to quotes from Wikipedia, and from Boiron USA's own website, and some simple mathematical calculations.

Beyond that, I make no comment whatsoever.

Turone F (2011). Homoeopathy multinational Boiron threatens amateur Italian blogger. BMJ (Clinical research ed.), 343 PMID: 21840920... Read more »

  • August 16, 2011
  • 01:28 PM

It was twenty years ago today . . .

by Marco Frasca in The Gauge Connection

With these beautiful words starts a recollection paper by the founder of arXiv, Paul Ginsparg. This is worth the reading as this history spans a number of years exactly overlapping the computer revolution that definitely changed our lives. What Paul also changed through these new information tools was the way researchers should approach scientific communication. [...]... Read more »

Paul Ginsparg. (2011) It was twenty years ago today .. arXiv. arXiv: 1108.2700v1

R. Aouane, V. Bornyakov, E. -M. Ilgenfritz, V. Mitrjushkin, M. Müller-Preussker, & A. Sternbeck. (2011) Landau gauge gluon and ghost propagators at finite temperature from quenched lattice QCD. arXiv. arXiv: 1108.1735v1

Axel Maas, Tereza Mendes, & Stefan Olejnik. (2011) Yang-Mills Theory in lambda-Gauges. arXiv. arXiv: 1108.2621v1

  • August 16, 2011
  • 10:44 AM

Women, romantic goals and science: The evidence just isn’t there

by Marie-Claire Shanahan in Boundary Vision

A critical examination of recent study suggesting that the pursuit of romantic goals hampers women's efforts in science... Read more »

  • August 15, 2011
  • 11:26 AM

Answer: MediQuiz #2: The Rhythm of Life

by Pranab Chatterjee in Scepticemia

Yeah, once again, almost everyone got it right. There are few songs that tend to stick in your head as much as stayin’ alive does, and indeed, it is just the right beat to make your CPR go along with. … Continue reading →... Read more »

  • August 15, 2011
  • 04:42 AM

Wikipedia: I Fought the Lore and the Lore Won

by Duncan Hull in O'Really?

Fighting the lore of wikipedia is an increasingly futile battle but there are people who resist using and improving the online encyclopedia. The remarkable thing is that some of this resistance comes from the scientific and academic communities, two groups of people who are supposedly concerned with the dissemination of knowledge. Wikipedia is the lore With [...]... Read more »

Neil L. Waters. (2007) Why you can't cite Wikipedia in my class. Communications of the ACM, 15-17. DOI: 10.1145/1284621.1284635  

Patricia L. Dooley. (2010) Wikipedia and the two-faced professoriate. WikiSym '10 Proceedings of the 6th International Symposium on Wikis and Open Collaboration. DOI: 10.1145/1832772.1832803  

Logan DW, Sandal M, Gardner PP, Manske M, & Bateman A. (2010) Ten simple rules for editing Wikipedia. PLoS computational biology, 6(9). PMID: 20941386  

  • August 15, 2011
  • 03:22 AM

A Ghostwriter Speaks

by Neuroskeptic in Neuroskeptic

PLoS ONE offers the confessions of a former medical ghostwriter: Being the Ghost in the Machine.

The article (which is open access and short, so well worth a read) explains how Linda Logdberg became a medical writer; what excited her about the job; what she actually did; and what made her eventually give it up.

Ghostwriting of course has a bad press at the moment and it's recently been banned by some leading research centres. Ghostwriting certainly is concerning, because of what it implies about the process leading up the publication.

However, it doesn't create bad science. A bad paper is bad because of what it says, not because of who (ghost)wrote it. Real scientists can write bad papers without a ghostwriter's help.

When pharmaceutical companies pay a ghostwriter, they are not doing this to get access to special dark arts that real scientists are innocent of. As far as I can see, it's just more efficient to use a specialist writer to do your scientific sins, when you're doing it all the time.

Rather like every evil sorcerer has an apprentice to do the day-to-day work of sacrificing animals and mixing potions.

Logdberg says:
My career came to an end over a job involving revising a manuscript supporting the use of a drug for attention deficit-hyperactivity disorder (ADHD), with a duration of action that fell between that of shorter- and longer-acting formulations.

However, I have two children with ADHD, and I failed to see the benefit of a drug that would wear off right at suppertime, rather than a few hours before or a few hours after. Suppertime is a time in ADHD households when tempers and homework arguments are often at their worst.

...Attempts to discuss my misgivings with the [medical] contact met with the curt admonition to ‘‘just write it.’’ But perhaps because this particular disorder was so close to home, I was unwilling to turn this ugly duckling of a ‘‘me-too’’ drug into a marketable swan.Many scientists will recall being in that kind of situation, albeit in a different context.

When writing a grant application, for example, you are almost literally trying to sell your proposed research to the awarding committee, on several levels. You need to sell the importance of the scientific question; the likely practical benefits of the research; the chance of success using your methods; what makes you the right person to do this work, and so on.

Writing a paper is much the same, although in this case you're selling research you've already done, and the data you collected.

Turning ugly ducklings into fundable, or publishable, swans, is part and parcel of modern science. Of course, the ducklings are not always as ugly as in the case Logdberg describes, but they are rarely as beautiful as they eventually end up.

Logdberg, L. (2011). Being the Ghost in the Machine: A Medical Ghostwriter's Personal View PLoS Medicine, 8 (8) DOI: 10.1371/journal.pmed.1001071... Read more »

  • August 14, 2011
  • 05:50 PM

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 12, 2011
  • 12:30 AM

A Case for BioHydrogen

by Sean Gibbons in Ars Scientifica

The hydrocarbon economy is faltering as oil reserves dwindle worldwide (Hirsch, 2008). Commodity prices have begun to fluctuate drastically due to the uncertain cost of petroleum, which resulted in food riots around the world in 2008. With a steadily decreasing energy supply and the demands on energy systems continually growing, the planet is in dire economic, geopolitical, and environmental straits. In order to halt the advance of climate change, prevent ecological collapse, rescue the global economy, and ensure our energy security, humanity must find a way to harness currently available (non-fossilized) energy.... Read more »

Agapakis, C., Ducat, D., Boyle, P., Wintermute, E., Way, J., & Silver, P. (2010) Insulation of a synthetic hydrogen metabolism circuit in bacteria. Journal of Biological Engineering, 4(1), 3. DOI: 10.1186/1754-1611-4-3  

Bendall, D., Howe, C., Nisbet, E., & Nisbet, R. (2008) Introduction. Photosynthetic and atmospheric evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1504), 2625-2628. DOI: 10.1098/rstb.2008.0058  

Blankenship, R., & Hartman, H. (1998) The origin and evolution of oxygenic photosynthesis. Trends in Biochemical Sciences, 23(3), 94-97. DOI: 10.1016/S0968-0004(98)01186-4  

Cleaves, H., Chalmers, J., Lazcano, A., Miller, S., & Bada, J. (2008) A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres. Origins of Life and Evolution of Biospheres, 38(2), 105-115. DOI: 10.1007/s11084-007-9120-3  

Fontecilla-Camps, J., Amara, P., Cavazza, C., Nicolet, Y., & Volbeda, A. (2009) Structure–function relationships of anaerobic gas-processing metalloenzymes. Nature, 460(7257), 814-822. DOI: 10.1038/nature08299  

Ghirardi, M., Posewitz, M., Maness, P., Dubini, A., Yu, J., & Seibert, M. (2007) Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms . Annual Review of Plant Biology, 58(1), 71-91. DOI: 10.1146/annurev.arplant.58.032806.103848  

Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., & Serrano, L. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature, 452(7189), 840-845. DOI: 10.1038/nature06847  

NISBET, E., GRASSINEAU, N., HOWE, C., ABELL, P., REGELOUS, M., & NISBET, R. (2007) The age of Rubisco: the evolution of oxygenic photosynthesis. Geobiology, 5(4), 311-335. DOI: 10.1111/j.1472-4669.2007.00127.x  

Schutz, K., Happe, T., Troshina, O., Lindblad, P., Leitao, E., Oliveira, P., & Tamagnini, P. (2004) Cyanobacterial H2 production ? a comparative analysis. Planta, 218(3), 350-359. DOI: 10.1007/s00425-003-1113-5  

Tamagnini, P., Leitao, E., Oliveira, P., Ferreira, D., Pinto, F., Harris, D., Heidorn, T., & Lindblad, P. (2007) Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiology Reviews, 31(6), 692-720. DOI: 10.1111/j.1574-6976.2007.00085.x  

Tsygankov, A. (2007) Nitrogen-fixing cyanobacteria: A review. Applied Biochemistry and Microbiology, 43(3), 250-259. DOI: 10.1134/S0003683807030040  

WILLE, M., KRAMERS, J., NAGLER, T., BEUKES, N., SCHRODER, S., MEISEL, T., LACASSIE, J., & VOEGELIN, A. (2007) Evidence for a gradual rise of oxygen between 2.6 and 2.5Ga from Mo isotopes and Re-PGE signatures in shales. Geochimica et Cosmochimica Acta, 71(10), 2417-2435. DOI: 10.1016/j.gca.2007.02.019  

  • August 10, 2011
  • 07:01 AM

Cancer diagnoses going viral

by Charles Harvey in Charles Harvey - Science Communicator

A genetically modified virus that can make hidden tumours light up may lead to a new and more effective way of screening for cancer. Some cancers are helpful enough to give off obvious clues to their existence. Prostate cancer, for example, can be detected as it raises the levels of a protein called PSA in the blood. Many, however, leave no such trace. Sufferers of these diseases can, therefore, remain in the dark about their condition, delaying treatment and lowering their chances of survival.... Read more »

  • August 10, 2011
  • 03:17 AM

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:/

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