Research / Scholarship posts
- January 4, 2012
- 08:22 PM
- 714 views
5 Reasons to Love Academia
by Bradley Voytek in Oscillatory Thoughts
1. Freedom to set your own scheduleAcademia's not a 9 to 5, cubicle slave job! We didn't go to school for 20+ years to work a measly 8 hours per day for 40 hours a week.You see, there's a certain... "culture"... of academia that equates "good, smart work" with "endless hours in the lab".This kind of mentality leads to famous suggestions such as the following from my PhD institute (also referenced in Nature):1. Every one works at least 50 hr a week in the lab (e.g., 8+ hr a day, six days a week). This is by far lower than what I am doing every day and throughout most of my career. You may be smarter or do not want to be as successful, but I am not asking you to match my time in the lab2. By working, I mean real bench work... I suggest that everyone puts in at least 6 hr concentrated bench work and 2+ hr reading and other research-related activity each day. Reading papers and books should be done mostly after work. More time can be spent on reading, literature search and writing during working hours when you are ready for writing a paper....I expect everyone to have made sufficient progress in the research so that a good paper is in sight (at least to the level of J. Neuroscience). If you cannot meet this goal at that time, I will have to ask you to prepare to leave my lab by the end of August.Or this gem from Caltech:I have noticed that you have failed to come in to lab on several weekends, and more recently have failed to show up in the evenings. Moreover, in addition to such time off, you recently requested some vacation. I have no problem with vacation time that is well earned, but I do have a problem with continuous vacation and time off that interferes with the project. I find this very annoying and disruptive to your science.I expect you to correct your work-ethic immediately.I receive at least one post-doctoral application each day from the US and around the world. If you are unable to meet the expected work-schedule, I am sure that I can find someone else as an appropriate replacement for this important project.You may be a unique and beautiful snowflake when you're being recruited, but once you're in, you stay in, science slave!2. Swimming in your pools of moneySeriously though, the time spent in lab is worth it. If for no other reason than the strong pay. Why go into industry when you can make $28-30,000 per year during your 4-7 year PhD, especially when that will be followed up by 1-5 years as a post-doc making upwards of almost $39,000 annually?!Look at those Ivory Towers!So sketch up some quick grant on climate change and make it rain!"What a strange business this is: We stay in school forever. We have to battle the system with only a one in eight or one in ten chance of getting funded. We give up making a living until our forties. And we do it because we want to help the world. What kind of crazy person would go for that?"—Nancy Andrews, Vice Chancellor for Academic Affairs and Dean of the Duke University School of Medicine(Source)3. Expanding humanity's knowledgeSo the work environment is nice and lax, the pay is great, and your spouse certainly isn't rethinking their life decisions when it comes to marrying you.But who needs those things?! We academics eschew time, family, and money for a higher purpose! We are adding to humanity's knowledge. One tiny (insignificant) nudge at a time:(Source: Matt Might)As long as you're fast enough:(Source: Jorge Cham: PhD Comics)4. Interacting with brilliant peersBecause in the end, pushing those insignificant boundaries of knowledge afford you the esteem of your peers. This, in turn, allows you to perpetuate the circle of scientific life!Because someday, you too get to review scientific manuscripts and help build upon the foundations of progress.* The writing and data presentation are so bad that I had to leave work and go home early and then spend time to wonder what life is about.* This paper is desperate. Please reject it completely and then block the author’s email ID so they can’t use the online system in future.* The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style.* I suppose that I should be happy that I don’t have to spend a lot of time reviewing this dreadful paper; however I am depressed that people are performing such bad science.(Source)Enclosed is our latest version of Ms. #1996-02-22-RRRRR, that is the re-re-re-revised revision of our paper. Choke on it... Hopefully, we have suffered enough now to satisfy even you and the bloodthirsty reviewers...To handle [the reviewers' suggestions], we have modified the Introduction and added, after the review of the relevant literature, a subsection entitled "Review of Irrelevant Literature" that discusses these articles and also duly addresses some of the more asinine suggestions from other reviewers.We hope you will be pleased with this revision and will finally recognize how urgently deserving of publication this work is. If not, then you are an unscrupulous, depraved monster with no shred of human decency. You ought to be in a cage. May whatever heritage you come from be the butt of the next round of ethnic jokes. If you do accept it, however, we wish to thank you for your patience and wisdom throughout this process, and to express our appreciation for your scholarly insights.(Source)5. Educating young mindsBut all of these awards pale in comparison to the cornerstone of academe: the student. As academics we are privileged with the highest of honors of educating tomorrow's thought-leaders!One student complained that a professor was not posting lecture slides to the course’s Web site:Is this a technical glitch, or are you being a jerk about it? I don’t think you know what your doing in this class. I have gone to the deprtment chair about it and she doesn’t know either. How can I study and take the exams without the notes? Its bad enough your lectures don’t have sound and video."I didn’t come to class today because i had a soar throat and couldn’t hear. I think it might be strep," the student wrote."Hello, Student X. I’m sorry you’re not feeling well. Did you intend to send this message to someone else? You’re not registered for any of my classes this semester. Oh, and I’m pretty sure that strep doesn’t cause loss of hearing," the professor replied."Ouch! i clicked the wrong address. can you forward that message to dr. DifferentProfessor for me? i can’t open the directory cuase my computer memory sucks and i have another program running. except change the hearing to talking. thanx!"(Source 1 and 2)(In all seriousness, despite these things, I really do love this job. "What kind of crazy person would go for that?" What kind of crazy person indeed.)... Read more »
Cyranoski, D. (2011) Neuroscience in China: Growth factor. Nature, 476(7358), 22-24. DOI: 10.1038/476022a
Glass, R. (2000) A letter from the frustrated author of a journal paper. Journal of Systems and Software, 54(1), 1. DOI: 10.1016/S0164-1212(00)00020-0
Lawrence, P. (2009) Real Lives and White Lies in the Funding of Scientific Research. PLoS Biology, 7(9). DOI: 10.1371/journal.pbio.1000197
Powell, K. (2006) Winning ways. Nature, 442(7104), 842-843. DOI: 10.1038/nj7104-842a
- January 4, 2012
- 03:36 PM
- 369 views
miRNA special reprint in Nature
by zacharoo in Lawn Chair Anthropology
A while ago I had a small post about RNA interference (RNAi), linking to a really awesome and educational animation and slideshow on the topic. Again, RNAi refers to gene regulation by very small strands of RNA. There are a number of types of RNA in your cells, and a several of these are involved in RNAi: in the last post I cursorily mentioned piwi-interacting RNAs (piRNA), small interfering (siRNA) and long intergenic non-coding (lincRNA).One type I neglected to mention is "micro" (miRNA), and this is the one about which the journal Nature has a special on-line issue. miRNA, like other types in RNAi, binds to messenger RNA in cells to prevent gene translation. The special issue of Nature focuses on miRNA in various diseases involving tumors and skeletal abnormalities, and so far as I can tell, it's completely free to all!What really caught my eye about this issue is its highly interactive medium, produced by some company called zmags. This "zmag" (I guess you'd call it?) has been rendered so that you view and leaf through actual magazine-like pages in your browser. I've got a 1+ yr old Macbook and the 2-finger zoom on the trackpad also works within the browser. Want to read and mark up some of it in your preferred program? Well you can save selected pages from the issue as a pdf, giving you flexibility in what content you download (though I did have some issues with this). A while ago I noticed Nature also used a somewhat interactive in-browser, pdf-viewing app called Readcube, though I admit I haven't really toyed with that program.It's a bit challenging but also interesting to follow the possible obsolescence of the (literally) printed word. Amazon's Kindle and other e-book platforms have all but buried the expensive, clunky hardcover tome. Academic publishers like Springer offer not only articles but also whole book chapters as pdfs available online (though they tend to require some type of university or other affiliation), and major newspapers offer most of their content on their websites.On this topic, Carl Zimmer had a neat piece in Nature a few weeks ago about the "rise of the e-book." He raises some excellent points regarding the pros and cons of e-books, some which I think could be extended to digital media more generally. I for one am like millions of others, relying on my handy computer and the internet for nearly all information I need to be a fully-functioning student, teacher and member of society. Still, as Zimmer points out at the end of his article, the permanence of e-books and the like is uncertain. I mean, what to do if we're hit by another devastating Y2k?Read onNature special issue hereZimmer, C. (2011). Technology: Rise of the e-book Nature, 480 (7378), 451-452 DOI: 10.1038/480451a... Read more »
Zimmer, C. (2011) Technology: Rise of the e-book. Nature, 480(7378), 451-452. DOI: 10.1038/480451a
- January 4, 2012
- 03:04 PM
- 354 views
Hot Sex Prevents Breast Cancer
by Neuroskeptic in Neuroskeptic
Breast cancer is caused by sexual frustration. Women should ditch their unsexy husbands and find a real man to satisfy them if they want to reduce the risk of the disease. That's according to An Essay on Sexual Frustration as the Cause of Breast Cancer in Women: How Correlations and Cultural Blind Spots Conceal Causal Effects, a piece that was published today in The Breast Journal.Really -Endocrinological processes are important targets in breast cancer research. These processes are also important in human sexual behaviors. I hypothesize that these processes are capable of adjusting or distorting biological active forms of specific sex hormones depending on experienced sexual stimuli. These aberrantly metabolized sex hormones will ultimately lead to breast cancer....My thesis is that breast cancer is essentially caused by sexual frustration. The focus of this hypothesis is aimed at the (un)consciously experienced tension and sexual dissatisfaction between the chosen mate based on socio-economic, intellectual, ethnic or cultural motives and the nonchosen potential mate who has more appealing sexual incentive properties.In most western societies the improved economic independence of women has not changed to such a degree that long-term partners are chosen entirely according to sexual incentive properties. If the selected partner has no or weak sexual incentive properties for the other member of the couple, it is likely that sexual frustration will follow in the long run (6), which ultimately will cause breast cancer in some women...WHY HIGHER SOCIOECONOMIC GROUPS OF WOMEN ARE MORE AT RISK...higher socio-economic group of women pay more than average attention to the assets or status of the potential partner(7)....The chances of some women from higher socio-economic classes to find a sexually compatible mate are considerably reduced. This is due to an often self-imposed very limited range of potential partners. In this group of women, high status of the potential partner compensates for the acceptance of physically less attractive men (9)...HEIGHT AS RISK FACTOR IN BREAST CANCER...These women have a disadvantage because they have a smaller pool to choose from if they want a man they will not tower over. This increases the chances to settle for a sexually incompatible partner...BREAST CANCER RISK IN NUNS... There are 15 references, but they're all about sex, not cancer. Thus we get a citation to support the statement that "If the selected partner has no or weak sexual incentive properties for the other member of the couple, it is likely that sexual frustration will follow in the long run (6)", but not for the rather more controversial idea that disappointment in the bedroom somehow leads to malignant mutations in the DNA of cells of the mammary epithelium.Well except the line that "aberrantly metabolized sex hormones" are responsible, which is the scientific equivalent of waving your hands and saying "woo".How did this happen? The Breast Journal, so far as I can see, publishes lots of sensible research. It may not be a major journal but it's MEDLINE indexed and ranked 143/184 for impact in the field of oncology, which means there are 40 cancer journals in the world that have less impact than it. If I had published there, I'd be a bit miffed that my work was appearing in the same pages. Thankfully I haven't but as a scientist I'm still insulted that this has been published in a scientific journal, and will be appearing on the shelves of libraries around the world under the heading "science". Stuger, J. (2011). An Essay on Sexual Frustration as the Cause of Breast Cancer in Women: How Correlations and Cultural Blind Spots Conceal Causal Effects The Breast Journal DOI: 10.1111/j.1524-4741.2011.01206.x... Read more »
Stuger, J. (2011) An Essay on Sexual Frustration as the Cause of Breast Cancer in Women: How Correlations and Cultural Blind Spots Conceal Causal Effects. The Breast Journal. DOI: 10.1111/j.1524-4741.2011.01206.x
- January 2, 2012
- 07:37 AM
- 497 views
2011: The Year in Drugs Deaths and data fraud
by Neurobonkers in Neurobonkers
A round-up of this year’s drugs news along with the latest available statistical data which shows that helium killed more than ecstasy, cannabis, mephedrone and GHB combined.... Read more »
Nutt, D., King, L., & Phillips, L. (2010) Drug harms in the UK: a multicriteria decision analysis. The Lancet, 376(9752), 1558-1565. DOI: 10.1016/S0140-6736(10)61462-6
Measham,F. Moore, K. Østergaard, J. (2011) Mephedrone, ‘‘Bubble’’ and unidentified white powders: the contested identities of synthetic ‘‘legal highs". DRUGS AND ALCOHOL TODAY, 137-146. info:/
Editorial team. (2010) The EMCDDA annual report 2010: the state of the drugs problem in Europe. The European Monitoring Centre for Drugs and Drug Addiction, also published in Euro surveillance :European communicable disease bulletin, 15(46). PMID: 21144426
- January 2, 2012
- 02:07 AM
- 850 views
Principles for Patient Safety
by Dr Shock in Dr Shock MD PhD
Buffer Teaching patient safety starts in medical school. Hospitals can be weired chaotic places. It’s often a wonder everything keeps working as it should although failures do occur. Medical professionals come to realize that mistakes happen and they adapt their working procedures to those of the so called high reliability organizations such as aircrafts, airline [...]
No related posts.... Read more »
Prasanna, P., & Nagy, P. (2011) Learning From High-Reliability Organizations. Journal of the American College of Radiology, 8(10), 725-726. DOI: 10.1016/j.jacr.2011.06.020
- January 1, 2012
- 10:02 AM
- 467 views
New Year’s Resolutions – Doomed to fail?
by Stuart Farrimond in Guru: Science Blog
New Year’s Resolutions: Do they work? What’s so magical about the stroke of midnight on December 31st? Many of us pledge to get fit, save money or stop smoking. Many of us also know how often these attempts end in failure. Perhaps Oscar Wilde had it right: Resolutions are “pure vanity. Their result is absolutely nil”. Oscar [...]... Read more »
Norcross JC, Mrykalo MS, & Blagys MD. (2002) Auld lang syne: success predictors, change processes, and self-reported outcomes of New Year's resolvers and nonresolvers. Journal of clinical psychology, 58(4), 397-405. PMID: 11920693
- January 1, 2012
- 09:41 AM
- 682 views
Copyright vs Medicine: If this topic isn’t covered in your newspaper this weekend, get a new newspaper
by Neurobonkers in Neurobonkers
According to the New England Journal of Medicine, after thirty years of silence, authors of a standard clinical psychiatric bedside test have issued take down orders of new medical research.... Read more »
Newman, J., & Feldman, R. (2011) Copyright and Open Access at the Bedside. New England Journal of Medicine, 365(26), 2447-2449. DOI: 10.1056/NEJMp1110652
- December 31, 2011
- 02:54 AM
- 884 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 30, 2011
- 08:04 AM
- 348 views
How Realistic is fMRI?
by Neuroskeptic in Neuroskeptic
How representative are fMRI experiments? Is "the brain" that we investigate with fMRI the same brain that we use outside the MRI scanner?A new paper from Bernhard Hommel and colleagues of Leiden in the Netherlands offers some important caveats. They looked to see what effect playing some recorded MRI scanner sounds had on people's ability to perform some simple cognitive tasks, while sitting outside the scanner.MRI is notoriously noisy. When you have an MRI scan you have to wear earplugs to protect against the sound but they only block out some of it. Opinions differ on whether the sound is pleasant or not. Personally I find the repetitive tick-tock rather soothing now, but then I've heard it many times over the years. First-timers can find it quite overwhelming.Anyway, Hommel et al found that while scanner noise had no overall effects on reaction time or accuracy, it actually improved performance on three measures of "cognitive control".For instance in a task in which participants had to respond to the colour of a circle by pressing the left or the right arrow key, they were slower to react when the circle appeared on the "wrong" side of the screen, i.e. on the left when the correct answer was the right arrow. This slowing of responses caused by a stimulus-response clash is called the Simon effect.The results showed that the Simon effect was reduced by noise. The same thing happened in two other studies: noise meant better performance.All of the noise effects were modest and the sample sizes were also quite small (14-18 per task, with everyone studied twice, noisy vs silent) but this paper joins a number of others raising questions about the representativeness of fMRI, with evidence that fMRI activates the brain and maybe even improves mood (although I doubt that last one). The authors' interpretation is that the noise made people pay more attention to the tasks, to compensate for the distraction, and that this means that fMRI studies may be biased in their measurements of cognitive control:Generalizing from fMRI findings to behavioral observations and vice versa seems to be more problematic than commonly thought, at least as far as control processes are concerned. In a sense, then, investigating cognitive processes by means of fMRI... is inevitably facing Heisenberg’s (1927) uncertainty principle, according to which the act of measurement can change what is being measured.To my mind the biggest weakness of this is that it only looked at noise. While scanners are noisy, that's not the only distracting thing about them: during an fMRI study you also have to lie down, in a small confined tube, and your only way to see the "screen" on which experimental stimuli are shown is indirectly via a small mirror which often doesn't give a good view.So ironically, I'm not sure how realistic this study is... Hommel, B., Fischer, R., Colzato, L., van den Wildenberg, W. and Cellini, C. (2011). The effect of fMRI (noise) on cognitive control. Journal of Experimental Psychology: Human Perception and Performance DOI: 10.1037/a0026353... Read more »
Hommel, B., Fischer, R., Colzato, L., van den Wildenberg, W., & Cellini, C. (2011) The effect of fMRI (noise) on cognitive control. Journal of Experimental Psychology: Human Perception and Performance. DOI: 10.1037/a0026353
- December 27, 2011
- 11:00 AM
- 379 views
Scanning The Brain While Looking At Scans
by Neuroskeptic in Neuroskeptic
A new study investigated what goes on in the brain when doctors make a diagnosis.Radiologists use X-rays and other imaging techniques to diagnose diseases - but in this study, they went into the scanner themselves. Brazilian researchers Marcio Melo et al used fMRI to record neural activity while the radiologists were shown an array of chest X-rays.Some of the scans showed evidence of disease, which the doctors were required to diagnose. There were also two control conditions, in which the stimuli were still X-rays but with little pictures of either animals or letters embedded in them, instead of diseases.The image above shows how it worked. As well as pneumonia, one patient has a severe case of Alligator Lung, while the other looks like they've got the Influenza 'B' virus.Now, the point of all this was to compare the mental process of making a diagnosis to that of seeing an object. The idea is that a trained radiologist sees particular diseases in the scans, in the same way that anyone can see an alligator.Activity during diagnosis, object-recognition and letter naming was very similar (compared to doing nothing); this presumably represents the visual and language areas involved in looking at the image, recognizing what it is, and saying it out loud:There were some slight differences, with the left inferior frontal cortex and the posterior cingulate cortex being more activated by diagnosis than animals. But this difference disappeared after controlling for the number of different possible descriptions the radiologists reported thinking about for each image.The authors conclude thatThese results support the hypothesis that medical diagnoses based on prompt visual recognition of clinical signs and naming in everyday life are supported by similar brain systems.Which seems fair enough, although it's important to remember that the diagnoses in this study were quite easy ones. The mean response time was just 1.3 seconds and only 6% of those split-second diagnoses were wrong. Unfortunately diagnosis is not always that easy.Anyway, this study is all very well, but why stop at chest X-rays? Last year I speculated on the fun neuroscientists could have with a real-time fMRI machine:You could lie there in the scanner and watch your brain light up. Then you could watch your brain light up some more in response to seeing your brain light up...We really need to scan people while they're looking at brain scans. Only then will we be able to understand the neurological basis of being a neurologist, and find the brain's looking-at-a-blob blob.Melo M, Scarpin DJ, Amaro E Jr, Passos RB, Sato JR, Friston KJ, and Price CJ (2011). How doctors generate diagnostic hypotheses: a study of radiological diagnosis with functional magnetic resonance imaging. PloS ONE, 6 (12) PMID: 22194902... Read more »
Melo M, Scarpin DJ, Amaro E Jr, Passos RB, Sato JR, Friston KJ, & Price CJ. (2011) How doctors generate diagnostic hypotheses: a study of radiological diagnosis with functional magnetic resonance imaging. PloS one, 6(12). PMID: 22194902
- December 27, 2011
- 11:00 AM
- 486 views
Optics research and the eye in Spain during the XX century: a brief history
by Pablo Artal in Optics confidential
A brief historical account on optical and vision research in Spain in the XX century... Read more »
Marcos, Artal, Santamaría, Aguilar, Plaza. (2006) Research in Physiological Optics in Spain: A historical revision. Opt. Pura Apl. 39 (3) 189-197 . info:/
- December 26, 2011
- 05:26 PM
- 525 views
Impact factor predicts unreliability of research papers
by Björn Brembs in bjoern.brembs.blog
Last week, we've already seen that the most prominent way of ranking scholarly journals, Thomson Reuters' Impact Factor (IF), isn't a very good measure for predicting how many citations your scientific paper will attract. Instead, there is evidence that IF is much better at predicting the chance that your paper might get retracted.Now, I've just been sent a paper (subscription required) which provides evidence that the reliability of some research papers correlates negatively with journal IF. In other words, the higher the journal's IF in which the paper was published, the less reliable the research is. This particular evidence holds only for genome-wide association studies (GWAS), but given the high correlation between IF and retractions, it likely holds for other research as well. Now what is the data? The paper contains one figure:On the X-axis you see the impact factor and on the Y-axis a measure for the bias of the GWAS data on a logarithmic scale. How did the authors calculate this bias score? In their own words:We divided the individual study odds ratio (OR) by the pooled OR, to arrive at an estimate of the degree to which each individual study over- or underestimated the true effect size, as estimated in the corresponding meta-analysis. We have recently used this method to identify a biasing effect of research location and resources. (Munafo MR, Matheson IJ, Flint J. Mol Psychiatry 2007; 12: 454–461)Thus, the authors plot a value that indicates by how much a single study over- or underestimates the actual effect (estimated by taking many studies into account) of a gene-phenotype association. The size of the circles on the graph indicates the sample size of the study. The overall "R squared" value, or the Coefficient of Determination for this correlation is only 0.13, but at a highly significant P=0.00002. This means that the correlation is pretty weak, but it is statistically significant.This sort of correlation, low R2 but statistically significant, corresponds roughly to the pattern of correlations one can see with citations: IF is predicting citations of a paper to some degree, but not very reliably. Likewise, IF is predictive of a GWAS unrealiability, but not very reliably. Or, phrased differently, IF is about as predictive of a paper's unreliability as it is about its citations, which I'd consider quite bad for something that decides about scientific careers.But another important point can be seen in the graph: IF is also predictive of the sample size of the GWAS study: the higher the IF of the journal in which the study was published, the lower the sample size. One could interpret this as evidence that high-IF journals are more likely to publish a large GWAS effect, even though it is only backed up by a small sample size, while low-IF journals require a more solid amount of data to back up the authors' claims.Taken together, this study provides some evidence for one of the potential mechanisms underlying the very strong correlation between IF and retractions we've seen before: authors are more likely to publish unreliable data with predominantly overestimated effect sizes in high-IF journals. Importantly, this constitutes a mechanism which cannot be explained by high-IF journals being more closely scrutinized than low-IF journals. Instead, it suggests that at least a portion of the retractions in high-IF journals is due to the studies published there being more likely to be flawed than studies in low-IF journals.In the words of the authors:Our results indicate that genetic association studies published in journals with a high impact factor are more likely to provide an overestimate of the true effect size. This is likely to be in part due to the small sample sizes used and the correspondingly low statistical power that characterizes these studies. Initial reports of genetic association published in journals with a high impact factor should therefore be treated with particular caution. However, although we cannot necessarily generalize our findings to other research domains, there are no particular reasons to expect that genetic association studies are unique in this respect.Munafò, M., Stothart, G., & Flint, J. (2009). Bias in genetic association studies and impact factor Molecular Psychiatry, 14 (2), 119-120 DOI: 10.1038/mp.2008.77... Read more »
Munafò, M., Stothart, G., & Flint, J. (2009) Bias in genetic association studies and impact factor. Molecular Psychiatry, 14(2), 119-120. DOI: 10.1038/mp.2008.77
- December 26, 2011
- 11:39 AM
- 544 views
A New Model for Scientific Publishing
by Bradley Voytek in Oscillatory Thoughts
There's a new paper out in Frontiers in Computational Neuroscience that is relavant to my interests. The paper is by Dwight Kravitz and Chris Baker from the NIMH and is titled "Toward a new model of scientific publishing: discussion and a proposal".About two weeks ago Dwight emailed me his paper saying that he'd read a post I'd written last month for the Scientific American guest blog called "What is peer review for?" (you can check out my interview on Skeptically Speaking on this topic as well).After reading Dwight's paper I want to make sure it gets as much exposure as possible. I can't it justice because it's so well-written and clear. But before I shuffle you off to read it I wanted to highlight their proposed system and ask you all what you think.What are the barriers to instantiating their proposed system?In the SciAm piece I concluded by saying:But the current system of journals, editors who act as gatekeepers, one to three anonymous peer-reviewers, and so on is an outdated system built before technology provided better, more dynamic alternatives.Why do scientists-–the heralds of exploration and new ideas in our society–-settle for such a sub-optimal system that is nearly 350 years old?We can–-we should-–do better.Well, it looks like Kravitz and Baker put a lot more thought into this problem than I and they've come up with an incredibly novel alternative system to peer review.They nail it. There's almost nothing that I disagree with.I love this paper.They succeed here not because of their criticisms--which abound in the sciences--but rather because of their inclusion of a viable, creative, intelligent solution that addresses problems of motivation, utility, practicality, and even finance for an alternative model for peer review and scientific publication.They begin by describing the current peer review system in the context of the neurosciences. They have an amusing graph that highlights the 17 levels of hell that is the peer review process loop. These guys crack me up."In the case of a rejection the Authors generally proceed to submit the paper to a different journal, beginning a journal loop bounded only by the number of journals available and the dignity of the Authors."(click to enlarge)Before I outline what their alternative proposal is, I want to highlight some of the problems regarding the costs and problems of the current system that Kravitz and Baker identify....what is striking is less the average amount of time [it takes to publish a paper], which is quite long, but more its unpredictability. In total, each paper was under review for an average of 122 days but with a minimum of 31 days and a maximum of 321. The average time between the first submission and acceptance, including time for revisions by the authors was 221 days (range: 31–533)......Beyond the costs of actually performing the research and preparing the first draft of the manuscript, it costs the field of neuroscience, and ultimately the funding agencies, approximately $4370 per paper and $9.2 million over the approximately 2100 neuroscience papers published last year. This excludes the substantial expense of the journal subscriptions required to actually read the research the field produces and the unquantifiable cost of the publishing lag (221 days) and the uncertainty incurred by that delay......Authors are incentivized to highlight the novelty of a result, often to the detriment of linking it with the previous literature or overarching theoretical frameworks. Worse still, the novelty constraint disincentives even performing incremental research or replications, as they cost just as much as running novel studies and will likely not be published in high-tier journals.Okay, so what is their alternative model?(click to enlarge)It breaks down like this:* No more editors as gate-keepers ("Their purpose is to serve the interests of the journal as a business and not the interests of Authors").* Publication is guaranteed, so no more concern over "novelty".* Editors instead coordinate the process and ensure that double-blind anonymity is maintained.* Reviews are passed on to the authors as part of a "pre-reception" process which allows the authors to revise or retract their work before making it publicly available.* Once public, the post-publication review process begins.* An elected Editorial Board acts as an initial rating and classification service to put the paper in context.* Members of the Board are financially incentivized... but the money doesn't go into their pockets, rather it can be put into their own research fund coffers.* Papers are put into a forum wherein members of that forum can ask questions and offer follow-up suggestions.* Forums provide a more living, dynamic quality to papers, as well as metrics for each manuscript.* With better metadata for papers, ads could be more targeted by paper topic (no more ads for PCRs in cog neuro papers, for example).* Kravitz and Baker note that something like a Facebook page for each paper could serve this purpose.The Kravitz-Baker system saves money and time wasted by the needless "walking down the impact factor ladder" that usually occurs.They address a lot more issues beyond what I've described above. They note that a common counter-argument to double-blind review, for example, is that a reviewer can "often guess" who the authors of the paper they're reviewing are because sub-fields are so small. But Kravitz and Baker point out that "the identity of the Authors might be guessed by the Reviewers, any ambiguity should act to reduce this bias". This seems so obvious.The Kravitz-Baker system seems really well thought out, and one I'd love to see in place. But I'm worried I'm missing some critical fault here.Anyone see any glaring issues?Kravitz, D., & Baker, C. (2011). Toward a New Model of Scientific Publishing: Discussion and a Proposal Frontiers in Computational Neuroscience, 5 DOI: 10.3389/fncom.2011.00055... Read more »
Kravitz, D., & Baker, C. (2011) Toward a New Model of Scientific Publishing: Discussion and a Proposal. Frontiers in Computational Neuroscience. DOI: 10.3389/fncom.2011.00055
- December 24, 2011
- 08:44 PM
- 675 views
Look who’s talking now, but be careful
by Daniel Mietchen in Wikimedian in Residence on Open Science
So far, none of the Open Access Files of the Day had sound, not even the two videos amongst them. This fits into the wider picture of multimedia being neglected in the scientific corners of Wikimedia projects, or in terms of reuse … Continue reading →... Read more »
Marshall, D., & Hill, K. (2009) Versatile Aggressive Mimicry of Cicadas by an Australian Predatory Katydid. PLoS ONE, 4(1). DOI: 10.1371/journal.pone.0004185
- December 22, 2011
- 06:34 AM
- 675 views
Scientists discover why diet may prolong life
by United Academics in United Academics
Researchers at the Catholic University of Sacred Heart in Rome have discovered the molecular process that is activated when people diet. They hope this will lead to the development of a drug that mimics this process.... Read more »
Fusco, S., Ripoli, C., Podda, M., Ranieri, S., Leone, L., Toietta, G., McBurney, M., Schutz, G., Riccio, A., Grassi, C.... (2011) A role for neuronal cAMP responsive-element binding (CREB)-1 in brain responses to calorie restriction. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1109237109
- December 21, 2011
- 11:24 AM
- 716 views
An effective malaria vaccine may be near
by United Academics in United Academics
There is strong evidence that this experimental vaccine has the potential to stop every strain of the parasite Plasmodium falciparum, responsible of the most dangerous form of malaria.... Read more »
Douglas, A., Williams, A., Illingworth, J., Kamuyu, G., Biswas, S., Goodman, A., Wyllie, D., Crosnier, C., Miura, K., Wright, G.... (2011) The blood-stage malaria antigen PfRH5 is susceptible to vaccine-inducible cross-strain neutralizing antibody. Nature Communications, 601. DOI: 10.1038/ncomms1615
- December 21, 2011
- 08:21 AM
- 291 views
School kids outshine adult commenters in thinking critically about evidence. And so what?
by Marie-Claire Shanahan in Boundary Vision
Students come out on top when their responses are compared to a comment thread from Popular Science.... Read more »
Shanahan, M.-C., de los Santos, J., & Morrow, R. (2009) Hybrid adapted primary literature: A strategy to support elementary students in reading about scientific inquiry. Alberta Science Education Journal. info:/
- December 20, 2011
- 01:04 AM
- 762 views
Who Benefits from Serious Gaming?
by Dr Shock in Dr Shock MD PhD
Buffer Multimodality or using a combination of visual, auditory, haptic,and other sensory modalities in the presentation of knowledge in serious gaming improves learning outcome. Interactivity or the communication between player and the digital gaming system in serious gaming also improves learning outcome. But these are two design elements and not psychological attributes of users of [...]
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Lee, Y., Heeter, C., Magerko, B., & Medler, B. (2011) Gaming Mindsets: Implicit Theories in Serious Game Learning. Cyberpsychology, Behavior, and Social Networking, 2147483647. DOI: 10.1089/cyber.2011.0328
Ritterfeld, U., Shen, C., Wang, H., Nocera, L., & Wong, W. (2009) Multimodality and Interactivity: Connecting Properties of Serious Games with Educational Outcomes. CyberPsychology , 12(6), 691-697. DOI: 10.1089/cpb.2009.0099
- December 18, 2011
- 08:06 AM
- 452 views
NHS research ethics procedures: a modern-day Circumlocution Office
by Dorothy Bishop in bishopblog
A discussion of the impact of research ethics and governance procedures in the UK... Read more »
Kielmann T, Tierney A, Porteous R, Huby G, Sheikh A, & Pinnock H. (2007) The Department of Health's research governance framework remains an impediment to multi-centre studies: findings from a national descriptive study. Journal of the Royal Society of Medicine, 100(5), 234-8. PMID: 17470931
- December 16, 2011
- 09:47 PM
- 3,146 views
Daily Mail misunderstand and misconstrue cannabis-schizophrenia research
by Neurobonkers in Neurobonkers
A study in to how the tabloids can misrepresent academic research.... Read more »
Kucewicz MT, Tricklebank MD, Bogacz R, & Jones MW. (2011) Dysfunctional prefrontal cortical network activity and interactions following cannabinoid receptor activation. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(43), 15560-8. PMID: 22031901
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