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  • January 14, 2012
  • 10:42 PM
  • 1,159 views

When Satire Becomes Reality

by Neurobonkers in Neurobonkers

On Friday political satirist Stephen Colbert entered the U.S. presidential race. A significant proportion of Conservatives in fact fail to understand satire and instead believe Colbert to be a Conservative commentator opposed to liberal thought.... Read more »

RAMSAY, C., KULL, S., LEWIS, E., & SUBIA, S. (2010) Misinformation and the 2010 Election. Published online at WORLDPUBLICOPINION.ORG by University of Maryland. info:/

  • January 14, 2012
  • 04:32 AM
  • 1,038 views

26 reasons not to trust what you read in the newspaper

by Stuart Farrimond in Dr Stu's Science Blog

So we all know we shouldn’t believe everything we read. Tabloids and science have never been the best of bed fellows (or should that be tabloids and the truth?). But just how widespread is fallacious newspaper reporting? An intriguing little investigation from University College Chester made an attempt to measure the terribleness (or not) of … Continue reading »... Read more »

  • January 12, 2012
  • 08:00 AM
  • 1,056 views

Error bars

by Zen Faulkes in Better Posters

Comparing averages should be one of the easiest kinds of information to show, but they are surprisingly tricky.Most people know that when they show an average, there should be an indication of how much smear there is in the data. It makes a huge difference to your interpretation of the information, particularly when glancing at the figure.For instance, I’m willing to bet most people looking at this...Would say, “Wow, the treatment is making a big difference compared to the control!”I’m likewise willing to bet most people looking at this (which plots the same averages)...Would say, “There’s so much overlap in the data, there’s might not be any real difference between the control and the treatments.”The problem is that error bars can represent at least three different measurements (Cumming et al. 2007).Standard deviationStandard errorConfidence intervalSadly, there is no convention for which of the three one should add to a graph. There is no graphical convention to distinguish these three values, either. Here’s a nice example of how different these three measures look (Figure 4 from Cumming et al. 2007), and how they change with sample size:I often see graphs with no indication of which of those three things the error bars are showing! And the moral of the story is: Identify your error bars! Put in the Y axis or in the caption for the graph.ReferenceCumming G, Fidler F, Vaux D 2007. Error bars in experimental biology The Journal of Cell Biology 177(1): 7-11. DOI: 10.1083/jcb.200611141A different problem with error bars is here.... Read more »

Cumming G, Fidler F, & Vaux D. (2007) Error bars in experimental biology. The Journal of Cell Biology, 177(1), 7-11. DOI: 10.1083/jcb.200611141  

  • January 11, 2012
  • 01:37 AM
  • 1,038 views

Recruiting study participants through Facebook

by Dr Shock in Dr Shock MD PhD

Buffer Read an interesting article about this subject. Interesting not in the sense of costs or efficacy but mostly on how they did it. It’s done for an epidemiological study on a mother child cohort. They wanted to include pregnant women for their study with facebook beside other forms of recruitment such as: active collaboration [...]
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Richiardi, L., Pivetta, E., & Merletti, F. (2012) Recruiting Study Participants Through Facebook. Epidemiology, 23(1), 175. DOI: 10.1097/EDE.0b013e31823b5ee4  

  • January 9, 2012
  • 05:51 PM
  • 655 views

ESA still not supporting open access

by Zen Faulkes in NeuroDojo


The Ecological Society of America drew attention to itself last week for a statement regarding open access for scientific publication. Jonathan Eisen covered it here.

I posted the link to Eisen’s post this on ESA’s Facebook page, and today, there was this comment:

ESA’s recent letter in response to OSTP’s Request for Information has generated discussion in the social media realm. This is perhaps a good example of the inherent conflict between the interests of those who believe research publications should make their content freely available to all and the reality that there are significant costs associated with publishing scholarly research journals. This topic will continue to be one with which the scientific community must grapple and one that will continue to evolve.
My response was that they seemed to be confusing “access” with “profit.” PLoS ONE has proved that open access journals can be profitable. Other publishers (Brill; see here) have recognized this.

If journals are worried about losing their subscriptions, I suggest this: Keep the technical articles free and print other, original content that people will pay for.

For instance, let’s go back the the journal Science, which I suggested would be a good target to convert open access. Only a small fraction of the original technical articles in Science are going to be relevant to any particular reader. As it stands, a subscriber to Science is getting a lot of non-targeted articles that are irrelevant to them.

What Science has been really good at is providing news and commentary. That is much more widely relevant to a broader spectrum of readers. I think if all the technical articles were still free, people would probably still be willing to pay money for all the other original writing. The conference reports, the policy analysis, and so on. That original work by professional writers is something that people realize should not be free. At least, the arguments for making it free are different than the usual ones used to justify open access, that is that publicly funded scientists are doing all of the intellectual work.

But oddly, the tendency for general journals has been to do the exact opposite. Journals have tended to make a few of their comments freely available, while locking down all the original science.

So, ESA, if you want people to stay members of your society, to give them reasons to do so besides original journal articles. I doubt it’s the main reason that most people join scientific societies. In fact, ESA, you yourself have surveyed why people joined your society.

The number one reason given in a membership survey for joining ESA was, “Supporting the field of ecology.” For young members, under the age of 35, “opportunities to present or publish my work” was third in the last but that's difficult to interpret because it includes presenting at conferences and not just the journals. Regardless, it's not just for the journals you publish.

When they asked lapsed members what might make them rejoin the society, the three main reasons were for information and career development. These were things that require more than just original journal articles. For example, the first item on the list was, “Help me stay abreast of developments in my field.” Sure, that is something that is partly about original research, but good original analysis and news reporting would also seem to be valuable to members. So why not give it to them?

Reference

ESA. 2012. ESA membership survey, February 2011 summary of results Bulletin of the Ecological Society of America 93(1): 13-23. DOI: 10.1890/0012-9623-93.1.13... Read more »

  • January 9, 2012
  • 01:35 AM
  • 1,016 views

Patient Safety in Medical Education

by Dr Shock in Dr Shock MD PhD

Buffer When searching in pubmed for the two mesh terms “patient safety” and “medical education” results in 8 hits. Some research articles and editorials. One quote with literature reference about the extend of the problem is: Our health care system today has an adverse event rate approximately equal to that of driving an automobile putting [...]
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Wagner, D., Noel, M., Barry, H., & Reznich, C. (2011) Safe Expectations. Academic Medicine, 86(11). DOI: 10.1097/ACM.0b013e3182327c81  

  • January 6, 2012
  • 08:00 AM
  • 905 views

Questioning Permanence: Would You Get a QR Code Tattoo?

by Krystal D'Costa in Anthropology in Practice

Are you inked? I’m not, though I’ve thought about it seriously and have a pretty good idea of what I would get and where I would put it—if I could work up the nerve to get in the chair. I’ll tell you one thing: It most certainly is not a QR code like Fred Bosch, who [...]









... Read more »

Dye, I. (1989) The tattoos of Early American Seafarers, 1796-1818. Proceedings of the American Philosophical Society, 133(4), 520-554. info:/

Schildkrout, E. (2004) Inscribing the Body. Annual Review of Anthropology, 33(1), 319-344. DOI: 10.1146/annurev.anthro.33.070203.143947  

  • January 6, 2012
  • 05:51 AM
  • 818 views

Are Bible-bashers scientifically stupid?

by Stuart Farrimond in Dr Stu's Science Blog

It never used to be like this. Sir Isaac Newton, one of the influential scientists to grace the Earth would be horrified. An outspoken Bible-believer, Newton believed that his observations of the Universe made the existence of God irrefutable. How times change. ‘New Atheism’ is the increasingly popular movement within top science thinkers. Its advocates say … Continue reading »... Read more »

  • January 4, 2012
  • 09:39 PM
  • 1,184 views

A Walkthrough To Find Credible Souces and Answers to the Controversies of Vaccines, Evolution, Holocaust, and Global Warming

by DJ Busby in Astronasty

Where do you get your facts?
Hopefully, a reliable source.
So what's an online reliable source, and how can a regular Joe get a hold of this information?

A very easy way to be confident is to make sure that you're reading from an .edu or .gov page. One of the easiest (and quickest) ways to find your topic is through the citations on Wikipedia. Some people doubt the validity of Wikipedia in fear of hecklers. The nature or self-maintaining issue of Wikipedia aside, the citations at the bottom are a real treasure trove.
... Read more »

Bonhoeffer J, & Heininger U. (2007) Adverse events following immunization: perception and evidence. Current opinion in infectious diseases, 20(3), 237-46. PMID: 17471032  

Demicheli V, Jefferson T, Rivetti A, & Price D. (2005) Vaccines for measles, mumps and rubella in children. Cochrane database of systematic reviews (Online). PMID: 16235361  

Committee on Revising Science and Creationism: A View from the National Academy of Sciences, National Academy of Sciences and Institute of Medicine of the National Academies. (2008) Science, Evolution, and Creationism. The National Academies Press. info:/9780309105866

  • January 4, 2012
  • 08:22 PM
  • 1,002 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 »

  • January 4, 2012
  • 03:36 PM
  • 502 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
  • 474 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 »

  • January 2, 2012
  • 07:37 AM
  • 650 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 »

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
  • 1,101 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 [...]
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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
  • 640 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 »

  • January 1, 2012
  • 09:41 AM
  • 938 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
  • 1,049 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 »

  • December 30, 2011
  • 08:04 AM
  • 463 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
  • 527 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 »

  • December 27, 2011
  • 11:00 AM
  • 752 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:/

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