Daily Archives: March 25, 2014

I do science – not social interactions

The media likes to show scientists sometimes as the stereotypical socially incompetent dweebs. In my case that stereotype is based on real life. To keep this even a little bit professional, I will mention no names (partially, because I hope anyone involved in these scenarios does not remember) and try to describe the scenarios with scientific detachment.

This “study” consists of one test subject (N=1) and any data is anecdotal. The study subject has limited social skills. This allows us to observe a socially underdeveloped phenotype in several interactions across time and in different cultures. During the data collection period between 2004 and 2011 there was a significant shift in the test subjects level of self perceived confidence. This results in shift of the data quality towards the end of the time period. The data points are recorded when test subject detects self-stupidity and/or unintended hilarity from surrounding individuals. The data are divided to three categories: 1) interactions with the opposite sex, 2) linguistic mishaps, and 3) workplace related interactions. These categories produced the most significant data points and provide a representative sample of the test subjects social interactions.

Stupidity2004to2011Category 1 data points are concentrated to the beginning of collection period. An example of mild case of embarrassment can occur due to lack of planning. The subject was engaged in a verbal interaction with a representative of the opposite sex. The need to leave the interaction increased and the classic phrase “Oh, look at the time! I have to go” was employed. Unfortunately the necessary prop, wrist watch, was not present.

Lack of foresight can also affect promising conversations. While deep hate towards accordion music is a topic close to test subjects heart, the enthusiastic description of it has to be reserved for select audiences. As a first conversation with the opposite sex the risk of the object to love harmonica is unknown. The risk reached 100% in a club, when conversing unknowingly with a harmonica enthusiast with 10 years of playing the damn instrument.

The situation could be alleviated by inserting a filter between brain and mouth. This could also alleviate the more subtle mishaps including over sharing. In an example situation the subject requested the use of a chap stick from a love interest. The inquiry “is it okay if it has already been used?” should not have been answered with “I have never cared that much about hygiene”.

 Category 2 data, linguistic mishaps, is sparse due to data collection being biased. Loss of minor events is inevitable when the subject is unaware of any mistakes made. Dealing with English grammar and finding correct words on the spot requires skill and attention span unfamiliar to the subject. Replacing a word with another of similar meaning would be fine, if the meaning and spirit of the communication is retained. Practical applications of this are tricky. Substituting vasectomy with castration even in casual conversation is frowned upon.

Category 3 data concentrates to time period between 2009 and 2011. The collection of data is on going and offers opportunities for future analysis. Work place architecture can give false sense of security from social interactions. It should be kept in mind that after the fast elevator’s doors open you need a good explanation as to why you were holding your arm up like a superman. The chance that someone is waiting for the elevator can approach 100% between 6am and 6pm.  Another obstacle for solitary existence in workplace includes shared office space. One has to navigate a minefield of social niceties and be careful of verbal output. When a new co-worker asks if your hobbies include riding, do not answer “What? Do you mean with a horse?”. The mental pictures projected to surrounding audience will be highly inappropriate.

In conclusion, the quality of self reported stupidity changes in time. Severity of cases varies considerably even within categories. More data is constantly collected and increased number of test subjects could provide a more representative picture of social in-adeptness. Highly controlled human studies are not possible at the level I would like to conduct them. Apparently use of human subjects in long term confinement from birth is frowned upon.


Open access to disease and other research – PLoS Pathogens

The appearance of open access journals is something I personally applaud. Having current research available for everyone with internet connection and understanding of English language, seems fair as some of the research is supported by tax money. This was also pointed out in Richard Van Noorden’s article “The true cost of science publishing” in Nature (2013) (1). To my mind it highlights, that my research is accountable to the general public instead of just my peers. Paying for my research to be distributed widely instead of to only the ones with access to high impact scholarly papers seems like a responsible thing to do.



PLoS is perhaps the most widely known open-access journal family with a good reputation. It concentrates on biological and life sciences. It has a very appealing web interface and is indexed in all the major archives we use in biological research to find articles like PubMed, MEDLINE, Web of Science, and Scopus.



PLoS stands for US Public Library of Science. The online journals of PLoS family include PLoS ONE, PLoS Biology, PLoS Medicine, PLoS Computational Biology, PLoS Currents, PLoS Genetics, PLoS Pathogens, and PLoS Neglected Tropical Diseases. I will concentrate on the PLoS Pathogens for now to illustrate the PLoS family of journals. PLoS is a non-profit organization. In 2001 it announced to start publishing electronic open-access journals, after an attempt to persuade other publishers to release their journals for the public for free after a delay (2-6 months post first publication of the issue) (2). The goal of PLoS is to provide the public access to research, not depending on financial resources. PLoS Pathogens has been published as a separate journal since 2005, as evident from the journal’s archives.

Scope of PLoS Pathogens include research on bacteria, fungi, parasites, prion, and virus related diseases which impact medical, and agricultural fields, and economies everywhere. The study of this microbial world gives insights into basic functions of cells and organisms, expanding basic science knowledge. Due to the impact of pathogens in everyday life, I find it appropriate that this publication is open-access. A separate issue arises to enhance the general public’s understanding of these scientific texts. Should we have a separate abstract to the public outlining the results? Or should scientific community present their information more aggressively in other mediums like blogs, tweets, and forums?


Notice the easy access tabs to metrics and comments, and subject areas tags. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003959

PLoS Pathogens, like all PLoS journals, adhere to Creative Commons Attribution license (CC BY). This means that authors still own their research, but anyone can copy, modify, reuse and reprint the articles as long as the researchers are cited. You don’t have to ask for publishers or authors permission. This seems fair compared to the publisher obtaining the rights to the work. Taylor however in his article in Scripted- A Journal of Law, Technology and Society, calls for a balance between the copyright practices (3). He points out, that the copyright is mostly on the side of the author. His point of view also includes the academic publishing done in book form, which to me is a whole different animal compared to publishing in research journals.

PLoS Pathogens has the impact factor of 8.14. Compared to non-open-access journals with long history and high prestige like Nature Immunology’s 26.2, or Cell Host and Microbe’s 12.6, it seems a bit low. When comparing to other open access journals like BMC Immunology’s 2.61 it is rather good.  However impact factor is not the best statistic to evaluate a journal. To me the width of the scope a journal presents affects my appreciation of the journal. Ones that take in articles from varied fields of research tend to select articles that have the  WOW-factor. Journals specializing to a topic seem to take in articles, that don’t necessarily have the WOW-factor, but are important in bridging the research to that future WOW! moment.

Part of Jorge Cham's PhD comic about rivalry between Nature and Science magazines. http://www.phdcomics.com/comics/archive.php?comicid=1200

Part of Jorge Cham’s PhD comic about rivalry between Nature and Science magazines. http://www.phdcomics.com/comics/archive.php?comicid=1200

The following quote from Van Noorden (1) shows the opposition from subscription journal publishers.

“The costs of research publishing can be much lower than people think,” agrees Peter Binfield, co-founder of one of the newest open-access journals, PeerJ, and formerly a publisher at PLoS. But publishers of subscription journals insist that such views are misguided — born of a failure to appreciate the value they add to the papers they publish, and to the research community as a whole. They say that their commercial operations are in fact quite efficient, so that if a switch to open-access publishing led scientists to drive down fees by choosing cheaper journals, it would undermine important values such as editorial quality.

Maybe I don’t know enough about the publishing industry, but to me the extra value gained from editorial quality is not clear. The open-access journals, like PLoS Pathogens, use peer-review and have very nice e-publication formats. The publishing in them is less expensive too, and the research can be seen by more people than the subscription based publications. Does anyone know exactly what the editorial quality refers to? I would really like to know what extra value I would get compared to open-access.


1. Van Noorden, R. 2013. Open access: The true cost of science publishing. Nature 495:426-9. http://www.nature.com/news/open-access-the-true-cost-of-science-publishing-1.12676

2. Vicki Brower, 2001. Public library of science shifts gears. EMBO reports. Nov 15, 2001; 2(11): 972–973.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1084138/

3. K Taylor, “Copyright and research: an academic publisher’s perspective”, (2007) 4:2 SCRIPTed 233 < http://www.law.ed.ac.uk/ahrc/script-ed/vol4-2/taylor.asp >