December 2011

Crowdsourcing biochemistry and molecular biology


Crowdsourcing is responsible for the wonderful success of Wikipedia—who would ever have predicted that volunteer editors from around the world could generate a resource that is so valuable for all of us? Another type of crowdsourcing is used by computer games that simulate protein and RNA folding. David Baker and colleagues at the University of Washington have created a competitive protein-folding game called Foldit that takes advantage of the problem-solving skills of amateurs to tackle how polypeptides fold in three dimensions (1). Scientists at Carnegie Mellon and Stanford universities have created EteRNA, a computer game that enables amateurs to design RNAs that fold well (2). If a player wins the weekly competition, his or her RNA is synthesized and then scored for how well it folds. These games make use of the power of crowdsourcing to find solutions and offers new ways of looking at problems that workers in the field may have missed.

 pres_msg_brenner  pres_msg_schekman 
 Brenner           Schekman 

Are there additional ways that biochemists could benefit from crowdsourcing? What if there was a website for biochemists to compare notes in their roles as customers regarding their experiences with journals and with vendors. For example, 2011 has been a good year for my research group in terms of paper publishing. Four original research articles made it through the evaluation process, and two more are about to be submitted. Each of these will appear in a different journal, and my experience with each journal was distinct. The manuscript-submission websites varied in terms of ease of use, clarity and time required to complete the submission; the time for review varied significantly; the quality of the reviews differed; and each paper was subject to a different level of academic editor oversight.

Scientists gossip about such differences, but what if there were a website with reviews of our experiences as “customers” of different journals? Whenever I am planning a trip to a new destination, I check out to read reviews of hotels in the city I will visit. I also contribute reviews to that site to help other travelers. Hotel managers are monitoring such sites very closely because travelers listen to the comments of other travelers. Although the online rebuttals of hotel managers sometimes seem gratuitous, managers are surely making changes at their hotels to avoid bad reviews in the future. We, as scientists, should speak out and understand that we have choices in the marketplace, and editors should care about the customer experience.

Journals need our feedback. Editors need to learn when their behavior is unacceptable. If referees are asked to provide feedback within two weeks, authors should not have to wait more than four. There are journals that send a manuscript out to four reviewers, and then the editors aren’t quite sure which of the four reviews is most important. One of my lab mottos is that I have never seen a manuscript that was not improved upon revision. That being said, four reviews are likely more than what is actually necessary, and editors have every obligation to provide timely and constructive feedback to authors.

ASBMB publishes three journals: the Journal of Biological Chemistry, Journal of Lipid Research and Molecular and Cellular Proteomics. The activities of these journals is overseen by the ASBMB Publications Committee, currently chaired by Charles Brenner of the University of Iowa. ASBMB journal editors also report to the ASBMB Council twice a year and must keep the publications committee and council members apprised of manuscript turnaround times and rates of acceptance. If you have complaints about one of our journals, the publications committee would like to hear from you.




A new type of manuscript review is coming to a new online Journal, eLife, recently established by the Max Planck Society, the Howard Hughes Medical Institute and the Wellcome Trust. With ASBMB member Randy Schekman as the new editor-in-chief, this journal will assign papers for oversight by a member of a board of reviewing editors. The editor and one or two other experts will read each manuscript, and they will then confer to merge opinions into one coherent message to the corresponding author, offering specific guidelines for one round of revision or a firm rejection on the basis of substantial criticisms of the work. The idea is to take advantage of the collective intelligence of three expert referees to provide authors with the most intelligent and rational reviews. This approach is very welcome. “It is my strong feeling that there is a need for a scientific journal at the very high end that is run by active practicing scientists embedded in an academic environment, individuals who experience both the frustrations and satisfactions of research,” says Schekman.

Faculty of 1000 
Another valuable, community-based service is provided by Faculty of 1000: Members contribute short, high-level summaries of papers they find interesting in their reading of the literature. I certainly appreciate papers being brought to my attention by colleagues in my field, and a single, weekly email summary makes it easy to stay up to date.

Scientists also need to share reviews of their vendor experiences. How many ASBMB Today readers have purchased an antibody or enzyme from a company and then discovered that it doesn’t work? There is one vendor known to members of my lab for sending out lousy antibodies, but I bet that company would be put out of business if all frustrated customers voiced their opinions on a single site. Think of how much money and time could be saved if we shared this kind of information. Let’s make use of the collective intelligence of our entire community of biochemists and crowdsource as much as possible to help each other be most successful.

  1. 1. Predicting protein structures with a multiplayer online game. Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović and Foldit players. Nature 466, 756-760 (2010).; 
  2. 2. 

Suzanne PfefferASBMB President Suzanne Pfeffer ( is a biochemistry professor at the Stanford University School of Medicine.

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