The arXiv is a server that hosts ‘eprints’ or ‘preprints’ of research papers, and is a key publishing platform for many fields, particularly physics and mathematics. Founded back in 1991 by Paul Ginsparg, it currently hosts over 1 million research articles, with more than 8000 submissions per month!
Despite now being in the running for 25 years, the arXiv still represents one of the greatest technological innovations to utilise the Web for scholarly communication.
While the majority of the content submitted to the arXiv is subsequently also submitted to traditional journals for publication, there is still content which never goes beyond its confines. Irrespective of this, communities engaged with the arXiv still cite articles published there, whether or not they have been formally published in a journal elsewhere.
This is the whole purpose of the arXiv: to facilitate rapid peer-to-peer communication so that science accelerates faster. The fact that all articles are publicly available is incidental, and just happens to be a topic of major interest with the growing open access movement.
However, the arXiv is not peer reviewed in the formal sense. It is moderated, so that junk submissions can be removed, or manuscripts recategorised, but it lacks the additional layer of quality control of traditional peer review.
So while some might think this poses a risk, ask yourself this question: do you re-use articles critical to your research without making sure that you have checked and understand the research to a sufficient degree that you can appropriately cite it? Because that’s peer review, that is, and it applies irrespective of whether an article has already been peer reviewed or not.
Last week, we kicked off a series interviewing some of the top ‘open scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’re bringing you another open science star, Dr. Gal Schkolnik, who recently published a really cool Collection with us on the bacterium Shewanella. Here’s her story!
Hi Gal! So can you tell us a bit about your research background, and how you originally got interested in science?
I did my BSc in Chemistry at the Tel Aviv University and my MSc at the Weizmann Institute, analyzing the chemical composition of deforestation-fire smoke from the Amazon, where farmers and corporations yearly set hectares of rainforest on fire for agriculture and pasture. For my PhD at the Technische Universitaet Berlin I measured the electric fields at protein surfaces and self-assembled monolayers. Now I’m researching Shewanella, an electroactive bacterium that can transfer electrons across its outer membrane. As you can see, I always start on a completely new field, because my greatest passion in life is acquiring knowledge – so learning something new is my favorite kind of challenge. I’m basically just a kid who never got over the “why” stage, haha. Plus I had some very inspiring teachers at school – two wonderful women who nurtured my natural tendency to go deep in pursuit of answers to the hardest questions.
People who have no access to journal subscriptions can use ScienceOpen to gain more knowledge about electroactive bacteria and their possible applications.
Last week, we kicked off a series interviewing some of the top ‘open scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’ve got something completely different, with Daniel Shanahan of BioMed Central who recently published a really cool PeerJ paper on auto-correlation and the impact factor.
Hi Daniel! To start things off, can you tell us a bit about your background?
I completed a Master’s degree in Experimental and Theoretical Physics at University of Cambridge, but must admit I did my Master’s more to have an extra year to play rugby for the university, rather than a love of micro-colloidal particles and electron lasers. I have always loved science though and found my way into STM publishing, albeit from a slightly less than traditional route.
Open science is a rapidly evolving field, with a huge diversity of actors involved. We want to highlight some of the superstars helping to spearhead the evolution of scholarly communication, who are real positive forces for change. The first of these is with Joanne Kamens PhD, who currently is the Executive Director for Addgene, a repository for the life sciences. We asked her about open science, the impact this can have on diversity in research, and the value of repositories. Here’s her story!
Hi Joanne! So can you tell us a little bit about your background to get things started?
After graduating University of Pennsylvania I went directly to graduate school in the Harvard Medical School Division of Medical Sciences where I received a PhD in genetics. For you historians, it was the first year that the Division existed allowing students to move around PIs in many departments. I defended my thesis while 6 months pregnant and had my son while still working in that lab. I had a great mentor in Dr. Roger Brent (now at the Fred Hutchinson Center in Seattle). I studied transcription using yeast and helped demonstrate that an acidic domain of the Rel protein was activating when brought in proximity to the promoter region. Again for historical perspective, PCR was invented while I was in grad school and I got to beta test the first MJ research PCR machine (M worked on my floor) which had no outsides. Roger Brent’s lab was one of the labs that created the yeast two-hybrid screening system and I have always been a lover of molecular biology technology which serves me well at Addgene.
We have new Collections coming out of our ears here at ScienceOpen! Last week, we saw two published on the bacterium Shewanella, and another on the Communication Through Coherence theory. Both should represent great platforms and resources for further research in those fields.
The latest is on the diverse field of Atomic Force Microscopy. We asked the Editor, Prof. Yang Gan, to give us a few details about why he created this Collection.
This collection is to celebrate the 30th anniversary of atomic force microscopy (AFM). March 3, 1986 saw publication of the land-marking paper “Atomic force microscope” by G. Binnig, C. G. Quate and C. Gerber (Phys Rev Lett, 56 (1986) 930-933, citations >8,800) with the motivation to invent “a new type of microscope capable of investigating surfaces of insulators on an atomic scale” with high force and dimension resolution. This can be used to measure local properties, such as height, friction, and magnetism, so has massive implications for science.
Since then, AFM has given birth to a large family of scanning probe microscopy (SPM) or SXM where X stands for near-field optical, Kelvin, magnetic, acoustic, thermal, etc. More than 100,000 journal papers, ~6,000 papers/yr since 2008, have been published if one searches the Scopus database with “atomic force microscopy” or “force microscope”. On ScienceOpen, there are over 6,000 article records if one searches using the keywords “atomic force microscopy” too. Nowadays, many disciplines — physics, chemistry, biology, materials, minerals, medicine, geology, nanotechnology, etc — all benefit greatly from using AFM as an important and even key tool for characterization, fabrication and processing.
ScienceOpen Collections are thematic groups of research articles that transcend journals and publishers to transform how we collate and build upon scientific knowledge.
What are Collections
The modern research environment is a hyper-dimensional space with a vast quantity of outputs that are impossible to manually manage. You can think of research like a giant Rubik’s cube: you have different ‘colours’ of research that you have to mix and match and play around with to discover how the different sections fit together to become something useful.
We view Collections as the individual faces of a Rubik’s cube. They draw from the vast, and often messy, pool of published research to provide an additional layer of context and clarity. They represent a new way for researchers to filter the published record to discover and curate content that is directly relevant to them, irrespective of who published it or what journal it appears in.
Advantages of Collections
Perhaps the main advantage of Collections to researchers is that they are independent of journals or publishers and their branding criteria. Researchers are undoubtedly the best-placed to assess what research is relevant to themselves and their communities. As such, we see Collections as the natural continuing transformation of the concept of the modern journal, acting in almost full cycle to return them to their basic principles.
The advantage of using Collections is that they provide researchers with the power to filter and select from the published record and create what is in essence a highly-specialised virtual journal. This means that Collections are not pre-selective, but instead comprise papers discriminated only by a single criterion: research that is relevant to your peers, and also deemed relevant by them.
Filtering for Collections occurs at different levels depending on scope or complexity of research. For example, Collections can be designed to focus on different research topics, lab groups or research groups, communities, or even departments or institutions. Collections can also be created for specific conferences and include posters from these, published on ScienceOpen. Youdefine the scope and the selection criteria.
Traditional models of peer review occur pre-publication by selected referees and are mediated by an Editor or Editorial Board. This model has been adopted by the vast majority of journals, and acts as the filter system to decide what is considered to be worthy of publication. In this traditional pre-publication model, the majority of reviews are discarded as soon as research articles become published, and all of the insight, context, and evaluation they contain are lost from the scientific record.
Several publishers and journals are now taking a more adventurous exploration of peer review that occurs subsequent to publication. The principle here is that all research deserves the opportunity to be published, and the filtering through peer review occurs subsequent to the actual communication of research articles. Numerous venues now provide inbuilt systems for post-publication peer review, including ScienceOpen, RIO, The Winnower, and F1000 Research. In addition to those adopted by journals, there are other post-publication annotation and commenting services such as hypothes.is and PubPeer that are independent of any specific journal or publisher and operate across platforms.
One main aspect of open peer review is that referee reports are made publicly available after the peer review process. The theory underlying this is that peer review becomes a supportive and collaborative process, viewed more as an ongoing dialogue between groups of scientists to progressively asses the quality of research. Furthermore, it opens up the reviews themselves to analysis and inspection, which adds an additional layer of quality control into the review process.
This co-operative and interactive mode of peer review, whereby it is treated as a conversation rather than a selection system, has been shown to be highly beneficial to researchers and authors. A study in 2011 found that when an open review system was implemented, it led to increasing co-operation between referees and authors as well as an increase in the accuracy of reviews and overall decrease of errors throughout the review process. Ultimately, it is this process which decides whether research is suitable or ready for publication. A recent study has even shown that the transparency of the peer review process can be used to predict the quality of published research. As far as we are aware, there are almost no drawbacks, documented or otherwise, to making referee reports openly available. What we gain by publishing reviews is the time, effort, knowledge exchange, and context of an enormous amount of currently secretive and largely wasted dialogue, which could also save around 15 million hours per year of otherwise lost work by researchers.
Open peer review has many different aspects, and is not simply about removing anonymity from the process. Open peer review forms part of the ongoing evolution of an open research system, and the transformation of peer review into a more constructive and collaborative process. The ultimate goal of traditional peer review remains the same – to make sure that the work of authors gets published to an acceptable standard of scientific rigour.
There are different levels of bi-directional anonymity throughout the peer review process, including whether or not the referees know who the authors are but not vice versa (single blind review), or whether both parties remain anonymous to each other (double blind review). Open peer review is a relatively new phenomenon (initiated in 1999 by the BMJ) one aspect of which is that the authors and referees names are disclosed to each other. The foundation of open peer review is based on transparency to avoid competition or conflicts born out through the fact that those who are performing peer review will often be the closest competitors to the authors, as they will tend to be the most competent to assess the research.
It’s not too hard to see that the practices of and attitudes towards ‘open science’ are evolving amidst an ongoing examination about what the modern scholarly system should look like. While we might be more familiar with the ongoing debate about how to best implement open access to research articles and to the data behind publications, discussions regarding the structure, management, and process of peer review are perhaps more nuanced, but arguably of equal or greater significance.
Peer review is of enormous importance for managing the content of the published scientific record and the careers of the scientists who produce it. It is perceived as the golden standard of scholarly publishing, and for many determines whether or not research can be viewed as scientifically valid. Accordingly, peer review is a vital component at the core of the process of research communication, with repercussions for the very structure of academia which largely operates through a publication-based reward and incentive system.