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Metabolism

The central engine of a laboratory is, unsurprisingly, research. Regardless of whether or not producing new knowledge is the direct objective of lab², research is the means to all of its ends. Much like an organism's metabolism, research consists of a complex network of interacting elements being progressively transformed, refined, and transported in different ways according to purpose. Establishing how knowledge is produced and communicated is a central part of lab²'s vision of science.

Incentives

There is no single right way of doing research, and valuable work has been done both in private, for-profit labs, public institutions, and everything in between. That being said, academic research is a truly unique system in that researchers are paid salaries for the act of researching, not for delivering its products (at least for the most part). Critics argue (often correctly) this is part of the reason why research tends to move at a faster pace in industry, but this model offers three key benefits, at least in principle.

1. It grants researchers freedom to explore fields and areas that may not be in high demand by the market, areas benefiting populations that cannot influence the market, or areas that may not be directly applicable at all at this time.
2. It allows researchers to more meticulously review and confirm their results.
3. It allows the products of research to be made publicly available to all, as argued by Peter Suber.

Industry may in fact advance at a faster pace, but it would have far more ground to cover were it not for the groundwork of generations of academic scientists making knowledge available to all. In addition, making knowledge publicly available is particularly valuable for those researchers working outside the world's central research hubs: in the academic and geographic periphery, first-hand, in-person expertise in a given specialized technique or area of knowledge can be hard to come by. In this regard (though possibly not others), academia acts as a de-centralizing force by democratizing knowledge. Thus, the benefits of academic research are valuable and we must endeavor to protect them.

On the other hand, accelerating the pace of science and ensuring public funds are being used efficiently are desirable objectives as well. For reasons like these, academic institutions condition career progression upon research output (hopefully among other things, as academic researchers often wear many hats). This places researchers under pressure to maintain a certain pace of research and publication, something science should strive for anyway. Unfortunately, it also results in certain disadvantages. For starters, pressuring academic output undermines to some degree the second benefit of the academic model outlined above, resulting in potentially lower quality research being published. Furthermore, it increases pressure to publish high-impact research that is likely to cause a stir, which often results in bottling up significant amounts of effort until enough has been accumulated to be able to publish in a prestigious journal. This results in research groups competing and racing against each other to publish the same large body of work. Bottling up research runs contrary to the natural, gradual course of scientific procedure. By making research advances available to all in a more timely manner, efforts can be pooled, more actors can be involved, and science can move more rapidly and efficiently.

Research

The Internet allows instantaneous, nearly cost-free sharing of information, something unthinkable in the early days of modern science. To stay true to the fundamental goals of academic research and maximize the benefits it offers, lab² conducts research in a completely transparent way, taking advantage of the platform offered by web technologies. The lab's ongoing research and methodologies are made available and updated in real time on the lab website. Similar ideas have been put forth before as part of the open-notebook science movement, first proposed by Jean-Claude Bradley in 2006. Multiple people have contributed their thoughts to the idea over the past years, as reviewed here.

Research webs using lab2web

One possible way of presenting research live is using an interactive mental map scheme such as the one shown below (may require updated browsers):

Try zooming, dragging, and clicking!
Made using lab2web.

To make these kinds of mental maps using a plug-and-play standard input file, check out lab2web.

Nodes on the map contain lines of research in the lab, with text color denoting research hypotheses or methodological/technology development. The color of a node denotes a hypothesis or technology's status as supported by evidence, disproven, or lacking enough evidence for a conclusion. Finally the border type signals a node's status as archived, current, or future line of research. Clicking on a node can present the evidence for or against the hypothesis or technology according to the lab's research, and link directly to the data and methods, protocols, and code used to acquire and analyze it. Data, protocols, and code are stored on a public, version-controlled repository such as GitHub, which allows easy tracking of where and when changes were made. Nodes are connected by directed edges, symbolizing logical or procedural dependence between different hypotheses and technologies. Highly connected clusters of nodes can signal a unit publishable as a research article. The Open Knowledge Maps project works with similar (and more developed) approach to representing information and research.

Clearly, science as a whole would benefit from open research practices such as these: other labs anywhere in the world could learn from the techniques and guide their own research questions according to recent, unpublished findings (with the caveat that they remain preliminary unless stated otherwise). However, lab² operates on the hypothesis that transparency in research also benefits the individual lab practicing it. Concretely, the lab² believes that clear signaling of research intentions and progress results in more collaboration, faster independent confirmation of good data, and more frequent correction of flawed data than it will result in "scooping", or other researchers taking promising research directions on their own and independently publishing the results in a peer-reviewed journal before lab² does. Of course, as with everything else in lab², this is a hypothesis that needs empirical testing. However, the success of preprinting, first in physics and now in many other branches of science, shows that similar practices can not only allow research to thrive and flourish, but coexist with current practices and structures of research, funding, and publishing. Given the spread of preprints, journal concerns about prior publication conflicts should also be lessened.

Publishing

Making the small steps of research public instead of bottling them up to make for a massive release can bring much good to science. Nevertheless, this is not to say that publishing large collections of work is redundant or unnecessary: review articles are invaluable resources that collect and curate the advances in a field and condense the evidence and status of higher-order models and theories. This also does not mean that journal research articles should be done away with: writing and submitting a research article constitutes a benchmark for what the authors consider to be sufficiently confirmed knowledge, and publishing in a journal signals that other researchers agree, through peer review. Both benchmarks and peer review are important aspects of research practice, and although neither one strictly requires a journal, journals provide useful venues to implement them in. Moreover, journals are valuable assets when they fulfill their original purpose: contributing to effective communication of science. Science is like advertising, as is said by Stevan Harnad (paraphrased by Peter Suber): you get paid to make your work, not sell it, and then offer it to the widest possible audience for free. Scientific publishers, when doing their job right, can help advertise your work in this way. Unfortunately, the job is often not done right, and structural changes at the policy level are long overdue to correct this.

Nevertheless, there is much that can be done–and is in fact done–at the level of individual researchers. The logical way of publishing to a wide audience is removing paywalls and other barriers of access. At lab², making completed research available through open access publishing is fundamental. More and more publishers, funders, and authors have joined the ranks of the open access movement one way or another, although the road to achieving this has certainly not been a smooth one. As others have explained, publishing in natively open journals ("gold" open access) and publishing parallel, archived copies of pre- and post-print research ("green" open access) are both perfectly legal and highly helpful practices that can coexist and complement one another. Repositories such as arXiv, biorXiv, medrXiv, psyArXiv, and many others have taken the scientific world by storm, with clear benefits for both the authors and their readers. Others have taken to publishing their work on other repositories, such as Github. It is important to underscore that this preprint ecosystem not only coexists but synergizes with established scientific journals. Once again, this is not to say they are indispensable: perhaps widespread implementation of real-time publishing strategies like the one discussed above, coupled with rolling peer review, will eventually lead to a fundamental shift in what a journal is and what it does. Established science funders such as the Wellcome Trust are experimenting with these ideas in publishing. The merits and myths behind these proposals continue to be discussed by multiple authors. But it is both encouraging and reassuring that we do not need to burn the current system to the ground before we implement a new one. These kinds of shifts in the role of scientific publishers have already happened organically in the past, with both the arrival of peer review to publishing in the seventies (much more recently than many people realize) and with the publication and media revolution that has been brought about by the Internet, online databases, and search engines.

Leaving a door unlocked certainly allows more people to walk through it, but it does not really mean more people will. One must also show people to the door and help them through it if necessary. Communicating science, both within science itself and to actors tangential to it, is an active affair. Engaging audiences at conferences, via email, and even through social media can help advertise the lab's research. Social media such as Science Twitter has provided a platform for circulating interesting work, troubleshooting methods with original authors, catching mistakes, and improving science at a rapid pace. Newer, specialized platforms are emerging, catered to researchers, specifically. Breaking down other barriers of access, including political censoring and the digital divide, is just as important, and lab² can contribute to these in different ways. Science is set in motion if knowledge is used, and knowledge must be actively made available to all to be truly known.