Open Access and the self-forming journal hierarchy

I recently posted a piece on Occam’ Corner explaining why I think instituting radical changes in science publishing should not be a major focus of scientists at this juncture. As those who have read the post will realize, my point is that we scientists need to band together to impress the public – and the politicians – that we are losing a generation of young scientists right now due to inadequate funding. And we may be on the verge of losing a mass of researchers from middle and senior levels as well.

But let’s be optimistic; suppose funding improves greatly over the next few years. What would I then propose?

I do support the idea that a scientist’s career should be judged by one’s contributions to science – and definitely not arbitrarily calculated by something as irrelevant as an  “impact factor.” It does not make sense to credit someone merely by their publishing in a big name journal – a “super-journal” – as the trio of Cell, Science and Nature are frequently known. Credit should be given for publishing quality science – I agree with that altogether.

However, I sense that there is a level of naivete surrounding the desire to “level the playing field.” I’d like to raise some of my concerns with certain aspects of open access publishing that worry me.

First, in the interest of full disclosure, I serve as an editor or editorial board member for 4 journals: 2 are open access (PLoS ONE since 2009 and Scientific Reports), 1 is a ‘society journal’ that belongs to the American Society for Biochemistry and Molecular Biology (Journal of Biological Chemistry) and the 4th is a new journal called Frontiers in Cell and Developmental Biology. I have every interest in seeing open access journals thrive, and I spend long hours supporting these journals.

Having made my disclosures, I will now say that the open access journals are currently in the process of setting their own hierarchies. I don’t see this as wrong or bad; it’s natural. Science is competitive, and everything science-related will ultimately be drawn into a cycle of competition. So for those who believe that their careers have been ruined or impaired by not publishing in top tier journals – news flash – open access will not change the attrition in the tenure system. Researchers may not be weeded out for not publishing in Cell/Science/Nature (and that’s a good thing), but other hierarchies will likely take their place. Perhaps more emphasis will be placed on research merit. Perhaps. One would like to hope. But a new hierarchy will ensue. It is already happening.

Every other day I receive requests to serve on editorial boards; mostly for new open access journals. Some journals – e-Life for example, have assembled editorials boards comprised of well-known scientists. These journals will attract submissions and be considered “high impact journals” – even if no ‘impact factor’ is ever calculated. Other journals will slide to the bottom of the totem pole – or already inhabit the bottom of the pond. I have seen one such journal that has a message from its editor-in-chief on its website. The message is replete with typographical mistakes, spelling errors, bad grammar and awkward language. Would anyone take a paper published in such a journal seriously? I’m sorry, but I would not.

Another fine example that highlights the complexities in the publishing world is illustrated in an e-mail request that I received yesterday to review a paper for an open access journal. With my expertise in membrane trafficking and endocytosis – the cell biology of how proteins get from point A to point B within the cell – I was shocked to find a request to review a cardiology paper dealing with electrical pulses in the mouse heart. Just to make it absolutely clear: I don’t and never have done any mouse physiology/cardiology work, and certainly have no expertise (or even much knowledge) in that area. How desperate can a journal be? How bad can the editorial process and peer review be? Pretty bad, I surmise. Unfortunately, this was not the first – or the second – such odd request to review a paper that I’ve received.

I’d also like to delve a little deeper into the issue of hierarchy – but this time examining why hierarchies tend to form, even within the “good” journals (leaving out the super-journals). Here is my personal perspective, which although true in my field, may well not reflect all others in science.

A quality science publication typically consists of one or more novel finding that advances the field. A mere collection of data – while it may well merit publication for its usefulness to others – is typically not considered the strongest form of publication. Of course if the method is new, or a huge amount of data has been compiled, such a publication may be considered more meritorious. However, generally publications that follow a ‘story’ – that develop and address a hypothesis or series of hypotheses and strive – as much as possible – to make sense of our universe – are those that are most appreciated.

In my field a simple example would be the following: if a researcher identifies (by one method or another) a new interaction between proteins – and then carefully ‘maps’ the interaction to discover how this binding occurs – that could merit a ‘no-frills’ publication. However, if the researchers are able to take the next step, and figure out the significance of that interaction – what the physiological ramifications of this interaction are – that would clearly enhance the merit of the study.

In the field of my wise and respected colleague, Dr. Stephen Curry, solving the crystal structure of a protein is often the standard for a basic publication. A study that reports solution of a complex of several proteins together, or has perhaps made predictions based on a solved structure and tested them – in the realm of structural biology such a paper would have enhanced scientific merit.

Now certainly from the examples above, if both such types of papers are published in the same journal – the more ‘basic’ and ‘deeper’ types of papers – discerning readers will realize that the latter studies (for each example) have more merit. But if there are journals with more established scientists on their editorial boards, they will be more likely to draw submissions (and accept submissions) of the latter type. Inevitably, like a self-forming gradient, journal hierarchies will arise – whether the journals are open access or not.

I don’t have a perfect solution; in fact, I’m sure there isn’t one. Those who know me understand that I am anything but a procrastinator, so my indecision on how to settle this debate is both atypical and symptomatic of the inherent complexities. I need more time to think – but during that time, I am committed to preventing the loss of another generation of scientists from our ranks. So please, let’s fight for the funding first – that’s where the consensus lies.



About Steve Caplan

I am a Professor of Biochemistry and Molecular Biology at the University of Nebraska Medical Center in Omaha, Nebraska where I mentor a group of students, postdoctoral fellows and researchers working on endocytic protein trafficking. My first lablit novel, "Matter Over Mind," is about a biomedical researcher seeking tenure and struggling to overcome the consequences of growing up with a parent suffering from bipolar disorder. Lablit novel #2, "Welcome Home, Sir," published by Anaphora Literary Press, deals with a hypochondriac principal investigator whose service in the army and post-traumatic stress disorder actually prepare him well for academic, but not personal success. Novel #3, "A Degree of Betrayal," is an academic murder mystery. "Saving One" is my most recent novel set at the National Institutes of Health. Now IN PRESS: Today's Curiosity is Tomorrow's Cure: The Case for Basic Biomedical Research (CRC PRESS, 2021). All views expressed are my own, of course--after all, I hate advertising.
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5 Responses to Open Access and the self-forming journal hierarchy

  1. Pingback: Ninth Level Ireland » Blog Archive » Open Access and the self-forming journal hierarchy

  2. Laurence Cox says:

    While I agree with what you say, this is not just a problem for scientists in academia. Over a nearly 40-year career (since completing my PhD in early 1975) as an industrial scientist in the defence industry and in government research establishments, I have seen a steady decline in the funding of science. While we could all understand the reduction in defence funding with the end of the Cold War, this is something that has continued for more than 20 years since then with defence research being squeezed between the rock of paying our troops and the hard place of defence procurement. You can find similar sentiments in this OT posting

    Academia, by its nature is a highly competitive environment where only a small proportion of PhD students will eventually achieve tenure. We need a flourishing industrial sector that can use the students who choose not to stay in academia, because it is their innovations that will produce the taxes to support the university sector. For, perhaps, twenty-five years after the end of WWII the defence sector provided this stimulus: I will quote just two examples, the Internet was created by DARPA in the USA, while liquid crystals were developed at RSRE, Malvern. This is not to suggest that these innovations would not have come about without the defence sector, just that they would have been much later and probably far slower in development.

    Looking back, it seems like the early 70’s were the turning point. In the UK this coincided with the Rothschild report. At first the decline was gradual and may not have been unhealthy, but its continuation has led to a very much attenuated industrial sector, even in those areas like pharmaceuticals where the UK is still a big player. Even usually well-informed politicians like Julian Huppert (Athene’s MP) seem to think that defence R&D can be treated as a cash-cow without any adverse effects. This is his paper:

    which apart from the criticisms I voiced is actually quite good.

    • Steve Caplan says:

      You are absolutely correct that a healthy private sector (industry) is key to the success of the system in many ways. However, I think there is an under-appreciation particularly for the basic sciences. The balance between science-leading-to-immediate applications, and science for the sake of knowledge is becoming alarmingly slanted to the former, mostly because of the ignorance of the public/politicians about how crucial basic science IS for industry and every other scientific sector. The days when Arthur Kornberg would stand and say that “without basic science, medicine becomes witchcraft” are long gone. And he was absolutely correct.

      • Laurence Cox says:

        I accept that the balance between pure and applied research is important but I do not think it is the most important factor. If you look at the start of Julian Huppert’s paper, you will see that he identifies the lack of spending by UK industry on R&D as being the major factor in not reaching the 3% of GDP target.

        Also if you look at

        specifically Figure 1.6 on Page 14 you can see that only 3.5% of PhDs end up in permanent research positions including 0.45% as Professors (full Professor in your US terminology). Doubling the funding for pure research would only increase this to 7% and 0.9% providing that there was no corresponding increase in PhD studentships. You still have 93% who will either end up in careers outside science, or in non-university research.

        I think that if you want to ensure that the best and brightest stay in academia you need to address this. More money spent by industry and government on applied research will create a demand for scientists so the person with a newly-minted PhD or with some post-doctoral experience has more alternative career paths and because of this does not have to risk so much in going down the academic path.

        Seen this way, pure and applied research are more synergistic than antagonistic and this is why I questioned your “balance” metaphor.

        Checking Wikipedia, I noted that US is at 2.7% of GDP on R&D spending, compared with 1.7% for UK, but still significantly behind both Japan (3.67%) and South Korea (3.74%). Amongst the smaller countries, Israel (4.2%), Sweden (3.3%) and Finland (3.1%) are also ahead of US. The low level of defence R&D for all except Israel probably means that you need to be spending over 4% of GDP to be comparable with Japan and South Korea.

  3. Thane Kerner says:

    First, completely agree that the development of hierarchies is inevitable and universal, and further that ‘Open Access’ as a model to fund science publishing is and will be subject to that natural ordering.

    Second, Green OA (in which funders require open access delivery either upon publication or after some specified embargo) has the potential to further erode research funding by diverting resources to develop infrastructure for delivery. (Indeed, the OSTP Public Access directive in the US explictly requires “identification of resources within the existing agency budget to implement the plan.”) In addition to the costs for new repositories, article accession and encoding, etc, that may result from Green OA mandates, new burdens are placed on researchers to jump through additional hoops to submit papers to multiple outlets.

    CHORUS ( is an initiative that seeks to leverage existing publishing infrastructure to make articles publicly accessible while avoid duplication of costs and effort. The system allows publishers to assist authors with compliance, provides public access to articles on publishers’ sites, and does so at no cost to authors, universities, governments, or other funders. CHORUS is now in an active pilot phase that demonstrates the solution with six major scientific publishers. Moreover, nearly 100 publishers have become CHORUS signatories (, including AAAS (Science), Elsevier (Cell), and the overwhelming preponderance of significant scholarly publishers worldwide.

    Some mistrust and skepticism have emanated from the more ideological quarters of the spectrum (“publishers won’t actually do it;” ‘publishers can’t be trusted;”), but allow me to propose a thought experiment. Imagine for a moment that publishers complied fully with funder mandates through CHORUS. In such a case, would it not be better–for the sake of research funding– for the research community to participate in a system that delivered access without additional resource diversion from research itself? Of course it would. Thus the energy should be directed to developing agreements and auditing systems sufficient to ensure compliance. These considerations and safeguards are a central element of the collaborative process currently being developed by CHORUS, publishers, and funders.

    CHORUS is an innovative and collaborative solution to minimize the diversion of research dollars into the publication and knowledge delivery process.

    [Full disclosure: I serve on the Board of Directors of Chor Inc., an independent 501-c-3 not-for-profit public-private partnership to increase public access to peer-reviewed publications that report on federally funded research.]

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