In this article I dig a little into the world of preprints. I use the field of mathematics to explore how an inclusive view of preprints and published articles leads to a research ecosystem that is greater than the sum of the parts.

So much of our world is divided by identity. Politics, people, beliefs — even scholarly publishing! I see deep divisions among us. There are some who cling to the notion that traditional journals are the only way to publish. These traditionalists see no need to look further afield to alternative expressions of intellectual thought. Others are exploring new models around preprints and peer review, especially in the life and biomedical sciences. And even others believe that the journal article and the journal itself are irrelevant to the future of open science.

It seems each camp is in deep and engaged discussion of their future, but failing to pause and consider a more holistic view of what a publishing ecosystem may look like. And yet the need to focus on a culture of research integrity is something all, at least in principle, can agree on, so why the discord? In essence it boils down to a deep distrust of the for-profit motive, pitted against the ideals of science. While it is certainly true that a for-profit view of science is only one perspective, it is also true that without that, scientific research and the publication of research would not be a successful endeavor. And then again, science should be open and collaborative without the need to consider projected financial gain.

Writing this piece was triggered by reading a recent Scholarly Kitchen article, entitled “Preprints Serve the Anti-science Agenda – This is Why We Need Peer Review” by David Green. I bristled at comments such as:

“Yes – there are benefits to more freely and quickly sharing science. But preprints join predatory publishers and paper mills to fuel a growing challenge for our society: distinguishing credible science from inaccurate, biased, and misleading work. This is encouraging a race to the bottom, where good science can carry the same weight as bad science, ‘alternative facts,’ and ‘truthiness’ – which is actually no weight at all.”

To me, this reaction to preprints is symptomatic of the seductive nature of a culture of identity, one that almost denies the benefit of a part of the publishing ecosystem that is clearly important and essential to scientific research collaboration.

On the other side of the coin I also recently read through a fascinating  workshop report that I came across from the ICOR organization (Incentivizing Collaborative and Open Research). A public meeting, entitled New Paradigms in research Communication – Continuing the Discussion led to a report demonstrating how truly remarkable creative thinking around open research and communication can be, yet excluding some potentially difficult voices that need to be heard. Without going into too much detail (better you read the report yourself) the participants of the workshop

“…gathered at HHMI’s Janelia Research Campus in late 2024 to discuss principles and visions for the future of open science communication, moving from abstract ideas and existing one-off experiments toward a holistic model of research communication that promotes robust science and aligns the incentives of scientists, institutions, and funders. This is a daunting task, but this group is optimistic that the time is right, that scientists and funders are ready for a new paradigm, and that there are many opportunities to facilitate convergence of current and future open science initiatives and to work toward a science communication environment that strengthens and accelerates science.”

The 41 participants focused on the future, rather than dwelling on current issues, and creative minds headed towards an agreement that

“…science would benefit from publication of scientific results in an integrated research ‘container’ and ‘environment’ that facilitates both more complete reporting of scientific information and a post-publication ecosystem for reviewing, summarizing, synthesizing, and interpreting scientific results.”

I was struck by the inventiveness and creativity here. I was also struck that some stakeholders were absent from the conversation — for example scholarly societies.

I would love to see such discussions be more inclusive and open to incorporating diverse voices – even those that may not all be on the same page.

I do worry. There is somewhat of a nihilistic view of the academic publishing landscape depending on where you sit in the community. We should recognize that ideals are essential, and that business, in both a non-profit and for-profit context, is not the enemy. The enemy is paralysis of thinking.  Perhaps we can recognize we have more in common than not and build our future together?

How do we start? Well, funny you should ask. Let’s take a look at the field of mathematics.

A mathematician will write a paper and share it on the arXiv, often at the same time they submit it to a journal. The arXiv post can immediately spark a conversation with others in their field that could have many different outcomes: improvements, new collaborations, identification of duplication, etc. This may result in the posting of new versions or sometimes retraction. All of this runs in parallel to the journal’s refereeing process. So there is a public vs private discourse aspect, which I would say is part of the culture of being a mathematician. Some mathematics publishers, including the American Mathematical Society (AMS), allow the author accepted manuscript to be posted on the arXiv as the final version; others only allow it after an embargo.

I turned to Ramin Zabih, Professor of Computer Science at Cornell and Executive Director of arXiv, and to Steinn Sigurdsson, Professor of Astrophysics at Penn State University and Scientific Director of arXiv, for their insights.

Ramin pointed out, that  in computer science, content is posted on arXiv at all points; before and during peer review, after acceptance etc.. Most of this work derives from a conference presentation. Ramin and Steinn also noted that one of the main reasons arXiv has been able to live in a happy coexistence with researchers, funders, societies and publishers is that it has never been at the mercy of the for-profit motive and the for-profit publishers. While arXiv is housed at Cornell, in practice it operates independently as worldwide resource. Ramin suggests that the cultural impact of a preprint in mathematics is very different from that seen in a biomedical context.

To elaborate; in math, the preprint exists in publishing spectrum.  The sum of the accumulated work builds confidence in a body of research and provides a coherent picture for promotion and tenure discussions. In math, peer review is often a slow and rigorous process – how else may a mathematician review a 70-page proof? The process and output build confidence. Peer review is left to the journal, but the build-up of versions on arXiv mean that there is often little difference between the final published paper and what sits on arXiv. The journals remain highly respected and regarded and arXiv is seen as an essential tool in a continuum of scientific expression. Indeed, is there a mathematician that does not receive a daily feed of relevant preprints to read from arXiv?

We should touch on preprints and AI. There is no question that preprints on arXiv are being ingested into LLMs. There may be ways for AI generated papers to skate past arXiv monitoring – although these threats apply to journal publishers also. It is wrong to think that journal article peer review will protect against fraud. Instead, perhaps the way to combat fraud in mathematics for example is to build trust among researchers at all stages of the publishing life cycle so that by the time the final article is published, the work is understood and its origins verified – thus establishing the value of arXiv as a way to establish provenance.

From Ramin’s perspective the future is bright for arXiv, and it is bright largely because of its essential place in the ecosystem of research in math, computer science and physics and the many other fields arXiv serves.

Where does this leave us?

From my perspective, running publishing at the AMS, researchers, funders, institutions and libraries, scholarly societies and publishers have more in common than set them apart. All care deeply about research integrity, the future health of science and the value of a research community. Perhaps all disciplines can look at the world of mathematics for inspiration on how the community’s coherent ecosystem generates more than the sum of the parts.