Notes on Engineering Health, February 2024: Notes on Academic Publishing

In 1936, Albert Einstein submitted for publication an article on gravitational waves in the Physical Review, a prominent North American physics journal. After he received a negative critique from the peer review process (his only paper to go through this gauntlet), he became so upset that he withdrew the article from the journal and published it in the Journal of the Franklin Institute in Philadelphia instead.

From Einstein’s time (1940s), the scientific publishing industry rapidly evolved to clarify its essential missions: register, certify, disseminate, and preserve the scholarly record through the production of what has come to be known as “the version of record” (the final published version of an article). Scientific publications have been the lingua franca of scientific discovery and knowledge, the edifice on which trust is built. The level of trust researchers can place in the scientific literature and, ultimately, the public’s trust in science are at stake. To understand how academic publishing got to the structure we know today and think of ways to improve it, it is helpful to understand the story of scholarly publishing, the technological advances that occurred along the way, and the forces and incentives that shape current behaviors and challenges.

The Early Days
The inception of academic publishing can be traced back to the 17th century with the establishment of the first scientific journals, such as the "Journal des sçavans" in France (1665) and the "Philosophical Transactions of the Royal Society" in England (1665), now the longest-running academic journal. These publications began a formal process for disseminating research findings to a broader audience. Before this, scholarly works were primarily shared through private letters, pamphlets,, and public lectures. These first publications were run by scientific societies, such as The Royal Society, with no intention to turn a profit on them but solely to advance knowledge through an open exchange of ideas.


The Expansion
Although the publishing of academic journals started in the 17th century, it expanded greatly in the 19th. The expansion of the printing press and other technological advances promoted both an explosion of scientific discoveries and a way to share them with the world and communicate their importance. It also had the surprising effect of reducing disputes over who was first to discovery. During the 19th and 20th centuries, the journals went through more and more specialization, creating separate tracks for mathematics, physics and chemistry, biological sciences (botany, physiology, zoology), etc.


The Modern Journal
There are currently more than 30,000 academic journals, and the number continues to increase by about 5% per year. In the last few years, on average more than 5 million scientific articles have been published annually, including short surveys, reviews, and conference proceedings.

In the middle of the 20th century three key practices arose that have defined the modern scientific publication:

1. IMRaD
Until 1945, articles were organized more like book chapters, mainly with internal headings associated with the subject. They did not follow the current standard structure of Introduction, Method, Results, and Discussion (or IMRaD):

Introduction
Why was the study undertaken? What was the research question, the tested hypothesis, or the purpose of the research?

Methods
When, where, and how was the study done? What materials were used, or who was included in the study groups (patients, etc.)? This section should allow other scientists to reproduce the results described in the following section.

Results
What answer to the research question was found? What did the study find? Was the tested hypothesis true?

Discussion
What might the answer imply and why does it matter? How does it fit in with what other researchers have found? What are the perspectives for future research?

The IMRaD structure was partially adopted in the 1950s and 60s, it became widespread after 1965, and ubiquitous in the 1980s.

This structure fulfilled multiple needs of the time. First, it focused scientific articles around only one or two critical hypotheses being tested. Second, with all publications primarily accessed in print form, space constraints demand an efficient structure and layout. Finally, because of the exploding number of publications, scientists were needed to decrease the time spent reviewing each article and to efficiently find the specific aspect of research for which they were looking.

2. Peer review
The introduction of peer review has been popularly attributed to the Royal Society of Edinburg, which compiled a collection of articles that had undergone peer review in 1731. By the 1960s, peer review was becoming widely-accepted; and is now a standard metric of scientific productivity (for the researchers) and validity (for the study).

Peer review means that a manuscript submitted to a journal will be reviewed by other (typically two or three) experts in the field (peers) to assess the paper before recommending publication.  In most cases, peer reviews are blind, in which reviewers and authors are anonymous to each other. Peer review was built as an important check-and-balance mechanism in scholarly publishing, ensuring that academic standards are met and published academic research is of high quality.

3. Impact factor
Another major aspect of scientific publishing changed in the middle of the 20th century with the introduction of the journal impact factor. It was created in the early 1960s by Eugene Garfield, the founder of the Institute for Scientific Information (ISI), which would morph into Clarivate, to help select a group of highly cited journals for the Science Citation Index. The journal impact factor was designed for only one purpose—to compare the citation impact of one journal with other journals regardless of their size.

A journal’s impact factor is an average based on two factors: (1) the number of citations in the current year of any article published in the journal in the previous two years, over (2) the number of articles in the last two years.
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While initially intended to help libraries decide which journals to purchase, the impact factor soon became a key metric for assessing the quality of research and the prestige of researchers and their institutions. As such, it became an essential tool for determining the quality of candidates for academic positions.

Since the middle of the 20th century, publishers have fulfilled their missions—registering, certifying, disseminating, and preserving the scientific record—without much challenge. They have become the orchestrators of scientific dissemination, sitting between scientists, reviewers, and readers. This central position has allowed the publishing houses to amass pricing power over scientists seeking to publish their research and over readers kept from freely accessing the literature by expensive paywalls. Large publishers have used their position to enjoy record revenues and profits.


The Internet and Decentralized Access
The supremacy of the publishers has come under heavy criticism, and the 21st century is perhaps set to see a new chapter in the history of academic publishing due to a confluence of developments:

Digital format
Most journals have stopped producing print versions, and with preprints becoming routine, it won’t be long before every article is published online at least once before it is published as a version of record. With the limitations of printed copies lifted, the democratization of access should broaden the reach of scientific research, allowing for a more global exchange of knowledge and collaboration across geographical and socio-economic boundaries.

Digital tools
The recent scandals around doctored data in scientific publications have called into question the publishers’ ability to fulfill one of their core missions — ensuring high quality and integrity in scientific publications. Digital tools and independent reviewers have become more common and are spotting erroneous figures and data missed by the publishers, whether innocent or not.

Review process
Online publishing has introduced new challenges and opportunities for the peer review process. Digital platforms facilitate more diverse and rapid reviews, including open peer review (where authors and reviewers know each other’s work and comments) and post-publication review. However, the increase in publication volume has put pressure on the peer review system, raising concerns about quality control and the potential for reviewer fatigue. Efforts to innovate in peer review practices continue to evolve as the system can still be seen as antiquated and opaque, often supported by publishers themselves for their own interests in maintaining their role as profitable gatekeepers.

New metrics
Online publishing has led to the development of new metrics for measuring the impact of research beyond traditional impact factors. Altmetric, for example, tracks the online attention and engagement that research articles receive. These metrics offer a broader view of an article's influence and reach, reflecting the changing ways scientific information is consumed and shared in the digital age.

Open access
The open access movement advocates for free, unrestricted access to research publications. Open-access journals do not charge readers to access articles but often charge authors publication fees to cover the costs of the peer review and publication process. This model aims to remove financial barriers to accessing research. Facing mounting costs of access, institutions are canceling their subscriptions to major journal conglomerates such as Elsevier. This has forced all major publishers, including Wiley, Springer-Nature, AAAS (Science), and Elsevier, to develop sustainable open-access models.


There is still a lot to say about the evolution of academic publishing, and some already have asked whether journals are needed at all, given the rise of other processes and platforms. But it is clear that the peer-review process, a heresy for Albert Einstein in 1936, has contributed meaningfully to building trust and integrity in the scientific system. And, although it will continue to evolve with new technologies and practices, it remains a crucial feature of scholarly publishing. As the ways science is produced evolve, how publications are put together, shared, and consumed will continue to progress, hopefully increasing access and collaboration.

– Jonathan Friedlander, PhD & Geoffrey W. Smith




First Five
First Five is our curated list of articles, studies, and publications for the month.

1/ Nature is healing
This month, the very serious Scientific Reports (a publication from Nature, what else?) published a study hoping to prove that “A walk in nature enhances certain executive control processes in the brain above and beyond the benefits associated with exercise.” The randomized controlled trial shows that participants who walked in nature reported their walk to be more restorative than those who walked in the urban environment, provided of course one isn't eaten by a bear. Researchers confirmed the self-reporting using electroencephalography to explore three aspects of attention—alerting, orienting, and executive control—from a behavioral and neural perspective.

2/ The (chromosomal) butterfly effect
New research from the Wellcome Sanger Institute and the University of Edinburgh showed that despite the high diversity in butterflies and moth species, their chromosomes have remained largely unchanged since their last common ancestor more than 250 million years ago. Over 200 chromosomal complete lepidopteran genomes were analyzed, showing that out of 32 ancestral lineages, only eight had undergone extensive reorganization. This should enthuse more than the occasional lepidopterist as it sheds light on specific mechanisms of chromosomal evolution.

3/ Smoking is terrible, immune edition
A team of scientists based in France (where else?) showed that smoking profoundly alters the immune system. The study published in Nature showed that smoking is a major contributor to variability in cytokine response, with effects of comparable magnitudes with age, sex, and genetics. While the innate response recovers quickly after smoking stops, the effect on the adaptive response persists for a long time. This could explain the increased risk of developing infections, cancers or autoimmune diseases.

4/ Vegan and ketogenic diets, immune edition
A recent study published in Nature Medicine showed that two weeks of controlled dietary intervention is sufficient to impact the immune system significantly and divergently. Using a multi-omics approach, scientists revealed that the ketogenic diet was associated with a significant upregulation of pathways associated with the adaptive immune system. In contrast, a vegan diet significantly impacted the innate immune system, upregulating pathways associated with antiviral immunity. This discovery could have implications for precision nutritional interventions.

5/ Or stop eating altogether, immune edition
A team from the University of Cambridge may have uncovered how fasting could reduce systemic inflammation, a phenomenon known but unexplained. Researchers showed in a Cell publication that levels of plasma IL-1β were lower in fasting compared to fed subjects, while the lipid arachidonic acid (AA) was elevated. AA acts on macrophages through the NLRP3 pathway, just like nonsteroidal anti-inflammatory drugs (NSAID), potentially solving a second mystery!




Did You Know?
In this section of our newsletter, we seek to demystify common terms and practices in our work as investors.

‍Fundraising
Fundraising is the process by which a venture capital firm seeks to secure capital from external investors, known as limited partners (LPs), to establish a new venture capital fund. The firm defines its investment focus, strategies, and target sectors during this phase. It then actively engages in marketing and outreach efforts to attract potential investors, which may include institutions like pension funds and high-net-worth individuals. The success of fundraising determines the size of the fund, impacting its capacity to invest in startups and early-stage companies. Fundraising is critical in forming a venture capital fund, setting the stage for its investment activities. The venture capital fund's fundraising process involves the development of legal agreements, including the private placement memorandum (PPM) and limited partnership agreement (LPA), which outline the fund's terms and investment strategies. Once investors commit capital to the fund, they become limited partners, and the fund is then equipped to make investments and support emerging companies. Successful fundraising relies on factors such as the venture capital firm's reputation, track record, and its ability to articulate a compelling investment strategy to potential limited partners. It serves as the essential foundation for the fund's investment endeavors and its potential to generate returns.

– Haiming Chen & Dylan Henderson

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