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Accelerating Scientific Publication in Biology
Ronald D. Vale
TL;DR
Publication practices have become slower and more demanding, while publication remains important for career progression and communication within the scientific community. The paper analyzes changes in biology publication practices and discusses preprints as one possible mechanism for accelerating communication. The analysis finds that the time to first-author publication has increased and is now approaching the length of graduate training.
Problem
Publication practices have become slower and more demanding, while publication remains important for career progression and communication within the scientific community.
Method
The paper analyzes changes in biology publication practices and discusses preprints as one possible mechanism for accelerating communication.
Results
The analysis finds that the time to first-author publication has increased and is now approaching the length of graduate training.
Takeaways & Limitations
Accelerating communication may require removing barriers and providing better incentives for preprint publishing.
Takeaways & Limitations
Universal consensus on preprint adoption may not be achievable.
Abstract
from arXiv · showhide
Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. More experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.
A trend toward increasing data required for publication
The amount of experimental information in biology papers increased substantially from 1984 to 2014, while publication expectations also ratcheted upward through journal competition and peer review.
- Observed changes: Print-version figure counts did not change significantly, because journal guidelines remained largely similar, despite the rise in experimental panels.The increase was therefore concentrated in panel density and supplemental material rather than the number of print figures.
- Observed changes: Experimental panels increased 2-4 fold from 1984 to 2014, indicating substantially more data in contemporary biology papers.The number of distinct datasets remained about two-thirds of labeled panels and that ratio changed little, supporting a real increase rather than relabeling alone.
- Observed changes: Supplemental figures and panels became comparable to or greater than print-version figures, further increasing the data associated with each paper.Supplemental information began appearing around 1997; supplemental panels were comparable to print panels in Cell and exceeded them in Nature.
- Associated changes: Contemporary papers also had 2-4 fold more authors than papers from 1984, consistent with more data and more diverse or complex techniques.The authors caution that additional authors are probably not the sole mechanism for acquiring the added data.
- Drivers: Publication expectations rose through competition, demands for mature stories, and referee requests that often added experiments before acceptance.The authors describe a feedback loop in which editors and reviewers continually reset expectations, while sequential submissions further delay publication.
What is a minimal unit for publication?
The paper argues that modern publication favors comprehensive stories, whereas earlier breakthroughs often appeared as successive papers reporting key findings or hypotheses.
- Modern standard: Modern publication makes it harder to publish a key initial finding or bold hypothesis before a mature experimental story is assembled.The paper contrasts this trend with the earlier publication of the Watson-Crick model and other foundational work in installments.
- Historical examples: Earlier discoveries in DNA, cholesterol, ubiquitination, and axonal transport emerged through multiple papers that progressively disseminated pieces of broader breakthroughs.The authors argue that these installments could now be delayed and compressed into fewer publications.
- Trade-off: Scientists want rapid publication for career advancement, priority, and protection from being scooped, yet top-journal ambitions encourage delaying submission for more data.These opposing incentives create pressure to postpone publication until a larger experimental story is available.
Consequences on the exchange of information within the scientific community
Delayed publication reduces access to new findings and may shift scientific meetings away from sharing work in progress toward already published results.
- Catalytic effects: Publishing key experiments quickly places ideas in the public domain, where other investigators can test them, extend them, and connect them with their own work.The paper presents this collective activity as a benefit of exposing results before every implication is resolved.
- Scientific meetings: The protracted and uncertain publication process makes students and postdocs increasingly wary of sharing unpublished data at scientific meetings.The paper links this reluctance to concerns about publication and career consequences.
- Scientific meetings: Scientific meetings are consequently becoming more filled with recently published or soon-to-be-published results than with exciting work in progress.The authors identify this as a change in the character of information exchange at meetings.
Consequences for Training
Longer and more demanding publication pathways make career transitions and scientific training harder, especially when publication is required for jobs, grants, and advancement.
- Career transitions: Training-time limits may not solve the problem unless publication systems also change, because trainees and PIs may extend training while waiting for publishable work.The paper argues that publication requirements are intertwined with decisions about how long trainees remain in laboratories.
- Publication timelines: Current UCSF graduate students took 1.3 additional years on average to publish their first first-author paper, bringing publication time close to the 6.3-year average graduation time.For students who published, the current average time to first-author publication was 6 years, near the desired upper boundary for training.
- Career transitions: Publication has become harder for graduate students, and this delays milestones needed for postdoctoral positions, jobs, grants, and career advancement.Thesis committees and applications may require an accepted first-author paper, while a manuscript in submission cannot be listed on an NIH grant application.
- Training benefits: Earlier publication could accelerate career transitions, improve writing and data-organization training, and give trainees flexibility to pursue new research or other career preparation.The paper also notes that longer data acquisition and publication leave young scientists fewer opportunities to write papers and practice these skills.
Possible solutions for accelerating communication
Existing open-access and peer-review innovations improve publication, but the paper argues that accelerating scientific communication requires a larger-scale mechanism than creating more journals.
- Recent platforms have introduced immediate open access and reforms to peer-review transparency, but these efforts do not by themselves satisfy the proposed scale and implementation criteria.
- New journals are unlikely to provide the transformative solution because they are expensive to operate and must compete for strong manuscripts.
- A transformative communication mechanism must operate at large scale, capture the field’s best work, launch within years, coexist with journals, and remain cost-effective.
Lessons from the Physics Community: Should Biologists Adopt an Internet Pre-‐Print System?
The physics community’s experience with arXiv provides a model for rapid, journal-compatible dissemination, while biology’s limited uptake reflects unresolved quality, overload, and policy barriers.
- ArXiv demonstrates large-scale pre-print use: one million papers had been submitted by January 2015, with 67 million downloads in 2013.
- Biology has not reached critical mass: bioRxiv received 888 pre-prints compared with arXiv’s 97,517 in the cited year, despite more life-science publications.
- A same-day bioRxiv submission reached a large audience and received extensive comments, emails, and discussions before anonymous journal reviews arrived.
- A biology pre-print repository could transmit results rapidly, provide earlier and broader feedback, and coexist with journals serving different communication needs.
- Pre-prints raise concerns about irreproducible or lower-quality work and information overload, although screening, investigator reputation, and improved search filters may mitigate them.
- Policy changes proposed to reduce adoption barriers include accepting pre-prints for discovery priority, grant productivity, and life-science journal submission.
Help from the journals: creating a new “Key Finding” format
The paper proposes a journal format centered on a compact “Key Finding” figure to limit data volume while preserving communication of a cornerstone result.
- Existing short communications mainly limit words, while researchers continue increasing the amount of data in figures and supplemental material.
- The proposed journal format would focus on limiting data, addressing an escalating publication requirement that communication-focused formats do not necessarily solve.
- A new format could restrict papers to eight panels across up to four figures, without supplemental data, and designate one figure as the “Key Finding.”
- The restricted format is presented as feasible because comparable concise article formats existed in earlier scientific publishing.
- Its broader adoption would depend on whether authors and readers find the format popular.
Conclusions
The life-science publication system is approaching a breaking point as publication requirements and delays increasingly conflict with graduate training and career progression. Electronic preprints, alongside journal reform and broader stakeholder action, are proposed as ways to accelerate communication while preserving flexibility across biological disciplines.
- Publication constraints: Publication requirements have ratcheted upward, with the time to first-author publication approaching the length of Ph.D. training.This creates tension with efforts to shorten graduate and postdoctoral training and with requirements to publish before career transitions.
- Scope and culture: The authors argue that the life-science community must take ownership of a communication system serving both scientific and public needs, while recognizing that subfields may adopt new practices unevenly.Universal consensus is not expected, and some communities may embrace preprints more readily than others.
- Implementation: Adopting preprints would require removing barriers, improving incentives, and changing behavior on a large scale before their value for biologists can be properly tested.Existing mechanisms are available, but broad participation is presented as the central practical challenge.
- Alternative reforms: Journal-system reforms such as more transparent reviewing and better evaluation metrics may help, but their effectiveness without new incentives remains uncertain.The discussion also questions whether such reforms would materially change the daily lives of graduate students and postdoctoral fellows while referees remain overwhelmed.
- Stakeholder action: The paper calls for stakeholders—including scientists, funders, societies, philanthropists, and editors—to discuss how to accelerate biological communication.The NIH is identified as especially influential because rapid access serves its public-good and trainee-career interests.
Figure 1
Figure 1 compares publication statistics across Cell, biology papers in Nature, and JCB for January–June 1984 and 2014. It tracks publication counts, figures, panels, and authors, combining long- and short-format papers.
- Figure 1: The analysis combines long and short formats, including Nature Articles and Letters and JCB Articles and Reports or Rapid Communications.Separate category analyses are provided in Fig. S1.
- Figure 1: The figure measures publication totals, average figures, panels per paper, and authors per paper.Figures include print and online supplements, whereas panel counts use lettered figure designations and tables.
Figure 2
Figure 2 follows cumulative PDF views and tweets for an article’s original bioRxiv version. The accompanying account describes readership and social-media activity after posting.
- Figure 2: Figure 2 tracks cumulative PDF views and tweets for the article’s original bioRxiv version.The record begins at posting and follows subsequent media exchanges.
- Figure 2: The figure concerns readership and social-media activity after the Perspective was posted on bioRxiv.The posting date was July 11, 2015.
- Figure 2: Abstract views exceeded PDF views by more than twofold.Daily-view information was supplied by bioRxiv.
SI Methods
The SI Methods define how panels and distinct experimental data were counted in Cell and Nature papers. They acknowledge that panels are an imperfect proxy and assess scoring consistency.
- SI Methods: Panels were counted from lettering in figures, while distinct data represented separate experiments or significant new analyses.Tables, data-containing schematics, and figure schematics were counted as panels, but schematics and model figures were not counted as data.
- SI Methods: Panels are an imprecise proxy for experimental data, motivating the separate distinct-data estimate.A single experiment can span multiple panels, while one panel can contain multiple experiment types.
- SI Methods: Multiple views, probes, quantifications, or related analyses from one experiment were generally counted as one piece of data.The rules also grouped identical experiments across cell lines and counted sequence alignments and tables as single data pieces.
- SI Methods: Distinct-data scoring was performed within a single figure rather than across different figures.The method therefore distinguishes data among panels but not between figures.
- SI Methods: Two independent scorers showed close agreement, with averages of 7.33 and 7.16 distinct data pieces per article.This consistency check used January and February 1984 Cell articles; remaining months were scored by one person.
Analysis of UCSF Graduate Student Publications
The study compares publication records of experimental-science UCSF graduate students from earlier and recent cohorts. Recent students took longer to graduate and publish first-author work, while several lacked completed or anticipated publications.
- Analysis of UCSF Graduate Student Publications: Recent UCSF graduates took an additional 1.3 years on average to publish their first first-author paper.The comparison uses publication records from students in four experimental-science PhD programs.
- Analysis of UCSF Graduate Student Publications: The analysis excluded students conducting exclusively theoretical or modeling work and counted only experimental-science programs.Graduate-school entry and degree dates came from the UCSF registrar.
- Analysis of UCSF Graduate Student Publications: Publication counts were based on PubMed records, excluding reviews and methods papers that mainly described previously published methods.The study also used author order to compare authorship across periods because co-authorship conventions differed.
- Analysis of UCSF Graduate Student Publications: The recent cohort included students without anticipated first-author or first/second-author publications, while some earlier students lacked publication records.Seventeen recent students had anticipated publications incorporated using estimated timelines, which may not match eventual publication.
Q&A Regarding Pre-‐prints
The Q&A weighs preprints as a faster, complementary route for sharing biological work while examining risks involving accuracy, quality, priority, careers, and medical use. It argues that safeguards, discovery tools, and community-specific policies are needed for adoption.
- Reproducibility and quality: Immediate public exposure may encourage accuracy, but preprints can also disseminate mistakes before peer review and potentially lead researchers down wrong tracks.The authors suggest commenting systems and further data collection on reproducibility as possible responses.
- Journals and discovery: Preprints would coexist with journals, while filters and integrated search across preprints and journals could help readers identify relevant or higher-quality work.Suggested filters include scientists, funders, and user recommendations; discovery could be integrated into PubMed or a new search engine.
- Priority and competition: Biology raises priority concerns because rapidly moving experiments may let others build on preliminary results, although public preprints could establish a widely visible record of priority.The discussion contrasts biology’s fast-moving systems with physics and notes that preprints must carry recognized priority.
- Implementation and policy: Preprint adoption faces practical barriers, including unclear career value, journal and grant restrictions, possible scooping, and unresolved policies for releasing reagents and source data.The authors propose community policies such as a grace period after posting for public release of reagents, strains, and source data.
- Ethical and practical issues: Medical communities may need separate decisions because erroneous preprints about procedures or drugs could have disastrous consequences for patient care.The paper treats biology as heterogeneous, allowing different communities to decide when or whether preprints are appropriate.
- Potential benefits: Preprints could accelerate feedback, expose work before journal publication, support trainees’ applications, and shorten delays in communicating results.The proposed benefits include earlier community feedback and evidence of scholarly work for graduation or postdoctoral applications.