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So, You Want to Publish a Scientific Paper?

An open notebook.

By Douglas Braaten, PhD

Learning how to craft a scientific paper so that it is accepted for publication takes practice. It also requires attention to details across many domains. Many advice resources are available, and I encourage any young scientist to carve out time to focus on what to do — and what to avoid — when writing scientific papers.

Before starting to write, give some thought to preparation, process, attitude and goal. Some key points I’ve learned from reading and editing hundreds of papers at Annals of the New York Academy of Sciences and Nature Immunology follow.

These two journals have very different aims, scope and readership, but similar goals of publishing well-written, well-constructed papers for the sake of readers’ understanding and clarity. Note the points below are not presented in order of importance or temporality — all are useful.


Part of the preparation is learning as much as possible about scientific publishing in general which will help to make the process both more enjoyable and successful.

The writing of a scientific paper begins when a lot of hard work has been done already. Completion of a series of experiments that demonstrate a statistically relevant discovery is the foundation of all good scientific papers.

That’s not to suggest that one can’t have a reasonably clear picture of what a paper might look like along the way of performing experiments. Indeed, designing experiments — the order and what’s required — is often critically informed by one’s experience in crafting a good scientific paper.

However, it’s never a good idea to start before a complete set of experimental results has been gathered. Doing so can reverse the circle from “now that I have a set of data how best can it be presented?” to “what experiments do I need to do to finish my paper?” the latter being the wrong way around.

Don’t get caught in the trap of needing to do an experiment in order to finish a paper. Instead, set out to perform the complete set of experiments necessary for readers (in particular peer reviewers!) to agree with you that the conclusions are supported by the data. And then write.


Consider who will need to read your paper before it is accepted for publication.

Among the best papers I’ve read are those that have been prepared for a particular journal and its readership. Writing to achieve those goals may not seem as important as simply describing the data. It’s critical, however, to write for readers and to prepare a paper with specific audiences in mind. These two points are often ignored. The journal editors must find it suitable for their journal, believe a given paper presents good data, and does so clearly enough to send it out for peer review. Next, while the process of peer review can vary among journals, papers at most journals are sent to at least two external peer reviewers. These individuals — very busy scientists, often pressed for time and overloaded with work — volunteer their time to comment on papers.

More than anything, peer reviewers hate papers that are overly long, vague and not crafted for readers. By accepting to review a paper, reviewers by and large give benefit to any doubt that it presents interesting information and data. Give them what they want without distractions.

Reviewers and editors are busy individuals — don’t hobble yourself by ignoring the fact that they can be easily put off by sloppy and careless writing.


Some of the above considerations of process are also considerations of attitude. It’s critical for authors to set and maintain a level of respect and collegiality for everyone involved when preparing and submitting a scientific paper — from submission, to peer review, production and every step through publication.

In my experience, the most successful authors are those whose attitude reflects the ideals of both achievement of work and an earnest, genuine desire to share important new information with the scientific community.

In contrast to that, an attitude of entitlement to be published is immediately noticeable to editors and, especially, to peer reviewers. I have seen good papers that may have only needed minor improvements as recommended by reviewers, upended by rejection because the authors believed they were in the right and didn’t need to make changes.

Even the most experienced scientists know it’s their responsibility to maintain an open, respectful attitude during the publishing process. Ignoring this imperils your aims for little more than an overly needy ego. Consider it a privilege to have your scientific paper evaluated and published.


Much of the above could have been included in a discussion of scientific author goals. The right preparation, a well-considered process, and a collegial and respectful attitude are certainly worthy goals.

Less obvious, yet equally important is considering the audience from the perspective of readers who want Open Access (OA). The interest in scientific papers to be OA is now so intense that it’s important for authors to consider OA for every one of their papers.

Indeed, so many funders are pushing for not only OA, but for other forms of pre- and post-publication access to scientific data that it behooves every author to consider both the laudable goals of OA and the ramifications for scientific publishing. Fortunately, many online forums present extensive discussions — e.g.

As the OA movement grows — and there’s no doubt that it will — authors must consider whether they will submit only to OA journals to support the goal of open information. At the same time, they should consider that publishers of OA journals will feel increasing pressure to seek more and more submissions to cover their publication costs as subscription revenue declines. Authors will surely experience this increasing pressure, as it will undoubtedly affect the publishing process.

For example, more papers to evaluate increases the burdens on everyone involved — editors, reviewers, production staff. Ensuring you do all that you can as a responsible scientific author will likely help achieve your personal aims of publishing and of contributing openly to scientific progress. And while much more can be said about how to publish successfully, keeping in mind preparation, process, attitude and your goal should help.

Publishing Evolves in a Connected World

A shot of planet Earth taken from space.

In many ways, the process from paper submission to publication has not changed much in 40 years. However, some changes are underway.

By Ann Griswold

Douglas Braaten, PhD, Chief Scientific Officer, Scientific Publications Editor-in-Chief, Annals of the New York Academy of Sciences

In the days before artificial intelligence mined obscure gems from the scientific literature; before preprint servers posted study results without pausing for peer review; when social networking meant cocktail conversations at the industry conferences — science publishing looked very different than it does today.

“When I started, authors submitted paper manuscripts produced on a typewriter,” says Douglas Braaten, PhD, chief scientific officer responsible for the Academy’s science journals and books, and editor-in-chief of Annals of The New York Academy of Sciences. “Happily, not everything stays the same.” But as technology continues to reshape academic publishing he says, “it’s useful to think about the things that do.”

In many ways, the process from paper submission to publication has not changed much in 40 years. Researchers still submit papers to journals. Papers are peer reviewed. Journal editors share the reviews with authors. Revisions take place. And then submissions are transformed into carefully copy edited, typeset manuscripts. This system has survived because it works, Braaten says.

But critics have long called for change. Some note that the peer review process can stretch on for months or even years. Others point out that the $25 billion academic publishing industry is dominated by a handful of major players who make a profit from the public investment in research.

Braaten and others don’t deny that the system could be improved, but they say the situation is more nuanced than critics suggest.

“I’d love for the industry to be less concerned with profit-making,” he says. “But there are some fundamentally important and useful things about peer review and having vetted, polished papers published in journals with global footprints.”

Still, technologies aimed at tweaking the process have increasingly flooded the market — and are gradually transforming the business. “It’s hard to keep track of these innovations because there are so many of them out there,” says Steven Ottogalli, Publisher, Life & Physical Sciences at Wiley. “Start-ups are coming online and impacting every part of the publication process, affecting every aspect of the value chain that used to lie solely with the publishers or with the academic societies.”

Preprint servers, for example — long a standard in the math and physics communities — are gaining in popularity with biologists. Scholarly collaboration networks are connecting researchers from diverse fields and distant locations, allowing them to share their findings in real time. Artificial intelligence-based search tools are tipping off scientists to papers they might otherwise overlook — creating new synergies. Novel technologies such as blockchain aim to increase accountability and transparency in the review process by encoding each article with a record of its origins, revisions and peer reviews. And younger generations of investigators are replacing static figures with embedded multimedia and interactive data.

Collectively, these innovations can bring the world to a laboratory’s doorstep and allow siloed projects to spread in new, unexpected directions. But how will these new technologies fundamentally change the traditional model of scientific publishing?

“There’s such a sociology surrounding scientific publishing,” Braaten says. “Think of what it means for grant funding, and tenure evaluations. And for what it means for the careers of young investigators when they publish in a top-tier journal. One would have a very hard time replacing all of these significant benefits with changes just in technology.”

Yet it’s hard to deny that the field is in transition. “I’ve been in this business for almost 20 years, and things have changed so drastically,” says Ottogalli. “Who knows what it will look like in another decade.”

Variations on a Theme

Steven Ottogalli, Publisher, Life & Physical Sciences, Wiley

Most of the innovations Ottogalli mentions are variations on the theme of open access, a business model that shifts the financial outlay from academic institutions to authors and funders (such as the Wellcome Trust) by replacing subscription fees and paywalls with open access license fees and free access to published papers.

Critics complain that subscription-based journals restrict access to publicly funded research by creating subscription paywalls. This, they say, forces the very academic institutions that produce the findings to pay for access to the published work. Open access could potentially fix that by providing immediate public access to papers upon publication.

“But this ‘fix’ doesn’t address the whole story,” Braaten says. “If by open access, you mean access to the information, there are a lot of ways now that one can access all published research, publicly funded or not.”

For example, most journals allow authors to post the submitted version of their manuscript on a lab website or, after peer review and acceptance, on the post-publication websites such as PubMed Central. And with the advent of preprint servers, Braaten says, there’s a huge amount of accessible information for free. “If someone wants access to a paper, it’s often available on one of several sites — just in a different format than one finds in a published journal.”

Subscription paywalls don’t keep science from the people, he says. Rather, they provide publishers and journal owners the funds required to produce published peer reviewed and polished papers on websites in HTML and PDF form, and in print journals. “The typeset published version — not the actual science in the article — is the thing that’s owned by a journal or publisher — it’s the product of their work. I think people may not be aware of this distinction,” he says.

Access to Published Science in a Connected World

One upside to all publishing models — including open access and pre- and post-publication servers — is that published papers are available for such things as AI text mining. In turn, this can improve discoverability within disparate disciplines, for example, ecology and economics. “AI will help humans make connections where they didn’t think of making connections before,” Ottogalli says.

The AI tool IBM Watson, for example, can search published content and find papers on climate change that a researcher might be interested in — and then make connections to other papers that might unexpectedly support work on climate change.

AI will help humans make connections where they didn’t think of making connections before,” Ottogalli says.

In the meantime, researchers are finding ways to share their findings outside of the traditional publishing process.

“Scholarly collaboration networks, which are like Facebook for researchers, are providing greater opportunities for working together,” Ottogalli says. ResearchGate and other scholarly collaboration networks (SCNs) build ties among researchers in similar and disparate fields, and can put relatively obscure labs in developing countries in touch with larger, well-funded ones abroad.

“The international collaboration piece is very important,” Ottogalli says. The publishing landscape is dominated by Western Europe, the U.S. and China, so “sites like this open up doors for researchers who may not be known to researchers in Europe or the U.S. At the end of the day, I think SCNs are a valuable tool in advancing science.”

But There’s a Downside, Too

ResearchGate and other SCNs can be aggressive in encouraging authors to upload versions of their published PDFs in violation of copyright. “This is clearly wrong,” Braaten says. Publishers have routinely issued take-down notices, informing the authors and ResearchGate that they must remove the content because it is in violation of publishers’ policies.

Echoing Braaten, there’s another way to provide access to research findings says Ottogalli: “preprint servers.” In a 2016 policy forum, Science lauded the advantages of preprint servers for authors, journals and funders. These sites expedite publication and offer a forum for sharing new tools or negative results, potentially accelerating the pace of research. It’s also possible that preprint servers could help weed out questionable scientific papers in the pre-peer review phase, when other researchers comment publicly on the study. “Some authors may value the feedback before the paper is submitted to a peer-reviewed journal,” Ottogalli says.

The concept is rising in popularity. Some journals have launched their own preprint servers for papers under review. And a few major federally funded programs require their investigators to post preliminary findings to the servers.

“We’ll see really interesting advancements in the next few years,” says Ottogalli. “It’s a time of big change.”

The New York Academy of Sciences – A Concise History

An illustration of the Academy's original home in 1817.

By Douglas Braaten, PhD

Founded in 1817 as the “Lyceum of Natural History in the City of New York,” by a small group of science enthusiasts, led by Samuel Latham Mitchill, a polymath and prominent politician who represented New York in the U.S. Congress, determined to create an organization that anyone interested in natural science could join in order to learn from experts, and that provided a venue for public consumption of scientific ideas and advances of the time.

For the next 100 years, the trials and tribulations of the Academy were in many respects the trials and tribulations of progress of science in New York and other states of the new American republic. In March 1817, James Monroe became the fifth American president. That same year he was elected an honorary member of the Lyceum, along with the third American president, Thomas Jefferson.

The intentionally anti-patrician nature of the Lyceum not only distinguished it from other institutions of the day, it served as the basis for a new type of democratic institution that later was instrumental in the progress of science, especially in the New York City area, though this was also felt throughout New York State and beyond.

On the national scene, Philadelphia, originally owing to its centrality as the first American capital and birthplace of major figures in politics and science—e.g., Benjamin Franklin—was home to the first science societies in the nascent country, although with the exception of Franklin’s Academy of Natural History the societies were aristocratic and elitist. They were institutions largely, if not exclusively, for men of wealth who were not themselves scientists; nor probably even much interested in science. Membership was a symbol of status, indicating, among other things, that a person had the financial means to support these 19th century social clubs.

Even by name—Lyceum: an institution for popular education providing discussions, lectures, concerts, etc.—the first incarnation of the Academy was fundamentally different from other societies. Its raison d’être was not social climbing and show, but the dissemination of science, and bringing people who were keenly interested in science, together.

This fundamental democratic principle determined the course of the Academy’s history, and with it the development of key institutions of science and learning in New York City today, including Central Park, the American Museum of Natural History, the New York Botanical Garden and New York University. It was by inclusion of people on the basis of only their interest in science that the Academy could bring together so many different stakeholders—indeed so many key individuals at just the right moments—to influence, if not forge the development of many New York City institutions.

The founding meeting of the Academy, then the Lyceum, occurred on January 29, 1817. To tell the history of the Academy’s accomplishments since then is to tell the history of science in New York State and America, and beyond. It is the history of an institution, but more importantly of the tens of thousands of individuals who have been Academy Members since 1817, from around the globe and from many diverse institutions, cultures and walks of life.

Indeed the history of the Academy would not have been possible without the devotion, energy and creativity of its Members. This collective engagement—today we refer to this as the Academy’s network—has enabled and driven fundamental changes in the landscape of science and science-based institutions in New York City and throughout the world. This is history worth telling, and re-telling.

Two centuries later, on January 29 2017, the Academy unveiled a permanent 200th Anniversary Exhibition in the lobby of its headquarters at 7 World Trade Center in New York City (see photos below). The folded timeline insert in this issue of the magazine provides a concise history of key Academy events, members and accomplishments since 1817. A prominent feature of the physical exhibition is a 17-foot-long timeline with images and text that tells the story of some of the enormous challenges and successes over the Academy’s 200 years.

In addition, as part of the 200th anniversary celebration, the Academy is publishing a revised edition of a critically acclaimed history of the Academy and of science in New York City and the early United States, Knowledge, Culture, and Science in the Metropolis: The New York Academy of Sciences, 1817–2017 by historian and professor Simon Baatz (John Jay College).

Originally published as special issue of Annals (Ann NY Acad Sci 584: 1–269) in 1990, professor Baatz’s book provides an, “engrossing account of the role of the sciences within the great American metropolis”… “this masterly account of science in its social context will be of the greatest interest to everyone who cares about New York, about the growth of knowledge, and about the importance of voluntary associations in our national life.” The revised edition, published in January 2017, contains a new chapter on the Academy’s history from 1970 to 2017.

An even earlier account, A History of the New York Academy of Sciences, formerly the Lyceum of Natural History, published in 1887 by Herman Le Roy Fairchild, is also available in electronic form by contacting the Academy at Fairchild’s account is a detailed discussion of many facets of the Lyceum’s early days, including biographical sketches of many of the important founders, lists of all of the first Lyceum officers and administrators, dates and addresses of locations of the Academy during its early peripatetic days, copies of the original constitution, by-laws and other legal documents.

Finally, a very brief history, “The Founding of the Lyceum of Nature History,” by historian Kenneth R. Nodyne, was published in 1970 (Ann NY Acad Sci 172: 141–149).

Some Prominent Members of the Academy

From its inception, the Academy has been a member-driven organization. And while it was a democratic organization that welcomed anyone, the Academy, for its first 100 years or so, proposed and voted on bestowing memberships.

As specified in the original constitution of 1817, admittance to the Lyceum was by three categories of membership. Resident members were from NYC and “its immediate vicinity” and thus could take part in Academy meetings, while Corresponding members, largely on account of travel times in the early 19th century—it took a day and a half to travel to Boston!—were less involved; Honorary members were selected on the basis of “attainment in Natural History,” no matter where they resided.

Categories of membership changed over the years. In the 1980s there were eight: Active, Life, Student, Junior, Institutional, Certificate, Honorary Life and Fellows. The total number of members had reached its highest, 48,000 from all 50 states and over 80 countries around the world. This membership apogee was in large part the result of two factors. One was the enormous influence of the Academy’s executive director from 1935 to 1965, Eunice Miner, whose zeal and “stubbornness” increased membership from 750 in 1938 to over 25,000 by 1967! The other influence was a membership policy in the 1980s of mailing out membership certificates to people worldwide.

Today’s Academy membership of 20,000 is composed of Professional, Student and Postdoctoral, Supporting and Patron, and—continuing a long tradition—Honorary Members. Over the course of our history there have been well over 200 Honorary Members, including 110 Nobel Laureates. Below are profiles of just a few of the Honorary Members.

Lord Kelvin (1824–1907)
Elected Honorary Member 1876

William Thomson, 1st Baron Kelvin, a Scots-Irish mathematical physicist and engineer who did important work on electricity and thermodynamics. Absolute temperatures are stated in units of Kelvin in his honor.

Louis Pasteur (1822–1895)
Elected Honorary Member 1889

A French chemist and microbiologist known worldwide for his work on understanding vaccination, microbial fermentation, and pasteurization. He was director of the Pasteur Institute, established in 1887, until his death. He was made a Chevalier of the Legion of Honour in 1853, promoted to Commander in 1868, to Grand Officer in 1878 and made a Grand Cross of the Legion of Honor—one of only 75 in all of France.

Niels Bohr (1885–1962)
Elected Honorary Member 1958

A Danish physicist who won the Nobel Prize in Physics in 1922 for making fundamental contributions to the studies of atomic structure and quantum theory. He spent much of his life and worked in Denmark, where he founded the Institute of Theoretical Physics at the University of Copenhagen.

Barbara McClintock (1902–1992)
Elected Honorary Member 1985

An American cytogeneticist who won the Nobel Prize in Physiology or Medicine in 1983 for her discovery of genetic transposition. Her work concentrated on studies of maize, for which she developed techniques for visualizing the chromosomes; she produced the first genetic map for maize and demonstrated the important roles of telomeres and centromeres. McClintock spent her entire professional career in her own laboratory at Cold Spring Harbor Laboratory.

Rosalyn S. Yalow (1921–2011)
Elected Honorary Member 2006

Born in New York City, Yalow was a medical physicist and co-winner of the Nobel Prize in Physiology or Medicine for the development of the radioimmunoassay (RIA), an in vitro technique used to measure concentrations of immune proteins called antigens. This revolutionary technique helped to marshal in the modern era of immunological research. Yalow also won the prestigious Albert Lasker Award for Basic Medical Research (1976) and the National Medal of Science (1988).