How to write an A+ research paper

This article lists some of the stages involved in writing a library-based research paper.

Although this list suggests that there is a simple, linear process to writing such a paper, the actual process of writing a research paper is often a messy and recursive one, so please use this outline as a flexible guide.

  1. Discovering, narrowing, and focusing a researchable topic
  2. Finding, selecting, and reading sources
  3. Grouping, sequencing, and documenting information
  4. Writing an outline and a prospectus for yourself
  5. Writing the introduction
  6. Writing the body
  7. Writing the conclusion
  8. Revising the final draft

Discovering, narrowing, and focusing a researchable topic

  • Try to find a topic that truly interests you
  • Try writing your way to a topic
  • Talk with your course instructor and classmates about your topic
  • Pose your topic as a question to be answered or a problem to be solved

Finding, selecting, and reading sources

You will need to look at the following types of sources:

  • Library catalog, periodical indexes, bibliographies, suggestions from your instructor
  • Primary vs. secondary sources
  • Journals, books, other documents

Grouping, sequencing, and documenting information

The following systems will help keep you organized:

  • A system for noting sources on bibliography cards
  • A system for organizing material according to its relative importance
  • A system for taking notes

Writing an outline and a prospectus for yourself

Consider the following questions:

  • What is the topic?
  • Why is it significant?
  • What background material is relevant?
  • What is my thesis or purpose statement?
  • What organizational plan will best support my purpose?

Writing the Introduction

In the introduction you will need to do the following things:

  • Present relevant background or contextual material
  • Define terms or concepts when necessary
  • Explain the focus of the paper and your specific purpose
  • Reveal your plan of organization

Writing the body

  • Use your outline and prospectus as flexible guides
  • Build your essay around points you want to make (i.e., don’t let your sources organize your paper)
  • Integrate your sources into your discussion
  • Summarize, analyze, explain, and evaluate published work rather than merely reporting it
  • Move up and down the “ladder of abstraction” from generalization to varying levels of detail back to generalization

Writing the conclusion

  • If the argument or point of your paper is complex, you may need to summarize the argument for your reader.
  • If prior to your conclusion you have not yet explained the significance of your findings or if you are proceeding inductively, use the end of your paper to add your points up, to explain their significance.
  • Move from a detailed to a general level of consideration that returns the topic to the context provided by the introduction.
  • Perhaps suggest what about this topic needs further research.

Revising the final draft

  • Check overall organization: logical flow of introduction, coherence and depth of discussion in body, effectiveness of conclusion.
  • Paragraph level concerns: topic sentences, sequence of ideas within paragraphs, use of details to support generalizations, summary sentences where necessary, use of transitions within and between paragraphs.
  • Sentence level concerns: sentence structure, word choices, punctuation, spelling.
  • Documentation: consistent use of one system, citation of all material not considered common knowledge, appropriate use of endnotes or footnotes, accuracy of list of works cited.
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Posted in Communication, Editing, Education, Impact Factor, Interdisciplinary research, Journal article, Journal Selection, Manuscript format, Medical Communication, Medical Writing, Peer Review, Science, Scientific editing, Scientific writing, Writing

What is open peer review?

History of traditional (closed) peer review

Even though scientific publishing has been around since the 17th century, formal peer review of submitted articles by external academics is relatively new. The journals Science and JAMA, for example, introduced formal peer review in the 1940s, and Nature didn’t introduce it until 1967.

The peer review system adopted in the 20th century has now become the norm for many journals. It involves an editor (usually a practicing researcher, but sometimes a journal staff member in the case of journals like Nature) sending out a paper to a few experts in the field, who then provide comments for the paper’s authors. Although the reviewers can generally see who the authors are, they themselves remain anonymous to the author, and only the editor knows everyone’s identity.

Problems with traditional, semi-blind, peer review

This “single-blind” system is not without problems. Anonymous reviewers can be biased against the authors of the paper, and lean toward rejection or acceptance for unscientific reasons. Often, the closest “peers” in someone’s area of research are also that researcher’s direct competitors! One solution is to remove the authors’ names from the manuscript, but this double-blind system is not fool-proof, and a reviewer will still often recognize which lab a paper comes from. In addition, any bias towards competitors of the reviewer still remain, even if that competitor is anonymized.

Another drawback of traditional peer review is that the referee reports are visible only to the authors and the editor. Nobody else can see what the reviewers thought of the paper. Especially in situations where reviewers disagree, and a single editor makes the final decision, it can be very informative to see what the reviewers thought of an article, and whether the editor’s decision was in line with their opinion. Reviewers are usually in a position to put the work in a broader context of the field, and often mention this context in their reports. They can also point out where the work could be expanded into new areas, and may still have some lingering questions. All of this is useful for everyone to read – not just the authors. It’s also important to remember that not all journals use the same criteria for publication. Some journals may turn a great paper down just because it doesn’t fit the scope of the journal. Other journals publish all sound science, including some papers that get extremely high praise in the referee reports.

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A timeline of open and transparent review

Within the life sciences in particular, several journals have opened their peer review process to address some of the issues discussed above. Sometimes this involves publicly naming reviewers and/or editors. Other journals publish some or all reviewer comments.

1999 After studying various peer review models, BMJ starts revealing reviewer names to authors
2000 BioMed Central launches, and soon after that starts including reviewer names and pre-publication history for published articles in all medical journals in their BMC series of publications
2001 Atmospheric Chemistry and Physics introduces a system where manuscripts are placed online as a “discussion paper”, which is archived with all comments and reviews, even before approved and peer-reviewed articles appear in the journal.
2006 Launch of Biology Direct, which includes reviewer comments and names with published articles.
2007 Frontiers launches, and includes reviewer names with articles.
2010 EMBO journal starts publishing review process file with articles. Editors are named, but referees remain anonymous.
2011 BMJ Open launches, and includes all reviewer names and review reports with published articles.
2012 Several journals launch with an open peer review model:

  • GigaScience – publishes pre-publication history with articles and names reviewers (opt-out system)
  • PeerJ – Peer review reports published with author approval, reviewer names published with reviewer permission. (Info)
  • eLife – Decision letter published with author approval. Reviewers anonymous.
  • F1000Research – All peer review reports and reviewer names are public, and appear after article is published online.

Benefits of open review

Benefits for authors and readers

  • Author can see who reviewed their work
  • Reviewer comments put paper in context which is useful additional information for readers
  • Reduces bias among reviewers
  • More constructive reviews
  • Published reports can serve as peer review examples for young researchers.

Benefits for reviewers

  • Shows the reviewer’s informed opinion of the work
  • Demonstrates experience as a reviewer
  • Can take credit for the work involved in conducting the review

Challenges

Although open peer review is becoming more common, and addresses several of the issues of anonymous review, a few challenges still remain. A study in the early days of open review suggested that naming referees slightly reduced the likelihood of finding reviewers but did not affect the quality of review. Conversely, other studies suggest that open review provides more constructive reports.

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Posted in Communication, Education, Peer Review, Peer-reviewed Journal

Writing the first draft of your science paper — some dos and don’ts

Four steps to preparing your first draft

Here is the process I use:

  1. Think about the topic you want to present, for some days or weeks.
  2. Make figures and tables.
  3. Then write as quickly as possible, as if thinking out loud. Get everything down, ignoring spelling, grammar, style and troublesome words.
  4. Correct and rewrite only when the whole text is on paper.

Do not split the manuscript among the co-authors. It is better to write a first complete draft, and then the co-authors can amend and add new text. In this way, the internal coherence of the paper is ensured. Ask each reviewer to track their changes.

Polishing your manuscript

Use good English

Unfortunately for non-native English speakers, language is an important problem. If the language prevents reviewers from understanding the scientific content of your work, the possibility of acceptance will be lowered greatly.

At the minimum, you should use the best English you can manage in presenting your high-quality science. Get a skilled writer or someone fluent in English to check your manuscript before submission. Now, most publishers have a service of English correction with a cost around €250 ($285) per paper.

You must save your readers the trouble of guessing what you mean. Look at this complaint from an editor:

“(This) paper fell well below my threshold. I refuse to spend time trying to understand what the author is trying to say. Besides, I really want to send a message that they can’t submit garbage to us and expect us to fix it. My rule of thumb is that if there are more than 6 grammatical errors in the abstract, then I don’t waste my time carefully reading the rest.”

Write with clarity, objectivity, accuracy and brevity, presenting your scientific research in a way that is logical and understandable. To improve your language skills, you can practice reading and writing English in other parts of your work, for example, by keeping records in English during your research and reading as many papers as you can in English.

 Avoid these common problems:

  • Sentences that don’t follow each other logically
  • Sentences that are difficult to understand by non-initiated readers (e.g., “The Annex IV of the MSFD includes the definition of GES to be applied by MS.”
  • Grammatical errors
  • Spelling mistakes and typos

Simplify your language

  • Original: “Numerous studies in recent years, such as those by Miller (1995) and Smith (1998), have shown that low salinities enhance oyster recruitment.”
  • Suggested: “Low salinities enhance oyster recruitment (Miller, 1995; Smith 1998).”

Avoid long sentences

  • Direct and short sentences are preferred!
  • Long sentences do not make the writing more professional; they only confuse readers.
  • Nowadays, the average length of sentences in scientific writing is about 12 to 17 words.
  • It is said that we read one sentence in one breath. Long sentences choke readers.

Some languages (e.g., Spanish) tend to have long and complicated sentences, which can be expressed with fewer words in English. You have to change your style when writing in English. One idea or piece of information per sentence is sufficient. Avoid multiple statements in one sentence. In writing the following passage some years ago, I understood my science well – but with 78 words in a single sentence, it’s unlikely that anyone would have understood it.

… Conversely, applying M-AMBI the explained variability reaches until 43.4%, for linear regression, and 53.8% for logarithmic regression, and the highest explained variability was found in high and low mesohaline and polyhaline areas (53-63%), whilst the lowest explained variability was in the oligohaline area (6%), being the mismatch in the comparison of both methods in terms of degraded-undegraded equivalences was of 16.4% of the cases in M-AMBI, and 12.7% in B-IBI, with a high spatial level of agreement.”

After the reviewers recommended using shorter sentences, I modified it to the following:

… Conversely, applying M-AMBI the explained variability reaches until 43.4%, for linear regression, and 53.8% for logarithmic regression. The highest explained variability was found in high and low mesohaline and polyhaline areas (53-63%). In turn, the lowest explained variability was in the oligohaline area (6%). The mismatch in the comparison of both methods in terms of degraded-undegraded equivalences was of 16.4% of the cases in M-AMBI, and 12.7% in B-IBI, with a high spatial level of agreement.

science draft with question mark featured

Problems with long sentences:

  • Use of passive voice (e.g., “It has been found that there had been many …” instead of “Researchers found that many …”)
  • Poor sentence structure with incorrect conjunctions or dangling modifiers (e.g., “because …, so …”; “Although …, but …”; “considering …, it is …”). For example, avoid this kind of sentence: “The highest explained variability was found in high and low mesohaline and polyhaline areas (53-63%), because of the high concentration of organic matter, although it was …” It is better to say: “The highest explained variability was found in high and low mesohaline and polyhaline areas (53-63%). This is related to the high concentration of organic matter. Although it was…”
  • Excessive use of subordinate clauses in one sentence (e.g., “It has already been found that when salinity increases to the mouth of an estuary there would be higher benthic richness, which can result also in higher diversity, while in low salinity areas benthic richness tends to be low …”)
  • Mixing different levels of parallelisms connected by “and” in one sentence (e.g., “This research investigates the grain size of sediments in coastal areas and discusses the grain size and the coastal sedimentation based on grain size …”)

Length of the manuscript

Again, look at the journal’s Guide for Authors, but an ideal length for a manuscript is 25 to 40 pages, double spaced, including essential data only. Here are some general guidelines:

  • Title: Short and informative
  • Abstract: 1 paragraph (<250 words)
  • Introduction: 1.5-2 pages
  • Methods: 2-3 pages
  • Results: 6-8 pages
  • Discussion: 4-6 pages
  • Conclusion: 1 paragraph
  • Figures: 6-8 (one per page)
  • Tables: 1-3 (one per page)
  • References: 20-50 papers (2-4 pages)

Redundancies to avoid:

  • Overusing conjunctive words or phrases such as “However,” “In addition,” “Moreover.” Use these words sparingly.
  • Phrases without meaning. Learn from the following comments from an Editor: “Never say ‘and references therein.’ …  Any intelligent reader knows to look at the references in a paper in order to get even more information.” Delete “In present paper.” It is impossible for it to be in a different paper! You start the conclusions “In this paper, we have prepared…..” This is nonsense. The samples were prepared in the laboratory!
  • Repetitive words with similar meanings, such as “schematic diagram,” “research work,” etc. It’s better to use the words separately: “this scheme,” “that diagram,” “the research was …,” “the work done was …”

Other writing don’ts:

  • Passive voice for intransitive verbs (which do not have a direct object); only transitive verbs can have passive forms. Hence, you cannot say:  “are happened” or “was went.”
  • The third-person singular form of verbs used for plural subjects (e.g., “the concentrations shows that …” instead of “the concentrations show that …”
  • Dangling modifiers, in which the subject of the main clause is not the doer (e.g., “To improve the results, the experiment was done again.” The experiment cannot improve the results itself. It should be “We did the experiment again to improve the results.”)
  • Don’t use spoken abbreviations: “it’s,” “weren’t,” “hasn’t.”
  • Never begin a sentence with a numeral: “5 mg of sediment were analysed …” Use: “Sediment (5 mg) was analysed …”
  • Single-digit numbers should be spelled out; numbers of two or more digits should be expressed as numerals (you can write “four samples” or “25 samples”). In a sentence containing a series of numbers, at least one of which is more than one digit, all of the numbers should be expressed as numerals. (Of the 21 samples, 1 was muddy, 6 gravel, and 14 sandy.)

To make the reviewer’s life easier;

  • Keep the text and layout style consistent throughout the manuscript by using the same font (usually Times New Roman) and font size in the text, figures and tables. Double line spacing and 12-point font is preferred; this makes more convenient for reviewers to make annotations. Margins of 3 cm are also useful for reviewers.
  • Number all pages! This is very important because it helps reviewers show you the parts to be amended.
  • Number each row in the text (it is easier to identify the position of the comments from the reviewers).
  • Pay attention to the abbreviations; they should be defined on the first use in both abstract and the main text (also in the legends of figures and tables). Some journals even forbid the usage of abbreviations in the abstract. Refer to the journal’s Guide for Authors to see the requirements for abbreviations.
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Posted in Case report, Communication, Impact Factor, Journal article, Journal Selection, Manuscript format, Medical Writing, Scientific writing, Writing

Presubmittal peer review for high-impact research

In more collegial, less competitive times researchers used pre-submission peer review to obtain frank, constructive feedback from trusted colleagues before sending their manuscript to a journal. But pre-submission review now appears to be rare in the current publish-or-perish environment.

Journal-managed peer review sometimes fails to screen out unreliable research. The reasons why peer review can fail as a quality filter have been debated, and many calls have been made for better training for reviewers and editors. Yet dissatisfaction with journal peer review remains widespread and appears to be on the rise. And good reviewers are becoming increasingly hard to find, according to editors in some fields. Although reviewing for journals is undertaken voluntarily, problems with late, superficial, biased and promised but never-delivered reports suggest that journal reviewers do not always take their commitment very seriously.

Post-publication peer review identifies potentially unreliable information (as in this recent example at PubPeer 2014). Although often necessary to correct the record, post-publication peer review on popular sites such as PubPeer, Retraction Watch or ChemBark can become rancorous. If the errors that readers find are serious enough, the result can be retraction – a frustrating and demoralizing experience for researchers who submitted their manuscript in good faith and trusted the journal’s peer reviewers to save them from public embarrassment.

Retractions of peer-reviewed, published articles are on the rise. They occur even in the most prestigious journals, where “groundbreaking” work is more likely to be published, and where editorial policies to correct the scientific record are more likely to be in place. Prompt, transparent retraction is laudable, but every time a peer-reviewed article is retracted because of errors that were identified by readers shortly after publication, I can’t help wondering why the peer reviewers did not notice the errors before publication.

A retraction is stressful for all stakeholders because it is often slow, painful and expensive. For the authors, a retraction is potentially career-threatening. For readers who used the flawed article as a basis for their own work, a retraction can be a major setback if it means they have wasted time and resources. For journal editors and publishers, retractions are problematic because they may be viewed not as a sign that the journal cares about correcting the record, but as an admission of quality control failure.

Even reviewers for glamour journals, where editorial quality control is assumed to be the most rigorous, make mistakes and overlook errors. So even at journals with a double-digit impact factor, “passing peer review” is no guarantee that potentially career-making research is ready for prime time.

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Posted in Journal article, Peer Review, Peer-reviewed Journal, Scientific editing

Post publication peer-review: Everything stays, and changes the same

In the early days of scientific societies (i.e. the 17th century), scientists would share their experimental results with each other at meetings, and receive feedback about their experiments in person.  (The scientific journal wasn’t invented until later.)  As the scientific community grew, it was impossible for everyone to be in the same room to hear about results, and so the amount of immediate feedback offered was limited to a few conferences or other gatherings. Recently, publishers, scientific societies and entrepreneurs have begun using the web to bring back the era of immediate feedback: so-called “post-publication peer review.”

One of the hallmarks of scholarly scientific publication is the review process.  While it isn’t perfect, peer review is the process used by almost all scholarly publications to filter out bad-science, identify weak data analysis and make suggestions for better presentation of results. Traditional peer review was done before an article was published. In the age of print publication, this made the most sense because of the costs associated with printing.

Although most scientific journals are published online these days, peer review is still most often done prior to publication and the status of “peer reviewed” is held up to undergraduate students as an important hallmark of quality. Online publication makes post-publication peer review easier than ever – most often in addition to traditional pre-publication peer review.

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Several new ventures are allowing scientists to comment on published papers, engage in discussions online and even publish more formal reviews. Informally, it started with blogs. Independent bloggers would read an article from the scientific literature and want to share their thoughts on it. As we have done on this blog, the blogger would cite the paper and discuss it’s results and any limitations. Perhaps the blogger might disagree with the original findings based on their own research. But the original author of the paper might never know that it was being discussed because there was no connection between the publishers version of the article and the blog post.

Next came user commenting.  Taking a page from blogging platforms, publishers such as PLOS and BioMed Central experimented with allowing registered users to post comments on journal articles. This was only moderately successful. Some folks suggested that scientists were unwilling to directly criticize the work of others, although they might be willing to comment on a blog post discussing the article. While article comments kept the scientific dialog contained in one place, the conversations didn’t really take off, and some scientists I spoke with were skeptical about the idea of allowing anyone to comment on scientific articles. In recent years, third parties have started taking on the post-publication peer review mantle.

PubPeer allows users to make comments on almost any article that has a DOI, but the site is separate from publishers web pages. Scientists may be more willing to engage in frank criticism, but it is harder to connect the original paper to the comments. Importantly, PubPeer contacts authors when new comments are posted about their papers – in this way, PubPeer attempts to provide feedback directly to the authors that blogging doesn’t provide. PubPeer also attempts to preserve bling peer review by not publishing reviewer names.

PubMed Commons is the platform built into PubMed for using comments. Currently in a pilot phase, PubMed Commons invites authors of PubMed papers to join and comment on papers. Their names appear by their comments. By limiting who can comment on papers, PubMed Commons seems to want to reduce instances of non-experts commenting on papers. Articles related to politically controversial topics such as evolution, vaccines and climate change would theoretically be open to abuse if comments from everyone were allowed. Users will see these comments at the bottom of the PubMed entry for each article.

Open Review is the much hyped tool from the academic social network ResearchGate. Open Review encourages authors to publish a slightly more formal review than the simple commenting systems of PubPeer and PubMed Commons.  Reviews are tied to your research gate account and to the entry for the article on ResearchGate.

As others have pointed out, the growing number of commenting systems produces a distributed system that can make it difficult for people to know where to go to get information about an article. And I suspect that these systems will only multiple in the near future. These new tools are providing a way for scientists to make their private conversations about recent research public, and allowing them to expand the group of people they can chat with. Although the goal is to provide feedback and commentary, the limits of space (how many people can fit in the room, who has the office next door) no longer apply.

New scientists have grown up commenting on their friends pictures, their silly comments on Facebook and their favorite YouTube videos.  Will this practice carry over into their scientific publishing? Will publishers eventually link back to these commenting systems? Will database producers (e.g. Scopus, Web of Science) incorporate user comments into their systems? It will be interesting to find the answers to these questions and see how these systems impact scholarly scientific communication.

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Posted in Communication, Education, Open access, Peer Review, Review article, Science, Science and Technology, Scientific editing, Scientific Journal

Finishing your PhD thesis: 15 top tips from those in the know

Many PhD students are now in the final throes of writing their thesis. Turning years of research into a single, coherent piece of work can be tough, so we asked for tips from supervisors and recent PhD graduates. Below is a selection of the best tips.

1) Make sure you meet the PhD requirements for your institution

PhD students and their supervisors often presume things without checking. One supervisor told his student that a PhD was about 300 pages long so he wrote 300 pages. Unfortunately the supervisor had meant double-spaced, and the student had written single-spaced. Getting rid of 40,000 extra words with two weeks to go is not recommended.

2) Keep perspective
Everyone wants their thesis to be amazing, their magnum opus. But your most important work will come later. Think of your PhD as an apprenticeship. Your peers are unlikely to read your thesis and judge you on it. They are more likely to read any papers (articles, chapters, books) that result from it.

3) Write the introduction last
Writing the introduction and conclusion together will help to tie up the thesis together, so save it for the end.

4) Use apps
Trello is a project management tool (available as a smartphone app) which allows you to create ‘boards’ on which to pin all of your outstanding tasks, deadlines, and ideas. It allows you to make checklists too so you know that all of your important stuff is listed and to-hand, meaning you can focus on one thing at a time. It’s satisfying to move notes into the ‘done’ column too.

5) Address the unanswered questions
There will always be unanswered questions – don’t try to ignore or, even worse, obfuscate them. On the contrary, actively draw attention to them; identify them in your conclusion as areas for further investigation. Your PhD viva will go badly if you’ve attempted to disregard or evade the unresolved issues that your thesis has inevitably opened up.

6) Buy your own laser printer
A basic monochrome laser printer that can print duplex (two-sided) can be bought online for less than £100, with off-brand replacement toners available for about £30 a pop. Repeatedly reprinting and editing draft thesis chapters has two very helpful functions. Firstly, it takes your work off the screen and onto paper, which is usually easier to proof. Secondly, it gives you a legitimate excuse to get away from your desk.

7) Checking is important
On days when your brain is too tired to write, check quotations, bibliography etc so you’re still making progress.

8) Get feedback on the whole thesis
We often get feedback on individual chapters but plan to get feedback from your supervisor on the PhD as a whole to make sure it all hangs together nicely.

9) Make sure you know when it will end
Sometimes supervisors use optimistic words such as ‘You are nearly there!’ Ask them to be specific. Are you three months away, or do you have six months’ worth of work? Or is it just a month’s load?

10) Prepare for the viva
Don’t just focus on the thesis – the viva is very important too and examiners’ opinions can change following a successful viva. Remember that you are the expert in your specific field, not the examiners, and ask your supervisor to arrange a mock viva if practically possible.

11) Develop your own style
Take into account everything your supervisor has said, attend to their suggestions about revisions to your work but also be true to your own style of writing. What I found constructive was paying attention to the work of novelists I enjoy reading. It may seem that their style has nothing to do with your own field of research, but this does not matter. You can still absorb something of how they write and what makes it effective, compelling and believable.

12) Remember that more is not always better
A PhD thesis is not a race to the highest page count; don’t waste time padding.

13) Get a buddy
Find a colleague, your partner, a friend who is willing to support you. Share with them your milestones and goals, and agree to be accountable to them. This doesn’t mean they get to hassle or nag you, it just means someone else knows what you’re up to, and can help to check if your planning is realistic and achievable.

14) Don’t pursue perfectionism
Remember that a PhD doesn’t have to be a masterpiece. Nothing more self-crippling than perfectionism.

15) Look after yourself
Go outside. Work outside if you can. Fresh air, trees and sunshine do wonders for what’s left of your sanity.

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Posted in Communication, Editing, Education, Science, Scientific writing, Writing

Let’s shine a light on paywalls that deny open access to scientific research

Reviewing scientific literature can be a bit like trying to negotiate a maze with the lights turned off. For years I was fumbling around in the dark, but didn’t realise I was missing out. Now the Open Access Button campaign wants us all to hit the switch and turn on the lights.

After I left college, I worked in the hospitality industry. Science interested me, but my interest was limited to newspapers saying “A new study shows … ” and the occasional popular science book. I never tried to look up the actual source studies – I just assumed that the story was accurately reported and left it at that.

Access senied

Paywalls keep most of us in the dark.

Then a sudden illness made me more interested in population health. I started reading with a sense of purpose. On Twitter I followed the discussions among scientists working at institutions around the world. They often shared links to scientific papers with each other, stuff that sounded really interesting and that I wanted to read. But I couldn’t. If I followed such a link, I’d find that I needed to pay £25 or more to download a single pdf file. How the heck were these science types able to keep up with developments in their field? Were they all secret millionaires? I clearly couldn’t keep up when, living on the minimum wage, it would take me half a day’s work to earn the right to read a single paper. I realised I was being prevented from learning more, from examining the details and seeing the evidence for myself. I was shut out of knowledge.

The scientific publishing world is dominated by journals produced by companies such as ElsevierNature Publishing Group and Wiley. Journals are the basic scientific currency, the way ideas are communicated. But they’re often only available by subscription, and most subscribers are academic institutions and libraries. Readers usually rely on being part of an organisation that subscribes to them because subscriptions cost a small fortune. In fact, the subscription price of journals has risen at nearly four times the rate of inflation since 1986, so it’s hard to keep up any other way. Even some institutions and libraries are now dropping subscriptions to journals – they can no longer afford it. And as neither the authors of published papers nor the experts who carry out peer review for the journals are paid for their work, such charges can seem perplexing.

Thankfully this isn’t the case for all scientific publications. Online journals such as those published by PLOS (the Public Library of Science)BMC Seriesand Peer J are free to all. When I started out on my journey they gave me a torch to find my way, to gain experience of reading papers and discover how they are structured – without threatening me with bankruptcy. The ethos of these journals is that science is not a privilege but a right. It’s something for all of us.

But I needed a wider circle of light.

I didn’t realise how much I was missing until I went back to full-time education a year ago. Suddenly, through my university portal, I had access to subscription journals and my world opened up. It was like being able to see after a cataract operation, or being able to hear after getting a cochlear implant. But it also made me angry. It made me realise how little scientific information the average person sees – even though, through the funding system for research, it’s often our taxes and charity donations that pay for it.

In the past couple of years the science community has seen momentum for change building up around open access, based on the idea that paywalls inhibit further research, innovation and good old-fashioned learning. But how do we even know people are missing out when their only reaction to a paywall is a deep sigh of frustration? One of the most innovative ideas has been to give people a “button” they can press each time they hit a paywall that blocks their access to research findings. After a successful beta launch by creators Joseph McArthur and David Carroll last year, the Open Access Button project has tracked more than 6,500 paywalls. But they know they are only scratching the surface. The project is now seeking crowdfunding for a second phase, and to ensure a fully tested version can be launched in time for Open Access Week in October.

“For the team, tracking people being denied access to research is just the start,” says McArthur. “We’re committed to helping people find the research they need. We ensure the data makes it to the people who can change how this system works. We’re also building features into the Button which help people track down available copies of the research immediately.”

If my doctor prescribes me a medicine, I want to be able to look at the studies that led to the decision that this was the best thing for me. If someone tells me that eating a food has health benefits, is it so wrong to want to check the source studies of that story? Why should a keen astronomer or geologist be denied access to a new theory simply because they work in a bank, not at a university that can pay access fees on their behalf? It’s time to bring scientific knowledge out from the shadows, and turn on all the lights.

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Posted in Case report, Education, Journal article, Open access, Peer Review, Peer-reviewed Journal, Review article, Science, Scientific editing, Scientific Journal, Scientific writing

The inexorable rise of open access scientific publishing

A new study shows that the rise of open access publishing of academic research is faster than anyone had previously realized. Before 2000 the vast majority of research papers were published in journals that could only be read by academics if they — or their university libraries — paid a subscription. But since the turn of the millennium, the growth of the world wide web has been accompanied by the emergence of open access publishing, by which research papers are made freely available online.

The academic publishing game has changed irrevocably.

The change does not mean that academics have embraced the free-for-all file-sharing mentality that is the bug-bear of the music business. Rather it reflects the deep-seated amateur ethos of scholars, who have always seen the work of producing and reviewing their research findings as an intrinsic part of the job. While the dissemination of that research relied on the printing and distribution of academic journals, the publishers’ subscription model was a sensible way to manage this business. But the opportunities provided by the web for instant distribution has fused with the principle that publicly funded research should be freely available and propelled the open access movement to the forefront of academic publishing. The escape from the physical bounds of publishing on paper should also help us to realize significantly better value for money in this core part of the research enterprise.

The rise of open access has been hampered by opposition from some publishers, who see it as a threat to a lucrative subscription model, and by some quarters of the research community fearful of jettisoning an established process of publishing in familiar journals. Scientists may have invented the internet but some remain suspicious of its fast-moving and disruptive nature. Others, myself included, are more sanguine about the promise of open access, as indeed is the UK government. In July this year science minister David Willetts warmly welcomed the report of the working group led by Dame Janet Finch on how to expand access to publicly funded research. The government sees open access as a way of accelerating the free distribution of scientific results, not just to researchers but also to businesses looking to innovate new technologies, and as a necessary mechanism for developing new computer-based text and data-mining methods for interrogating research results with a breadth and depth that no individual could hope to match. Finch’s recommendations are now being implemented as policy by Research Councils UK, the body that oversees public spending on science and the humanities. In a bold move, the UK has committed itself to ensuring that from April 2013 all publicly funded research papers will be available free to readers.

The policy is not without its critics, many of whom are concerned about the cost implications, since the new policy has a strong preference for facilitating free access by paying publishers an “article processing charge” (APC) to ensure the paper is made freely available upon publication (one of the forms of gold open access). The cost calculations are uncertain but may be as high as £60m per year, which will have to come from the research budget, a sore point with researchers in these austere times.

A cheaper green route is also available, whereby the author usually deposits an unformatted version of the paper in a university repository without incurring a publisher’s charge, but it remains to be seen if this will be adopted in practice. Universities and research institutions are only now beginning to work out how to implement the new policy (recently clarified by the RCUK).

inexorable rise open access

They should be encouraged by Laasko and Björk’s study which, fittingly, is published in an open access journal. The Finnish researchers found not only that nearly 17% of research papers worldwide are now published in open access journals, a figure that is two to three times higher than was previously supposed, but also that the exponential rise in open access publishing shows no sign of slowing down.

In the UK, since about 35% of papers are reckoned to be made available through deposition in repositories — the green route — the total percentage of open access papers (52%*) looks like it has crossed the half-way mark. Whatever the difficulties universities and researchers might face in implementing the new RCUK policy, it is clear that there is no going back. We can look forward to a future in which there is a much freer access to research results, both for researchers, businesses and the public. The only question now is what can we do with it?

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Posted in Communication, Journal article, Open access, Peer-reviewed Journal, Science, Science and Technology, Scientific Journal

Peer review needs to expand so that more scientists are reviewing papers

A new tool that selects peer reviewers by algorithm could make the peer review process more reliable, by sources

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The more peer reviews on a paper from top scientists, the stronger the peer review signal.

Technology has changed some aspects of science tremendously. We have deep space telescopes that produce terabytes of data every day. We have tools to create synthetic living cells. However, the system of peer review – the mechanism by which scientific results are vetted – hasn’t materially changed since the 1600s when journal publishing was invented.

The reliability of the peer review process has recently come under the spotlight when the journal Science wrote a fake biology paper and submitted it to a number of open access journals. The fake paper made it through the peer review process of the majority of the journals.

Pharmaceutical companies have also drawn attention to the fact that the majority of peer reviewed papers in the bio-medical space are not reproducible. Amgen reported that 89% of peer reviewed articles are not reproducible. Bayer’s estimation stands at 64%. The Economist has also discussed studies that question the reliability of the peer review process.

Part of the issue is that in the traditional peer review process, only two or three scientists peer review a paper. The system places too much weight on what a small number of scientists think. There are more than 50,000 people working in a field like breast cancer. What two or three people think is too small a sample size: the signal is not statistically significant. We need to expand peer review so that there are vastly more scientists peer reviewing papers, sharing their thoughts and comments on each other’s papers.

In the past, it hasn’t been possible for journals to solicit peer reviews from a large number of people, because the process by which journal editors find peer reviewers for a paper is manual and labour intensive. That may change with large communities of scientists emerging online: Academia.edu has 5 million academics on its platform; ResearchGate lists over 3 million and Mendeley has 2.6 million.

If we combine these large communities with technology currently available, we can algorithmically determine the top scientists in a given field, and weight their peer reviews accordingly. The goal is to build a system that incentivises scientists to share their peer reviews and thoughts on the papers they are reading. Science is a conversation, and progress happens through the rapid discovery of errors, and quickly learning from those errors and moving on.

Cue the acquisition by Academia.edu of Plasmyd, a peer review and discussion platform for papers. The goal is to tackle the next building block in open science: building a better peer review system. The integration will combine Plasmyd’s experience in fostering peer review with Academia.edu’s research community and experience developing new ways of measuring reputation in research.

Humanity faces many problems that require science-based solutions. We need to find cures for Alzheimers, Parkinson’s, HIV, malaria and cancer. The planet is on a path to self-destruction with increasing carbon emissions and we need to develop a carbon-free source of energy that works at scale.

The goal of open science is to accelerate scientific discovery by making the process of science more open. Part of open science is getting every science PDF that has ever been written onto the internet and accessible for free. Another part is building a better peer review process, one that is more open and does a better job at separating the reproducible research from the non-reproducible research.

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Posted in Communication, Open access, Peer Review, Peer-reviewed Journal, Scientific editing, Scientific Journal

Why open access should be a key issue for university leaders

Universities are digital machines these days. But many of the decisions that have to be made as a result are not technical at all. They are about the nature of research and its public benefits, about how learning and teaching takes place, and how we confront difficult ethical issues. Strategic choices that are made now will have significant implications for the ways in which knowledge will be created and shared in the future.

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We couldn’t operate universities without the digital systems that run payroll, student registrations, finance and the teaching timetable. Our libraries spend more on electronic publications than paper. We reach large numbers of students online using increasingly significant digital media. But while bandwidth is now as basic a need as electricity and parking, there are critical choices ahead.

Central to these is openness – the extent to which those working and studying within the university and college system can get access to any digitally-based information they need without encountering a virtual gateway: a password, subscription requirement or payment.

Paywalls and passwords are an irritating but natural consequence of the privatization of the web; they are also essential for online security. For the future of research, though, the need for openness is far more than a convenience. It arises because the volume and rate of production of online publications and digital data sets has now outgrown the limits of conventional research methods and is changing the ways in which new knowledge is created. Without openness across global digital networks, it is doubtful that large and complex problems in areas such as economics, climate change and health can be solved.

There are two primary reasons why these changes to research are taking place:

1) The sheer volume of new, peer-reviewed publications is already too great for manual review in many fields of study. In medicine for example, more than two new papers are published every minute. The volume of research outputs is accentuated by China and India, the emerging giants in university-based research.

Thirty years ago, when today’s senior researchers were in their early careers, big university and copyright libraries could claim to stock printed copies of everything published in a discipline; today, many researchers never need to enter the library building at all.

2) The sharply declining unit cost of bandwidth, digital storage and processing capacity, combined with the breathtaking pace of technical innovation, is allowing massive, almost instantaneous flows of digital data across the world. In many cases, these flows are being constantly fed by devices linked together as the “internet of things”. Some of these devices are highly sophisticated – for example, real-time seismic measurements used to predict tsunamis and terrestrial earthquakes. Others are commonplace – citizen journalists using smart phones to upload images or the millions of daily financial transactions that track economic trends.

These massive digital data flows are the new raw materials for research. For highly complex problems such as climate change, epidemiology, financial stability and space exploration, access to global big data is already a basic condition for research to take place at all.

Protocols

Appropriate and effective policies and protocols that ensure openness are essential in ensuring access to both research publications and massive digital data sets. Automated searches of the publication record are not feasible if subscription requirements and paywalls constantly prevent access to the copy-of-record. This is why the current debate about “green”open access – delivered by repositories – and “gold” open access – delivered by journals – and article-processing charges is so important.

Access to massive digital data sets is invariably complex and contentious. Nation states are touchy about rights and security (all the more so, given WikiLeaks and Edward Snowden). Individuals and interest groups worry about rights to privacy and commercial misuse of personal data. Researchers are concerned about the premature release of research data and the ethics of openness when information is collected with assurances of anonymity. Each of these is a complex set of issues in its own right.

Openness is also central to the continuing development of learning and teaching – where pupils complete course material ahead of lessons to free up time with their teachers – is rapidly moving on, often putting social media at the center of course design.

Our universities were built from the principles of scarcity and closure: restricted access to libraries; special knowledge that could only be passed on in the lecture theater; closed communities of scholarship. Today we are drowning in digital information, available almost everywhere via interfaces and cheap devices that know where we are. Learning and teaching is about making sense of this bewildering open world, with all its opportunities and its increasing dangers.

Digital technologist specialists are important in every university; we need them to keep our systems running and to look ahead for coming innovations that will require investment and changes in the ways that we work. But the strategic and ethical questions that arise from the rapid and comprehensive advances in digital technologies – and particularly openness and its consequences – are for anyone in a leadership position, whether an academic programme convenor, a dean or a vice-chancellor. All universities are now digital, and all research and teaching will be shaped by continuing technological change.

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Posted in Communication, Education, Open access, Peer Review
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