An Overview of Peer Review and Science Publication

 

Science News and Information is a new blog featured on Cosmic Roots and Eldritch Shores. Here, you’ll find highlights of some of the most recent discoveries and breakthroughs in science and research. I’ll try and connect each topic to important societal implications, and I will do my best to remove my own opinions.

We want this space to be a source of fact. We want this space to be relevant, entertaining, and safe to explore interesting science and any underlying implications. That’s why I was so excited when Cosmic Roots and Eldritch Shores decided to put together a new science feature like this. I remember as a kid reading science fiction and fantasy and always wondering about the real science and reality behind the stories. I hope you enjoy what will appear here in the coming weeks and months, and hopefully, years.

Today we’ll start not with the excitement of the seven planets orbiting TRAPPIST-1 or the controversies of CRISPR technology (both topics I promise to return to), but with the subject of peer review and publication. Okay, I know! There’s not a great way to make the term ‘peer review and publication’ incredibly appealing. But it’s the foundation of the entire scientific enterprise and well worth a discussion. I thought this would be the best place to build our foundation as we venture to the outer rim of what we know and don’t know.

The important thing to keep in mind is that science is a process. Scientists can be wrong; we’re human after all. In the laboratory, we constantly get our hypotheses wrong, our experiments end in failure, and we knock our heads against the lab bench hoping for inspiration. Quite often we just don’t have the tools to solve the big questions and we must splash in the waist-deep waters for years until the right technology is developed to really dive into the deep end.

But when a discovery is made, it needs to be reported. This part of the scientific process is where I want to spend the rest of our discussion: peer review.

Peer-reviewed journals are the most important source of scientific information and all scientific researchers work towards publishing their findings in peer-reviewed research journals. Journals like Nature, Science, The Lancet, New England Journal of Medicine, Physical Review Letters, and Journal of the American Chemical Society all review and publish new science and often compete with one another for the most impacting work.

The process begins when a researcher believes they have enough data to convince other scientists their findings are valid and true. Depending on the subject matter, this data collection could be a small pilot project or a major research endeavor that encompasses thousands of hours of work and dozens of experiments. Typically, once the arrangement of the data is outlined, the researcher puts on his or her author’s hat and begins crafting a manuscript to present their new findings.

In a way, scientists are story-tellers and their research manuscripts present a data story. But a defense of the hypothesis is essential. Questions should be addressed, such as: Why was this experiment performed? What was observed? Why should the public care about these results? What does it mean in context of what is already known? Do the findings challenge previous findings or build upon it? Typically, the methods must be specific enough that someone else picking up the paper could repeat the experiments in their own laboratory.

Once the manuscript is completed and all the authors have signed off, it’s sent to a journal. There, it meets the first person that will review the article: the editor. Journal editors are usually experts and will read the cover letter, the abstract…ideally the entire paper…and decide right then and there if the topic of the manuscript is relevant to the journal they are working with. Just like publishing in science fiction and fantasy, certain works and topics are better fits for certain journals.

Journals like Science and Nature only publish ground-breaking work that advances a specific field or features novel approaches, methods, or technologies. Some journals are more specific: Cancer Research isn’t going to feature a paper about behavioral cognition, just like Analog probably won’t feature a classic fantasy tale about dwarves attacking a dragon’s horde…probably, unless there’s time travel!

If the editor decides to pass, the authors must decide where next to submit. However, if the editors feel the manuscript may be a good fit, the next step in the process begins. They will contact anywhere from 1-3 external reviewers to do a critical and thorough read of the entire manuscript. These reviewers are also experts in the field and contacted by the journal to provide their opinion about the quality of the science, the findings, and their interpretations. It’s the reviewers’ task to judge the entire work on its own merit.

The reviewers usually provide a written reply that is a point by point consideration of the work, with specific comments, questions, or suggested improvements to the manuscript. Comments can range from simple typographical mistakes to the proposal of several additional control experiments that must be included. Typically, the reviewers decide whether the manuscript should be accepted as is, provisionally accepted with minor corrections, provisionally accepted with major corrections, or rejected.

The editor’s collect all the reviewer’s comments for the authors and then make a final decision. It’s not unheard of for an editor to go against a reviewer, or to offer their own interpretation of the manuscript to the authors.

If a manuscript is invited for resubmission, the researchers will get a chance to look over the comments, address the concerns, and resubmit (with no guarantee of acceptance). The manuscript’s authors will write a rebuttal to the reviewers if needed, and occasionally a manuscript will bounce back between editor and author a few times. Depending on the journal, the specific guidelines, and the corrections needed, it can take anywhere from a few months to years for a research article to be published.

This dialog is arguably the most integral and important aspect in science communication. It’s essential, really, but the important point to keep in mind is that it’s not infallible. Mistakes are made and it’s not until results are reproduced in other independent labs that important findings are taken as truth in a field. Often, disagreements between laboratories and individuals can arise.

This social discord is a healthy part of the process. For example, in 2011 Science published a report that DNA, the blue print of life, could incorporate the element arsenic into the ‘backbone’ of its structure. It’s fact that DNA’s backbone contains phosphorus and by showing that arsenic could be used in its stead, the authors of this paper argued this was proof that life could have evolved elsewhere in the universe using different starting elements and molecules.

The news sent ripples throughout the scientific community. There were many skeptics and ultimately it was shown that the data could not be reproduced outside of the publishing laboratory. After debate in the field, and multiple attempts by various labs to replicate the results, the results were shown to be nothing more than anomalies. Skeptics of science will note that because of these discrepancies, science can’t be trusted. But independent validation of research results is an integral and important aspect of peer review and in these cases is called post-publication peer review. The editors and peer reviewers at each journal get the data as presentable as possible; the rest is up to the community at large.

However, breakdowns in this entire process do occur and can lead to publication of erroneous data (unfortunately, at times, due to fraud and bias by the publishing authors), which means it very important that the scientific community critically evaluate published work. A landmark paper in 2005, written by Professor John Ioannidis at Stanford University, presented the argument that a large portion of publish research is irreproducible. This set off a flurry of introspection within the scientific community to address the growing problem that some published results can’t be replicated in independent laboratories, just like the arsenic paper. There are even watchdog groups that publicly catalog retractions of journal articles that can’t be reproduced or which contain errors.

That’s not to say that scientists are willfully publishing bad data. Far from it. Papers are retracted for a variety of reasons, including for innocuous errors in experimental design or data collection. So, it’s a very good thing the scientific community polices itself and makes this known to the rest of the world.

But there is no doubt science is facing a reproducibility crisis. Major contributors to this problem are lack of appropriate use of statistics, lack of specific detail in the methods section, and lax peer review at some journals. Journals like Nature have used crisis as an opportunity to shore up their publication and review procedures, including asking for independent validation of key experiments before publication, verification of reagents and chemicals, and open access to all of the data.

Open access is a vital component for peer review and validation. Open access means that all the raw data discussed in a manuscript is provided online for anyone to access it, including you! Anyone in the world can access the data and use it for validation and repeat important experiments.

This type of validation is another aspect of post-publication peer review and it helps identify those papers that need more scrutiny. Journals such as Scientific Reports and PLOS One are entirely open access with their publications and free for anyone, anytime, to download and view.

Some researchers even use a newer innovation called pre-publication peer review. Typically, most scientists can get input on their work before it is published by presenting their data at conferences. However, draft manuscripts can be submitted and published online at places like the bioRxiv, with the hope that people provide critical commentary as the manuscript is prepared for publication elsewhere.

Taking this a step further, Nature Human Behavior published a manifesto on how to improve publication bias, reproducibility, and transparency. Nature Human Behavior has also recently established a new type of peer review process for their registered reports. Researchers can begin the publication process with this journal before any experiments are performed. The research design, methods, and introduction of a manuscript are written before any experiments and are peer reviewed by the journal’s editors and external reviewers. Then, and only then, is the experiment performed, the results analyzed and examined, and the rest of the paper written. The entire manuscript is put under peer review again to check for adherence and then published regardless of the findings, positive or negative.

In this way, Nature Human Behavior hopes to reduce experimental bias and increase reproducibility, all using the standard peer review process. I expect to see more innovations like this adopted by more journals in the coming years.

To wrap up, I hope this has helped clarify a little about what peer review really is and why it’s so important. Coming up in the coming weeks and months, we’ll explore a variety of topics and findings in science and all of it will have been examined by peer review.