How do scientific papers get published?

I had a busy week last week.  Besides doing experiments, I was also working on a manuscript about sustainability in biobanking. I’ve talked in other posts about what a scientific paper generally looks like (see here), but not what it takes to get from experiments in the lab to publication.  This is what I’m going to talk about today.

First, you have to know enough of the field to have an understanding of what is known and not known.  Second, you have to identify a hole in that knowledge that you could fill by doing experiments to test hypotheses. Third, you needed to do well-controlled experiments that will hold up to careful analysis.  These will be the basis of your manuscript’s results section.


From the NYT article

Let’s talk about this point a bit more, but first, go to the New York Times and take this little puzzle (it’ll only take a minute or so). This puzzle boils down the essence of doing a good experiment.  You start with a hypothesis (e.g., the numbers are all even). You test that hypothesis and see the result. If you get a negative result, you come up with a new hypothesis and test that.  If it’s a positive result, you can do a few things.  You can decide that your hypothesis is correct and try to guess the answer or, in the case of the laboratory, publish a paper about your new amazing result.  However, it won’t get published because you could be wrong. You will have to find other ways to confirm your hypothesis using different or complimentary experiments.  You should also do your best to disprove your hypothesis. Even in the NYT puzzle, you should try to find negative results. This will help you better understand the limitations of your hypothesis and the results you obtain.  In the lab, it will likely also lead you down roads of abject failure that will never see the light of day, but that’s the reality of science.

Now that you have your experiments completed, your forth step is to actually write the paper.  My undergraduate research adviser always had a draft outline of the paper in process as experiments were being done. That way, he could fill in results as he went along. Most researchers aren’t that organized and they get to writing the paper when their adviser (or the head of the lab) looks at them essentially tells them to “get their butt in gear and write the damn paper, already!” Why is starting a manuscript so difficult? Mostly because it involves synthesizing information. Results on their own are beautiful pieces of success that could go anywhere and do anything.  Synthesizing these into a “story” and discussing the implications of these results on the broader field is hard work. And the wrong analysis can affect the chances of the paper being published or your reputation in the field.

The other challenge when starting to write is figuring out what journal to submit the manuscript to – and keep in mind, there are thousands of possibilities.  Depending on the scientific significance, novelty of the results, and general scientific interest, you may submit your paper to one of the top journals (like Nature, Science or Cell) or you may submit to one that isn’t.  Maybe you’re wondering why this matters?  Each journal has an impact factor, which indicates how often papers published in that journal get cited by other authors.  The more prestigious the journal, the more citations your paper gets, indicating generally, that your research is more influential.  This affects how likely it is for you to (fill in the blank): get a job, get tenure, get invited to give talks at meetings around the world, get a raise, get more grants, get more students, be more successful overall etc. Therefore, the higher the impact factor, the more likely it is for you to become a wildly famous (in the ideal) or successful (in reality) scientist.


The first page of a publication I wrote about the DNASU plasmid repository published in the journal Nucleic Acids Research

Once the journal is decided upon, and the manuscript is reformatted to fit the requirements of that journal (which is a whole other pain in the butt sometimes requiring you to cut the manuscript length by 60%) you submit your manuscript and wait. And you may wait a long time.  I’m not a journal editor so I can’t provide all the insider details, but once at the journal there are  levels of review.  Internal reviews by the journal editors sending the manuscript out for review by other scientists in the field, additional editorial review, etc.  At each stage the manuscript can be rejected and each step takes time.

The manuscript reviewers take on an essential role in the scientific process. They help to ensure that the research is high quality and that the claims made in the paper are valid and supported by evidence. Any scientist can be a reviewers (I’ve reviewed a half a dozen manuscripts), but they should ideally have knowledge of the scientific topic being addressed in the manuscript. Typically each manuscript that is sent out to review to three scientists, and they each anonymously provide their comments back to you and to the editors.  This is where the process can get messy.  The reviewers could just flat out suggest your paper should be rejected or accepted.  Then again (and more likely), they may ask for edits – these can be as simple as fixing typos and adding a few clarifying sentences to doing years worth of additional experiments. And the reviewers may not agree – one reviewer could accept the manuscript, one could reject it and one could ask for edits.  It’s then up to the journal editor to decide what to do. For more about reviewers, check out this Sci Snippet about who these reviewers actually are and the crazy things they sometimes do and say.

When you get the reviews back, if your paper hasn’t been immediately accepted, you can choose to make edits, do the suggested experiments and resubmit to the same journal.  If this is your choice, just by re-submission, you are not guaranteed to have your paper accepted.  You may spend months doing experiments, just to have your manuscript rejected at the end of the day.  If the reviewer comments are too negative or the paper was rejected, you may realize that you set your sights too high and you should submit to a different journal that may have a higher likelihood of acceptance.  At that point, you start the review process all over again.

If this sounds frustrating to you, it is.  I have friends who have had papers in the review, edit, review process for over a year.  I have friends who have submitted papers over and over and haven’t been able to get them published. I also have friends that submit to a high profile journal and get accepted right out of the gate.  However, with the stakes being so high and affecting you scientific career so directly, the publishing process is a necessary frustration and if done correctly, can make your science and your research better.


7 Fun and Interesting Science Websites

I spend a lot of time on my computer; most of my day at work, a few hours when I get home, and every weekend writing this blog and working. Like everyone else, I have high hopes that I’ll focus and power through the day without surfing the web, but I fail miserably every time.  Besides my go-to fluffy news and fun sites (SlateNot Always Working, Dooce), I try, at the very least, to stay on topic and look at science-related website.  Often this means browsing the Table of Contents for hardcore science journals like Nature, Science or Cell, but more often lately, I’m looking at interesting general science websites with stories posted by my scientist friends on Facebook or Twitter. I realize that you, my readers, may not have hundreds of scientist friends regularly sharing  science posts, links and websites with you over social media, so I’ll share some today. Here are seven fun websites that I think you might enjoy.

IFLScience1. I F**king Love Science (IFLScience)

With 21 million followers on Facebook, I’m guessing you’ve heard of this one, but if not, it deserves a follow.  Although there has been some recent controversy about IFLScience posting inaccurate or misleading stories and then failing to correct them, overall this is a fun site that posts multiple times a day about topics from health to space an everything in between.

Ignobel2. Ig Nobel Awards  

Some people wait all year to find out who gets nominated for the Academy Awards and they throw Oscar parties to see who won.  As stereotypical as it may sound, I have that level of excitement for the Nobel Prize announcements. The Nobel website is great, but since I’m guessing you aren’t as obsessed with this yearly event as I am, I’m going to suggest the Ig Nobel Award website instead! Modeled after the Noble Prizes, these awards highlight improbable research that also makes you think. For example, this year the Ig Nobel for Medicine went to researchers in India for treating “uncontrollable” nosebleeds, using the method of nasal-packing-with-strips-of-cured-pork (aka bacon). REALLY FUNNY!

radiolab3. Radiolab

Technically Radiolab is a podcast on NPR, but they do have a website with archives of their podcasts. The two hosts Jad Abumrad and Robert Krulwich are amazing storytellers who focus each of their episodes on a single topic like Sleep or Speed or Sperm. What’s so creative is how they use sound throughout their stories to bring the science to life. I saw them speak about science communication at a meeting, and they ended their presentation with a video that was created based on their episode about Death call Moments. Watch it. It’s incredible.

wired4. Wired Science Section

Wired is a magazine for nerds, and since I’m a total nerd, I love it. vWhat I like the most is that they weave an interesting story without forgoing the important details when dealing with complicated scientific topics, for example, the recent article on the genome editing system CRISPR. I know a lot about CRISPR and genome editing, and I didn’t feel like they watered the topic down, but it was still accessible to a non-scientific audience.

scientificamerican5. Scientific American

One of a few popular science magazines, this is the only one that I look at regularly The articles are fun to read plus in every issue they have a profile of a scientist, which I think is a pretty great way to help people get to know who scientists are as people.  Also, in honor of Jon Stewart leaving the Daily Show (*sigh*), they posted the Top 10 list of  best Science Moments from the show. What’s better than that for Daily Show withdrawal?

NYT6. The New York Times

I love the science section of The New York Times. Matt Ridley (who wrote one of my book club choices Genome), Carl Zimmer and Gina Kolata are only three of many fabulous science journalists who take the time to research a story extraordinarily well providing a real depth and understanding in their pieces.

sciencemag7. News sections for Nature and Science

I know that I said that Nature and Science are hardcore science-for-scientists website, but their News sections hit on the top stories of the week and are more accessible than the science articles.  They also compile in-depth special sections, like the recent “Ebola: Did we Learn?” that has articles about the new Ebola vaccine, what we learned from this ebola pandemic, and how we might respond better next time.

Why did I choose these websites and not others?  Mostly because they were the first that came to mind.  There are thousands of others, and many are listed on the sidebar of this blog. I will also post lists like this every so often so you can get more info about some of these sites.  And please share in the comments your favorite science websites!