Hello again! Welcome to Post #4 at ‘The Canadian Postdoc’ where I try to make science relatable and sometimes even fun.

I’ve had some excellent feedback about the blog from some very smart people and I was happy to see a decent number of people read my piece on the Stem cell controversy. On the advice of a fellow blogger, I am going to try and cut down on my length on these things. Sometime I just get excited and ramble, so I’ll try to cut down on that from now on, even if it takes me 2-3 posts to get through a topic.

As the stem cell controversy was going on, I’d been spending a little bit of time reading comments, tweets, and reddit posts about the situation, and one thing kept coming up. It became obvious after a while that some people don’t really understand how a scientific paper goes from an idea, to a manuscript, through peer-review, and into a scientific journal.

It’s also clear that some people don’t really understand what primary literature IS, let alone where to find it, or even understand it. So today I’m going to delve into that a little, and I promise, I’ll keep it brief.

Scientific Publications

You’ve probably got a couple of friends, or at least know someone who tells you to ‘read the primary literature!’ (well, I know I do), but what exactly does that MEAN?

Primary literature is the stuff of science. It’s the articles written by scientists, for scientists, and is typically reviewed by scientists. So last time when I talked about Nature as a journal, that’s what I meant. Now, it gets kind of difficult for the general public to get access to these, as the subscriptions are sometimes ludicrously high.On the other hand, there is a new phenomenon called “Open Source Journals”, which allow free access for the public. One of the biggest is PLoS, or the Public Library of Science.

So there you have it, that’s a primary source. Of course there are other sources out there, for instance, my blog, while it may be accurate, and may be well referenced is a ‘secondary source’ or even a ‘tertiary source’. That means that I go to primary, and sometimes secondary sources for information, and then relay them to you. So you can’t really reference my blog as a source, because a lot of it may be opinion based. This of course is a problem in many debates. Primary literature is what you should be looking at to make an informed opinion, or at the very least, well written secondary literature that consistently and accurately references primary material.

Okay, so now that that’s established. How does an idea get from your head, to the lab, and then to publication? Well let’s walk through the process. (Most of this information is from my own experience and knowledge, so if I get anything wrong, feel free to comment)

A laboratory makes a discovery. A good lab will repeat the experiment that showed the discovery 3-4 times to make certain it wasn’t something weird with the experiment, and to get enough data to run the proper statistics. You never want to rush into publication with something you haven’t replicated a number of times yourself. You write the manuscript and include authors on the paper. Typically (at least typical in the biology world), the person who did the most work, and writes the paper comes first, usually this is a graduate student (someone doing a Masters or Ph.D), or a post-doc (see my first blog post if you’re unsure what a post-doc is). The last author is almost always the supervisor, or Professor who runs the lab. Everyone in between are the contributors, someone who gave intellectual input during the process, or helped carry out the experiments. You’ve produced your data, you’ve written your paper, you’re polished that paper until it shines. Now you need to decide where to publish it. From a geneticist/biologist point of view, you have a tonne of options. You can go somewhere with a general genetics readership like the American Journal of Human Genetics, or if your paper is REALLY good, Nature Genetics or Cell. You can also publish in a specialty journal (eyes, viruses, etc.), where the general readership may not be as big, but there will be more people who will be in your field, and will find your work more useful. Journals are typically graded on a scale called “Impact Factor”, which essentially boils down to ‘how many people per year reference articles in your journal’. Which makes sense. If you publish good papers, more people will read them, and use them as references in their own papers. A good Impact score ranges from about 3-10. A GREAT score is about 30-40, for instance, Nature Genetics as of today is listed as 41.063

Finally, you’ve submitted your paper to a journal, so what happens now? A number of steps happen once you’ve submitted your paper, and this is called “Peer Review”. It’s exactly as it sounds, your paper will be read, reviewed, and scrutinized by people in the scientific community. So since I’m on a kick for number lists today, here’s another:

Once your paper is submitted, it is first sent to the journal editor. This person is effectively the journal’s gatekeeper: The journal editor is the first line of defense for a journal. He/She will usually take a quick read of the paper (keep in mind that they probably see hundreds to thousands of paper a year), and determine whether the paper is suitable for the scope of the journal (did you submit a liver disease paper to an eye journal? shame on you! REJECTED), or if it’s up to snuff (i.e. if the science is sexy enough for their journal considering their readership). Your paper is sent by the journal to a panel of (usually two or three) reviewers. This process is entirely blind, so you never know who the reviewers of your paper are (though sometimes you can probably guess). The reviewers can be suggested by you when you submit your paper (to write a paper, you obviously have to read a lot, so you’ll generally know who would be suitable), some journals will also allow you to recommend people to NOT review your paper. If there’s someone you don’t get along with, or have a bad experience with, you may want to list them in this section when you submit. The review process can take anywhere from two to eight weeks, in my experience. This gives ample time for reviewers to read the paper, analyze the figures, and decide whether or not the paper is suited for publication. The reviewers usually decide one of four things:

i) Accepted without revision (rare)

ii) Accepted with revisions (minor or major)

iii) Major revisions, which will be reviewed again (this will usually require additional experiments/data)

iv) Reject You’ll get a notification as to what the reviewers thought, along with the comments. If you’ve been determined as either ii) or iii), you’ll get a chance to fix the paper, add in new figures or data, and then respond to the reviewers. Sometimes, reviewers can be very helpful, other times they can be vague, or even hateful, but 80-90% of the time, the comments are very cordial and helpful. You then resubmit your manuscript, and it is reviewed a second time, and may come back for further additions/changes if necessary. Steps 2-3 keep happening over and over until your manuscript meets the necessary quality for the journal, or you’re finally rejected. Yes. After 4-5 revisions, you can actually be rejected. It doesn’t happen often, but it can happen. Usually you’ll come out the other side with a much strong paper, accepted or not.

Hopefully this all leads to a publication in a scientific journal, where fellow scientists can read, enjoy, and most importantly, use, your data and findings for future experiments. So really, the point of this whole post was to show you what goes into a scientific publication. Once you’ve actually prepared your manuscript, it can take anywhere from three to eight months, dependent on speed of reviews, deadlines, and press-setting (actually make it fit onto a page nice and neat for the journal).

As I said before, THESE are the sources that you should be referencing if you want to make an informed opinion. If you find them hard to understand, and frankly they are hard to understand if you’re not acquainted with the knowledge or language, look for places like this blog to try and break it down. Is there a paper or topic you’d like to see broken down? A scientific discovery you’d like to see covered? Well, let me know! I’ll leave a contact form below which will be sent directly to my email and you can ask anything you like! Thanks again for reading!