In this next module, we're going to talk about writing the Methods section. The Methods and Materials section should give a clear overview of what was done. It is the recipe for the study. It gives sufficient information so that someone else could replicate the study. You want to be complete in your materials and methods section. You want to give enough information that somebody can replicate your study, but try to minimize the complexity. Try to make life as easy as possible for your reader. So there's a couple of things you can do to make life easy for your reader. You can do things like break your methods into smaller sections with subheadings or cite a reference for commonly used methods rather than going into all the details of a well known method. And wherever possible, display methods information in a flow diagram or even a table. Get creative! There are a lot of things in the methods and materials section that are better presented as a table or flow diagram Rather than as text. Finally, in the methods section, we're going to jump ship on some of the things that I've told you before. The materials and methods section is the one place where you may opt to use the passive voice, and where you may use jargon more liberally. At the start of this unit, I mentioned a series of articles that are about the different parts of the scientific manuscript. That was written by Thomas Ansley in the journal Clinical Chemistry. This series is freely available online and it's not just for chemists. And I've pulled a few key figures from his articles that I really like. This is a busy slide and I'm not going to go over it in detail, but I'll leave it for you to peruse, because I really like how he's framed the method section. He thinks of it as the who, what, when, where, how and why of your paper. And he goes into details for each of those. Who maintained the records? What was used? When was it done? Where were the records kept? This is a nice checklist to go through. As you're writhing your method section. What do you need in your materials and methods section? You need to give information about the materials, things like drugs, buffers, chemicals, gasses, reagents, Sell wines. You need to give specifics like pH, temperature, ingredients, doses, all of those things. It's a recipe, so they need the exact specifics so they can recreate it. If your research involves human or animal subjects, you'll need to state that the research was approved by the appropriate ethics committee at your institution. You actually need a official statement of that in your method section. You also need to give details about the experimental protocol. You need to say also how you measured you variables. How did you measure your dependent and independent variables? What instruments did you use? Telescopes, microscopes, weighing scales, questionnaires, etc. And then finally, what analysis did you do? How did you analyze your data at the end of the day? The exact components of materials and methods will, of course, differ depending on your discipline. So I'm just giving you a broad overview here. But these are the basic elements that you might see. As I've said before, I want to encourage you to make life easy for your reader. The method section is not the most fun section to read it's likely that your reader is just going to skim the methods section to look for the key things that they want to know. So one way to help your reader navigate the methods is to break your method section into subsection Section within formative subheadings. We just going to give some examples of this, so this was from a paper and viruses, so their subsections where they had general approach, biosafety, isolation of the virus Serologic Analysis, Pathological and Immunohistochemical Studies and Molecular Analyses. The reader then can easily find what ever they need to because they can just go to one of those subsections. Here's another example. This one was looking at flying albatrosses. So they have subjects and experimental protocols. The subjects here are the flying albatrosses. Then hardware, and then they were using GPS tracking. So they had to say how they were processing the GPS data. And then, wind was a very important variable here because we're talking about flying. One more set of sub-heading, just as an example. This one had cell culture and transfections, antibodies, plasmids, recombinant virus production and infection, and so on and so forth. But you get the idea. Whatever your topic, breaking the methods into subsections is a good way to go. Another way to make life easy for you reader is for commonly used methods or methods you've already described in a previous paper. You could refer the reader to those references rather than going into all the details. This works especially well if you can assume that most of your readership is already familiar with the method. It may help the reader to not have to read through a large number of experimental details that are already well-documented elsewhere. And what would this look like in the paper? Well, when you get to the method that's already well-known, you can just say as previously described and give readers the reference, and I'm giving you two examples here. It helps with concision. Another way to make life easy for your readers is to use flow diagrams or tables, to help simplify the explanation of methods. One common flow chart that you see in clinical studies is the a participant flow chart which shows how participants flowed through your study. Here 174 persons were asked to participate, 103 enrolled, and 97 completed all the labs. You can see that it's incredibly easy to glean information. Formation from a diagram like this, imagine if the same information was presented in text. It would be hard to read through and make sense of. And it would also be really boring to read. A picture is much more efficient for imparting this kind of information. Now, your comments we'll see participants flow diagrams like this in papers. But there are probably many other instances where we ought to make more use of diagrams. If you have studies with complex experimental protocols, complex dosing of drugs, this information might be better in a diagram or a table. So be creative, and look for instances where you can represent experimental details visually. The verb tense for the method section is exactly the same as in the results section. You're going to report methods that are already completed in the past tense, because they are already done. So we measured, we enrolled, we analyzed, and so on. But you're going to use the present tense to describe how the data are presented in the paper. Because when the reader reads the paper, the data are still presented in that way. So you would say the data are summarized as, notice the passive voice there. That's in the present tense, because the data are still summarized that way when the reader is reading the paper. All right, so I've been admonishing you about the use of passive verbs. But now, I'm going to tell you that for the method section it's actually okay to use the passive voice or even a combination of passive and active. It's fine to go back and forth between passive and active as long as it's not too jarring on the reader. There's a couple of reasons why I'm okay with the passive voice in the method section. One is that in the passive voice, it emphasize the what is measured, the what was done, rather than who did it. And arguably, what was done is more important than who did it. For example, oral temperatures were measured. That's in the passive voice. That emphasizes the oral temperatures as opposed to the researchers who was taking the temperatures. The active voice here would be we measured oral temperatures. And that's okay, it's more lively I think but again, it feels to emphasized the material method or variable of Interest and one could argue that you want to emphasize that material or method in the method section. The other reason that I think it's okay to use the passive voice here is that most people don't read the method section word for word. So it's okay, I think, if the method section is a little boring. You can expect that your readers just going to skim the method's section for the key things that they want more information on. Also, in the active voice, the method section may end up with most sentences starting with we. If you try to put it in the active voice, you're going to have a lot of we measure. We observe, we analyze. That's fine to have a lot of sentences starting with we, but it's also a little boring. And if you're very creative, you can find ways to avoid starting every sentence with we, but I'm not sure it's worth that effort. So just to give you an example of a method section with lots of passive voice and jargon. We have the peptides were synthesized by the Biopolymer Core Facility. Now, we get a lot of jargon here, we get another passive voice, were coupled to and then keyhole limpet. Hemocyanin, which I don't know what that is, but the jargon is okay here, we need the jargon here. And again, it's okay I think to put this in the passive voice. Just to show you an example where the active voice was used in the method section, you can use the active voice in the method section. Here's a fun example that relies mostly on the active voice. For this unit, I'm going to pull a few examples from the British Medical Journal, the BMJ Christmas Issue. And if you're not familiar with the BMJ Christmas Issue, it publishes humorous research. So they make for some fun examples. And this is from a paper on academic spam. Just to give you a little background, I like many scientists get multiple emails a day requesting that I submit a paper to some journal or attend some conference. And most of these are completely unrelated to what I do and are basically spam. And I just delete these. But in the 2016 BMJ Christmas issue for fun. So researchers actually studies this phenomenon more systematically, and here's a paragraph from their results section. They write, we assessed the number of spam emails received in each collection phase. Detailed analysis was undertaken of spam received in April 2014, June 2014, and April 2015. The investigators rated their spam and invitations as being of no, low, medium, or high relevance to their academic careers. We determined the number of duplicate spam invitations. When possible, we recorded the publisher for journal invitations and organizing body for conference invitations. Finally, we conducted a qualitative analysis. Focusing on memorable spam. I think this works just fine. It's mostly in the active voice notice of the second sentence. Does switch to the passive voice so again, it's okay to switch if it's not too jarring on your reader. You'll notice that they also did end up using we an awful lot as the subject in the sentence. But I think it reads well and it's easy to understand. And it's okay that they have a number of sentences starting with we. So there are certainly many ways to put the methods in the active voice, and the choice is really up to you. I'm just going to end here with a little bit more detail on academic spam. I'm going to use this study on academic spam as an example in some of the upcoming modules. Again, it's from the BMJ Christmas Issue so, it's meant to be humorous. It's a short paper that accurately follows this standard format of a scientific manuscript and it's fun, so it makes a great example. So just for you to understand the context every time I bring this study up, I went into my email box today and pulled out two academic spam emails that I received yesterday. I'm showing you those here so you'll know what I'm talking about when I refer to this academic spam study. The first one on the left here was set with high importance and it says, greetings for the day, hope you are doing well, two exclamation points after greetings for the day. With the support of editorial board members and organizing committee, we would like welcome you, you can see that it's grammatically incorrect on that one, we wish if you could join as a keynote speaker in this grand event. The one on the right, very similar. It says, this 2017 may you output the best papers of your career and get the best number of citations. We sincerely hope this to be true and many more good things happen to you in this year. And you can see that these are very funny and clearly spam. You get the idea. So one of the papers I'm going to be using as an example this week is going to be about academic spam.