 Yes, my writing's all done. I've got a complete manuscript. It's the right length. It says everything I need. I've got the figures I've got the abstract. I've got the title. What more could I need to do? Huh, I haven't edited anything yet. Uh, I can only imagine what the text actually reads like now that I haven't looked at it for a month Well in today's episode, I'm gonna share with you my top 10 tips to better and more effective editing Stay tuned to PIs because there's a little rant for you at the end Hey folks, I'm Pat Schloss. Over the past several months, I've been working on a manuscript here on YouTube You can go back and look at the previous 60 or so episodes to see its evolution Recently, we've completed all of the text. All of the text is there in the manuscript but As I look back over the text, it looks a little bit like a Frankenstein's monster There's a little bit of this, a little bit of that. Maybe it doesn't quite flow that well My process of writing is to get all the text down that I can without editing myself as I write I've done very little editing as I've gone The reason I do this is because I find that if I'm editing my text as I write well Then I run into the problem of just constantly editing and wordsmithing every sentence and I then don't get very far For me and I find for trainees that work with me and my collaborators That it's most effective to get the text down and then to go back and do a lot of editing to clean things up Like I said, it's a lot of editing so what I want to share with you today are 10 tips that you can use to make your editing more effective and You know if you follow these tips What I think you'll find is that the next time you write a manuscript that your writing will be even better tip number one Editing should be iterative. I find that when I'm editing the first time through or the first several times through That I make a lot of changes There's a cat Steven song that was covered by Cheryl Crowe and a number of others from when I was in high school Cheryl Crowe Called the first cut is the deepest that is certainly true with writing as I've been editing this manuscript I've had that song Just going through my head constantly the first cut is the deepest It's enough singing anyway. So know that initially you're going to make lots of changes your manuscript is not perfect It is not ready to submit. It needs a lot of work still. I Prefer to edit the text text directly in the manuscript On a physical document. So I like to use my iPad I also like to print things off and have some physical tangible thing that I can work with I find that if I'm doing things electronically like in a word processor That I kind of lose sight of the overall thing Manuscript and I I easily get distracted right I go to the web. I go to other sections of the paper I just get easily distracted and so by having this kind of physical token of my writing that I can interact with I Find that I make much better edits and that the process goes much more smoothly as I share with you what mine looks like Here on my iPad You'll see that I've got a variety of things highlighted for things. I need to come back to I've got things in red to stand out to me. Some people don't like red. So, you know, use whatever color works It's a nice contrast in color And then I've got a fair amount of text in here One other thing that I do is I write as you saw when I was talking about inserting references They like to leave in placeholders Kind of like what I have here For this text right I didn't exactly know the E coli coordinates that I was referring to so I put an xxx again If I spent the time then to go back and find the coordinates that would have like totally killed my momentum in writing But now I can come back and I can I can fill in those X's right So there's a variety of those things that I need to fill in Version numbers and things like that as I go through the editing the amount of editing I do will hopefully become less and less until I get to a point where it looks pretty clean and Perhaps I've got a headache from looking at it so many times and I'm just like Let's move on to something else tip number two Let it breathe as I just said sometimes I edit so many times and so many Interpretations that I got a headache and I'm just sick of looking at the thing right well a few episodes ago I was talking about this also in terms of my analysis and letting the analysis breathe and giving it a chance to percolate and kind of Ruminate on that and to think about what the analysis actually says to make sure everything fits together Well, if I put the manuscript to the side for a few days and then come back to it I'll read sentences. I'll be like what the heck did that mean? So as an example in my abstract, I noticed that I had a sentence right here in the middle That doesn't really add anything doesn't really say anything and I'm not exactly sure what that meant to say I think that was supposed to be a statement Summarizing all the results, but as I can already see I'm gonna be doing some other editing this abstract I think was exactly 249 words so one letter one word underneath the limit And so I could get rid of those seven or eight words and and kind of perhaps Free up the text a little bit in case I need to add things But again by giving the text some room to breathe I see sentences in here that don't make any sense oftentimes what I'm looking for are subjects Where I'm assuming that the reader knows what the subject of the verb is But again looking at it with fresh eyes. It's not quite clear what the subject of that sentence is Tip number three strengthen your sentences by putting the action up front again Looking at my abstract here. I See a sentence Right around here right for full length 16 s aren't any gene sequences. There was an average blah blah blah of that gene, right? So Where's the action? Where's the most important part right? I think it's back here at the end, right? So there was an average of point six ASVs per copy of the six chance RNA gene For full-length sequences, right? So the most important thing in that sentence is that as you find more Copies of the 16 s gene in a genome you're gonna find more ASVs, right? And so I want to move that up front in the sentence People talk about in journalism. Don't bury the lead. Well, I think each sentence kind of has a lead So don't bury the lead don't bury the important part at the end put the action up front by the same token I'm not a fan of saying as figure one shows blah blah blah blah blah Like you're kind of just killing the momentum of the sentence when you say that Say what the figure shows and then at the end of the sentence in parentheses put figure one, right? So again, put the action up in front of the sentence and that way your reader knows what's most important as they're reading through your document Tip four get your tenses right. I know this is like elementary school My kids are working on tenses as they're learning writing skills themselves in elementary school in junior high For most scientific writing the tenths should be past tense the work that we did we did in the past, right? Rarely very rarely do you want something to be future tense future tense would be for things like in the future We will do x y and z or someone else should x y and z and that will be future tense Sometimes we do use present tense and that would be for kind of statements of fact, right? So like E. Coli has seven copies of the 16s RNA gene, right? That is a it's not in the past right E. Coli used to have seven copies and now it has something else But it does have seven copies. So as I look through my own document here I find several cases where I botched the text. So for example right about here I say at the time of submission. This is the most current version of the database. Well Someone's gonna be reading this in the future past the time of submission, right? So I should say at the time of submission, this was the most current version of the database And we can kind of go through that elsewhere again the kind of two sentences later the rndb provides Could instead say well at the time that I wrote this it provided downloadable versions and again going through the manuscript and thinking about When did this event occur? Did it happen in the past? Well, it should be in the past. Is this a generalizable fact? That should be in the present tense up here in my intro I do have an example of using present tense, right? So one an example of both is seen in the comparison of Staph aureus and Staph epidermis where each genome has present tense five copies of the sixty-nose RNA gene, okay? So again most of the time your tense should be in the past If it's a statement of fact, it's usually present very very rarely is it going to be a future tense? Tip number five vary your sentence length, but ten towards shorter sentences It's very difficult to keep track of concepts subjects of the direct objects or end up in direct objects in long convoluted sentences Maybe I'm just too simple, but I like short punchy sentences the same time if everything is a short punchy sentence Then it becomes like see dick run see Jane toss right and that's kind of too simple, right? But as kind of a general principle, we're also looking for wordiness and we don't want overly wordy sentences You know so an example would be in order to blah blah blah to say to Right in order to test this hypothesis replace that with to test this hypothesis There's no need for those extra words an example here in my manuscript Is here on page 4 at line 96? This makes it more challenging to attempt to fit a distance threshold, right? So I could just say this makes it challenging to fit a distance threshold or this makes it impossible to fit a distance threshold, right? I can remove four words and replace it with one. That's a win Of course as we're editing and making things more compact We don't want to make it so compact that we again confuse the reader by dropping out useful information like what is the subject of the sentence? Tip number six forget what Mrs. Shaw taught you in high school English. Mrs. Shaw was a dear woman She was my sophomore year English high school teacher. She had sheep. Maybe that's part of the reason I have sheep Who knows but she was a great woman, but What she taught me in writing probably didn't serve me super well in the long term for scientific writing, right? So we don't want to be flowery with our languages. We don't want to use lots of adjectives We don't want to change up our vocabulary. We want to be consistent We want to be tight We are not writing the great American novel, right? I am not writing this great Pros that's flowing like poetry. I'm writing a scientific manuscript that should be direct and to the point one of the big problems that I have especially with my writing strategy of kind of writing in parts Before I edit is being consistent with my terminology an example that I find in this manuscript Is what am I calling the things that we split that ASV is split genomes into right so in the title I say unit of inference Further down I say clusters elsewhere. I say bin right and An on and on and on right and I've got unit of inference in the text as well. So I Need to tighten that up and be consistent in my language You might think well, it needs to be more variety or it's going to be boring But instead of being boring and lively by using lots of different terms for the same thing It becomes confusing because someone might read this and say well What's the difference between a unit of inference and a cluster or a bin? He's got these three different terms So if I limit that to one term that it's much clearer to my reader what I'm actually saying So I'm not sure what I want to use do I want to use unit of inference cluster or bin So what I did was I took this title and I gave it to my lab In a slack channel as I did in the last episode when I was kind of testing different titles and my lab came through with Responses to these three titles that I wrote and I find that most of the people in the lab Prefer example to where I say clusters and I think clusters where it's at because it's it's clear that this is a cluster of Sequences related sequences, and I think that's what I'll go with and I'll I'll trust their judgment Kelly in my lab gave a good comment that she likes clusters because we talked about Clustering sequences into O2 use so that title then with clusters has more of a nod to O2 use as the alternative to ASVs than the other options, and so she's right I don't mention O2 use in these three different titles And so again having clusters is more of a nod to having O2 use and I think she's right And I think the lab agreed with her so we'll run with example 2 Tip 7 enlist a friend to read your manuscript before you give it to a collaborator or your PI When you do this, it's a two-way street. So first tell your friend what you want help with Are you looking for copy editing where you want them to correct your grammar and your punctuation? Do they you want them to tell you that you haven't italicized your bacterial names? Or are you looking for more structural information? Right, there's no need doing copy editing if you still have questions about the structure of the manuscript If you're looking for the overall flow of the story That's more of a structural question than copy editing It's critical critical critical that you tell your friend and that you trust them and that you will not be hurt by Any feedback they give you because your writing might suck Right my writing often sucks. This manuscript sucks in its current writing and that's why I have so many edits We need to be professional about that if you're asking somebody for help you should be willing to take the help Okay, so tell them that you're willing to take any critique you give them Tell them, you know it's rough, but you need their help to make it better now friend. I'm talking to you now Be honest with your with the person giving you the manuscript You do them no favors you give them no favors by handing them back a manuscript with minimal edits They know the manuscript is bad. That's why they gave it to you for help They did not give you the manuscript so that you could say this is amazing This should be published in like cell-nature science, right? No, they gave it to you because they need your help give them help Not putting comments is not helpful Fill that thing with comments and so that they can learn and they can do better And they'll do the same thing for you when you give them a manuscript Tip number eight change things up a bit. I talked about letting your document breathe Well, sometimes we don't have the the time to let things breathe for weeks, right? And we kind of want to move this story along and get the thing submitted So what can you do to help change things up a bit? Well, you can change the font you can change the margins You can change the font size what that does psychologically is it allows you then to see Phrases in different contexts as you read a manuscript over and over again in the same format You know where all the sentences are you kind of memorize the structure of your manuscript and then as you read you gloss over different things But by changing the font the size the orientation the margins those types of things you now see the manuscript in a different light because those phrases aren't kind of Lockdown or anchored to the place you expected them in the manuscript. I've been writing my manuscript in our markdown It's written as a text file again. That's one of the things that helps me avoid I was spending too much time on editing especially things like bolding and italics It also gives me a lot of power and the ability to put our code and output directly into my text. Anyway In this header, I can do a variety of things to change the format So these two lines on lines 9 and 10 are giving me a Helvetica or or sans-serif font I can comment those out. I could also make my font size at 12 point to make my margin one and a half inches And so then I can make my manuscript And we'll then see how that changes the appearance of the manuscript So that again, what we're looking for is to see sentences in different places Of the manuscript so that I I don't gloss over that text when I edit it. So again now we have a serif font We've got wider margins, which kind of moves things around a little bit Instead of being on like three fourths of a page my abstract and important sections are now over a page and again, I can then take this and edit it and By using the different font and structure to the document I can then see text anchored to different points in the manuscript to again Help me to see things with new eyes and then before I submit I'll go ahead and put it back to the format that I want to put it in Usually adhering to the recommendations of the instructions to authors for the journal I'm submitting to so here's another question for you all If you're a trainee or a junior scientist What's one thing that you wish your PI could do to help you write better and to make the editing process easier? Conversely if you have PI, what do you wish your trainees knew about writing, right? So what's something that you if you could tell people coming into your lab that you wanted them to know about writing? What's the tip that you would give them and feel free to put all that information down in the comments below Because maybe, you know, we could accumulate these ideas and we could share them with people and we could do another video to kind of summarize People's ideas. So if you're a PI and your trainees don't know this bit of information Why don't they tell them tell them and if you're a trainee and you wish your PI knew something You might think of ways that you can constructively tell them what information you need To improve your writing. We call that mentoring up. I believe right, okay? The final two tips are gonna be a little bit controversial, but stick with me. I think it's important tip number nine Don't use track changes. I know this is controversial Most people will think what the hell is Pat talking about but really don't use track changes I think it's I think it's a crutch and I do not think it helps anybody So first of all if you take things from your trainees perspective And and they get a document back that you have made all sorts of modifications on say in a Microsoft Word document What are they gonna do right? Are they empowered to say no Pat's an idiot. I'm not gonna change this No, they're most likely gonna just change everything And and not learn a whole lot from that process and they perhaps don't feel empowered to push back and say hey Pat You know, I wrote the sentence this way because of X Y and Z I mean, I hope they would but the reality is probably that they're not going to The other thing is that track changes then become a bit of a bulldozer, right? So I get your document. I put it in a Microsoft Word I start making all sorts of changes and then fire it back to you There isn't much give and take there isn't much learning Inherent in that process. So I like to work on an iPad or on printed material as I said earlier and When I when I do this it really slows me down because I write by hand much slower than I type and I I don't want to give my trainee a sea of red ink, right? I don't want to give them a bazillion track changes I also don't want to write the paper for them. I've got my own stuff to write I've got my own things to do and I you know, perhaps I can write the paper for them or do a lot of heavy copy editing for Them on this paper, but what's that gonna do for the next paper, right? Not much So what my strategy is working with a trainee is that I will spend an hour working on the document and I'll start maybe At the title or the abstract and go as far as I can or maybe I'll start with the results section and kind of Work outwards kind of in the process that I would write And as I'm reading that I'm not gonna be so focused on the first couple iterations of the manuscript on Copyediting or wording of things I might you know notice things and I'm gonna leave comments more in the margins We're all highlight examples and say, you know You're using all sorts of tenses throughout here or you're burying the lead like I said earlier, right? And I'll highlight examples and then I'll give it back to them after I've worked on it for like an hour and say These are some things I noticed Rework the manuscript with these things in mind and then give it back to me and we'll do this give and take many times Eventually we do get to a point where we are ready to do copy editing and work on the wording But again doing the track changes is just it's just a bulldozer, right? And it's not teaching the trainee anything about the writing process by giving them comments and then asking them to see an example See how I would fix the example and then work on that through the rest of the manuscript I think they learn a great deal one of the other things that I just absolutely love doing And a colleague of mine Greg Dick at Michigan told me about his post-doc mentor I think was Jill Banfield did this with him. I think I've got the story right Is that she would sit down side by side with people and literally write the manuscript with them? I don't I think I think this is true But I think it was a great role model that Jill would do that with people And so what I like to do at least one time One on one paper per trainee is to sit side by side with the trainee going through their draft and Helping them to see the draft the way I see it I recall working with a former student Alex Schubert And I remember reading a sentence and maybe it was like the first sentence of the paper And I read it out loud and she started giggling and she's like I have no idea what that sentence means, right? And so again seeing it in a different context or seeing it the way I see it Helps you to write better and what I find is that yeah I might spend 20 hours over the course of a couple weeks sitting side-by-side with somebody which is something I love doing I love doing it takes a ton of time, but I love doing it But the next paper that Alex wrote was great, right? It was it was so much better written because we had gone through that process And so instead of seeing it as like a 20-hour time sink It was an investment and it really paid rewards down the road in her future papers and again That's worked really well with my other trainees So PIs please take the time to work with your trainees to give them feedback on what they need to know to write better trainees listen right don't see that example sentence fix that and then like ignore The cases of that throughout the rest of the manuscript really take their training and what they're trying to give you to heart Tip 10 now. This is for the PIs Cover your ears read the damn paper really come on One of the biggest complaints that most trainees have is that their PI will not read their paper They have put so much effort into writing this paper And you can't spend an hour to give them initial feedback on your thoughts of the paper You know what that tells them it tells them that either you don't care or that you think it just sucks, right? And and maybe it does suck right Hopefully you don't hopefully you do care But maybe it does suck but they need to be told that in a nurturing way and letting things drag out for weeks Just is not helpful, right? It's just painful my wife's master's advisor named Steve Krasovic Had a discipline where he would get the manuscript back to his trainees within a couple of days And he said that exact same thought to me. He said Pat, you know these trainees they put in a lot of work to Write the manuscript. It's the least I can do To edit and help them to write better. My name is going on that paper Steve's name went on that paper Let's make the paper better because they're doing us a great service and helping our career It's the least we can do to make their careers better So PIs read the damn paper really Put everything else to the side and work on that if you can't get back to it in a couple of days Tell the tell the author, you know, I'm working on this grant proposal. I've got a crunch deadline You know, I'm not gonna be able to get to it this week But I promise you I've got time in my calendar blocked out Monday morning to work on it for two hours Okay, again, I think they appreciate that but leaving them in limbo where they don't know the status of the paper It's very harmful and it is just super frustrating to your trainees So that's the PI Collaborators, please read the damn paper. So again What I advise my trainee is that we will go through give and take we'll get it to a point where we really like The look of the manuscript and we like the flow of things. I think it's ready to go, right? But because I don't know everything and as a courtesy all our co-authors should see the paper I then tell them give it to the co-authors, but in the email Tell them that we think it's in pretty good shape. We want their feedback and we know they're busy So if they don't get back to us in the next 10 days or five days or some period of time We're gonna go ahead and submit it But if they have comments or if they need more time, please let us know So again by giving them a period of time that you want the manuscript back by They can plan their time around that and if they don't get back to you even just to say hey I need another like week or two Then you're free to submit it in my opinion Okay, so and that's another place where the PI should be able to step in and you know for like an important Collaborator that's done some heavy lifting on the paper and say hey, you know Mary You've done a lot of work on this manuscript. We submit it. We want to submit it But we want your feedback first. Have you had a chance to look at it and and so again the PI can step in maybe throw around a Little bit of muscle to help move that collaborator around along if you really do want their feedback. Alright, so those are my 10 tips I'm sure I have more tips My lab knows that I have many many pats pet peeves of writing But I think these are the 10 most important tips that I see in my own writing the writing of my trainees and the overall Editing process that I'd really encourage you to think about so if you have other tips that you think are important for writing Or you know if you don't think PI should be reading the papers in a timely manner Go ahead and leave a comment below and we'll send the Twitter trolls to attack you. No But if you have other comments or feedback or ideas on what makes your editing and writing process better Please let us know down below in the comments We all learn from hearing other people's experiences. You might not agree with my process But I think there's a few things in here that you can hopefully take away to improve your own writing All right, so as we go ahead We're getting close to submitting this manuscript and so in the next issue episode or two We're gonna go ahead and submit the manuscript so I can show you the process and what it looks like To submit the manuscript and to be finally done so you can lean back and say I am done writing until you get the reviewers comments back and then you think they're just a bunch of idiots. Anyway Keep trying to work these ideas and concepts into your own writing and your own research practices and Practice that tell your friends about what we're doing here on these code club episodes and we'll see you next time