Writing Tips: Improving Clarity on the Sentence Level

(This post is authored by Lana Martin.)

Clarity is especially important when writing scientific methods papers, proposal, and reports. Journal referees and grant reviewers typically read many submissions in one sitting; they expect to quickly and easily understand the mechanics, significance, and potential contributions of your work. Once a project is published, readers expect to quickly and easily understand how they can use and apply your method in their own work.

Improving clarity of writing is an iterative process that involves a lot of practice in writing, editing one’s own writing, and editing the writing of others. Clear, orderly writing is not a natural tendency for most of us because we don’t normally speak that way in conversation! Similarly, academic specialization leaves us in the dark concerning the amount of detail necessary to make a piece accessible to a broader audience. For most people, developing an intentional practice around routine writing tasks is necessary in order to improve writing skills.

The first draft of any document can always be improved with multiple editing passes. One strategy to improve editing efficiency is to designate each editing pass to a specific editing component, keeping in mind your own personal weak areas. For example, you may first clean up mechanical errors such as spelling and grammar. Second, you may re-write sentences while considering a specific list of writing principles. Finally, editing for over-all cohesion and completeness of ideas can be easier once you have clean copy to work with.

Here, we present five principles for clear writing on the sentence level. These guidelines are universal, yet particularly relevant to scientific and technical non-fiction writing.

1. Directly modify a verb. Often, when describing an action, our default inclination is to add a verb modifier later in the sentence—well after the verb appears. For example:

“…considering simultaneously the population structure…”
“…considering population structure simultaneously…”

This structure makes sense in conversation, because you can emphasize how you did something with tone and inflection. We read in a more linear fashion than we speak; in writing, consistently placing the adverb before the verb makes it clear to the reader which action the modifier belongs to. Consistently ordering verbs and verb modifiers is especially useful when listing a series of actions that are each modified differently, such as in a protocol.

“…simultaneously considering population structure…”

 

2. Front-load the star topic of a sentence. Another habit that we carry from conversation to writing is to bury the most important part of a sentence at the end. This may cause the reader, particularly those less familiar with your subject matter, to re-read the sentence. Here, the specific concept—the star topic of the sentence—follows the general concept:

 “As a result, a large number of false discoveries may be found in the common case where the cell type composition is correlated with the phenotype.”

When reading about a methodology problem, we usually want to first know what is specifically interesting about a concept, and then learn about the concept’s significance on a larger scale. These “flipped” sentences are common in first drafts and can be easily edited in a single pass.

“As a result, the cell type composition is commonly correlated with the phenotype, and the methods produce a large number of false discoveries.”

 

3. Refine use of the dependent clause. A dependent clause is a group of words with a subject and a verb; alone, it is not a complete sentence and does not express a complete thought. We tend to use dependent clauses in writing because we tend to use dependent clauses in our own thought processes. This may suffice for problem-solving in our head-space vacuum, but, in order to effectively communicate with other people, we must completely describe these ideas in writing.

For example, this statement has two dependent clauses next to each other:

“Detecting allelic heterogeneity in regions that are more complicated is not intuitive.”

Given the provided information, the object of “more complicated” and/or “less intuitive” may not be clear. Adding a conjunction (“that”) between the two clauses clarifies that detection is the object of “less intuitive,” and regions is the object of “more complicated.”

“Detecting allelic heterogeneity is less intuitive in regions that are more complicated.”

 

4. Replace a vague dependent clause with a compound sentence. Dependent clauses help present contrasts by defining the scope in which the given statement is valid, but they can also be vague and confusing. For example:

In contrast to Mendelian traits, the extent of AH at loci contributing to common, complex disease is almost unknown.”

When reading scientific and technical writing, we want to see contrasts clearly described—especially for readers who may not have an in-depth understanding of the background concepts. We, as specialists, may not clearly define these concepts because we are not accustomed to working our way through the logic of fundamental ideas. Re-engineering the overly vague clause with a compound sentence can efficiently get the novice reader on the same page as the expert reader. The dependent clause is now a complete thought that stands on its own:

The genetic causes of Mendelian traits are well understood, but the extent of AH at loci contributing to common, complex disease is almost unknown.”

 

5. Add, remove, or modify an article used before a noun. An article is a word (the, a, an) that is placed before a noun to indicate the type of reference being made by the noun. The use of articles is tricky and, at times, a matter of stylistic choice. However, in scientific and technical writing, there are a few best practices for using articles to improve clarity. For example, articles can specify the volume or numerical scope of the noun. When articles are used to clarify numerical scope, first decide if the noun is one (singular) or many (plural), then choose to include or omit the appropriate article.

Use the definite article “the” when you are referring to the one unique item or set of items. In descriptions of methodology, this type of article is commonly used to signal that the noun is a general concept, a broad system, or a one-and-only example.

Immunological properties is a general concept, which the author may separately define in detail:

“…the immunological properties of a B cell receptor…”

Adaptive immune system is a broad system comprised of many parts:

“A key function of the adaptive immune system is…”

GTeX v6 project is one-and-only; future GTeX will presumably be v7!

“…the Genotype Tissue Expression (GTeX v6) project…”

Use the indefinite articles “a” or “an” when referring to a general type or group of items. In descriptions of mythology, this type of article is commonly used to signal that the noun can be any member of a group. “A” is placed before a noun that begins with a consonant; “an” is paired with a noun that begins with a vowel.

Assay-based protocol is a type of protocol:

“In contrast to an assay-based protocol…”

Useful tool is a type of tool:

“…ImReP provides a useful tool for mining large-scale RNA-Seq datasets …”

When using a plural noun, we typically omit the indefinite article.

“In contrast to assay-based protocols…”

In a hypothetical scenario, if ImReP actually provides not one—but many—useful tools:

“…ImReP provides useful tools for mining large-scale RNA-Seq datasets …”


Developing an intentional writing practice can be as simple as scanning your work for sentences with potential for improvement. By designating editing passes to specific mechanical errors or types of sentence-level improvement, writing in a consistent, clear manner may become more habitual—and feel less like an exercise in foreign language class. In upcoming blog posts, we will discuss more ways to efficiently improve the structure and readability of papers.

In addition, we have written numerous blog posts on strategies for writing papers:

Our group has also published numerous blog posts on managing scientific labs and strategizing a graduate career. Articles presenting our advice on these subjects have become the top-viewed posts on our website: http://zarlab.cs.ucla.edu/advice/.

Writing Tips: An Authorship Policy that Maximizes Collaboration

(This post is authored by Eleazar Eskin.)

Assigning authorship and determining the order of authors on scientific papers is an issue that every research lab deals with. Authorship ranking can be a frequent source of conflict among members of a research lab. In many labs, multiple students involved in a project compete for first- or high-ranking authorship throughout the life of the project. Competition for authorship in a lab culture lacking a clearly-defined policy disincentives students from obtaining other lab members’ help, because the project leader may ultimately lose their first-authorship position to the students they recruit for help. These issues can reduce the quality of inter- and intra-lab communication and collaboration. Ultimately, authorship conflict can reduce lab productivity, create lots of bad feelings, and, in some cases, poison the work environment.

Here we share our labs’ authorship policy. Of course, the actual authorship of papers published in our lab reflects the amount of work and contributions that each author made to the project.  However, during the course of the project, there are ample opportunities for different members of the group to contribute more or less than anticipated. Acknowledging flexibility in contribution amount and authorship shapes the final ranking and achieves several other goals. First, our authorship policy is designed to encourage inter- and intra-lab collaboration, increase the overall productivity of the lab, expand training opportunities for students in the lab, and improve the overall productivity of each individual member of the lab.

In our lab, we use the following key principles to assign authorship:

  • No last minute changes. It takes months (if not years!) to complete a research project and finish writing a paper describing the process. Many authorship conflicts arise just before paper submission, which can be a hectic process even without disagreement. In our lab, we never make last minute changes on the eve of submission.

    Instead, we explicitly address author-order issues after the paper is submitted. The revision process always requires more work, so there is plenty of time to resolve conflicts in a calm and constructive way. We often contact journals to change the author order after submission of original and revised manuscripts, and we have even changed the order of authorship on accepted papers just before submitting a camera-ready version. The advantage of this policy is that we remove the majority of drama in authorship conflicts.

  • Each student has their own first-author projects. Competition for high authorship ranking is inevitable in academia, where one’s publication record has a crucial impact on their career. In addition, graduate students in many programs are required to publish a specific number of first-author papers in order to complete their degrees.

    In our lab, each student has clearly defined projects that lead to first-author papers. Except in exceptional circumstances, such as leaving the lab before finishing their project, the student will be the first author of the paper. Other students in the lab are welcome to join the project and contribute (with the first-author student’s permission). In this case, they have authorship rights but cannot dislodge the project leader’s first-author position. With the authorship outcome established in advance, each student involved has clear expectations and can budget their involvement in the project accordingly.

    The advantage of this policy is that we no longer have students competing for first-author positions. Students are genuinely encouraged to collaborate and obtain help from peers in their projects. In addition, junior students often recruit senior students to help with their first projects. This is a win-win scenario; senior students benefit from the mentoring experience, and the advanced graduate students’ research experience often substantially speeds up completion of the junior students’ project. In addition, encouraging senior students to help with all lab papers also lightens my mentorship load and frees up time for my research, writing, and teaching.

  • First-author students help determine the author order. Lack of a clear protocol for determining authorship ranking throughout the course of a project can lead to conflicts as publication nears. In our lab, we create a culture of granting authorship-assigning agency to the first author student, who has substantial input into the author order and is responsible for monitoring their co-authors’ productivity.

    During the course of the project, the first-author student is responsible for gently nudging them to contribute if a student co-author has contributed relatively little time to the project. If a co-author has contributed a tremendous amount, the first author can decide that the two students should share first author. The advantage of this policy is that the first-author student has a lot of ownership over their projects and is responsible for ensuring, over the course of the project, that the workload is split to reflect the final authorship ranking.

  • Students are recognized for pulling more than their anticipated weight. Many very talented students often substantially contribute to multiple projects in the lab, including the other students’ papers in which they are not the first author.

    In our lab, we greatly encourage this behavior. I explain to the students that I will notice their additional investment of time and effort, and they will be recognized for this in letters of recommendation that I will write for them. I also explain to students interested in taking on extra project workloads that the experience and recognition—regardless of their specific authorship ranking on each project—will provide for them many future opportunities and collaborations.

Our policy leads to a highly collaborative environment where each student who graduates from the lab co-authors a paper with the majority of the other students in the lab. Senior students gain invaluable experience mentoring junior students through the paper writing process. When they graduate from the lab, my students are very generous with credit and authorship to others involved in the lab. This makes me proud of them as both scientists and people.

Even with this policy, I would say that every six months to one year we have an authorship conflict among lab members that I must get involved in. In part, this is because authorship is so discrete that, even with the best intentions, the constraints of a ranked list sometimes fail to completely reflect the individuals’ contributions. Using joint first authors and joint corresponding authors can help with this issue, but jointly-authoring still may not introduce sufficient complexity to accurately reflect the efforts and contributions of all individuals involved. However, the collaborative culture of our lab, as well as our collaborative relationships with other labs, usually helps us resolve these disputes in short time.

Writing Tips: Why we Publish Methods Papers

by Eleazar Eskin

Computational genomics is a field where many diverse academic groups collaborate, each bringing to a project their own distinct academic cultures.  In particular, each academic discipline involved in computational genomics has its own publication strategy in terms of the types of papers they publish and how they package methods and results in these papers.  Publishing papers is extremely important to careers in academia and science, because all scientists are reviewed for tenure or promotion based on our publications records.  An important factor in our review (unfortunately) is the impact factor of the journals that we publish in.  Here, we describe our lab’s publication strategy and the reasoning behind it.

Our lab is a computational lab, and the main contribution of our lab to Bioinformatics is the development of methods for solving important biological problems, particularly in the area of genetics.  These new methods are implemented in software packages that (hopefully) are used by others to enable biological discovery.  Naturally, the key papers our group produces are papers that describe and explain potential applications of these new methods.

Roughly speaking, there are two strategies for publishing methods in our field.  The first is to focus on writing methods papers that are primarily dedicated to describing the computational advances.  The second is to focus on publishing our novel methods as part of more comprehensive papers that present a biological contribution. In this case, our method is primarily described in the supplementary materials. Over the span of my career, I have seen computational researchers receive more pressure to follow the second strategy in order to have papers published in a high impact journal.  Unfortunately, following the second strategy often delays publication (sometimes for years), because peer review often involves applying the method to a new dataset and/or performing extensive functional validation.

Our group primarily follows the first strategy.  In addition, we work with other groups and, as collaborators, publish papers focused on biological contributions.  This strategy works out well for us, and we feel that writing methods-focused papers is the best way for us to make a contribution to science.  We hope that other computational biology groups will follow our example and publish more methods papers.

Here are some of the reasons we feel this is a good strategy:

  1. Doing Justice to our Work. We can fully explain the methods only in papers dedicated to methodology. Since our contribution is methods, the best way to push the science forward is to clearly describe our method and the context of its development and application. In a dedicated paper, we are most likely to have enough space to fully describe the method and explain how the approach works.  Methods papers also have the space (and are typically required) to compare the proposed method with previous methods. This comparison puts the performance of the paper in perspective to the work of others.  Methods papers ideally provide enough details that other groups can build upon our method and compare their results to our published results. Sharing authorship on these papers also allows students who were involved in the development of these methods to demonstrate their strong technical skills.  In my view, computational biologists should be evaluated by the quality and impact of their methodology development and departments when making hiring decisions should consider this impact.  The impact can be measured by the number of users of the software implementing the methods, the number of citations of the papers describing the methods and the discoveries that these methods have enabled.  These factors are more important than the impact factor of the journals where the methods are published.
  1. Self Determination of Publishing. There are no outside bottlenecks preventing us from finishing our papers quickly, and we can control the publication process of our papers. A methods paper is primarily written by members within our lab, and authors evaluate the method using both simulated and established datasets.  This structure means we need not wait for outside collaborators or experiments to finish.  Finishing the paper faster means that have more time to work on new papers.
  1. Increased Number and Improved Quality of Collaborations. The methods paper is a widely-distributed, often freely available, finished product, and many prospective collaborators approach us after reading a paper from our group. More importantly, in our collaborations, we have very little competition over authorship.  Students in the group are happy to work hard on a project just to be in the middle of the collaborative paper, because they already are first author on their own methods papers.  Our methods development students are not competing for credit with the students in the collaborators group.
  1. Project Longevity. Writing a methods paper forces the method to be finished, evaluated, and documented, and publishing the paper forces us to release the software. This process encourages the project to have more longevity. Once the method is fully developed, new students can easily pick up and build upon the previous method.  Once a student leaves the lab, the method can persist with new lab members as it is stable, well-documented, and de-bugged.  Long after they have left the lab, many of the students who wrote methods papers in our group continue to author papers related to applications of their method.

In full disclosure, we do identify one negative aspect of the methods paper publishing strategy.  High impact papers require collaborations, and it is less likely that methods developers can publish high impact journals as a senior or corresponding authors.  While it is less likely to occur, members of our lab do occasionally gain senior authorship in high impact journals through collaboration.  We have found that the combination of methods papers, where you are the senior or first author, and high impact papers, where you have middle authorship and it is clear that your role was the application of the method, is overall a positive outcome and looks good in your publication record.

For example, Eran Halperin and I published a 2004 paper in the lower-impact journal Bioinformatics that described the HAP haplotype phasing method.  The HAP method was later used in a Perlegen-led paper that was published, with Halperin and I as co-authors, in the notably high-impact journal Science. The 2005 Science paper helped me get my job at UCLA; it was clear what my contribution was as I also authored the methods paper in Bioinformatics.

Our lab has produced several other examples of methods papers paired with high-impact collaborations. Kang et al. (2008) presents the EMMA method in Genetics (impact factor of 5.963), and a collaboration with the Jake Lusis group on the HMDP presents results in Genome Research (impact factor of 11.351) (Bennett et al. 2010).  More recently, we published the CAVIAR method (Hormoziari et al., 2014) in Genetics and collaborated with Dan Geschwind’s group in applying the method to a Nature paper (Won et al. 2016).

Citations of papers mentioned in this post:

Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, Daniel H

Chromosome conformation elucidates regulatory relationships in developing human brain. Journal Article

In: Nature, 538 (7626), pp. 523-527, 2016, ISSN: 1476-4687.

Abstract | Links | BibTeX

Hormozdiari, Farhad; Kostem, Emrah ; Kang, Eun Yong ; Pasaniuc, Bogdan ; Eskin, Eleazar

Identifying causal variants at Loci with multiple signals of association. Journal Article

In: Genetics, 198 (2), pp. 497-508, 2014, ISSN: 1943-2631.

Abstract | Links | BibTeX

Bennett, Brian J; Farber, Charles R; Orozco, Luz; Kang, Hyun Min; Ghazalpour, Anatole; Siemers, Nathan; Neubauer, Michael; Neuhaus, Isaac; Yordanova, Roumyana; Guan, Bo; Truong, Amy; Yang, Wen-Pin; He, Aiqing; Kayne, Paul; Gargalovic, Peter; Kirchgessner, Todd; Pan, Calvin; Castellani, Lawrence W; Kostem, Emrah; Furlotte, Nicholas; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

A high-resolution association mapping panel for the dissection of complex traits in mice. Journal Article

In: Genome Res, 20 (2), pp. 281-90, 2010, ISSN: 1549-5469.

Abstract | Links | BibTeX

Kang, Hyun Min; Ye, Chun ; Eskin, Eleazar

Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Journal Article

In: Genetics, 180 (4), pp. 1909-25, 2008, ISSN: 0016-6731.

Abstract | Links | BibTeX

Hinds, David A; Stuve, Laura L; Nilsen, Geoffrey B; Halperin, Eran ; Eskin, Eleazar ; Ballinger, Dennis G; Frazer, Kelly A; Cox, David R

Whole-genome patterns of common DNA variation in three human populations. Journal Article

In: Science, 307 (5712), pp. 1072-9, 2005, ISSN: 1095-9203.

Abstract | Links | BibTeX

Halperin, Eran; Eskin, Eleazar

Haplotype reconstruction from genotype data using Imperfect Phylogeny. Journal Article

In: Bioinformatics, 20 (12), pp. 1842-9, 2004, ISSN: 1367-4803.

Abstract | Links | BibTeX