It takes a village to write a scientific paper

Every scientist I know (myself included) underestimates how long it will take to write, edit, and submit a paper.  Despite having 22 publications to date, I still set laughably-high expectations for my writing deadlines.  Even though scientists go into a project with a defined hypothesis, objectives, and workflow, by the end of data analysis we often find ourselves surprised.  Perhaps your assumptions were not supported by the actual observations, sometimes what you thought would be insignificant becomes a fascinating result.  Either way, by the time you have finished most of the data analysis and exploration, you face the difficult task of compiling the results into a meaningful paper.  You can’t simply report your data without giving them context and interpretation.  I’ve already discussed the portions of scientific manuscripts and how one is composed, and here I want to focus on the support network that goes into this process, which can help shape that context that you provide to your data.

One of the best ways in which we can promote rigorous, thoughtful science is through peer-review, which can take a number of forms.  It is worth noting, that peer-review also allows for professional bullying, and can be swayed by current theories and “common knowledge”.  It is the journal editor’s job to select and referee reviewers (usually 2 – 4), to compile their comments, and to make the final recommendation for the disposition of the manuscript (accept, modify, reject).  Reputation, and personal demographics such as gender, race, or institutional pedigree can also play a role in the quality and tone of the peer-review you receive. Nevertheless, getting an outside opinion of your work is critical, and a number of procedural changes to improve transparency and accountability have been proposed and implemented.  For example, many journals now publish reviews names online with the article after it has been accepted, such that the review does not stay blind forever.

Thorough reading and editing of a manuscript takes time.  Yet peer-reviewers for scientific journals almost unanimously do not receive compensation.  It is an expected service of academics, and theoretically if we are all acting as peer-reviewers for each other then there should be no shortage.  Unfortunately, due to the pressures of the publish-or-perish race to be awarded tenure, many non-tenured scientists (graduate students, post-docs, non-tenure track faculty, and pre-tenured tenure-track faculty) are reluctant to spend precious time on any activity which will not land them tenure, particularly reviewing.  Moreover, tenured faculty also tend to find themselves without enough time to review, particularly if they are serving on a large number of committees or in an administrative capacity.  On top of that, you are not allowed to accept a review if you have a conflict of interest, including current or recent collaboration with the authors, personal relationships with authors, a financial stake in the manuscript or results, etc.  The peer-review process commonly gets delayed when editors are unable to find enough reviewers able to accept a manuscript, or when reviewers cannot complete the review in a timely manner (typically 2 – 4 weeks).

I have recently tried to solicit peer-review from friends and colleagues who are not part of the project before I submit to a journal.  If you regularly follow my blog, you’ll probably guess that one of the reasons I do this is to catch spelling and grammatical mistakes, which I pick out of other works with hawk-like vision and miss in my own with mole-like vision.  More importantly, trying to communicate my work to someone who is not already involved in the project is a great way to improve my ability to effectively and specifically communicate my work.  Technical jargon, colloquial phrasing, sentence construction, and writing tone can all affect the information and data interpretation that a reader can glean from your work, and this will be modulated by the knowledge background of the reader.

I’ve learned that I write like an animal microbiologist, and when writing make assumptions about which information is common knowledge and doesn’t need a citation or to be included at all because it can be assumed.  However, anyone besides animal microbiologists who have been raised on different field-specific common knowledge may not be familiar with the abbreviations, techniques, or terms I use.  It may seem self-explanatory to me, but I would rather have to reword my manuscript that have readers confuse the message from my article.  Even better, internal review from colleagues who are not involved with the project or who are in a different field can provide valuable interdisciplinary perspective.  I have been able to apply my knowledge of animal science to my work in the built environment, and insights from my collaborators in plant ecology have helped me broaden my approach towards both animals and buildings.

No scientific article would be published without the help of the journal editorial team, either, who proof the final manuscript, verify certain information, curate figures and tables, and type-set the final version.  But working backwards from submission and journal staff, before peer-review and internal peer-review, there are a lot of people that contribute to a scientific article who aren’t necessarily considered when contemplating the amount of personnel needed to compose a scientific article.  In fact, that one article represents just the tip of the iceberg of people involved in that science in some way; there are database curators, people developing and maintaining open-source software or free analysis programs, laboratory technicians, or equipment and consumables suppliers.  Broadening our definition of science support network further includes human resources personnel, sponsored projects staff who manage grants, building operational personnel who maintain the building services for the laboratory, and administrative staff who handle many of the logistical details to running a lab.  It takes a village to run a research institution, to publish a scientific article, to provide jobs and educational opportunities, and to support the research and development which fuels economic growth.  When it comes time to set federal and state budgets, it bears remembering that that science village requires financial support.


Featured Image Credit: Kriegeskorte, 2012

Summer outlook

I’ve got quite a busy summer ahead!  You’ll be able to find me at:

June 22, 2018: The HOMEChem Open House at the UT Austin Test House , University of Texas at Austin’s J.J. Pickle Research Campus.  I’ll be meeting with BioBE collaborators to discuss pilot projects exploring the link between indoor chemistry and indoor microbiology.

July 15 – 20, 2018: The Microbiology of the Built Environment (MoBE) Gordon Research Conference, University of New England in Biddeford, ME.  BioBE’s Dr. Jessica Green is meeting Vice Chair.

July 22 – 28, 2018: Indoor Air 2018 Conference in Philadelphia, PA.  I’ll be presenting some of the work I’ve been part of, exploring the effect of weatherization on bacteria indoors.

August 12 – 18, 2018: The 17th International Society for Microbial Ecology (ISME17) in Leipzig, Germany.  Here as well, I’ll be presenting some of the work I’ve been part of, exploring the effect of weatherization on bacteria indoors.






USDA AFRI NIFA Agricultural Production Systems grant awarded to Menalled et al.

In 2016, I was a post-doc in the Menalled Lab, which studies plant and weed ecology in the context of agricultural production and sustainability.  There, I assessed soil bacterial communities under different farming management practices and climate scenarios.  I also helped to develop a grant proposal, which was just accepted by the USDA AFRI NIFA Agricultural Production Systems!  Leading this project is Dr. Fabian Menalled (as Principal Investigator, or PI), along with a number of other PIs; Dr. Amy Trowbridge, Dr. David Weaver, Dr. Tim Seipel, Dr. Maryse Bourgault, and Dr. Carl Yeoman, and collaborators Dr. Darrin Boss, Dr. Kate Fuller, Dr. Ylva Lekberg, and myself as a subaward PI.  I will again be providing microbial community analysis for this project, and collectively the project investigators will bring expertise in plant ecology, agronomy, economics, soil and plant chemistry, microbial ecology, agroecosystems, and more.

This research and extension project focuses on the needs of dryland agricultural stakeholders and it was designed in close collaboration with the NARC Advisory Board. While I was only able to attend one meeting, other team members regularly meet with Montana producers to discuss current issues and identify locally-sourced needs for agricultural research.  During this project, we will continue to meet with the NARC Advisory Board to share our results, evaluate implications, and better serve the producer community.

Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield and economic returns.

Project summary

The semi-arid section of the Northern Great Plains is one of the
largest expanses of small grain agriculture and low-intensity livestock
production. However, extreme landscape simplification, excessive reliance on
off-farms inputs, and warmer and drier conditions hinder its agricultural
sustainability. This project evaluates the potential of diversifying this region
through the integration of cover crops and targeted grazing. We will complement
field and greenhouse studies to appraise the impact of system diversity,
temperature, and precipitation on key multi-trophic interactions, yields, and
economic outputs. Specifically, we will 1) Assess ecological drivers as well as
agronomic and economic consequences of integrating cover crops and livestock
grazing in semi-arid systems, 2) Evaluate how climate variability modify the
impacts of cover crops and livestock grazing on agricultural outputs. Specifically,
we will 2.1) Compare the effect of increased temperature and reduced moisture
on agronomic and economic performance of simplified and diversified systems,
2.2.) Assess the impact of climate and system diversity on associated biodiversity
(weeds, insect, and soil microbial communities) and above- and belowground
volatile organic (VOC) compound emissions, and 2.3) Evaluate how changes in
microbially induced VOCs influence multitrophic plant-insect interactions.


  1. Assess key ecological drivers as well as agronomic and economic consequences of integrating cover crops and livestock grazing in semi-arid production systems
    • Compare the agronomic and economic performance of simplified and diversified systems
    • Assess the impact of cover crops and livestock grazing on the associated biodiversity (weeds, insects, and the soil microbiota)
  2. Evaluate how climate conditions modify the impacts of cover crops and livestock grazing on semi-arid production systems
    • Compare the effect of temperature and soil moisture on agronomic and economic performance of simplified and diversified systems
    • Assess the impact of climate and system diversity on associated biodiversity and above- and belowground volatile organic compound (VOC) emissions
    • Evaluate how changes in VOCs emissions influence important multitrophic interactions such as resistance to wheat stem sawfly and natural enemy host location cues
  3. Integrate the knowledge generated into an outreach program aimed at improving producers’ adoption of sustainable diversified crop-livestock systems

Spring Updates

It’s been a really busy spring so far, so much so that I haven’t had much chance to write about it!  Here is a brief overview of what I’ve been up to.


This past year has easily produced the largest number of research topics I have been working on concurrently.  In addition to publishing a paper on the rumen in cattle last September, I have been working on a paper on the rumen of yearling rams which is currently in preparation and due to be submitted to a scientific journal for review soon.  I still have several small projects in development from my post-doc in the Yeoman lab, as well as a number of grad-student-led papers that are still pending, and was invited to contribute to a scientific review which is also in preparation.

I’ve been working through the large dataset of soil samples from my post-doc in the Menalled lab.  That large project has blossomed into four papers thus far, two of which I’m writing on the soil bacteria, and one of which I am co-authoring on the legacy effects of climate change.  Those four are also due for submission to scientific journals for review soon.  The Menalled lab just received a grant award from USDA AFRI NIFA, on which I am a (subaward) PI and to which I will be contributing soil bacterial community analysis.

The rumen and soil work over the past year has been entirely in my spare time, however, as my position in the Biology and the Built Environment Center has kept me delightful busy.  I have been collaboratively processing a large and complex dataset on weatherization, home operation and lifestyle, indoor air quality, and microorganisms in dust, which I will be presenting at two (possibly three) conferences this summer.  I have also been collaboratively writing grant proposals, and while those are still in development or pending review, they span everything from light, to chemistry, to plants and living machines, to hospitals, to social networks in buildings.  I hope to further develop some of these collaborations with a short trip at the end of June to the University of Austin, Texas’ Test House.

In addition, I have been assisting in the planning, development, and launch of the University of Oregon’s Institute for Health in the Built Environment.  The Institute will facilitate collaboration and information sharing between researchers and industry professionals, with the goal of researching, building, and promoting healthier built environments.  The Institute just hosted its #BuildHealth2018 Consortium meeting in Portland, OR, at which I presented some of the results from that large weatherization study regarding indoor plants.  The meeting was fantastic, and spurred in-depth discussion on problems facing industry professionals, innovative research goals, and a wealth of new possibilities.


In the past few months, I’ve spent a lot of my spare time helping to develop the Eugene Pod of 500 Women Scientists, an organization created to promote diversity, equity, and inclusion in science, and to promote education and interactive between scientists and the general public.  We have focused on hosting monthly Science Salon events, four to date, to do just that.  I presented at the first one, and have helped organize and MC the others.  The Eugene Pod’s activities were just featured on the central 500 WS page, as Pod of the Week, and you can also follow our updates and events on our Facebook page.

Running trivia on fire and fungi.


While it has been a struggle to maintain regular contributions, I still maintain Give Me the Short Version, along with a few intrepid contributors, which summarizes scientific articles for easier consumption.  This spring, I spent several days judging STEM and robotics competitions for several local Eugene middle and high schools, which has been a lot of fun.  The student projects are enthusiastic and creative, and I appreciate the chance to assist in these programs in some small way.


I have continued to mentor UO students.  The post-bac student from the BioBE lab that was learning bioinformatics with me, Mitch Rezzonico, was accepted to the University of Oregon’s Bioinformatics and Genomics Master’s Program!  Mitch wrapped up his work this spring to prepare for the intensive program, and with his interest in health research, BioBE hopes to work with him again in the future.  BioBE recently hired an undergraduate student for science communication, Mira Zimmerman.  Mira has been making some upgrades to the BioBE and ESBL websites which will continue to be rolled out over the next few months.  In addition, she will be helping me develop informative blog posts on the built environment, and helping to grow our information dissemination capabilities.  Hiring a student as a science communicator was something I had been hoping to test out, and so far it’s been a smashing success.


My course proposal for “Introduction to Mammalian Microbiomes” was accepted by the University of Oregon Clark Honor’s College for the fall term!

In April, I gave a guest lecture to Mark Fretz’s Design the Unseen course at the University of Oregon, on the Indoor Microbiome.  The class was populated by architecture students, who were learning about integrating health considerations into design strategies.  As a final project, students design a brief field experiment or intervention strategy for a design assistance project with Portland firms. I assisted one group in designing a small experiment on natural daylighting in an office and the effect on E. coli growth on culture plates – more on those results soon!


Later that same day, I have a lecture at the Oregon Museum of Science and Industry in Portland, as part of their OMSI After Dark series which opens the museum after-hours to adults for hands-on activities and lectures.  The lecture was on the gut microbiome, and I was able to present in the Planetarium!



OMSI After Dark Presentation on the gut microbiome

Last night I participated in the Oregon Museum of Science and Industry (OMSI) After Dark event: “It’s Alive! (Mind and Body)”.  OMSI regularly puts on After Dark events, where adults can check out the museum, listen to lectures in the planetarium, and engage in interactive science experiments and activities, all while enjoying an open bar.  Last night, I had a great time giving a short presentation on “Ishaq OMSI After Dark 20180425“!

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Photo Credits: Lee Warren

I’ll be teaching “Introduction to Mammalian Microbiomes” this fall!

I’m very pleased to announce that I’ll be teaching a course this fall on “Introduction to Mammalian Microbiomes”, with the University of Oregon Clark Honors College.  I hope that this will be the first of many courses taught at UO, beginning with my background in “host-associated”, and expanding out into “house-associated”.

Course Description: Introduction to mammalian microbiomes.

The learning objectives of this course are to introduce students to basic concepts in host-associated microbiomes. Some background in microbial ecology, genetics, anatomy, bioinformatics, or immunology would be helpful, but is not required. While difficult concepts will be discussed, the course is intended to teach students about the basic principles: what is a microbiome? How does host anatomy drive microbial ecology? How does that community develop over time? How does it change? How does technology inform our understanding of these systems, and what limitations does that technology introduce? When we read about host-associated microbiomes in the news, especially regarding health, how can we assess if the study is rigorous and how should be interpret the scope of the findings? The skill-set objectives include learning to review complicated journal articles, distilling their findings while understanding their limitations, and developing science communication skills in a variety of formats.

500WS Eugene Science Salon: “Hot Mess: Biodiversity in the Sky Islands and following fire.”

500 Women Scientists Eugene is hosting another Science Salon at First National Taphouse; “Hot Mess: Biodiversity in the Sky Islands and following fire.”

Carolyna Piña Páez

Graduate Student at Oregon State University

Title: “Population structure of Rhizopogon in the Madrean Archipielago: The Sky Islands of Southwestern United States and Northwestern Mexico.”

Bio: Carolyna Piña Páez is a graduate student at Oregon State university. Her adventures in Mycology began in 2005 in the Sonoran Desert, working with gasteroid fungi. Since 2011, she’s been working with truffles and other ectomycorrhizal fungi associated with true fir, pine and oak in the central part of México. In 2013, she moved to Oregon and was amazed with the diversity that this place hosts.

Talk slides: ScienceSalonMarch25_Carolina_fungi_ScienceTalk

Amanda Stamper, M.S.

Fire Management Officer, a.k.a. “Burn Boss”, Nature Conservancy, Oregon

Title: “Burning for Butterflies, Birds & Blooms”

Bio: Amanda started her career in fire management as a member of a 20-person contract crew in 1999. In 2001, after finishing her BA in Philosophy at the University of Oregon, she returned to fire management, working on hotshot crews, handcrews, and engines; as a fuels technician on the Deschutes National Forest; and assistant fire management officer in fuels management on the Ochoco National Forest and Crooked River National Grassland.  She studied Natural Resources at Oregon State University and completed a Masters in Natural Resources, Fire Ecology, and Management at the University of Idaho in 2012. She has since worked for the Prineville Bureau of Land Management as a natural resource specialist coordinating post-fire emergency stabilization and rehabilitation; as invasives program manager for the Deschutes and Ochoco National Forests and Crooked River National Grassland; fire management officer for The Nature Conservancy in Oregon and Washington; and chair of the Oregon Prescribed Fire Council.

Talk slides: 20180325_Salon_Amanda_fire

Acknowledgements to our wonderful support network

500 Women Scientists Eugene would like to thank the organizations that helped make this event possible.  First and foremost, First National Taphouse in Eugene, who shared their wonderful space with us and where we will be putting on future Salons, and donated a keg to the event!  We are also extremely grateful to several organizations which contributed raffle or trivia items for us to raise additional funds, including Leslie Dietz and the Eugene Science Center.  Our beautiful logo was crafted by Cassie Cook,  our amazing event posters were designed by Serena LimFertilab generously lent us a sound system.  And of course, we want to acknowledge the national leadership of 500 Women Scientists, who brought us together, gave us a voice, and who suggested these Science Salons as a way to help CienciaPR, a organization which similarly supports science education and infrastructure.

I’d also like to acknowledge the powerhouse team of women who came together to organize this event: Karen Yook,  Leslie Dietz, Jessica Flannery, and our wonderful speakers; Carolyna Piña Páez and Amanda Stamper.  500 Women Scientists was formed in the spirit of cooperation and support, and this team truly took that to heart.  I can’t wait to organize the next one with you ladies, and the next one, and the next one, and the next one…