Friday, August 5, 2022

Ph.D. position in our lab available starting Spring 2023 semester

 We’re Recruiting a PhD Student

The School of Forestry, Northern Arizona University, seeks a motivated Ph.D. student starting in Spring 2023. The student will be advised by Matthew Bowker and potentially co-advised by other faculty members. Potential research foci include but are not limited to: 1. Ecological role of biological soil crusts (biocrusts) in varied ecosystems, 2. Developing ecological restoration materials and techniques using biocrusts, 3. Resistance of biocrusts to climate change, 4. Ecology of dust, 5. Other soil ecology and restoration ecology topics. 

Initial funding would be provided through a Teaching Assistantship (TA) in the School of Forestry, transitioning to a Research Assistantship when possible. The candidate will be expected to participate in seeking funds for an RA, through the NSF GRFP program or comparable program. We will provide an annual stipend of at least $20,000, tuition remission, and student health coverage, in addition to research costs.     

TA duties would include assisting Dr. Bowker in teaching an undergraduate Soil Ecology and Management Course in Spring and other Forestry offerings in Fall.

Qualifications: (1) Master of Science in Forestry, Biology, Environmental Science OR (2) Bachelor of Science in Forestry, Biology, Environmental Science or related field plus research experience (undergraduate thesis, capstone or internship, or employment-related experience). Candidates with greenhouse or field research experience, and previous experience or relevant coursework  in soil ecology/soil science and/or bryophyte/biocrust ecology will be preferred

The candidate must satisfy all requirements set by the School of Forestry, and Northern Arizona University. 

Admissions requirements (Deadline Oct 15, 2022):

    GPA of 3.0 or greater on a 4.0 scale in all college and university work


    If English is not your native language:

    a score of at least 80 on the internet-based TOEFL or

    550 on the paper-based TOEFL or

    213 on the computer-based TOEFL

    Three letters of recommendation

How to apply:  First contact me directly ( to state your research interests, and motivations for attending graduate school, with “soil ecology graduate student inquiry” in the header. In this email, also briefly state why you meet the qualifications. Please attach a resume or C.V. and GPA. If we agree that you are a good match for the position, we will encourage you to formally apply to the program. We will make our final selection from those applicants. All kinds of human are welcome in our lab.

Friday, October 30, 2020

Ph.D. position in our lab, starting Fall 2021....Fire mosses!


Photos: a & b. Henry Grover, c. Kyle Doherty

We’re Recruiting a Funded PhD Student

The School of Forestry, Northern Arizona University, seeks a motivated Ph.D. student to conduct field and greenhouse experiments in and near Flagstaff, Arizona starting in Fall 2021. The student will explore the utility of using greenhouse-grown mosses to enhance ecological restoration of burned forests. Specifically, they will: 1. Improve greenhouse cultivation techniques 2. Determine if mosses can support desired soil microbiota, 3. Develop methods to pelletize mosses for deployment in the field, 4. Quantify the effect of added moss pellets on soil health in post-fire environments. Funding would provide a research assistantship consisting of an annual stipend of $26,660, tuition remission, and student health coverage, in addition to travel and project costs. We expect 4 years of funding.  

Qualifications: Master of Science in Forestry, Biology, Environmental Science is preferred. Candidates with Bachelor of Science in Forestry, Biology, Environmental Science or related field plus research experience (undergraduate thesis, capstone or internship, or employment-related experience) will also be evaluated. Candidates with greenhouse or field research experience will be strongly favored. Candidates with previous experience in soil ecology and/or bryophyte/biocrust ecology will also be favored. The candidate must satisfy all requirements set by the School of Forestry, and Northern Arizona University. 

Admissions requirements (Deadline Feb 15, 2021):

    GPA of 3.0 or greater on a 4.0 scale in all college and university work

    GRE scores in the top 40th percentile

    If English is not your native language:

    a score of at least 80 on the internet-based TOEFL or

    550 on the paper-based TOEFL or

    213 on the computer-based TOEFL

    Three letters of recommendation

How to apply:  First contact us directly ( with a statement of  your research interests, and motivations for attending graduate school, with “Fire moss graduate student inquiry” in the header. Please provide a resume or C.V. and provide your GRE scores (if taken) and GPA. If we agree that you are a good match for the position, we will encourage you to formally apply to the program. We will make our final selection from those applicants.

Thursday, January 9, 2020

PhD research position available in our lab: ecological restoration

Image result for mpg ranch biocrust bowker

The School of Forestry, Northern Arizona University, seeks a motivated Ph.D. student to conduct field and greenhouse experiments in Flagstaff, Arizona and field sites in the Bitterroot Valley of Montana starting in Fall 2020. The student will be co-advised by Matthew Bowker and Anita Antoninka and will collaborate with partners at MPG Ranch in Montana. The student will: 1. explore the fundamental ecological role of biological soil crusts (biocrusts) in intermontane grasslands and shrublands, 2. continue our efforts at developing ecological restoration materials using biocrusts in Montana, and 3. Examine the relationship between biodiversity in moss and biocrust communities and their resistance to climate change stressors. Specifically, the project includes: a. Creating a biocrust trait database and elucidating the role of trait diversity in ecosystem function of biocrusts, b. Refining greenhouse and outdoor based methods of production of biocrust materials, c. Exploring new cutting edge ideas for preparing biocrust materials for field use, and d. Field tests of biocrust materials in restoration sites. We anticipate annually renewable funding to be available to the student for at least 4 years of study. Funding would provide a research assistantship consisting of an annual stipend of $26,660, tuition remission, and student health coverage, in addition to travel and project costs. 

Research Environment: The School of Forestry is one of the top Forestry Schools in the nation, and a productive research environment, with faculty members specializing in a variety of ecological topics such as landscape ecology, ecological restoration, plant ecophysiology, entomology, hydrology, and soil ecology among other topics. Northern Arizona University is also a hotspot for soil ecology research.

Qualifications: Master of Science in Forestry, Biology, Environmental Science OR Bachelor of Science in Forestry, Biology, Environmental Science or related field plus research experience (undergraduate thesis, capstone or internship, or employment-related experience). Candidates with greenhouse or field research experience will be strongly favored. Candidates with previous experience in soil ecology and/or bryophyte/biocrust ecology will also be favored. The candidate must satisfy all requirements set by the School of Forestry, and Northern Arizona University. 

Admissions requirements (Deadline Feb 15, 2020):
    GPA of 3.0 or greater on a 4.0 scale in all college and university work
    GRE scores in the top 40th percentile
    If English is not your native language:
    a score of at least 80 on the internet-based TOEFL or
    550 on the paper-based TOEFL or
    213 on the computer-based TOEFL
    Three letters of recommendation

How to apply:  First contact us directly ( to state your research interests, and motivations for attending graduate school, with “Montana biocrust graduate student inquiry” in the header. Please provide a resume or C.V. and provide your GRE scores (if taken) and GPA. If we agree that you are a good match for the position, we will encourage you to apply to the program. We will make our final selection from those applicants.

Useful Links:
School of Forestry -

Sunday, September 1, 2019

How to write an Introduction that is effective and relatively easy


  1. This advice is for my field and the type of journals I publish in which fall under ecological and biological sciences. Different fields likely have different definitions or expectations. 
  2. My advice is strongly influenced by, but not identical to, writing advice provided to me by Tom Whitham during a graduate class. I internalized it and find that I still largely follow it to this day. Thanks, Tom.
  3. One size does not fit all, but these suggestions will help you get a first draft on paper that can be modified in any way you or your coauthors wish. 

General advice:

  1. An introduction involves some review of the literature but is not in itself an exhaustive review of the literature.
  2. An introduction must lay out the rationale, context, and basis for understanding a study. Information not directly germane to the coming study does not belong.
  3. Practice thinking bigger than the particulars of your study. 
  4. Don’t get derailed struggling for the perfect sentence structure or working in a first draft, or that you can’t remember the year of that citation. Just write according to a well-defined structure, and clean it up later. Get words on paper.
  5. An introduction seldom requires more than 4 paragraphs. Really. 3 might be fine. Save some blab for the discussion or your next paper, or just skip it.
  6. Introduction structure is an inverted triangle, broad at the top, narrow at the base (except for the very last sentence which gets broad again….Ok it’s a short-stemmed martini glass).

A structure to begin with:

Paragraph 1: Must establish the broad context of the study, the general topic. 

If you are doing basic science it should involve a scientific theory which you wish to test, refine, debunk, etc. If you are doing applied science, this is the problem affecting nature or people that you hope your work might solve.

Sentence 1- State the central theme in a clear, uncomplicated topic sentence. Since it is an overall summary of an area of inquiry, it will probably have multiple citations.

Examples: “The stress gradient hypothesis predicts that as abiotic stress increases, the prevalence of facilitative species interactions also increases.”

“Since the 1990s, a consensus has emerged that greater richness of ecological communities tends to be positively related to ecosystem functions”

“The extent and severity of western wildfires have rapidly increased in recent decades and has been linked to climate change and management legacies”

The next few sentences will flesh out some details and logical outcomes of the central theme. For example we might point out that in the American southwest, specifically changing vapor pressure deficit is linked to fire behavior, and climate predictions suggest the vapor pressure deficit is likely to decline even further by mid-century. It may be appropriate to highlight any alternative hypotheses or models about how the world works here, or that there is controversy in the literature. Do cite studies, just don’t feel like you have to cite everything ever written. Focus on the most important citations, and do not get into study details here.

Last sentence – You will state something general that is still not known, and that is in a general sense the knowledge that you wish to contribute. If you are doing basic science, this is the chink in the armor of our knowledge, the missing piece. If you are doing applied science, this is a possible solution to a problem (broad sense).

Examples: “Despite the hundreds of studies establishing a clear link between terrestrial plant richness and productivity, there have been only a handful of studies and no consensus on whether the richness of other communities also affect ecosystem functions.”
“To date all research has addressed the influence of vascular plant seeding of post-fire erosion, and there is a paucity of information about the utility of non-vascular plants for this purpose” 

Since paragraph 1 is such a tone setter, here’s a real example, consistent with the advice above:
The drylands of the world present some of the more challenging land degradation problems, driving the expansion of the desert biome (Millennium Ecosystem Assessment 2005). It can be exceptionally difficult to rehabilitate degraded drylands for various reasons (Allen 1995), including: 1. The scarcity of resources–especially water– that recovering biota need (Bainbridge 2007), 2. Persistent dominance of invasive plants (Miller et al. 2011), and 3. The propensity for soil erosion to become a self-reinforcing process that precludes the recovery of desired biota (Ludwig and Tongway 2000; Miller et al. 2012). Rehabilitation approaches may have to focus not just on reintroducing desired biota, but also restoring a system’s ability to both capture and retain resources (Tongway and Ludwig 1996; Jacobs 2015) and resist invasion (Chambers et al. 2014). Drylands also are distinct in that there can be substantial interspaces between the canopies of grasses and shrubs, even when they are not degraded (Kéfi et al. 2007). The soil surface of these interspaces is the habitat of a highly functional assemblages of soil-aggregating organisms (cyanobacteria, mosses, lichens, fungi), which together compose biological soil crusts (biocrusts). Rehabilitation of biocrusts could benefit degraded drylands by increasing erosion resistance (Chaudhary et al. 2009), by creating and maintaining soil fertility (Reynolds et al. 2001; Belnap 2002), influencing the capture or redistribution of water (Eldridge et al. 2010; Chamizo et al. 2012), and discouraging some problematic exotic invasive plants (Serpe et al. 2006; Peterson et al. 2013). A real or perceived weakness of biocrusts in a rehabilitation context is their variable but often slow natural recovery from disturbance (Weber et al. 2015), but recent research indicates that assisted recovery of biocrusts can be achieved (Wang et al. 2009; Lan et a. 2014; Liu et al. 2013). Development of viable and economical biocrust rehabilitation techniques can be viewed as an opportunity and a pathway to enhance the function of degraded drylands (Bowker 2007). 

{If I engage in some self-critique here it would be that my paragraphs tend toward the lengthy side. But, they flow well in my biased opinion.  I really want to focus on the structure and  flow in this post; you can go for brevity in your writing if you like, and I'll work on being less wordy in the future}

Paragraph 2: Must establish the specific topic of the study. 

Supply key facts, and some relevant details about what you identified in the last sentence of paragraph 1.

“Like plant communities, corals may also be highly diverse communities of sessile organisms that potentially contribute to a different set of ecosystem functions. These functions include…….{pertinent details here}.  Also like plant communities, corals are threatened by anthropogenic stressors which compromise biodiversity. The identity of the stressors is again different from vascular plants…{pertinent details here}”

Last 1 or 2 sentences will identify more specific unknowns about your specific topic.

Here’s a continuation of the previous real example:
Biocrust rehabilitation is a young field that has only become a common research topic in the last ~15 years. A recent proliferation of research on this topic has emerged, especially from China (Tian et al. 2006; Li et al. 2010; Liu et al. 2013), but many questions remain unresolved (Zhao et al. 2015). Biocrusts can be rehabilitated in dryland ecosystems using salvaged natural biocrust material as inoculum (St. Clair et al. 1984; Belnap 1993). This practice may result in enhancement of ecosystem functions such as soil aggregation, and the creation of soil fertility (Maestre et al. 2006; Chiquoine et al. in press). However, it is uncommon to have a ready supply of salvageable biocrust materials on hand. To fully realize the potential of biocrusts as a rehabilitation tool, ex-situ cultivation techniques must be developed and optimized (Bowker 2007; Zhao et al. 2015). With a few exceptions (Xu et al. 2008; Xiao et al. 2011), most work in this arena has focused on culture of biocrust cyanobacteria with notable successes (Liu et al. 2013). Cyanobacteria may be isolated and grown in liquid media, which can be scaled up to produce inoculum in large quantities (Rao et al. 2009; Liu et al. 2013). Research on the other common biocrust autotrophs, mosses and lichens, has not progressed as far as the research on cyanobacteria (Zhao et al. 2015). Despite this, mosses are also generally culturable, either vegetatively from fragments of gametophytes or from spores, and can be grown on sand or agar substrates (Stark et al. 2004; Xu et al. 2008; Bu et al. 2011). Despite this knowledge, there remains much work to do to optimize the moss culture process to make it efficient enough to produce sufficient quantities of material for use in field applications. To our knowledge, rapid culture of dryland soil lichens has never been achieved and was therefore a much more notable research gap. Because some lichens are nitrogen fixers (Belnap 2002), it would be especially beneficial to overcome the technological hurdle of lichen culture, so that they may be artificially grown as a rehabilitation material (Bowker et al. 2010).

{Did you catch that? We went from talking generally about the challenges of rehabilitating drylands, to the specific state of knowledge about biocrust rehabilitation for ecosystem outcomes.}

Paragraph 3: Establishes why your study system is ideal to address this topic

Note: There is often but not always a need for this paragraph. 

Example topic sentences:
“The widespread woody plant mortality observed during the 2003 drought in Northern Arizona, across broad elevational and edaphic gradients, make it the ideal location to identify determinants of different mortality rates.”

“The 2011 Wallow fire was the most extensive wildfire in Arizona state history, burning in a mosaic of high, moderate, and low intensities. Thus, it affords us an opportunity to explore the variation in hydrological outcomes of wildfire in a heterogeneous landscape”

Just lay out your reasoning for the selection of either your study organism, community, location, whatever. There ought to be good reasons, and you know them.

Paragraph 4: Must state your questions or hypotheses

Sentence 1: Summarize what you did in the study in 1 or 2 sentences
“We conducted a meta-analysis of the effects of biochar on crop productivity and soil fertility”

“We sought to determine the relative importance of community richness, evenness and spatial patterning on nutrient cycling rates in Northern Arizona.

Next few sentences: State your specific hypotheses and questions. 1 – 5 is a good number usually.

You may use a numbered list format if it’s useful. It helps readers follow too.
“Specifically, we tested the hypotheses that: 1. Blue, but not red skittles, correlate with lower cancer incidence in rural counties, and 2. This positive benefit is contingent upon navel width.”

The above may be sufficient, but in cases where hypotheses need a little explanation or justification, follow each with a statement explaining some nuance or novelty of the hypothesis.

Specifically we tested the hypotheses that:
1. Blue, but not red, skittles correlate with lower cancer incidence in rural counties. Previous research has overlooked this factor, focusing on genetics and environmental exposure to carcinogens.
2. The positive benefit of blue skittles is contingent upon navel width. Since wider navels can accommodate more blue skittles, subjects with wider navels can benefit from higher dosage”

Final sentence: An impact statement. State what we might gain from this study. It should link back to the general topic in the beginning.

“If these hypotheses are correct, we may begin to apply skittles to navels as an inexpensive yet effective cancer treatment in impoverished rural areas”.

Sunday, August 18, 2019

How to respond to a review of a scientific paper

[Prologue: We decided last year to talk about peer review in our lab meeting, as a training exercise for the students. First we covered how to review, then how to respond to a review (this subject of this post). In general, I think we should actively teach these things. Most of us learn by watching how our advisors do it, and it works for some of us....but why not make this standard graduate student education? 

As a coauthor and  editor and reviewer, I often see poor response letters, leading me to believe that many people are just not being given good instruction in how to craft a response. The lab meeting discussion topic led me to write my version of how to respond to a review. It's fairly consistent with some treatments like this, and this, but personalized to reflect what one guy does who has done this a bunch of times. I don't claim this is the one true way, just a way that has worked out for me.

When we discussed this, there were other faculty present who added their personal tips as well, which showed that we (the professors) mostly followed the same principles, but differed a little bit in our approach.  That was good for students to see. These kind of instructional lessons are best paired with real examples. We also spent some time looking at a couple of my real response letters. I can imagine turning this into an exercise, giving a student a comment and asking them to respond to it.]

How to respond to a review of a scientific paper:

Part 1. Choose your own adventure 

1. (Accept) minor revisions – Celebrate. Tell your coauthors so they can too. Get on the minor edits within a few days, while the editor still remembers the paper …it may speed things up.

2. Revise & resubmit – Read comments, share outcome with authors, alert them that you may be requesting input soon. If it’s easy, you can start revising as soon as you can.
If it’s not so easy, chances are you’ll be feeling sort of defensive about some of the comments. Put it away until next week. Don’t respond with a “hot take”.

3. Reject with invitation to resubmit – Read comments, share outcome with authors, tell them whether you are feeling like resubmitting or not and get their take. The decision to resubmit or not will depend on whether you are willing/able to rebut or apply all of the comments.  Usually, it is better to resubmit to that journal if willing/able to address the comments (you’ll stand a somewhat better chance there than another equal journal). 
These days, this is the new “revise & resubmit” so journals can talk about how exclusive they are. That’s my cynical take, anyway. So they might actually want your paper after all.
Again, put it away until next week. Watch a you tube video of “Hitler and reviewer 3”. It helps. 

4. Reject – Inform your coauthors.
Skim the review, don’t dwell on it.

After a few days, read the comments in detail.

Very rarely you may challenge the decision. The journal will have a formal process for this. To challenge you must be able to argue convincingly and succinctly that the reviewers were flat-out and demonstrably wrong, careless or biased and this led to a wrong decision by the editor. The subject/handling editor is the one who usually makes the decision. Absolutely do not make a habit of this, it’s kind of a nuclear option.

Assuming you are not challenging….
With a calm mind, determine whether there is good advice in the reviews. There almost always is. Even though you’re not bound to apply these comments, it is smart to seriously consider them since they may help armor you in future reviews. It is not unlikely that one of the same reviewers will review again for the other journal, and they will be annoyed if you ignored the hours they volunteered to do your review.

Part 2. So, you are revising for a resubmission to the same journal (adventures 1-3 above)

You need to produce a revised manuscript and a response letter to the reviewers.

1. Check journal instructions. They may want a revision where changes are marked somehow, in addition to a clean version. Know what they want before doing anything. Also check what the deadline is.

2. To make your response letter, copy all comments into a doc verbatim. This will become your point by point response. Always draft in a word processing file, so you can save the letter for your records.

3. (Optional) Annotate your manuscript with comments for you. It can be useful to copy the major comments, into comment bubbles into a version of your ms in the place where you think it should addressed. This is just for your own reference.

4. Work through the comments, making the needed change in the ms. If the journal wants your changes marked in some way, e.g. colored font or track changes, do that. In the appropriate spot in your response letter (after the corresponding comment) either (a) describe what you did to address that comment, or (b) explain why you didn’t make the requested change. Make it easy to distinguish response from the comment, e.g. I like to use bold italics for my responses. (Though, note that depending on the manuscript submission system you may have enter the info into a box online that does not allow special formatting….check first) 

5. (Recommended) Do the easy stuff first. Leave the comments you need to think about until later sessions. It will probably be easier psychologically for you that way, plus it gives you time to think through the tough ones.

6. It’s the corresponding author’s job to do handle the response, so if that’s you, take the lead. But it is also common to ask coauthors for input or thoughts on specific comments that they might be more qualified to tackle, e.g. the person who did the super specialized spatial model in your paper might want to handle questions about that. If you are a student, definitely solicit your advisor’s advice on your responses.

7. Add an opener to your response. Put a short paragraph on the front of your letter, in front of the detailed responses to comments. It’s basically a “thank you” note for everyone’s volunteer time to improve your work, and acknowledgement that the paper is better (hopefully you feel this way, otherwise maybe you caved a little too much).

Dear Dr. Famous –
We wish to thank you and the reviewer for your efforts. {you might point out something specific like: especially the statistical advice and the many thought-provoking suggestions for the discussion}. We have considered all of the constructive suggestions, and applied (all/the majority). As a result, we feel this draft is much stronger. Below you will find your comments and those of the reviewers reproduced verbatim, followed by our responses in bold italics (or whatever).

8. Offer your coauthors a chance to comment on your response before resubmitting. You’re communicating on their behalf, ethics dictate they should be offered a chance to see what you are resumbmitting & give a thumbs up. It’s not impolite to limit time because you usually have a deadline. 

Part 3. When responding, should you “fight” or bend the knee? Or compromise?

Usually your response is going to be a mixture of giving the reviewer what they want (and actually improves or at least does not harm the paper), saying “no thanks” on some comments, and meeting them partway on others.

Here’s the key things: 





1. Review all comments with a calm mind. Little known fact: reviewers are actually right pretty often! If 2 reviewers comment on the same thing, that’s a strong indication that there’s really something there to work on. When you pretty much agree with the reviewer, apply their suggestion. SO EASY! 

Also, go ahead and give them the minor stuff, even if you’re only kind of on board. They usually tell you exactly how to make them content.

If you can, bend the knee on most matters. Guess what?! Chances are you’re now at least halfway (numerically) through the comments.

2. When should you fight? It gets tricky when you don’t really agree with a comment….should you “fight” (mostly NOT do what the reviewer suggests and explain why in a rebuttal), or meet them halfway, or cave? 

As in life, fighting should not be your first option, nor your default. A smart person chooses their fights. They fight when it matters, and when they at least have a chance of winning. 
There’s 3 factors really: A. How strongly do you feel that you are right and the reviewer is wrong? B. Are you going to be able to clearly and effectively articulate your case without emotion to the decider (editor), and maybe even convince the reviewer? C. Are you fighting a lot already? Can you engage one more fight without appearing closed to constructive criticism (i.e. looking like an obstinate shit)?

3.  How should you fight? There are many shades of “fighting”, some overt, some subtle. It should be polite and respectful by default. Yes, you can fight politely. If someone else is rude, respond with emotionless language, do not escalate. Most instances of fighting actually result in meeting somewhere in the middle, i.e. you have fought to defend some of your ground. Here’s a few hypotheticals:

Scenario 1: I’m right, here’s why
Problem: The reviewers don’t seem to get why you used model selection. They think more people would understand a simple full-factorial ANOVA, than your overcomplicated fancy-pants showboating. You feel strongly that not only have you thought through the options, but you have valid reasons for your approach.

Solution: First try to see through the eyes of the reviewer. Did you express, in a way that a typical reader could understand, why you made the choice you did? If no, you clarify the wording in the manuscript. If yes take note of where this was clearly expressed. Then compose your clear-headed argument in support of your approach, with the intent to persuade. 

Then in your response letter you might apologize that you were unclear in the presentation of your reasoning, explain your change, and offer a little more lengthy explanation of why you are right. “We believe we failed to communicate our reasoning for selecting this approach, and that led to these comments. We apologize for the confusion. Now, the text states: “We applied model selection because we needed to identify only the most crucial experimental factors that should be carried forward into experiment two.” The model selection approach is optimized for this purpose. We do in fact include the full factorial model in our model set (see supplemental table 2), and found that it is not among the best models”

If you were clear from the beginning and you think the reviewers blew it, then skip the mea culpa, state your argument first, then tack on something like: “We feel this was explained succinctly on L334-336. If we have not been clear, we would be grateful for specific suggestions to improve clarity.”

Outcome: The reviewers and editor will see you actually considered the comment, that you are motivated by reason and you mean to do a good job (check!). Hopefully they will agree that your reasoning is sound (check!). If it works all the way, that’s a WIN. You keep the analysis 100% the way you think is right, yay!

Scenario 2: Divergent reviewers.
Problem: You have a section in your discussion you are really proud of. The writing is good, and it provides an interesting, unconventional interpretation of the data and some hypotheses for future researchers to test. Reviewer 1 finds it overly subjective and recommends removal to reduce the length of the paper. Reviewer 2 had some positive comments about it and is intrigued to follow up in their future research. You can’t make them both happy at the same time. 

Solution: With regard to the subjectivity argument, you can explain to Reviewer 1 that you feel the discussion is the main place in the manuscript where the author can interpret the data and that this is important to do. Show them that your language makes it clear that you are building a hypothesis to be tested rather than a firm statement of fact. You remind them that proposing new interpretations is one way that science may advance in new directions. As evidence, you point out that reviewer 2 did not level the same criticism and finds value in the new interpretation. You tell reviewer 1 that you understand their concerns about the length of the section, and as a result you were able to reduce the text by 20%.

Outcome: You show you listened to both reviewers, even though you agree more with one than the other. WIN! You keep 80% of the section that you love.

Scenario 3: Switcheroo a.k.a. I can’t give you that, how about this?
Problem: Reviewer 3 has a hard time believing the conclusions of your experiment. They think that in your diversity-function study, your design makes it impossible to distinguish distinct mechanistic explanations: complementarity, and the sampling effect. They argue that you really need a different experiment that is able to partition these two mechanisms, or you should stop focusing your discussion on the complementarity mechanism. You have no time or money for another experiment, so this comment appears to be a stake in your heart. You cannot deliver what they want, exactly.

Solution: You investigate some numerical methods of partitioning these two effects, and you apply them to the data you have. You have to add this to your methods, and results and make a figure. While you’re at it, you go back to your last 4 experiments with similar diversity gradients and do the same thing, allowing you to plot (in general) the degree to which diversity affects function via complementarity. You add that to your methods and results. You present it as kind of a mini-metanalysis, that enhances the evidence for the generality of your findings. 

Outcome: You could not deliver what the reviewer wanted, but you offered something totally different instead. With luck, both reviewer and editor will be satisfied with your effort. WIN! You’re not dead on arrival, you kept your experiment, you kept your complementarity-focused discussion (100% of your content), and with some extra work, you enhanced the interpretability of the results (bonus 20%).

4. As you gain experience you’ll find your comfort level in your choice to give in or fight on individual comments. You may become more or less fighty, and probably your fighting will be more subtle….like a stealthy ninja. 

Part 4. Ok, but what do you actually say in response to a comment, and how do you say it?

1. For comments that are simply grammar, spelling, word choice edits and the like, just say: Done. or Corrected. 
(i.e., No discussion is needed…we did it)

2. For more substantive comments in which you take the reviewer advice and addressed the comment, actually explain what you did. If its not obvious where the change is, you can either tell the editor/reviewer where the changed part now resides (e.g. L133), or just copy into your rebuttal the altered sentence (e.g. We have modified our statement to reflect the results of this study, and removed overgeneralizations. The sentence now reads: ________).

3. If you’re not going to apply the comment (i.e. you’re engaging in some form of “fight”), you must state a reason. Tone and clarity are key here, because you must convince the editor and the reviewer that you seriously considered the matter and have a reasonable argument for not going the suggested direction. 

You very well might have to pull out extra evidence like citations. Once in a while you might have to do an analysis or prep another figure to support your argument. This is uncommon, but it is a good test of your resolve in this fight.

4. Never, ever, ever insult someone. For example, don’t say “That is a rather disingenuous argument”. 

Instead say, “We strongly disagree with this argument for the following reasons:…..” or if you want to adopt a softer tone : “We understand your concerns, but respectfully disagree for the following reasons:…..”

5. Once in a while, a reviewer catches a key error, or suggests a great idea that you didn’t have before. 
Do: Briefly acknowledge such instances. 
For example: Great catch! That was a typo, and it led us to check the entire appendix again which is now error free.
Thanks! That was an excellent idea, and we agree that it improved the flow of the discussion substantially. 

Don’t: Thank the reviewers for every. single. comment. It reeks of the kind of slobbery deference to authority that is the antithesis of science. A blanket “thanks for the review statement”, and occasional acknowledgement of the most useful comments will suffice, and show that you appreciate this process. Hopefully you do, despite it's quirks.

6. If you did something really dumb, like put the same table in twice as 2 different tables (yeah, I did that), it is appropriate to briefly acknowledge the error and apologize for the confusion it caused. 

When you realize that your presentation errors led to confusion, go ahead and acknowledge that. 

For example: “Both reviewers appear confused by this section, indicating that we did not communicate our point effectively. We apologize for the confusion.”

Don’t: Apologize constantly. Same reason: slobbery deference to authority is the antithesis of science. 

7. This process is peer review. If you remember this simple fact, it will help you get your tone right. Always remember that and address the reviewers and editors respectfully and professionally, but as peers, i.e. equals. You are neither the inferior or the superior of the reviewers & editors. Communicate to them as you would like your professional peers to communicate to you. Just as they should respect the work you put into the manuscript, you should respect the volunteer time they are putting into reviewing.

Sunday, September 9, 2018

What we can learn about ecosystem collapse from Iceland

A large proportion of Iceland is either unvegetated completely or only very sparsely so. This is generally true of highland regions, but also some lowland regions where sand plains may be found.  These are called deserts: not in the sense of a dryland, but in the sense of a deserted place where the paucity of vegetation makes it exceptionally difficult to live. 

This could be the Atacama Desert or Mars. It's a highland desert of Iceland.

A view of Sandvatn, on the way to Langjökull glacier. Notice that little island of green by the lake...more on these islands below.

It is also curious that despite a mild climate for the latitude, the land does not support trees generally. Often, it seems that the dominant vegetation are mosses in rocky areas like lava flows, or grasses where there has been some soil formation. Maybe this isn't so strange in the highlands, where you might have expected more low-growing plants. But, this holds true even in areas closer to the coast which are well within the environmental tolerances of trees.

Your first instinct may be to look at the glaciers and ice sheets, the most extensive in Europe. You might think that after the last ice age, the land never really supported plants because of the recent glaciation. Or you might pin it on the several active volcanoes. And yet old writings, including the sagas, report a vegetated place. Another key to the past is in place names, for example many place names refer to a forest or woodland, yet if you go there there is no such thing present. There's also some hard physical evidence of more extensive vegetation. For example you can go to some nearly barren areas and find charcoal pits. The charcoal would have been made to fuel iron forges (settlers were iron age people), but where are the trees? Surely people didn't drag wood into some barren area just to make charcoal. A sensible person would produce the charcoal where the wood is, then transport the much lighter charcoal.

Then, most informative of all are the rofabörðs. Rofabörðs are actual remnants of vegetated land, usually in small patches with abrupt cliff-like boundaries, that border unvegetated land. I find it poetic that they are sometimes shaped like puzzle pieces. They are that final piece that allows you to solve the puzzle of Iceland's past. You only have to see one to guess the amazing truth: 1. Iceland had vegetation, 2. Now it's mostly gone, 3. The soil, sometimes alot of it, is now gone too. When you start piecing this together with some of the other lines of evidence,  you can further infer that: 4. people were a part of this change. 

A rofabörð at the bottom of a slope at Einifell.

The other side of the hill. Another rofabörð ends abruptly in a cliff-like edge of greater than 1 m.
You can see quite a bit digging into a rofabörð. First, they are deep! Second, they preserve a stratigraphic record of key events like volcanic eruptions. The long term presence of vegetation seems to associated with substantial soil development, and furthermore vegetated patches accumulate rather than lose soil over time, alot of it.

Oli Arnalds opening a soil pit into a nearby rofabörð. Note that the top is vegetated by heath including grasses and low growing shrubs.

We exposed over 1.5m of soil, and still did not reach a marker called the "settlement tephra layer", which is dated to the year 871. This patch must have gained all of that soil in the last 900 years or so. You can see a black tephra layer here, probably one of the more recent (a few centuries ago) Hekla eruptions. 

The scope of the ecosystem collapse is huge. Iceland's vegetation loss led to catastrophic erosion in about one third of the country. The ability of these severely eroded areas to support vegetation ever again is seriously compromised, and it doesn't happen very often without a serious shove from people (future post alert!)

Ok, why did this happen to Iceland? A perfect storm of multiple factors, here's my summary attempt:

1. From the beginning,  Iceland has some unique vulnerabilities. Volcanic ejecta (tephra: ash, cinders, etc.) can, has, and does sometimes bury low-growing vegetation, knocking back the productivity and coverage or snuffing it out completely. This has happened many times to greater or lesser degrees anywhere in the country. The record is captured in soil remnants with datable tephra layers that you can clearly see. Another more localized factor is that many meandering rivers emanating from the ice sheets can render large plains bare (e.g. Skeidarsandur), especially when there is an ice flood. Finally, the soils are andosols, derived from volcanic ash. Such soils may present some nutrient availability challenges, may poorly aggregate without vegetation and organic inputs, and may contain some unusually light mineral particles that can be easily transported by wind or water.

2. Over this fabric of vulnerability, settlers cleared the forests and woodlands to build and heat homes, conduct metal working, and make farmland. The Icelandic birch would have been the dominant species of the lowlands, growing in usually open canopies in small shrub to tree form. this is the only native timber. Such woodlands covered about one third of the country. The highland was likely vegetated with heath with low growing, spreading dwarf shrubs. This heath was not grazed by any native mammalian herbivores, there are none. So the introduction of sheep or goat grazing in the highlands was a new ecological pressure for this system and would further impact recruitment and porductivity of shrubs.

3. Without much tall vegetation anymore (very few trees, fewer shrubs), the former woodlands had lost their resistance to volcanic ash deposition. Some of these areas became deserts after ash fall smothered the rest of the vegetation.

4. Without vegetation, soil erosion is much more prevalent. All of this leads to permanent widespread soil loss, sometimes measurable in meters, and expansion of desert regions. Some sandy deserts also tend to encroach into adjacent areas, compromising vegetation more.

5. A last insult was the Little Ice Age, which was an unconducive period for plant growth, especially with all of these other pressures also occurring.

The prevailing story here is that multiple factors lead to the ecosystem collapse, but new anthropogenic pressures like wood harvest and grazing speeded, expanded and exacerbated natural disturbance regimes. This is difficult to reverse now, but a few ways have been developed by the oldest Soil Conservation Service in the world.

Thursday, August 30, 2018

Exploring Fire Moss in the Northwest

When I tell people that I study mosses in Arizona and New Mexico some folks give me a quizzical look and ask why I’m not working up in the Northwestern US. Thanks to the support of Jason Jimenez from the Colville National Forest and Pete Robichaud from the RMRS Moscow Forest Sciences Laboratory I have been able to heed that advice. Over the past two summers I have traveled to Kettle Falls, Washington to help monitor a Burned Area Emergency Response (BAER) mulching treatment on the 2015 Stickpin Fire. This has also fed my summer wanderlust as I have expanded my natural survey of fire moss colonization to the 2015 fires in Washington and the 2017 fires in Montana.

The Sunrise Fire of 2017, Quartz Montana
It was incredible to see just how important moss is for postfire recovery up there, everything that north westerners had told me was true! I saw the usual suspects Funaria hygrometrica and Ceratodon purpureus, and some new early successional species, Polytrichum juniperinum and the liverwort Marchantia polymorpha. One species that was conspicuously absent from the Northwest was Bryum argenteum. Total bryophyte cover was over 50%! And the speed of natural colonization and succession was incredible. After exploring fires less than one year old, it became apparent that moss was the largest contributor to cover immediately after fire, and thus is an important component of soil stabilization in this region.

Some crispy Marchantia and Funaria both releasing spores prolifically, two years after fire
Moss colonizing the Noisy Creek fire spring 2018, 8 months after fire
To better understand how mulching affected moss colonization on the Stickpin fire, I trained the soils crew from the Colville NF on my methods. Last fall, they sampled straw and wood shred mulched units, as well as an untreated unit. Moss cover was significantly lower on both of the mulches, but seemed to fill in around and under them quite well.
Maddie and Amber demonstrating perfect bryophyte sampling technique. It has been wonderful to share my research with land managers and learning from their experience in a new ecosystem. 
Moss eking out a living under low cover straw mulch.

We were interested in exploring mulching impacts byrophytes in more detail. Additionally we wanted to understand how postfire logging affects moss cover on a logging experiment that had occurred close by. Both mulching and logging are relatively common postfire management techniques and their impacts on vascular plants has been studied in detail. Broyphytes have received much less attention so I submitted a Joint Fire Science Program GRIN proposal to expand our research and it was funded! We will continue to monitor the impacts of postfire treatments on bryophytes this fall and will add some plots in logging units. We will also measure the impacts of mulching and logging on available soil nutrients and relate that to bryophyte cover. Finally, a major component of the GRIN is outreach to the management community so I will be attending BAER workshops, giving a webinar, and creating a fact sheet to continue sharing my research with land managers.