Conferences 2016

2015 was a good year for conferences. The Ecoblender lab attended the California Native Plant Society, Society of Ecological Restoration, the San Joaquin Valley Ecological Conference and the Centennial for ESA.  Lots of great ideas from these conferences that being reflected in up coming projects within our lab. What about 2016 though?

Unfortunately, both CNPS and SER operate bi-annually, which means we will have to wait until 2017 to attend again. The San Joaquin conference is a really fun one day conference in March that the Ecoblender lab will likely attend again. ESA is on the maybe list in Fort Lauderdale. Some other potential options?


Why @the_zooniverse and #openscience sharing platforms are also tools for social restoration

Person in Room with 500 Monitors --- Image by © Louie Psihoyos/CORBIS
Person in Room with 500 Monitors — Image by © Louie Psihoyos/CORBIS
Zooniverse is primarily a research platform with a big citizen science component.  Reasons to consider putting image data you collected (even smaller datasets or image/video libraries) include the following:
1. It raises your public reputation and gets your name out there.  This is really important as you get sometimes get surprise funding and collaborations too from places you might not expect.
2. It makes the project and the funding from agencies look great, and it is really another form of publication/dissemination.  It is also another financial return on the all those cameras and all your time.  REMEMBER – many of these tools also have an interaction component to engage people and not just flip through pics.
3.  We can engage with a wider audience and get local stakeholders to see the photos, see the odd animal, and begin to care more and appreciate their system from a very different perspective. Seeing those pics at ground level often at night etc is a total window into a world that ranchers, the oil staff, the managers, and even many biologists do not get.  I see this is an important social-restoration tool in that it promotes looking at and paying attend to plants and animals within the system.  I feel the exact same way about the pollinator videos.
Not only do natural systems need restoration but people need their social perspective on the ecology of systems restored.
4. This system (and flickr) provide the free cloud storage of ALL your photo data for us, ie this is our cloud backup.
5. We can show students what we do and teach them or volunteers to help.  Of course, it is best if each PI does it, but the students or techs can also look at other things for us at some point. Windiness, total number of plants, total number of false hits for us, etc… or do other things we have not imagined yet – filter some, change contrast, etc.  that is the point of these tools.
In summary, I see all these outreach efforts (flickr, youtube, blog, twitter, etc) as a really important process of ecology, restoration, communication, and doing some social good.
These ‘snapshots’ are also an opportunity to illuminate natural history for individuals to see the system you care about.

Positive interactions @ ESA100

Niche mediation/niche construction/niching: The dominant plant (shrub, cushion, tree, etc) can increases the suitable area for a plant species by reducing abiotic or biotic pressures. As E. McIntire has pointed out though, positive interactions generate more area with the same fundamental niche characteristics, rather than expanding the niche itself. Thus, removal of limiting factors on the beneficiary by the benefactor will not increase the realized niche beyond that of the fundamental niche. If biotic limitations are zero, then the realized niche will simply equal the fundamental niche.

Realized Niche = Fundamental niche – biotic limitations (sensu Hutchinson)

The dominant plant will therefore either 1) increase habitat availability by generating the same microclimatic conditions of the fundamental niche for a species; i.e. increasing the area of the fundamental niche or 2) Reduce biotic limitations, such as herbivory or competition, that prevent a species from occupying areas of their fundamental niche. Both these situations have the same perceived response (a range expansion), however, I believe they have different implications for ecology and conservation.

Semantics of facilitation: The original definition of facilitation stated, roughly, is a positive effect between two individuals that is non-trophic based. I think we have assumed that this means it remains within trophic level, but A. Liczner has pointed out that this may not be the reasoning behind the original definition. Instead, it may be to imply a positive effect that is not trophic. For example, a shrub would not be facilitating a deer by being eaten, but would facilitate a deer by providing shelter. I also think “facilitation” can be a challenging term because what would the opposite be for facilitation? Competition? But not all negative effects are competitive. For instance, a shrub deterring herbivory is often classed as facilitation, but if a shrub attracts herbivores what is it? I think the general classification of positive or negative interactions act as good umbrella terms, but not sure what to do when going more specific.

Beyond the stress gradient hypothesis: There was other semantic discussion on the term “stress” and how it may be time to move away from stress as if it were a quantifiable measure and instead discuss the gradient that is being measured (temperature, soil moisture, etc). Smit actually took this one step further and stated how we should also measure the response of stress on the plant. Simply correlating water availability with plant biomass or abundance is not sufficient to determine if a plant community is stressed, because these communities may have adapted different life-history traits (sensu Grime). Additionally, there should be a bigger push to study other approaches that are not singular mechanisms (similar to what I proposed in my review). Instead, as we concluded, there should be further work in other areas of research such as: animals, indirect interactions, “unpopular” mechanisms or mechanisms in combination.


#ESA100 in Baltimore

As a first time ESA goer the whole experience was pretty wild. There was nearly 4000 people in attendance of the conference and the number of sessions occurring simultaneously must have easily been over 10. I really liked manyof the talks and at times found it difficult to choose which rooms to go to. I missed out on a R-workshop but instead learned a lot about invasion melt down. Overall, good experience. Some key notes I took:

Data – Meta-data as always is very important when structuring datasets online, however ArcGIS data might require a more detailed description of the data presented. This is because ArcGIS is often a layered dataset will “planes” rather than “vectors” of data. The current standard is ISO-19115. This brings up another point, which is that excel is both power but maybe also problematic. Not all data fits best in excel and their may be other platforms that would be more advantageous.

Invasion theory – I learned a lot about invasion meltdown which I generally didn’t know before.  I also noticed more incorporation of theory into basing decisions about invasion. For instance, if a native+non-native grow poorer on their own than together (interspecific<intraspecific competition) this a consequence of niche differentiation theory where species use different resources. If the native+non-native grow poorer together than separately (interspecific>intraspecific competition) than this is neutral theory/co-existence. The other novel invasion talk discussed creating a metric of invasion. Although many would quickly challenge this I really do like the simplicity of the metric. I know Ontario uses a “coefficient of conservatism” to quantify a plants susceptibility to disturbance, which can be super effective in conservation management. I wonder if there were other applicable metrics we can develop to assist in restoration decisions.

Quick land assessments – The talk about REFA plus the CNPS strategy of quickly quantifying landscapes really shows how necessary this is. Coarse estimates of landscapes are such a great idea and can give great modeling power when combined together. Global datasets already exist for temperature, preciptiation, etc. However, at the local scale  ecologists can provided more refined information such as a general species composition list, topography and soil composition. If a standardized approach was used for all ecologist, this would also help with the creation of meta-data because there would be greater similarities between data sets. Lastly, I like them a lot because they are easy and can typically be done in less than half  a day.

Facilitation – I had the chance to meet with some great researchers to discuss positive interactions. It was  great experience and I got a lot of ideas from the discussions. I will do a separate post discussing the dialogue. The symposium also went very well and I thought it was a great balance of applied and theoretical that was specific enough to encourage listeners.

My talk – It went well actually. I was surprisingly nervous and it was early in the morning but still a good talk. Another one to add to the list.


How to streamline editing collaborative manuscripts with #openscience & some #zennotes hacks


Within the team, we share and edit very collaboratively. Often, individuals participate not as co-authors but as ‘friendly’ referees to improve our work and to ensure that we kept informed of evolving ideas within the lab. Graduate students in the lab and I also sign an agreement when we begin collaborating to ensure that our expectations are aligned and mutually acceptable.  One of the elements is the two-week rule.  We indicate that will do our best to turn around materials to one another within two weeks AND to give our collaborators two weeks before deadlines to make their contributions or write support letters or provide associated materials. We also have a few new rules to support a more healthy work-life balance.  No emails on weekends, wait till Monday, and do not ask for things over the weekend.  One of the challenges I have recently faced as a collaborative editor, is changing gears between editing different manuscripts.  I have noticed that the longer I wait to edit, the harder it gets, and the longer I continue to wait.  I have also noticed that retroactive interference is a big deal for me now that I am getting older and more toasty.

So, here a few ideas to deal with these issues.



1. We stick to the two-week rule turn-around time. Waiting too long makes everything slower, and we forget previous revisions. I am VERY guilty here. My turnarounds vary from 1 day to 6-8 weeks for poor Alex Filazzola.

Guideline: Do our outmost to adopt a two-week turnaround time for me and for you too. Do not include weekends in count.

Incentive: If we miss the 2-week window (we use shared, online calendar to track back and forth), I put $50 into a fun, lab account such as amazon for us to spend on lab stuff (like coffee pods and yummy treats). If you student misses deadline, a $25 penalty? Same fund for the lab.

2. Take one extra day before you send to collaborators, read it one more time from scratch. Use the highlight function only, not track changes, to ‘highlight’ any bits that you need clarification on.

Help the collaborators be more rapid and direct their attention to give you the help you need. MAYBE even make a list of Qs for the collaborators to consider when you send the ms back.

Guideline: Highlight needs for collaborators a priori.

3. Include alternative versions of figures (i.e., Riis you do not include or other effect size measures you calculate but did not use in ms), the data (ALL) plus summary data you used for plots, and code in a g-drive folder in case your collaborators want to look at. For instance, Alex was way ahead me, did Riis etc, had them ready to go, but I had to ask from them and wait a day bc of email lags. SO, let’s streamline that.

Guideline: Provide supporting materials that you helped you write manuscript to collaborators because it can also help them revise.

4. Prep cover letter, look up referees whilst you wait, and get the data ready to publish on figshare (for derived datasets) or knb for primary datasets. Recently, I have also discovered that writing the cover letter has really helped me hone my ideas on the value of the manuscript, even more so than that abstract, and that I have then returned to the manuscript and improved it.

Guideline: Prepare datasets & cover letter for publication whilst you wait.


Workflow tools
We currently flip ms docs back and forth. I like because I work offline a lot to minimize online shopping, twitter, and other distractions. I recognize some of the available tools also support offline mode then syncing. However, there are some limitations. We could consider using the following tools instead:


Google docs with commenting and the associated tracking function



Here are a few blog posts to consider:

5 Ways to Collaborate on Documents Online in Real Time

How to Collaborate on Documents Over the Internet

The big goal here for me is to be present, in the moment, and on the ball for each and every editing instance.  Plus, minimize stress and put some more zen into my writing & editing.


Concurrently, not orthogonality

Working on round 3 of a design for understanding the Ephedra-Brome relationship in the Panoche Hills. Based on our discussions I think I want to simplify the project a bit more to the roots. What are the major factors limiting Ephedra growth. Similar to my mechanisms paper, there are different pathways a shrub can facilitation a plant, there are also different pathways Bromus could be affecting Ephedra. Looking at the literature this could be interference, exploration of resources, etc. So why not test it all?

Density series of Brome vs Ephedra. Step one is to resolve whether or not Brome actually limits Ephedra in some way. Then step two is to layer on different factors that could be responsible for changing the relationship or interaction. These include:

– Nutrients

– Soil Moisture

– Shade/light

– Herbivory

– Soil substrate

The big revelation?! Concurrently but not crossed. We have discovered that beyond two interaction terms things start to get murky. What would a significant relationship for nutrients x shade x herbivory mean anyways? Let’s bring back the basics and understand the role of each factor on the Ephedra-Brome interaction independently. Then once we resolve which factors are most relevant we can design a “final” experiment be it in the field or greenhouse that combines these factors together.

This will also give us more insight into growing Ephedra, so even if the Brome link isn’t true we can still get some botany out of this.

Restoring Ephedra is within reach!!


A brief comment on writing frequently & well for #scicomm & #openscience

I have been thinking on my workflow (Chris Lortie) as of late. This is in response to the recent post by Alex reviewing a book on dissertation writing he received as a gift from a collaborator.



Image from humor post on topic.

I love to write. However, it is so tempting to rabbit hole and keep reading more stuff, exploring tangents and connections, and developing alternative visualizations for a paper. As of late, I have come to recognize that this is one part positive (think through a topic well and provides gestation time) and one part negative (procrastination). It is continuum of opportunity that requires balancing the benefits and costs. However, it is crystal clear to me that writing regularly, if not for large projects but for smaller communications, is beneficial and a key form of practice.  If an audience is included in the writing process, even better, as it encourages more careful wording and promoted open-science insights into the process vs. product of scientific inquiry. Tweets, blog posts, detailed notes at meetings (that you then subsequently share), and sometimes even emails are also excellent opportunities to ensure that you are precise and clear.

I have also purchased this book to check out the workflows of productive individuals.



Finally, I wanted to add that my fav book all time on this subject was by Italo Calvino. Science and literature converge.


The peeking around the corner is a bit cheesy, but it is a really awesome primer on writing.


After reading some of Dr. Bolker’s book, I think I can share some insights on writing. I know my own writing has significant room for improvement and if there was a giant take home message from the novel, it is that practice makes perfect. I should definitely be writing more frequently than I currently am. Additionally the book had some suggestions on how to generally improve writing as a graduate student beyond that of grammar. It touches upon many factors including how to pick a supervisor, researching a topic you enjoy and quality > quantity. Additionally, just as the title suggests, the book strongly promotes frequent writing to take bite-size pieces of a thesis rather than marathon writing it in the last month of a program.


Overall the book is an interesting read and gives the graduate student a little self-awareness into considerations for writing. One contribution I would like to make in addition to Dr. Bolker’s narrative is that writing should trend with the progress of a particular experiment. It may be a good idea to break up the writing of a manuscript throughout the duration of an experiment. For instance, have a hypothesis and predictions formalized during the experiments genesis, complete a detailed methods section before embarking to the field and subsequent results/analysis once returned. Not only does this make individual manuscripts easier to write, but better links the paper with the experiment maintaining the purpose from conception to birth.

Another trend I am trying to develop in my own writing is to have a conceptual workflow. Our lab is great in that we conduct a review on a topic first before conducting an empirical test of that subject. I would like to go one step further and add in an application stage where the thesis is not only examining ecological relationships but contributing towards environmental stewardship. This is in the form of developing a restoration program or mitigating anthropogenic effects. Ideally, my thesis would have a workflow of Review –> Tests –> Management. With the “test” stage being the largest. Hopefully it works!


Ephedra dendrochronology

Trying to resolve the age of the Ephedra’s found on top Panoche Hills is super difficult. As with trees in arid environments, precipitation is the factor limiting secondary growth development. Thus, drought years can produce extremely small tree rings or “missing” rings altogether. Ephedra is additionally challenging being a shrub, which generally are tougher to date than “true” trees. Some key things I’ve learned from conducting a proper tree aging is:

1. Replication – Often it is important to compare multiple samples of the same individual as well as other members of the population. As with other sciences, more is always better.

2. Consider abiotic or limiting factors – temperature, precipitation, or snow melt can all strongly determine tree ring presence. This is also true for microscale topographical changes. For instance a tree or shrub growing on a slope will likely have a different ring structure than its counterpart growing on a flat/plateau.

3. Cross-validation – Besides comparing it to other individuals of the same species, it is often good practice to compare with an additional species found in the same area.

That being said! I’m going to give this dating thing a shot. From a sample individual collected at the Panoche Hill plateau, an area limited particularly by precipitation, I was able to count 42 growth rings in a core sample. Unfortunately the center is rotted (a trend in ephedra cores) which probably has a higher density of tree rings than the remaining sample. However, if I assume the same number of rings/cm as the not rotted wood, there would be approximately 58 total rings.

But!! Panoche Hills experiences drought events such as the last two years. From my time out there, Ephedra only produced seed in 2013 which I am going to assume is a “successful” growth year and would produce a growth ring. Years like 2014 and 2015 produced no seed, and were therefore likely to have a missing growth ring. On average, for the last 58 years, precipitation lower than the seed producing threshold represented %20 of the years.

What does this all mean? Not much actually… it seems than Ephedra at Panoche Hills, could be anywhere between 70-1000 years old. There are just so many considerations that it will definitely require the assistance of a professional. It is interesting to think though that Ephedra could have only colonized Panoche Hills, post-European arrival to North America.

09 ephedra1 09 ephedra3