That feeling when you finish your dissertation…

I wrote the following as an immediate reaction to seeing that my dissertation had been approved by all my committee members back in April of this year:

This initial draft of my conclusion underwent further revision.

My committee just approved my final dissertation document with the graduate school, so that’s done I guess…

It feels a bit surreal – nearly 6 years devoted to reading, collecting data, writing, learning, analyzing data, writing, thinking, collecting more data, offering inexpert guidance, did I mention writing? and now there are a few check-boxes that say I’ve done it. I keep thinking that they might take it back, though I don’t know who “they” are, my committee definitely demanded rigor and helped me build my knowledge in the process.

The #impostersyndrome will never go away.

I continued making revisions based on committee feedback right up to the deadline. It’s still not perfect, but I think I understand the imperfections at least the tiniest bit better. Hopefully I will be able to address some of these as a finish preparing to submit manuscripts for two chapters for publication.


Snakes Hang Out in Douglas-fir Forests Too

I’m back in Sonoma County, California doing some fieldwork. One last season, mostly to pass the reins to another PhD student. It got me thinking about my last trip out in 2014, so here is a tale from the field.

We were on the lookout for snakes. Western rattlesnakes to be more exact. Doing fieldwork in Sonoma County, California these are probably the biggest immediate danger, next to twisting an ankle or fracturing something in a fall. A bite is unlikely to be fatal if you stay calm and get to help in a reasonable amount of time, or so I’ve been told. Much worse is the possibility of contracting Lyme disease from a tick bite. Fortunately, in five seasons of fieldwork I had never had to find out. So there we were, well off of any trail except what deer or rabbits (or snakes!) might use, traversing a hillside with clump grass and mixed chaparral vegetation. That means often dense, impassable shrubs with stiff, sharp branches at face height. Okay, that’s not what the vegetation classification means, but we make up our own meanings while cursing our way through. Rattlesnake habitat. Looking carefully before placing a boot down while hanging on to the branches threatening to whack you in the face on a steep hillside, while it’s 75 degrees F (or 45 and rainy) is hard work. Usually we’re doing both over ~7 weeks. Our vigilance seemed to pay off as we finished our scramble by exiting into a shaded, cool, soft, open, needle-carpeted Douglas-fir forest. The terrain flattened out, the understory dissappeared, the ground softened, and the temperature cooled.

The three of us stopped to catch our breath, and I told the others we were close now as I scanned down the hillside looking for the solar radiation shield that marks the center of each of our 200 plots. I knew we were within about 100 meters, and could probably just see that far, but couldn’t spot the site. I turned back around to see how the heavy breathing was coming along for the others. Joe and Kerri are standing about three feet away from me and starting to breathe a little more evenly. Then I see Joe point at the ground and say, “Kerri” on one of his heavy exhales. I follow his pointing finger, and there right next to Kerri’s boot, and I don’t mean nearby, I mean right. next. to. is a ~12-inch rattlesnake, stretched out long so that her boot is probably around the middle of its body. Kerri doesn’t follow Joe’s pointing finger, when he says her name she looks over at him instead. Kerri is the one who taught me about keeping a calm, clear head in the field, by example and some crazy stories. In an even voice (I think), I say “Kerri, there’s a snake right next to your right boot.” She looks down, calmly looks around to make sure she isn’t stepping into more danger, and takes a good large step or two away. Danger averted.

Now, often if you’re getting near a rattlesnake it starts rattling. They don’t really want to get into it with something that is so much bigger than them. Wasted energy on something that can’t be a meal. But this one had been silent. Upon closer examination this appeared to be due to recently having a meal, i.e. it had a distinctive bulge along the otherwise slender body. We were lucky. Out of the usual danger area we had relaxed, and even moved a little farther from the edge of transition from chaparral to Doug-fir forest, and one of us almost stepped on a snake. That was damn close. We gathered ourselves up, after a few pictures to document our encounter, started to make our way down toward the plot. I had taken about four steps and froze. Directly ahead in my chosen path, maybe 15 or so feet away was another rattle snake, and this one was no baby. Easily an inch in diameter and probably about three feet long. It hadn’t made a sound either. So, not that way.


The snake that we inadvertently got way too close to

One other thing about Douglas-fir forests: the trees drop their lower limbs as they grow. In addition to the ground being covered in needles, it is littered with sticks. Interestingly, these sticks and twigs started looking a lot like snakes. It was the longest 100 meters I have ever walked, Kerri and Joe following my path (perils of being the leader), and all of us playing “stick-or-snake?” the entire time.


Kerri & Joe coming up the trail after finishing the plot

Intro to R as GIS

For the past two years I have served as one of two student representatives on the US-IALE executive committee. One of the major things we do in addition to providing a student voice on the ExComm is organize a students-only half-day workshop at our annual meeting. This is offered at no-cost to students attending the conference and we try to do things relevant to the field. In 2015 our chapter hosted the IALE World Congress in Portland, Oregon and with an eye on software that many students are learning to use we (ambitiously) put together an introductory workshop on manipulating and analyzing spatial data using R. We were able to recruit three other people to help develop and deliver the workshop, and managed to cram the whole thing into 4 hours.


Karl providing some guidance during the workshop – equally possible that he’s saying, “I haven’t seen that error before…”

Given that we unleashed a barely controlled firehose of R on the attendees, I think that overall it went okay. Given the material I think it would work better as a 6-8 hour workshop with the option for attendees to bring/use their own data. Maybe this is the way it should be set up from the start, i.e. here is a dataset that I know it works with, now try and do it with your own. I haven’t organized or been a part of delivering many workshops, but I learned a lot and really enjoyed the experience.

If you want to check it out the workshop materials the are freely available here on GitHub.

Effects of diversity, topography, and interannual climate variability on pathogen spillover

Text from an abstract I submitted for the 6th Sudden Oak Death Science Symposium on the initial results from one of my dissertation chapters. Additional analysis is in progress.

Our knowledge of sudden oak death (SOD) disease dynamics indicate that without bay laurel (Umbellularia californica) there is seldom oak (Quercus) infection. This requirement of an alternate host species for disease transmission to oak species is an example of pathogen spillover. We developed a path analysis to test specific hypothesized relationships between physical and ecological factors affecting pathogen spillover. Path analysis enables simultaneous examination of direct and indirect effects from multiple factors, which can enhance our understanding of the multiple influences on pathogen spillover in SOD. We rooted our path model with the topographic wetness index, indicating potential soil wetness and moisture persistence, and examined the direct and indirect effects of species diversity, temperature, precipitation, and bay laurel density on potential inoculum load and infection of oak species.


Path model structure defining relationships between factors influencing pathogen spillover.

We applied 10 years of data from a long-term SOD-monitoring plot network in southeastern Sonoma County, CA. Each of the 200 15-m by 15-m plots was equipped with a temperature logger and plots were visited once per year from 2004 to 2012, and in 2014 to assess P.ramorum/SOD host species for disease symptoms and download temperature data. We inspected oak species for canker symptoms and indexed potential inoculum load by counting symptomatic leaves on each bay laurel stem for 60-seconds. We recorded the abundance of all tree species rooted in each plot during visits in 2005 and 2014 to quantify community diversity. Rainfall was measured at 15 rain gauges installed throughout the study area during this period.


A field crew member taking measurements at one of the plots.

We conducted a piecewise assessment of the path model, enabling us to account for the repeated measures structure of these data. Results from our path model of disease observations aggregated to the plot level revealed that diversity mediates the potential for pathogen spillover through a relatively strong direct negative effect on oak infection. Potential inoculum load on bay laurel had a direct positive effect on oak infection, with its overall influence moderated by temperature, topography, and diversity. Temperature and rainfall had relatively weaker influences on pathogen spillover compared to diversity and inoculum load. The net negative effect of diversity on oak infection is consistent with the dilution effect found in other studies of SOD. Topographic wetness had significant direct influence on diversity and inoculum load, where higher values of the wetness index tended to have lower values for diversity, but higher values for inoculum load. This is consistent with areas where moisture is likely to accumulate and persist providing a more favorable environment for P. ramorum sporulation.

The American Chestnut Epic


American Chestnut Trees. Source:

The American Chestnut (Castanea dentata) is a storied tree. An American epic with books written and legends told. It was a behemoth, not necessarily by the size of individuals, though plenty were taller than the Statue of Liberty and had trunks you could hang a basketball hoop from if it were lying on its side. No, the behemoth legend of the American Chestnut lies in its versatility and pervasive presence in the lives of people living in the Eastern United States during the its reign as the dominant tree in the forests of the Appalachian Mountain range.


Original range of the American Chestnut. Source:

Chestnuts roasting on an open fire…” were the sweet nut of the American Chestnut. The productivity of these tress provided fodder for pig farmer’s herds at no cost of sowing and harvesting. Homes, barns, fences, furniture, and firewood were hewn from these trees. The tannin content in the bark provided natural resistance to insects and made them a valued resource of the tanning industry. “The Perfect American Tree.”


Chestnuts, leaves, and burrs. Source: wikimedia commons (Timothy Van Vliet, 2004)

Like many giants of lore, or perhaps more aptly the alien invaders in H.G. Well’s War of the Worlds, the American Chestnut was reduced to nearly nothing by less than a speck of dust. Cryphonectria parasitica, the cause of Chestnut Blight was introduced to the East Coast of the United States in the early 1900s. It took less than 50 years for it to decimate the American Chestnut throughout its range. This ascomycete (sac fungi) was brought to the United States via plant material collected in Asia, where the Asian Chestnut had evolved resistance to the pathogen. Meanwhile the American Chestnut had no resistance, or at least none that people had the presence of mind to look for. Remember, this was the 1920s, 30s, and 40s. The nuances of passive mutations and genetic variation and heritability were far from mainstream knowledge. So, the demise of the American Chestnut was hastened by preempitive harvest of healthy trees, essentially eliminating the possibility of finding a native tree with inherent resistance.


Chestnut Blight. Source:

The American Chestnut still persists as a species throughout its original range, but mostly as a resprouting understory “shrub.” But the legend continues, as concentrated efforts are being made to restore this tree, if not to its former magnificence and dominance, at least to having American Chestnuts roasting on open fires once again.

*Here is a video from the University of Maine summarizing the story.

More about efforts to save/restore the American Chestnut:

News flash: genetic engineering may save the American chestnut tree

I haven’t been into genetics work since labs during undergrad, so I wonder how CRISPR might help/influence these efforts

The American Chestnut Foundation

A 95-foot tall Chestnut tree was recently found in Maine.

Note: The pathogen is also prevalent on chestnut trees in Europe. Hypovirulence of the pathogen was first discovered here.


Pathogens Causing Us Pain

Ebola, flu, HIV/AIDS, malaria, are a handful of diseases that most people readily recognize as causing us pain. There are also many microbes in forest ecosystems that cause us “pain.” This pain may be economic, public safety, or otherwise. Large trees suffer mortality from disease more frequently, reducing biological diversity and beauty. While death by tree is less likely than death by ebola, it can still happen. Like human diseases, forest diseases are a natural part of the system, but control and prevention is much more difficult. Trees don’t go to the doctor when they’re sick, and detection is the number one challenge for dealing with any disease.

Video identifying ash dieback

Some diseases are introduced to new places where the local hosts have no resistance, such as sudden oak death

Sudden oak death landscape. Photo by David Rizzo, UC Davis.

Forest diseases can be managed, but it requires concentrated efforts in finding out how the disease is transmitted from one host to the next. And what environmental and human factors are affecting this transmission.

What diseases are impacting the forests where you live?

This was inspired by Richard Cobb and the talk he gave in the NC State FER Seminar series and finished due to participation in the 2015 #SciFund Outreach course

What are you grateful for today?

I just got back from walking the dog this morning. It is a sunny and blue sky morning – a classically beautiful Colorado day.
Backpacking in the Lost Creek Wilderness
I crossed paths with a man who lives in the neighborhood, and I see regularly but have never spoken with. He stands a good six inches above my 5’10”, but moves slowly. He gently stops me on the sidewalk and says to me, “May I ask you a question?” I respond “Sure.” After all, the dog is in no rush. She tends to really mosey in the morning, thoroughly sniffing every third blade of grass. So, he asks with sincerity “What are you grateful for today?” I respond with “beautiful sunny day,” “good food” (I enjoy making our oatmeal breakfast). Then he immediately follows up by asking, “Would you like to know what I’m grateful for today?”
“Of course.”
“Today is my 25th anniversary of surviving incurable brain cancer.”
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