The University of Texas at El Paso (UTEP), in association with Boise State University, and the U.S.D.A. Agricultural Research Service (ARS), is recruiting a postdoctoral researcher to work on a recently funded National Science Foundation ‘Critical Zone Thematic Cluster’ grant to study carbon fluxes, ecohydrology, and nutrient availability in the carbonate-dominated soils of dryland ecosystems. The project has sites in Texas, New Mexico, and Idaho. While funded through UTEP, this position is located in Boise, Idaho and focused on the scientific field operations at the Idaho sites, including the Reynolds Creek Experimental Watershed and the Northwest Irrigation and Soils Research site in Kimberly, Idaho. We are specifically looking for a candidate who has experience working with eddy covariance towers and the data that they generate. Other useful areas of interest include soil science, soil biogeochemistry, knowledge of dryland ecosystem structure and function, and ecosystem-atmosphere gas exchange techniques. We seek a colleague who is interested in collaborative engagement with scientists and students and also in education and outreach activities. Up to four years of funding is available. We will begin to review applications on Nov 15^th but the position is open until filled. The target start date for the position is January 4, 2021. For more information, please email Anthony Darrouzet-Nardi (ajdarrouzetnardi@utep.edu), and copy Lixin Jin (ljin2@utep.edu), Jennifer Pierce (jenpierce@boisestate.edu), and Gerald Flerchinger (gerald.flerchinger@usda.gov). To submit an application, please visit this link and send one pdf file with a cover letter, CV, and contact information of at least three referees.

That link at the bottom is to the official listing on the UTEP HR site. If you have any issues, try clicking it a couple times. The system can be a bit clunky.

Today at AGU I’m doing a synthesis of the results of our 2010-2012 snowmelt experiment. Here’s a quick bibliography of the project papers.

Belowground responses
Darrouzet-Nardi, A., H. Steltzer, P. F. Sullivan, A. Segal, A. M. Koltz, C. Livensperger, J. P. Schimel, and M. N. Weintraub. 2019. Limited effects of early snowmelt on plants, decomposers, and soil nutrients in Arctic tundra soils. Ecology and Evolution 9:1820-1844.

2012 aboveground plant responses
Livensperger, C., H. Steltzer, A. Darrouzet-Nardi, P. F. Sullivan, M. Wallenstein, and M. N. Weintraub. 2016. Earlier snowmelt and warming lead to earlier but not necessarily more plant growth. AoB Plants 8.

Senescence
Livensperger, C., H. Steltzer, A. Darrouzet-Nardi, P. F. Sullivan, M. Wallenstein, and M. N. Weintraub. 2019. Experimentally warmer and drier conditions in an Arctic plant community reveal microclimatic controls on senescence. Ecosphere 10:e02677.

Soil cores vs. lysimetry
Darrouzet-Nardi, A., and M. N. Weintraub. 2014. Evidence for spatially inaccessible labile N from a comparison of soil core extractions and soil pore water lysimetry. Soil Biology and Biochemistry 73:22-32.

Microplate amino acid assay
Darrouzet-Nardi, A., M. P. Ladd, and M. N. Weintraub. 2013. Fluorescent microplate analysis of amino acids and other primary amines in soils. Soil Biology and Biochemistry 57:78-82.

Theoretical soil pore water N dynamics
McLaren, J. R., A. Darrouzet-Nardi, M. N. Weintraub, and L. Gough. 2017. Seasonal patterns of soil nitrogen availability in moist acidic tundra. Arctic Science 4:98-109.

N limitation
Melle, C., M. Wallenstein, A. Darrouzet-Nardi, and M. N. Weintraub. 2015. Microbial activity is not always limited by nitrogen in Arctic tundra soils. Soil Biology and Biochemistry 90:52-61.

It’s as if when p < 0.05 is achieved, suddenly our estimates of percent difference among treatments are accurate to 2-4 significant digits! Here’s an example I came across in a recent issue of Ecology.

Survival rates were 20.4% higher in the first cohort compared with the second (historical mean control) cohort (Dunnett’s test, p<0.001)

This is not from an article I would normally read. I just scanned recent articles for about 5 minutes till I found this one, but hopefully now that you know about it, it will annoy you as much as me when you start seeing it everywhere.

While this is not just a significant digits issue, the three digits presented in the above example (20.4%) represent what I think readers will often interpret as vastly better constraint on that value than is warranted. Even if the reader doesn’t interpret it as a value constrained to between 20.35 and 20.45%, I think most readers will underestimate how much greater the uncertainty is in most cases.

I’ll demonstrate with an R example (though you ought to still be able to follow here even if you are not an R user). Let’s say we have two treatments and the actual difference between them is that b is 50% larger than a, and there is some randomly distributed sampling error.

a <- 10 + rnorm(10)
b <- 15 + rnorm(10)
t.test(a,b)

This gives us output similar to the following:

Welch Two Sample t-test
data: a and b
t = -11.37, df = 17.997, p-value = 1.199e-09
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-5.783967 -3.979782
sample estimates:
mean of x mean of y
10.05559 14.93747

Ok, so we have an absurdly significant p-value of 0.000000001199! The difference is “real” and percent differences quite accurate we might think to ourselves. So let’s calculate the percent difference: (14.93747-10.05559) / (10.05559) * 100 = 48.54892. Hm, that’s a lot of digits in both cases, so we’ll just report that treatment b is 48.5% higher than treatment a (p < 0.001). Boom, quantitative analysis is complete.

But wait, wasn’t that difference supposed to be 50%? It was. And we got somewhere between 48 and 49% which is, let’s call it, “off by a bit” when we use the easy-on-the-eyes three significant digits system and these particular parameters. Keep in mind that in many studies, especially in ecology, variation is higher and sample sizes lower (in other words, not all p-values are 0.000000001199).

So this leads to a question: is there a good way to quantify this uncertainty that we are seeing in these percent differences? And it turns out for a simple problem like this that there is.

We can do a “ratio t-test” in which we take the logs of the data, run a t-test, and then un-log the values. Meta-analysis practitioners who want to synthesize a lot of treatment/control ratios often take advantage of this situation where the difference in the log values is related to the quotient of the un-logged values.

t.test(log(b), log(a))

Welch Two Sample t-test
data: log(b) and log(a)
t = 11.022, df = 16.039, p-value = 6.801e-09
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
0.3213321 0.4743339
sample estimates:
mean of x mean of y
2.701976 2.304143

Then we un-log and we can get a confidence interval for our percent difference

exp(2.701976 - 2.304143) = 1.488595
exp(0.3213321) = 1.378963
exp(0.4743339) = 1.606943

So, that 1.488595 looks familiar, it’s close to the 48.5% we calculated before. Why is it not exactly the same? Idunno and someone that is better than math and stats and R inner workings that me can figure that out, but you’ll find it’s always really close like this.

More interesting though is the 95% confidence interval: 37.8% to 60.7%. Pretty big! That third significant digit is starting to look ridiculous with what we now see is more of a 20% window. I would bet most scientists doing this type of analysis would not think it was so large when the p-value was so small. But it is, and we can demonstrate with 10,000 simulations:

set.seed(1)
ans <- logical(10000)
for(x in 1:10000) {
a <- rnorm(10) + 10
b <- rnorm(10) + 15
m <- t.test(log(b), log(a))
lwr <- exp(m$conf.int[1])
upr <- exp(m$conf.int[2])
ans[x] <- lwr < 1.5 & upr > 1.5}
summary(ans)

This gives 473 FALSE to 9527 TRUE, which is what we expect with a 95% confidence interval. Try it with other seeds, you’ll get the same answer. This shows that the ratio t-test confidence intervals (e.g., the 48.8% [37.8%, 60.7%] from above) are correct. And thus it follows that even if you have a ludicrously low p-value, you CANNOT assume or fairly present a percentage difference with 2 or 3 significant digits and no estimate of uncertainty. And remember if you see a p-value that is a lot closer to 0.05, that interval is probably something like 48.8% [1%, 90%]. In my view, scientists must start presenting these intervals done by ratio t-tests or similar approaches to avoid the percent difference fallacy.

In the first study, we explored the early effects of an infrared-lamp induced warming treatment and looked at correlations between fluxes and environmental variables. One of the cool things we saw was that crusts actively photosynthesized a lot in the winter, including under snow.

In this study we both add data on the other treatment in the experiment, a water treatment, as well as examined the experiment nine years later. A few things had changed about how the treatments were implemented but together the data show how long term effects can change over time. We also saw some interesting interannual variation that I believe is linked to plant effects.

I think in these chambers the effect of root respiration is actually pretty big, even though the chamber walls go down 30 cm. The roots of desert plants are just pretty enterprising when it comes to finding unexplored volumes of soil where they might be able to get water and nutrients.

Here’s the big summary of all the years that shows how the biocrusted soils in these different treatments exchange CO2 over time.

It was a fun study to work on, I was really pleased with the papers that ended up coming together, and I’m excited to be working on making a similar chamber system to study fluxes in the Chihuahuan desert.

The thing that is really neat about the show is that because Kristina understands the science herself, she knows what questions to ask to get her interviewees excited to talk about the things they are studying. I’ve learned all sorts of stuff listening to various episodes like that restoring plants as locally and site-specifically as possible is the way to go, and that mammals are really the only vertebrates who take chewing their food seriously. These are the type of fun facts I love to share with my introductory biology students, which I will surely do! It’s a great show, check it out.

Here’s my thoughts on doing occasional blogging over a 10-year period. When people ask about it, the first thing I tell them is that it’s a lot of work! Writing a decent post requires some effort and several rounds of self-editing if you don’t want it to suck. It’s not like facebook or twitter or reddit where you can crank out a first draft of your thoughts and it’s fine and it’s no work and it fits right in (at least I can’t do that). Blogs need more thought behind them, which is a strength of the medium. Weirdly for me, I feel like I’ve now seen blogs come and go as a trend on the internet, though I think they will always have their niche as an intermediate type of content somewhere between the level of polish seen on stream of consciousness social media and more formal publication media like scientific journals or journalism outlets.

One thing I like about blogs is being able to edit old content. I can always go back and change an awkward sentence or a factual error or a bad joke and the next person who finds that post won’t be subjected to it. In fact in having to go back and correct some hyperlinks with this new home for the blog, I fixed a few of these sorts of things. Although blogging is a real time commitment and I have to be careful with time allocation for any project in my job, I’m looking forward to sharing some new thoughts here on the usual topics of ecology and statistics, as well as some ideas on teaching, which is something I now have a few years experience doing here at UTEP. And so with that, onward to the next 10 years of Anthony’s Science Blog!

I was excited to attend the CZO meeting because I have long been involved in the LTER network and have been aware of CZO but had not seen a lot of CZO results up close. The community is impressively developed, with around 200 scientists attending the meeting and something like 500 researchers across all career levels in the whole network. It’s becoming an essential part of our nation’s science infrastructure. There was discussion of topics such as major findings from the CZO sites, the future of the CZO program, and its relationship to other environmental observing networks.

There was some debate about exactly what the boundaries of the “critical zone” are, though there was also quite a bit of consensus that it’s roughly something like canopy to bedrock. Peter Groffman (who by the way is a fantastic scientist and nice guy who without fail stops by my talks and posters to give me smart feedback about whatever I’m working on) made a great observation in his talk that the environmental and Earth sciences are now in the era of “network science.” I would have to agree with this assessment what with LTER, NEON, CZO, and many other environmental research networks continuing to grow and mature, not to mention distributed experiments like NutNet, WaRM, DIRT, and BIODESERT.

Some of the talks that were highlights to me were Susan Brantley’s plenary, Steve Holbrook’s talk on geophysical measurements, Daniella Rempe’s talk on “rock moisture” at the Eel River, and Emma Aronson’s soil microbial work at various CZO sites. Brantley’s talk emphasized the value of the CZO endeavor in informing crucial questions of interest to our civilization such as the environmental impacts of fracking. She also summarized a bunch of the coolest findings from across the different CZO sites. Holbrook’s geophysics team’s ability to “see” belowground features such as porosity and depth of various parts of the critical zone was amazing. One technique they used apparently involves whacking the ground with a sledgehammer to follow the seismic waves it creates. I think we can all agree we want to be the sledgehammer guy or gal. Rempe’s talk was cool because it showed how we are beginning to crack the mystery of how water interacts with fractured bedrock. I was always told that’s a black box until the water gets to the river. Aronson combined all of my favorite soil measurement techniques (nutrients, enzymes, etc.) with microbial community analyses and was really bringing the biology to the geology and hydrology heavy teams at the CZO.

The CZO network is set apart in a couple ways from LTER, NEON and other networks. It differs from the LTER objective of repeated long-term observation (in part due to the fact that many processes of interest to critcal zone scientists operate over deeper time periods), but similar to LTER the science is hypothesis-driven with questions tailored to specific sites. This sets both LTER and CZO apart from NEON, which is more of a large-scale observation tool with a huge strength being its consistency in methods across sites, a feat neither LTER nor CZO attempt at nearly the same degree. There were some good discussions at the meeting of how to integrate these different networks and I noticed that there is a fair amount of interest both from the community and from NSF to do this when warranted to answer ambitious questions. Overall, the CZO network has been really successful in bringing together lots of researchers to understand soil, ecosystem, and geologic processes. I give them an A+.

Wow, I had quite a bit to say about that meeting. Thanks for continuing to read! I will now forge ahead with my thoughts on the Soil Ecology Society Meeting.

I arrived at the Soil Ecology Society meeting on Wednesday morning, just in time to catch the end of the “Ecology of Soil Health Summit.” The current president of the Soil Ecology Society, Matt Wallenstein spearheaded this effort to bring together agricultural and industry folks with us soil ecologists. It looked to me like a big success and there is no doubt that all sides have a ton to learn from each other. I also really enjoyed getting to talk to Matt about his growing startup company Growcentia, which is now turning a profit selling their signature product “Mammoth P” primarily to Cannabis growers (though strawberry and tomato growers too they assured us!). It’s an amazing accomplishment for an ecologist like Matt to turn into a successful entrepreneur and the perfect demonstration of how decades of basic research in a field like soil ecology can all of a sudden be harnessed to drive our nation’s economy forward.

After the conclusion of the Soil Health Summit that morning, the “soil nerds” as we were called by one presenter (who to be fair is an insect nerd herself, my good friend, and now CNN personality Jane Zelikova) were unleashed. These are pretty much “my people” when it comes to science so it was a great pleasure to see all of their latest greatest findings.

Some talks that were highlights for me were Stuart Grandy’s talk on his new approaches to studying the nitrogen cycle, my postdoc advisor Mike Weintraub’s work building on our studies of soil pore water, and Kirsten Hofmockel’s talk on comparing cropping techniques in Iowa with respect to soil sustainability. Stuart is pushing our understanding of the nitrogen cycle backwards from the production of inorganic N in soils to better understand the process of depolymerization of the organic compounds that yield amino acids and other N-containing monomers. His approach includes an awesome sounding setup for doing 15N amino acid pool dilutions. Mike presented some data from deciduous forests in the Stranahan Aroboretum in Toledo testing to see they saw the same seasonal trends in soil pore water sugars that we had seen in the Arctic. He didn’t, but hey that’s research, especially in soils.

Finally, Kirsten’s talk had some shocking images showing for example corn being grown directly on a riverbank. This may not sound shocking but there were audible gasps from biogeochemists in the audience who understand the importance of denitrification-stimulating riparian buffer zones as a crucial stopgap to the so-called “nitrogen cascade” of environmental impacts caused by our overuse of N. Anyway, it was a great talk designed to show us how we can take advantage of soil ecology to inform cropping practices that maintain higher microbial biomass, soil fertility, and ultimately make farming more sustainable. I also always enjoy seeing the soil science being done at PNNL where Kirsten is the Lead Scientist for Integrative Research. Comparing their cutting edge analytical capabilities vs. average soil scientists like me is IMAX vs. VHS. (I note though many movies can still be appreciated without IMAX!)

All in all a great soil adventure. I look forward to heading home, seeing the kids, and jumping head first back into understanding tundra and desert soils next week.

Dr. Jayne Belnap, the world’s foremost expert on biological soil crusts, sharing some of her favorite crusts.

A closeup of Syntrichia from the Splash Lab.

Our team checking out plants and biocrusts at Sand Flats

Eva (right) and incoming fungal loop grad student Grace Crain working on some raceways

Isabel and Jimmy working on plant-soil-biocrust water relations.

On another project, master’s student Alex Lara has been working on building automated CO2 flux chambers that we are going to deploy at The Jornada at a site with an eddy flux tower run by my UTEP colleague Craig Tweedie.

Alex with his sweet chamber prototype

My first Ph.D. student Jane Martinez spent the summer up in the Arctic, mostly in Barrow, and also in association with one of Craig’s projects. She is bringing back boatloads of soil cores that we are going to use to take the plunge into some proteomics. Wish us luck!

Jane in the Arctic, looking chilly yet snug

A brand new Ph.D. student starting this fall, Shani Rivera, has been working on setting up sites for an international project, BIODESERT, run by Fernando Maestre in Spain. BIODESERT investigates the role of grazing on plant and soil properties in drylands around the world. I think they said they now have sites in something like 29 countries, which is amazing. We are really excited to be part of such a huge and neat collaborative project. Here’s a picture from one of Shani’s sites.

Bison at the Janos Biosphere Reserve in Chihuahua, Mexico

My UTEP colleague (and basically partner in crime at this point) Jennie McLaren and I co-advised two REU students, Shyla Cooks and Xavier Soto, who were looking at soil properties from a series of plots set up by Brandon Bestelmeyer, a collaborator from USDA/NMSU/The Jornada LTER. These plots were part of the Restore New Mexico project that seeks to restore grasslands in New Mexico by reducing shrub cover with herbicides. We are looking at what factors might help predict the success of the herbicide treatments. They had an eventful field season, with weeks of 100+ temperatures, run-ins with livestock, and a getting a vehicle stuck in a wash.

Shyla and Xavier measuring soil hydraulic conductivity. (Also our spare straw hat makes its third appearance!)

Finally, I had two more excellent undergrads working in my lab this summer, Jaime Morales and Daniela Aguirre, who helped with all of the above projects in addition to a few others. Jimmy has become pretty handy with a Licor 6400 and has helped to measure photosynthesis on some greenhouse experiments here on campus in collaboration with some students from the chemistry department. Dani has developed some excellent bench chemistry skills and has been running a ton of microplates, including some I think pretty novel data on soil pore water from microlysimeters in semiarid soils.

REU students hard at work corin’ soils

It’s been a great summer. I’m so grateful for all of the great work that has gone in to getting the lab off the ground.