Biodiversity: the Blog

Why are there so many species and what are we going to do about it?

Yes, young scientist, your field experiment IS doomed.

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Does it ever seem like the universe is has something against your field experiment? That’s not your imagination. Nature is definitely trying to undermine you.

Whether you’re in middle school searching for a science fair project, 84 years young and trying to determine what sort of animal is eating your garden, or a struggling PhD student hoping to make a career out of field research, I hate to tell you this, but your experiment isn’t going to work the way you thought it would. Instead, you’re going to learn so much more. Or you won’t, either way. So try to enjoy it.

I stole this from IFLS because it captures the nature of field research so perfectly.

I stole this from IFLS because it captures the nature of field research so perfectly.

My friend Ben Blonder learned a little about precipitation instead of plants when he arrived high in the Rocky Mountains of Colorado to set up a long term field experiment earlier this summer, and found the entire site was still under several feet of snow. You can read about his subsequent adventures that he detailed on his blog.

I also learned a little about precipitation after one of my fluorescent-tracking experiments was destroyed by a monsoon rainstorm.

I also learned a little about precipitation after one of my fluorescent-tracking experiments was destroyed by a monsoon rainstorm.

These are the steps that are usually left out of how the scientific method is taught in school. You thought there was only: 1. Make observations, 2. Form a question, 3. Define a hypothesis, 4. Design methods, 5. Collect and analyze data, 6. Draw conclusions, and 7. Communicate your results.

What they don’t tell you is that in between the steps of collecting and analyzing data, you have to insert: 4a. Realize your methods don’t work the way you expected, 4b. Redesign methods, 4c. Collect more data the new way, 4d. Repeat an unknown number of times.

I like to think that with more experience, those steps might drop out of the method. But I have a sneaking suspicion that instead, you simply become resigned to their presence and learn to expect them.

I have been learning a little about expecting the unexpected from some nocturnal research this summer. I have been trying all summer to get data from a field experiment on where pocket mice cache seeds (see my previous posts about this effort for details). I had designed an elaborate procedure to glean information about their movements from every spec of fluorescent powder they tracked away from my fluorescent dust covered experimental seed depots, combining that with video data to identify the animals. But then I realized two things:

  1. I could identify the trails and general movement if I just zoomed out, got my nose off the ground, and walked around (their little feet and tails and tummies track it around widely).
  2. This species does not tend to cache seeds outside their burrow as often as I thought they did.

Actually, I realized a third thing, too:

  1. Animals are jerks (they really are) and will do whatever you least expect them to do.

I realized I needed to examine a much larger set of instances of animals taking seeds from experimental depots I provided. I also realized this was possible to survey much faster with less detail, but greater understanding, if I walked around and generally looked at their movements – and that way, I might actually find some of the caches I was really interested in.

But of course my experimental depots were washed away by a large rainstorm in the driest part of the driest mountain range near Tucson. So, with a sinking feeling that I was wasting my time, I spent a few hours re-baited them all, even though it was predicted to rain again. This is monsoon season in the Sonoran Desert, after all. But it was a lovely few hours hiking in the desert, and hey, I probably needed the exercise.

Then, last week, armed with my UV flashlights, I headed out to survey for footsteps and caches.

I still had never found one of their caches. I knew what to look for by reading about them: signs of recent digging, with fluorescent dust in the apron of disturbed soil. I had seen the disturbed soil after recent digging was recorded by my game cameras. And on this rocky, hard-packed desert pavement hillside, recent digging is pretty rare and noticeable.

Fortunately, I brought a friend along who thought a night time hike in the desert with black lights sounded like a great way to see some scorpions, tarantulas, and other wildlife. (Lightning, too, as it turned out.) As we surveyed the second-to-last depot, he pointed at something glowing bright.

Uphill of the depot was a little pile of nine seeds, carefully piled between some pebbles. This was not a random arrangement of some seeds that had been dropped.

The first cache we found

The first cache we found

As we walked back along the rest of the depots, we found several more definite caches, and a few that were definitely non-randomly placed, but didn’t look very well hidden from pilfering neighbors, so I’m not sure what to make of those. But it turns out I wasn’t finding dug caches because these pocket mice don’t try to dig most of them – would you? If all you had was your hands and nails against the caliche and the rocks? Instead, it might be easier to cover them in a little pile with rocks in a crevice, or under a nice dense bunchgrass.

A cache of seeds fluorescing under a UV flashlight where they are hidden in a dense bunch of invasive grass.

A cache of seeds fluorescing under a UV flashlight where they are hidden in a dense bunch of invasive grass.

Just when I was ready to finally give up on this doomed field project, it reeled me back in by spitting out some data. This may be the most emotionally abusive research ever, or, well, just the usual doomed research process.

So with that thought, I provide you, fellow young scientist, with a field guide to handling the fact that your research is totally doomed:

  1. Have fun. If nothing is going to come of this anyway, make sure you got a lovely hike in, or listened to some rad music while collecting your useless data, or otherwise enjoyed the wasted time.
  2. Try to adopt a framework that includes variability in the environment as part of your understanding, rather than pretending it doesn’t exist.
  3. Be flexible, and ready to improvise.
  4. Get your friends involved, whether or not they’re experts in this arena. They have good ideas. Don’t be embarrassed to talk about the project with anyone you can bring it up to – you never know where that key suggestion or offer of equipment will come from.
  5. Don’t give up. Every research project is doomed, until it isn’t anymore. Maybe you can’t collect enough data to be useful in one season, but after 20 seasons, it might be pretty interesting.

Written by pacificsummer

August 3, 2015 at 6:52 am

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The social and ecological footprint of a carne asada taco

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What is the ecological footprint of your lunch today? Seriously, think about what you brought with you, or where you went out to today. How much land was required to grow the crops or raise the animals involved? How much water did they require? What additional processes go into that food beyond just growing it, like the oil burned to ship ingredients to you?

Driving in to Hermosillo for a visit last year, the view through my windshield at a traffic light.

Driving in to Hermosillo for a visit last year, the view through my windshield at a traffic light.

If you live in Tucson or in Hermosillo (or really in any city with increasing food cart culture now), your routine might include a visit to the nearest taco cart for some carne asada. And a team of researchers have now calculated the ecological footprint of all the carne asada from taco carts in Hermosillo. Their results will appear in a special issue of the Journal of the Southwest this fall.

Carne asada, as I recently learned from two of the authors, Nemer Narchi of ColMich and Alberto Burquez of UNAM in a presentation about their research, has a more specific cultural history and context than just beef that is grilled. This particularly North Mexican dish is a specific process of grilling beef on mesquite charcoal and is a relatively recent culinary invention dating from Jesuit arrival. Carne asada is typically served on wheat tortillas instead of corn tortillas. The article traces the way cattle and wheat together were major agricultural introductions that settled a traditionally nomadic indigenous dominated north, allowing it to be incorporated into the centralized Mexican state. As mining and cattle culture spread, carne asada served alongside tortillas and salsas was born from family celebrations after butchering cattle to serve miners in mining camps. As the population of Northern Mexico became more urban, unemployed butchers during recession cycles opened mobile restaurants serving snack-sized combinations of these ingredients: the taco carts.

A cow standing in a converted buffel grass pasture. I took this photo while visiting Alberto last year, near one of his study sites outside Hermosillo.

A cow standing in a converted buffel grass pasture. I took this photo while visiting Alberto last year, near one of his study sites outside Hermosillo.

The researchers then calculate the environmental and socioeconomic costs of the industry that has formed to produce the now ingrained culinary traditions. When you eat carne asada from a taco cart in Hermosillo, the cattle were likely raised on the extensive ranches surrounding the city. Throughout the state of Sonora, ranch lands are being converted from native Sonoran Desert thornscrub plants, including native grasses, to bulldozed and planted pastures of a grass introduced from Africa, known as buffel grass (Pennisetum ciliare). Yes, this is the grass that I have been studying for a good part of my dissertation research. It has a large effect on the native plant species. Between the bulldozing, the buffel grass planting, the water required, and the potential erosion and other effects of overgrazing, cattle ranching in Sonora to produce the legendary carne asada can have a heavy footprint, as well as a large one.

And then you must consider the wheat grown to produce the tortillas. And the native mesquite trees cut, frequently from ecologically fragile riparian areas, to produce the mesquite charcoal used to grill the beef. So what is the final footprint? You’ll have to check out their article this fall or some recent press coverage for more details.

A heavily grazed area that is not planted with buffel grass.

A heavily grazed area that is not planted with buffel grass.

But almost more importantly, this research focuses on the footprint of everyday objects, and provides a model for how to start researching that. You can plug your life statistics into online calculators to find out your overall ecological footprint, but it feels a little more abstract than knowing what this one taco required some specific amount of acreage and, increasingly importantly, some specific amount of water. They also examine why that footprint is what it is, what social and economic choices and policies and trends shaped that footprint.

What are the footprints of the small pleasures and cultural anchors of your daily life? What would be your taco cart if you were to follow the lead of Nemer, Alberto, and their coauthors, to find out what something you consume regularly costs ecologically and why it is made that way?

A neat view out my car window as I drove through Hermosillo last year.

A neat view out my car window as I drove through Hermosillo last year.

Written by pacificsummer

July 20, 2015 at 10:54 am

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Luminous footsteps of the dancing desert mice

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The protocol: Trays of seeds and fluorescent yellow powder are placed at sunset with a game camera to record who tracks the powder around.

The protocol: Trays of seeds and fluorescent yellow powder are placed at sunset with a game camera to record who tracks the powder around.

I can hear the cicadas buzzing outside, so I know it must be hot. The predicted high on NPR at dawn this morning was 99 degrees Fahrenheit. Not so warm for June in the Sonoran Desert, but uncomfortable. My fieldwork for several summers involved starting at dawn, but staying out all day in this, marking little seedlings on exposed hillsides. (You can see very preliminary – not peer reviewed yet – results of what I found at the Southern Arizona Buffelgrass Coordination Center website.) All summer. It was, well, tough. I have a rather unique data set as a result.

I was listening to the NPR weather report at dawn today because I was on my way to a field site to retrieve some plastic trays of seeds coated in fluorescent powder I had left out all night before. I am interested in the places nocturnal seed-eaters go. The wind picks up during the day, so I wanted to minimize the powdery spray between the time the seed eaters tracked it around, and when darkness falls and I can return to trace their pathways with blacklights (and friends!). I explained a little about the goals of the project in my previous post.

Looks like this tray got a visit! All the seeds are gone and there are scratch marks in the fluorescent powder, then tracks to the side of the tray...

Looks like this tray got a visit! All the seeds are gone and there are scratch marks in the fluorescent powder, then tracks to the side of the tray…

This dawn and dusk schedule is much more comfortable, convenient for me getting other writing done during the day, and also for attracting volunteers. Many animals adopt this schedule in hot deserts. The schedule even has a name: crepuscular, although I call it the siesta schedule. This will be key because I am detecting fewer pocket mice per night than I had hoped. So I may be in for many more crepuscular days of leaving little offerings to the desert, trying to increase my sample size.

Here is a teaser of the pocket mouse (genus Chaetodipus) jamming the fur-lined pockets next to its mouth full of seeds, then burying them nearby like a pirate with treasure, or a squirrel with nuts. Most animals that “scatterhoard” their seeds in many small caches near the source later return to move them to secondary caches, or even eventually to their “larder” in their burrow. I suspect these pocket mice behave in a similar way.

And as a bonus, when the little guy (or gal) first showed up, before eating anything, it did my favorite “dancing” behavior:

Was it marking this resource for itself? Attracting a mate? Doing an instinctive behavior in response to positive stimulus? We need an animal behavior specialist to get on testing this.

And a few last gratuitous shots of the experimental set-up during a beautiful Tucson sunset:

SONY DSC

Trays of seeds and fluorescent yellow powder are placed at sunset with a game camera to record who tracks the powder around.

Written by pacificsummer

June 7, 2015 at 10:51 am

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Some awkward footage of an interesting animal

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Ever wondered what a javelina (Pecari tajacu, syn. Tayassu tajacu) looks like from underneath? Yeah, me neither.

The setup: a seed tray dusted with fluorescent powder and a game camera to find out who tracked it about.

The setup: a seed tray dusted with fluorescent powder and a game camera to find out who tracked it about.

I did wonder, however, whether pocket mice (genus Chaetodipus, yes, the dancing ones), known for foraging under cover to avoid predation by owls, would tend to bury palo verde or other seeds under buffel grass (Pennisetum ciliare). Buffel grass is an invasive bunch grass spreading through the Tucson Mountains that inhibits native seedlings from establishing – and provides some nice cover to these mice, potentially attracting them to bury native seeds in the worst possible place: right under buffel grass.

To test this hypothesis, I left fluorescent-dusted seeds on fluorescent-dusted trays in the desert to see where mice would take the seeds, planning to return tonight with UV flashlights to follow their luminous footsteps. It felt like leaving sunset offerings to the tiny, dancing desert gods.

Much like the fantasy world of Game of Thrones, however, the Sonoran Desert has many gods who are more than happy to accept offerings. Most seed trays, it turned out, were visited by a roving band of javelina. Check it out:

You get a great view of their four-toed front feet, of their flexible snout at work, at their lumbering gait, and their curious investigation of the seed trays, marking flags, and cameras, and their powerful molars grinding the seeds of the foothills palo verde (Parkinsonia microphylla). One of the major reasons scatterhoarding rodents like pocket mice may be beneficial for the trees is that they protect some seeds from destructive consumers, like javelinas.

Often thought to be pigs, javelina are in a different family, although still related. This is an animal that is hunted for sport and meat, and is seen as a menace and a pest as it roves through town, knocking over trash cans. It lives in a wide variety of habitats, including even cloud forests and swamps as far south as Ecuador. Check out more information on them from the Arizona-Sonora Desert Museum, or visit in person to see some javelina yourself.

Written by pacificsummer

May 26, 2015 at 9:43 am

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A scaly problem

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Driving down the Catalina Sky Highway from the summit of Mount Lemmon, Tucson looks at first like a dusty blond blur. As you approach the base of the mountain, patches of brilliant lemon resolve themselves.

A good year for palo verde trees is a bad year for allergy sufferers.

A good year for palo verde trees is a bad year for allergy sufferers.

As anyone with allergies knows, the palo verde trees (genus Parkinsonia) are blooming in force right now. But which neighborhoods are so infused with the native trees? Where do they start and end? From thousands of feet up, drawing patch lines seems trivial, but walk through the streets under the branches themselves, and you feel less certain. Is this block in, or does the patch start one more over?

You may begin to notice patches even within neighborhoods. At what scale should the palo verde patches be drawn?

The patch size of interest probably depends on your question. If you are seeking palo verde trees in Tucson to photograph (or seeking to avoid their pollen), a map with the raw number of trees per block might be helpful without trying to draw lines around patches. So why bother delineating these categorical zones at all? Why not measure some continuous variable, such as the number of palo verde trees on the block?

In other cases, a patch size itself is an important variable, so you have to stand back, squint your eyes, and draw the lines. The local invasive bunch grass buffel grass (Pennisetum ciliare), for example, grows outward in roughly circular patches. To track the rates of its spread in the foothills of the Santa Catalina Mountains, researchers have used repeated aerial photographs and traced polygons around the visible buffel grass patches.

SONY DSC

We got into a snowball fight with an infrared game camera used for detecting wildlife on our mountaintop campus.

I just returned from four days at UA Science Sky School, where we had snowball fights between the pines and aspens! There are no palo verdes to be seen on top of Mount Lemmon, which is a Sky Island, a little patch of pine forest in a desert sea. But where does that patch boundary lie? In fact, the vegetation changes in several dramatic and distinct zones as you travel up the mountain, but trying to pinpoint the transition point is an exercise in frustration.

The groups of students from Flowing Wells High School that I mentored this week at Sky School also had to confront these questions as they conducted field-based scientific research. To answer their question about how resources for plants (and animals) changed as a result of forest fire, we needed plots on either side of a burn boundary. The boundary of a fire seems abundantly clear until you are forced to locate a 10m x 10m plot right along that boundary.

Fortunately, the students in my group were focused on what characteristics mattered for their question. The question of where a boundary lies, at what scale, can be a very scaly problem indeed, and they resolved it by drawing a thicker boundary line between the burned and unburned areas, on either side of which the light, vegetation, and water availability was less affected by proximity to the other type of area.

SONY DSC

Two students take a soil sample for measuring percent moisture.

Written by pacificsummer

April 26, 2015 at 12:03 pm

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Do people like you belong in the backcountry?

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Well, do they? Take a moment to answer that.

Honestly, answer it. Here are a couple beautiful photos my friend Ty took to enjoy while you think about it:

This photo casts serious doubt on whether I belong in the backcountry. (That's me doing "the walrus" up on to a redrock ledge in The Maze last January.)

This photo casts serious doubt on whether I belong in the backcountry. (That’s me doing “the walrus” up on to a redrock ledge in The Maze last January.)

A night camped on the Green River means pooping in bags and packing it out. Do you have what it takes?

A night camped on the Green River means pooping in bags and packing it out. Do you have what it takes?

What did you answer? And what did you take “people like you” to mean?

Your answer might depend on who you see represented in ads for outdoor brands, or in films at the Banff Mountain Film Festival, or who you see out on trails.

Or how often you yourself get outside.

There are lots of reasons some groups get out and enjoy nature more than others, which are beyond the scope of this post, but one factor is income (which is, of course, connected to many other factors). If you don’t have the money for a car (or gas, or gear) or the time off of a low-paying job, it can be hard to take your family to the nearest national park or wilderness area. If you’re not very healthy, or you have a hard enough time with daily life, the idea of tackling an optional challenge – physical exertion in a strange new place – may seem like a luxury.

And if you never have been out hiking, it’s sure hard to imagine yourself doing it. One way to solve that is to give more people (kids, families, everyone) the opportunity to leave the city and experience nature.

You think we're going to climb down WHAT to get to that river?

You think we’re going to climb down WHAT to get to that river?

I volunteer with an organization through the Sierra Club, that recently changed its name from the 30 year old “Inner City Outings” to “Inspiring Connections Outdoors,” but the goal of the all-volunteer nonprofit is to give kids an opportunity to experience nature who might otherwise not get out of the city. Volunteers who have passed background checks and been trained in outdoor skills and first aid partner with Title I Schools, halfway houses, and other groups that work with at-risk and underprivileged youth to provide opportunities to go hiking, caving, camping, and stargazing.

The primary expense the group has is transportation costs for the kids, although when we can, we like to provide healthy snacks so everyone has had more than a bag of Hot Cheetos to fuel their adventure.

A group of MBA alumni from Arizona State University that have an annual tradition of hiking the Grand Canyon Rim 2 Rim 2 Rim (47 miles and change… and a lot of elevation change!) are using their trip to raise money for this group. I appreciate these guys who feel they belong in the backcountry raising funds (and awareness) to help a new generation expand that pool of people who feel they belong there, too.

Want to kick in to support getting underserved youth outdoors in the Tucson area? Donate to their campaign: https://www.crowdrise.com/r2r2r2015/fundraiser/

And in somewhat a related note on representation in the outdoors community, for women who are annoyed that skis made for women’s sizes and shapes are often of lower performance aimed at intro-level skiers and snowboarders rather than the advanced and expert, check out this kickstarter of high performance skis and boards for women (sans the pink flowers, as a bonus!):

But it was a nice paddle once we were down.

But it was a nice paddle once we were down.

Written by pacificsummer

March 25, 2015 at 11:01 am

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Energy and sexual activity: the data says…

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Kangaroo rat pups born in a trap overnight (they are covered with millet from being dumped out of the trap).

Kangaroo rat pups born in a trap overnight (they are covered with millet from being dumped out of the trap).

Back in January, I speculated on this blog about some disorganized observations I had made of unusually high rodent reproductive activity (resulting in pups born in traps overnight in February).

Since I followed that with a post on the importance of systematic data collection, rather than relying on a series of anecdotes, I should probably follow my own advice and provide some data analysis on the rodent reproduction.

Fortunately, the observations I wrote about in January were made at the site of a long term experiment on the interactions of rodents and plants. Ecologists have collected thirty-eight years of data on rodent reproduction, along with systematic data on weather and plant life.

Base camp for the long term project started by Jim Brown in 1977.

Base camp for the long term project started by Jim Brown in 1977.

Erica Christianson, a doctoral student at Utah State University, is studying these interactions at Portal as part of her dissertation work, and she crunched some of the numbers on reproduction and weather conditions (and generously allowed me to share them here!).

Erica’s main hypothesis, and one I wondered about in January, was that the large rainfall in the late summer and early fall last year resulted in more seeds available in early winter. With sufficient energy to stay warm and active during the winter, females could afford to breed.

A very quickly constructed scatterplot reveals that years with higher rainfall in the late summer and early fall do indeed have higher rates of female reproductive activity observed the following January:

Precip&Repro2

You might notice a couple of things about this plot. First, you would be justified in pointing out that this is a correlation, and does not prove that the summer rain causes high January rodent reproduction. But it is consistent with a reasonable explanation for it.

You might imagine designing an experiment to test the causality more directly, in which all the plants are killed before they produces seeds after the next year with high summer rainfall. That would be an ambitious experiment on this landscape, involving a lot of person-hours with some herbicide or clippers, but it could be done.SONY DSC

You might also notice that fall precipitation does not perfectly predict female reproductive activity. Probably that interacts with several other factors. Ever noticed how you get hungrier in cold weather? Your body burns more calories to stay warm. (This is why mountaineers are advised to continue eating as much as possible if caught out overnight on a cold peak.) I suspect that if we also looked at the temperatures each winter, we might find that less rain is required in warmer winters to boost female reproduction, and the rainfall plus temperature would explain even more of the variation in reproductive activity. But that probably best left to future posts.

A lot of grass grew in the San Simon Valley following heavy late summer rains, providing substantial seed resources this winter.

A lot of grass grew in the San Simon Valley following heavy late summer rains, providing substantial seed resources this winter.

I should also point out that these results are extremely preliminary. Typically, to have some confidence in a conclusion, the full description of the methods for data collection and analysis should be subjected to peer review – that is, at least three or more other experts will critique it before it is published. That’s definitely not how my blog works.

If you are interested in getting out in the field to collect data used in real long term and large scale research projects, check out iNaturalist, National Phenology Network, and the Arizona Sonora Desert Museum. If you are in Tucson this weekend for the Tucson Festival of Books, visit Science City to meet some of these folks in person and pick up brochures for other Citizen Science opportunities as well!

One last photo: a cactus mouse (Peromyscus eremicus) that was released and immediately climbed the fence supposed to keep the rodents larger than that out. Let's hope the kangaroo rats are less bold.

One last photo: a cactus mouse (Peromyscus eremicus) that was released and immediately climbed the fence supposed to keep the rodents larger than that out. Let’s hope the kangaroo rats are less bold.

[Updated 3/17/15: I changed the label on the x axis of the grass from “Fall precip” to “late summer” to more accurately reflect how the plants seemed to respond to the rainfall and be more consistent with my text.]

Written by pacificsummer

March 12, 2015 at 9:51 pm

Posted in Uncategorized

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