R functions to bind together lists into a data frame: yet another plug for the tidyverse

When working with large datasets in R, I often have to split data manipulation jobs up into a large number of small tasks which I run in parallel on my university’s computing cluster. Once the tasks have all finished running, I load the output into my R workspace. Each task’s output is usually a single data frame, and I define a list with each element being one of the data frames. The next step is to somehow bind together the list of data frames into a single data frame. The data frames all have the same number of columns and the same column names, so they can easily be put together with R’s rbind() function.

The “naive” way of doing this would be to put rbind() into a for-loop. Here I make a dummy data frame into a list by copying it many times to demonstrate.

foo <- data.frame(a = rnorm(100), 
                  b = runif(100), 
                  c = rlnorm(100), 
                  d = rlogis(100))
foolist <- replicate(n = 10000, foo, simplify = FALSE)

Binding these data frames together in a for-loop is really not recommended, because it is both extremely slow and uses a large amount of RAM, because the entire constantly lengthening data frame is read back into the memory with each trip through the loop. Here is how you would do it, though (I added the system.time() wrapper to show how long it takes):

  foo_loop <- foolist[[1]]
  for (i in 2:length(foolist)) {
    foo_loop <- rbind(foo_loop, foolist[[i]])

This takes 594 seconds on my machine.

You can use a functional programming trick in R to make this a little bit more efficient. The function do.call() takes a function as its first argument, followed by a list. It constructs a function call with the function from the first argument, and the list as its arguments. As a toy example, do.call('c', list(1, 2, 3)) is equivalent to c(1, 2, 3). Here is how you would use do.call() to bind the list of data frames together.

  foo_do_call <- do.call('rbind', foolist)

This takes 184 seconds on my machine, and also uses less memory.

However, Hadley Wickham’s tidyverse family of packages, and its workhorse package dplyr, provide an even more efficient solution. The bind_rows() function takes a list of data frames as its argument, and returns identical output to the preceding base-R function calls.

  foo_bindrows <- bind_rows(foolist)

This takes only 0.03 seconds on my machine. That’s over 6000 times faster than do.call()!

You can confirm that these three methods return the same output by checking with identical(foo_loop, foo_do_call) and identical(foo_loop, foo_bindrows).

Overall, I would recommend using the tidyverse function here. It’s better both in terms of speed and memory usage.


Paradise on the forty-fifth parallel


This is your standard camping trip report (I will limit myself to no more than 2 social/environmental critiques). Mary and I spent a long weekend on Manitou Island, ten miles out in the brilliant waters of northern Lake Michigan. The short version: it was one of the most beautiful places we’d ever been.

After over a year living in south-central Michigan without making the trip to the northern part of the state, we finally used my birthday as an excuse to head up there. The trip started with a relatively short drive from Lansing to Leland, near the tip of the Leelanau peninsula, roughly where the tip of the ring finger would be on the mitten-shaped Lower Peninsula. Leland is a touristy fishing village squeezed into a narrow strip of land a few hundred yards wide between Lake Michigan and a smaller body of water. I’m not sure how much of it, if any, is still operational other than as gift shops and quaint restaurants, but the gray, weather-beaten fishing shacks looked authentic enough. We boarded the good ship Mishe-Mokwa, a ferry that took us on the hour-long journey through choppy waters. Mary got a little queasy when we ventured to the upper deck of the lurching boat to get a better view of our approaching destination, North Manitou Island.


Playing cards amid a pile of packs while waiting for the ferry in Leland


The Mishe-Mokwa pulling into the harbor to swap passengers


We boarded and were soon off


Our last close-up view of the mainland


Enjoying(?) the fresh air aboveboard

(Social commentary digression: On the boat, the discrepancy between the demographics of National Park visitors and the racial breakdown of the US population at large was clearly on display. The question is: How do you strike a good balance between these two things: 1- enticing people who don’t traditionally do any backcountry camping into parks while 2- avoiding developing some of the few places that still have a relatively small human footprint on the landscape? I have no idea, but maybe I will muse about it in a future post.)

You can read elsewhere about the history of North and South Manitou Islands. North Manitou was once home to a small community of homesteaders, and later some rich vacationers from Chicago kept summer cottages there. Now the buildings, orchards, and clearings they left behind are abandoned, and the land is managed by the National Park Service. It’s a big destination for backpackers because backcountry camping is allowed anywhere on the island. What’s more, it’s the perfect size–roughly circular and about 5 miles (8 km) in diameter. That’s small enough to explore from end to end in a couple days, but big enough for the ~100 backpackers on the island on a given summer weekend to spread out pretty darn thinly. And of course, the island abounds with natural beauty: dunes clad with thick beech-maple forests, dramatic windswept bluffs overlooking the lake, and beaches of many-hued smooth pebbles washed by bright bluish-green waves. The remoteness of the island means that we had our pick of isolated campsites in the midst of this splendor.


Packs on, we await clearance to hit the trail


An abandoned summer cottage near the dock


Mary tries to preempt blisters by the island graveyard


Humble concrete crosses mark most gravesites


Walking in the maple-beech forest inland


On a perch overlooking the lake near campsite #1


The first evening’s view of South Manitou Island

After we arrived and heard a safety briefing from the NPS ranger, Mary and I took off down the trail. We spent the next two days and nights circling the island, with numerous side detours to see abandoned barns, orchards, and the cemetery where the couple dozen hardy homesteaders are buried (including some who spent their childhood there and returned to their final resting place as recently as 2010). We were constantly serenaded by vireos, redstarts, black-throated green warblers, thrushes, and robins that breed on the island, and scolded by vast numbers of chipmunks. On the second night, we were treated to a show of three otters cavorting about 100 yards out in the waters of the lake! A gull and a tern were angrily harassing them, faking dive-bomb attacks and cawing harshly, but the playful otters did not seem to mind. Unwelcome additions to the fauna were mosquitoes and blackflies, but they were not too bad if you wore long sleeves except in a few marshier spots in the forest.

As for the quality of the camping, it couldn’t be beat. The first night we camped on a high, windy bluff in a grassy clearing overlooking the lake on the west side of the island, where the mid-July weather got downright chilly at night. The high temperature was about 70 F (21 C) each day, with sunny skies. The next night, we pitched our tent in the woods just back from a stunningly picturesque beach on the east side. Mary and I enjoyed a romantic time cooking such delicacies as Zatarain’s mixed with soy sausage and canned corn, carefully rationing a plastic water bottle filled with bourbon, and reading creepy Japanese short fiction from the early 1930s to each other.


Kitchen at campsite #1


Stirring the rice and beans for our first dinner


Sipping an adult beverage from a blue tin cup while reading and watching the sunset = living


It stayed light until around 10 PM


Apple pancakes for breakfast on Day 2: sort of successful on the camping stove


Navigating using the trail map


Swenson’s old barn on the west side of the island


Surveying the trail ahead


Cedar waxwings were eating fruit in an abandoned orchard

The terrain was mostly flat and forested, so the backpacking was pretty easy. Every couple of miles, the woods opened up into large clearings with orchards and the occasional barn, which provided interesting variety. Lake Michigan is so big that the lake at the center of Manitou Island is itself a mile or so long and great for swimming. (Yo, dogg, we heard you liked lakes, so we put a lake in your lake.) Of course, I took a dip in the Big Lake–that’s the Ojibwe meaning of the word Michigan–as well. Wonderfully refreshing.

(Environmental commentary digression: The Great Lakes are a unique and fragile treasure. We Americans, entrusted with 20% of the world’s fresh water shared among five lakes, have really messed them up. One thing we definitely noticed on our trip was the beautiful clear water that for some reason had lots of filmy algae floating around in it. Apparently, zebra mussels, which were introduced from ships discharging ballast water taken on in Eastern Europe, have proliferated, filtered particulates out of the water, making it clearer. This in turn releases algae from light limitation and causes huge booms in their biomass, with all sorts of negative consequences.)


We made a small side hike to gawk at this view on Day 2


One of the many obligatory “pure Michigan” selfies we took


Playing dice on an old truck hood in the middle of a bunch of ancient wrecked logging equipment


Mary ponders where to go next


This is the lake within the lake!


Eating Mary’s delicious homemade granola bars after swimming in Lake Michigan


The beach just next to campsite #2


Cooking Pasta-Roni on the second night




We hiked the last couple miles along the shoreline on Day 3


Piping Plover chick!


The dock where the ferry soon came to take us home

I’ll leave you with one final anecdote: On Day 3, which just so happened to be my 30th birthday, we made sure to show up extra early at the dock, not wanting to miss the ferry and be stranded for 24 hours with only a few extra rations of Zatarain’s to tide us over. There, just as we were preparing to head off the island, I started chatting with a Park Service employee who was glassing the beach with binoculars. After asking whether I had a life list, he pointed out four Piping Plover chicks that were foraging in a small puddle on the beach! One of the parents later made an appearance as well. The Piping Plover is an endangered shorebird that only nests on remote, secluded beaches, and North Manitou Island is its biggest stronghold in the Great Lakes region. What a way to end our sojourn on the island–a wonderful weekend in a beautiful place with an amazing wife!


“There is a sort of magic in the drama of the mile” *

tl;dr version: this is a shamefully self-absorbed blog post in which I brag that I ran a mile in under 5 minutes the other day. If you care to learn more, read on.

In a (not altogether rare) moment of introspection back in September 2016, Mary and I were talking about our plans for the future. As our careers develop and our lives go on through the stages of adulthood, and possibly in the future parenthood (no guarantees, Mom and Dad), our responsibilities are increasing. I realized that I had a couple of regrets, self-improvement goals that I had always wanted to do but not ever committed the time to. One was that despite being relatively adept at learning languages, I had only learned one fluently (German) and one decently (Spanish). The other was that I had never run a sub-5 minute mile. The closest I came was 5:10 in college. Almost as soon as I had those thoughts, I realized that those two things did not need to be regrets. They were both attainable goals–but both are skills that fade with time, so I immediately began to pursue them. I decided to go for the athletic goal first, followed by the linguistic goal. A few days later, on September 4, 2016, we headed to the running track at Clay High School north of the Notre Dame campus in South Bend where Mary timed me in a mile run.

can you name all of my running idols?

The mile is a very interesting distance for running. It’s one of the few non-metric distances that is still contested internationally–although it’s being replaced by the 1500m or 1600m run. One mile is exactly 1609.344 m, for you metric aficionados. That’s four laps around a standard 400-meter track with a couple extra steps thrown in. It requires a unique balance of aerobic endurance and anaerobic speed. Having neither of those things in sufficient quantity, I painfully eked out a time of 5:53. That marked the first time over the next 10 months that I would wear out Mary’s patience complaining about how slow I was.

Over the next months, including all throughout the Michigan winter, I kept up a steady schedule of training. The nice thing about the mile is that you don’t need to put in hours and hours at a time, as you would for the marathon. I never did any workout longer than about 1 hour, 5 to 6 days a week. The basic plan was to do 1 to 2 track workouts a week, starting with 200 m and 300 m repeats in the first couple months, then eventually 400 m, 600 m, and 800 m repeats. I also ran 5 to 8 miles a few times a week, sometimes doing a few sprints at the end of the run, and every few weeks a tempo run which was roughly a 5K at 6-minute mile pace. At first, running 200 m at “race pace” in 37 seconds felt like a dead sprint, but gradually longer and longer distances felt–not quite comfortable, but manageable.

The original plan was to have the whole thing wrapped up in 2 or 3 months. When that proved to be ludicrously ambitious, I decided to set a deadline of my 30th birthday: July 9, 2017. With support from a loving wife and encouragement from family and friends, my time dropped to 5:33 in October, 5:28 in November, and 5:20 in December. After a weird illness in February, I reeled off 5:15 in March and 5:09 in April. It was really gratifying to see such tangible progress and to feel fitter than at any other time in my life. I knew I could not get much faster by myself on the track so I had my eye on a few local races.

In late May, when we were visiting Mary’s family in Tennessee, they all came out to cheer Mary’s sister Carol and me in a road race. I managed 5:04 that day, followed by 5:01 a few weeks later. Now for the big reveal: On June 29 (with only 10 days to spare until my birthday), Mary and I headed to the “Bring Back The Mile” track meet at Okemos High School, just a few miles south down Hagadorn Rd. from our place in East Lansing. There, I toed the line with some fast dudes, and, the usual pre-race nerves and pessimism notwithstanding, crossed the finish line in 4:59.7! What an absolute feeling!!!

I won’t bore you any more with race report details or other self-aggrandizing minutiae. I don’t often brag on myself but I felt I deserved to just this once. Now on to the next goal, learning some spoken Mandarin–after I shave a few more seconds off my time, that is! See you at the track. (Pictures below)

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(*) quote by Sir Roger Bannister

Rally ’round the (ironic with a meme of Neil DeGrasse Tyson) flag

The above title is given with apologies to Steel Pulse.

This is a little late to be completely relevant, and any number of scientists and non-scientists have already weighed in on the March for Science, but I decided to add my opinion to the mix. First, I want to express my admiration for all the people who worked so hard to organize the event and who are continuing to promote the values and goals of science.


The crowd in front of the Michigan State Capitol in Lansing

Last Saturday, the wife and I headed to the satellite rally of the March for Science being held on the grounds of the State Capitol in Lansing. This was after a brief period of soul-searching on my part. I read some of the arguments (advanced by scientists) both for and against the March for Science, and I found merit in both sides. I strongly support the aims of the March for Science. That includes: maintaining the well-earned privileged status of scientists as voices of expertise to guide important decisions in government and society, making sure that researchers have adequate funds to expand human knowledge and serve applied goals, and mobilizing activists both among professional scientists and the public as a whole, in this time of urgent crisis. On the other hand, I appreciate the argument that the case might be weakened by portraying scientists as activists with a left-wing political bent, because well-paid propagandists have implanted the meme in people’s minds that science is part of a nefarious elite liberal agenda. At first, the latter argument held sway with me. I agreed with the goals of the march, but felt that the march itself would undermine those goals.

A talk I saw by Dr. Marcia McNutt, president of the National Academy of Sciences, at Michigan State University ended up pushing me to a solid pro-march stance. Dr. McNutt has a very impressive trailblazing resume, being the first woman to head the U.S. Geological Survey and to be editor-in-chief of Science. The talk she gave, about using science to guide policy decisions, was interesting but left me a little unsatisfied. She repeatedly affirmed that scientists seeking to guide policy should not present any biases or value judgments, but rather stick to “just the facts.” This stance struck me as so extreme that it denies reality. The very act of compiling facts for policymakers is inherently value-driven: one has to decide what facts to present and what topic is even worth studying to assess benefits or harms to society. I know that she had to be diplomatic and stick to a script, but I felt that she went too far. She expressed only the most tepid support for the March for Science for similar reasons: that it would portray scientists as biased. At that point, I was decided: it is not wrong to own the values and beliefs I hold, since it is my strong conviction that scientific decision-making is absolutely critical and will produce the best outcomes for society. Talking it over with my wife and with a good friend helped us to make that decision.


The wife and I with low-budget signs

So the die was cast and we headed to the march. It was time for another critical decision: funny ironic sign or serious boring sign? My agonized vacillating over whether to even attend the march made me stick to a very simple sign, but Mary split the difference by making a funny one. I am also conflicted about the use of humor and irony to achieve serious goals (Megan Garber has written much more eloquently than me about this in The Atlantic.) While many if not most of the signs were at least a little tongue-in-cheek, I think the march struck a decent balance between relatable, down-to-earth humor and serious activism. I would like to write more about that topic, but I’ll save it for another post.


As an R nerd, I couldn’t resist snapping a photo of this sign

To sum up: the march in Lansing had a pretty impressive turnout–I think the papers put it at 2500, which is similar to my eyeballed estimate. I enjoyed seeing colleagues and friends out there, and I hope I get a chance to vote for Abdul Al-Sayed for Michigan governor before I leave this state. Down with Tricky Ricky!


The above-mentioned ironic flag, held by a marcher dressed as Ms. Frizzle


A dark day

My feelings last night and into this morning include: anger, resentment, sadness, isolation, and existential fear. I doubt this post will be very eloquent or really express my feelings and thoughts well, but I wanted to write something down. Sadly, I am physically far from any of my loved ones today, which only adds to the black mood.

I have two points to make: (1) to remind everyone that the Trump win can’t be easily slotted into a media narrative, and much of the current narrative is wrong, and (2) that I am hoping this moment will be a motivator for myself, and other compassionate people, to leave my enclave of privilege and work harder to positively impact this broken nation and world.

(1) Commentators on the election are describing Trump’s win as a “rebuke to the elites” and a populist victory. We cannot lose sight of the fact that the “popul-” in that particular brand of populism is an incredibly narrowly defined demographic, one that defines huge swaths of the American population as other, as an outgroup to be despised. The implication in calling someone like Trump a populist is that he is appealing to the “real” people rather than minority or niche groups. Needless to say, that is ludicrous. Trump’s success comes from his appeal to a very narrow segment of the population, and we cannot lose sight of that. Not to mention the supreme irony that Trump’s status as an elite and his shameless pandering were seen as genuine by many voters, but Clinton’s less nakedly hypocritical behavior was seen as lying fakery. If anyone thought they were delivering a rebuke to the elites by voting Trump, I have to flatly say they were misguided and wrong.

(2) Speaking from my position as a privileged person, I am pretty insulated from some of the worst potential consequences of the upcoming Trump presidency. At this point, we can only hope that some of the gravest fears and predictions people have made will not come true (though it’s hard to hold out too much hope for healthcare, climate policy, etc.). I want to express my empathy for those I know who aren’t quite so privileged, and hope that things will not change too much for the worse in their lives. I also hope this horrible disaster will be a linchpin that will motivate compassionate people to work harder to make the world the way we want it, rather than relying on electoral politics to do the trick. I reserve the next day or two for moping, but if you see me wallowing in bitterness and cynicism, rather than working to effect change, any time in the next four years, remind me of these words I wrote. Engagement at the local level is what we need now–we’re in this together.

Women in science, and science studies

I know that it is a little bit tone-deaf for a man such as myself to opine on topics like this, but I really would like to express myself and I hope it is not interpreted as mansplaining. I just finished reading an article on The Atlantic, provocatively titled “The Constellations are Sexist.” The article itself was more or less forgettable clickbait, but it raised a number of issues that made me want to formulate my thoughts and respond. The article, linked here, correctly points out misogynistic and sexist aspects of Greek mythology, the historical scientific establishment that excluded and minimized the accomplishments of female astronomers, and the macho culture of space exploration. Unfortunately, it does so in a superficial, flippant way that makes some sweeping claims, claims which were immediately pounced upon by all kinds of trolls, but also more legitimate members of the internet commentariat. With regard to the article itself, there are two main points that I want to bring up: first, my personal experience as a card-carrying member of the (male-dominated, and particularly white-male-dominated) scientific establishment, and second, my opinion on science studies and the humanistic critique of the scientific enterprise.

My personal experience as a scientist: I work as a scientist and collaborate every day with brilliant people—currently most of my collaborators happen to be women. I am grateful to be part of a culture that acknowledges and values contributions from both women and men. I can really only speak specifically about ecologists; I don’t know the situation in the physical sciences that well. It’s too bad that ecologists are not a more racially diverse group, but I hope that will change with time. However, I have personally experienced the darker side of the “collegiality” of academic culture: male scientists who exploit power dynamics, especially over women, for their own gain. Worse yet, supervisors often turned a blind eye to what these men were doing until things got too serious to ignore, and women’s voices often weren’t heard. I would also say that while the machismo culture of ecology is (luckily) not quite to the level of the Mercury astronauts in The Right Stuff, it certainly is something I’ve noticed, especially when it comes to outdoing one another in fieldwork, or even one-upmanship about putting in long hours at the office. So, I certainly have empathy for those who critique the scientific establishment as being harmful to women. In my perspective, things are slowly improving, but a lot of issues still need to be addressed.

However, talking about flaws in the way the scientific establishment treats women and other groups outside of the inner circle of power brings me to another point, the humanistic critique of the enterprise of science. I will issue a disclaimer that I haven’t read most of the primary literature in this field, but lately I have read some about it, and have been thinking about it from the perspective of a scientist. The author of the piece on the sexism of the constellations is very invested in this critique, constantly pointing out in that piece and in other pieces (see her website) that science isn’t necessarily objective, tied up as it is with power dynamics of the society that creates it. (She is especially interested in gender dynamics but that point could easily apply to other types of power dynamic.) I agree with this point, and I would say that a rigid view of science as always shining the harsh light of truth and objectivity upon nature is a false and probably harmful view. After all, who can reasonably deny that science and technology have expedited the gutting and destruction of the environment, and have been a vehicle for capitalists to make off with boatloads of money at the expense of marginalized groups? However, I think the obsession with critiquing the practice of science can go too far. For one thing, it can be, and has been, used as ammunition by people with a vested interest in undermining science, such as evolution and climate change deniers. For another thing, the obsession with critiquing downplays the wonderful accomplishments that women scientists have made and are making. For example, the article about sexism in the constellations only mentioned two female scientists/engineers. One was an 18th-19th-century female astronomer (now largely forgotten, but what casual science fan can name any 18th-century astronomers of any description?). The other was in a derisive footnote that a female “Mission Operations Manager” for NASA is nicknamed “MOM,” which I don’t really think smacks of misogyny. I generally see the validity of the postmodern critique, but when it is delivered in such an echo chamber, stripped of any dialogue with currently practicing scientists, women or men, it’s pretty useless.

I would like to end by saying that I deeply admire the women scientists I know, and that I think my field of ecology, and the sciences in general, would benefit from two things. First, white men need to relinquish some of their grip on the power structure to allow greater diversity in identities and modes of thinking. Second, there does need to be an improved dialogue with the humanities and with science studies. When we step outside our narrow focus and think about the paradigms within which we operate, it can really lead to great insights. As it stands now, a critique of science by the humanities can’t be effective unless scientists both are aware of it and know what can be done to improve the way science is done. That requires positive suggestions in addition to negative criticism. As I’ve said in previous entries on this blog, a little humility, open-mindedness, and compassion (not the most macho of traits) can go a long way!


Midwest livin’

I’ve been living in the Upper Midwest for a total of about a year now, off and on, including a few stints with Mary in South Bend/Mishawaka, Indiana, and now in East Lansing, Michigan. I can’t say I have fully experienced the place, since I’ve mostly made myself scarce by the time winter rolls around. However, I think I have been here long enough to have developed some impression of the character of this area. Of course, Michigan is probably most known for being the buckle of the Rust Belt, with cities blighted by abandoned factories, run-down houses, crumbling infrastructure, and decay. That’s sadly what happens when we hitch our fortunes to globalized capital. Lured by the short-term prosperity it brings, local governments abase themselves before corporations, allowing them to loot the public coffers with tax breaks. But the moment that shareholder profits would be maximized by offshoring all the manufacturing, the capitalists peace out. It is the capitalists’ responsibility and their duty to do that, in this broken system—their responsibility is to their shareholders, and that’s that. However, the government has been way too lax in its responsibility to the citizens who can no longer survive without steady employment, instead vilifying and shaming people who need to use the (dwindling) social safety net. As a government-funded postdoc, I’m pretty insulated from all that, but it is sad to see these forgotten citizens trying to get by when both the “free market” (sarcastic quotes) and the government have screwed them over.



The rail station in Niles, Michigan (built 1892)

While that’s a pretty bleak take on life in the Upper Midwest, I have also really been enjoying living in a different part of the USA than I am familiar with. Even though media and pop culture have been steadily homogenizing this country (linguistically and culturally), it is fun to notice little regional differences. For example, the other day I took the Amtrak train from East Lansing to Niles, Michigan (just across the state line from South Bend), where Mary picked me up. I sat in front of an old farmer couple. As we rolled by the fertile farmlands of southwest Michigan, patches of different truck crops whipped past the window, to me appearing like a green blur. The husband, however, identified each type of vegetable for his wife: “Those’re potatoes.” “Looks like an asparagus patch.” “Huh, that’s a lotta cukes.” “Don’t know what those are, probably green beans.” I was very edified by his descriptions of the different soil types in different parts of the state, with their different glaciation histories leading to different sand and organic matter content. We passed right by the athletic complex of Western Michigan University in Kalamazoo (imagine a very nasal and flat Midwestern accent): “That’s Western Micheegan. Real good haakey team. Great haakey there.” Not something you’d hear much in North Carolina or Tennessee. They showed me the location of their hometown, Lapeer, in the time-honored Michigan method of pointing to its location on the outstretched palm, in this case around the base of the thumb. Call me a silly newbie, but I think that’s cute. When I arrived in Niles and met Mary, I enthused over the historic railroad station and said I wanted to go in and look around. A bystander interjected, “It’s nothing special.” I disagree, as you can see from the picture. And of course, I had to try some Faygo root beer the other day to fully consummate the Michigan experience. That definitely was nothing special, but I would still probably rather drink it than get sprayed by it at an Insane Clown Posse show.

A (possibly futile) plug for civil discourse

I would like to briefly comment on an issue that is causing me a good deal of personal anguish at the moment. Recently, I have seen a lot of posts on social media deriding “progressives” who are threatening to withhold their vote from Hillary Clinton as some sort of protest for what they see as corruption. Of course, the personal vendetta that some people seem to have against Hillary Clinton is misguided and pointless. I have taken up residence in an important swing state for the 2016 election (Michigan)—here it would be especially moronic for a reasonable person to vote for anyone except Hillary Clinton. However, what bothers me about the things I have been seeing on social media is that it is now fashionable to cruelly deride anyone who is uneasy with the constant rightward drift of the Democratic Party as an out-of-touch, privileged elitist who is so insulated from hardship that he or she would not even mind if Donald Trump were elected president to “prove a point.” I agree with this point to some extent, although I am not entirely sure that there’s not some “straw man” element to it.

However, on the other hand, I find it very unsatisfying that the Democratic Party has been relying on the good will of left-wing voters by simply staying a little to the left of the insane, reactionary, regressive, dehumanizing conglomeration that is the Republican Party. Of course all progressives would prefer Hillary Clinton’s Supreme Court nominations to Trump’s, and her appointees to head federal agencies, the list goes on . . . That said, when I vote for Hillary Clinton in a few months, my vote will be accompanied by feelings of sadness that the Democrats don’t fully live up to my ideals when it comes to equal distribution of wealth, reducing corporate influence in all aspects of society, and taking aggressive action to rectify environmental problems. However, those feelings can’t be conveyed in the ballot box and my vote will count the same as a voter who is delivering an enthusiastic mandate for every policy that Hillary Clinton embodies. I would be sad if I were thought of as a privileged elitist for saying this, because my political ideology is motivated by empathy for all people, privileged or not. I wanted to take the opportunity to write this and encourage people to discuss things civilly, avoid exaggeration and misrepresentation of others’ views, and actively seek points of agreement. I’m fully aware that social media doesn’t well reflect the way people interact face to face, and many interactions on social media are like traps that compel people to say the worst thing that pops into their heads. However, I think the only possibility for any part of the progressive agenda to be enacted is for people with different ideologies to cooperate with one another. At least, people who generally agree on most policy points should be able to find some common ground.

If you have read to this point, hopefully you have an opinion on my statement, and I would love for you to share it with me.

Fieldwork and some thoughts on what motivates science

I recently returned from a week or so in Colorado with what I am now calling my “old lab,” a.k.a. the Sanders-Classen lab group. I’m still certainly very much a part of what’s going on in that lab group, but nevertheless it was strange to be deposited back in the midst of the lab dynamic after a couple of months elsewhere. It resembled nothing so much as briefly visiting family and taking a detached, objective look at drama that was once a daily part of your life. An academic lab is like a family, though: while we only jokingly refer to Aimée and Nate as “Mom and Dad,” the German dictionary word for a PhD supervisor is Doktorvater or Doktormutter depending on gender. Of course, the Germans invented that paternalistic, hierarchical relationship. I really enjoyed catching up with the lab and chatting about the projects we have been working on.


An illustrious colleague conducting a field experiment; Almont, Colorado

Being out there and working on our field projects again inspired me to think about my philosophy of science. At the time that I began grad school, I was a convinced experimentalist who believed that the best means of ecological inquiry is to determine the mechanisms underlying patterns in nature using experiments. By manipulating organisms’ environment, we can figure out how they will respond to changing environments, and more importantly, why. While I still think this type of inquiry is extremely important, I am not sure that my personal niche as an ecologist is to carry out these types of experiments. To me, the main benefit of experiments is that you can use them to infer why things happen instead of just looking at the relationships between phenomena. Observational studies can only suggest causal relationships However, I think that ecological field experiments are so prone to artifacts, limitations of scale, and caveats that often their results are little better than a suggestion either. To find a good counterexample to this, you have to refer to one of the few classic and elegant ecological experiments—their rarity attests to the difficulty of getting good inference about mechanism from the complicated, contingent reality of the ecological world. I was reminded of this by reading Bob Paine’s obituary. Paine was an ecologist who conducted a path-breaking experiment that showed how a single keystone species (a predatory starfish) could structure an entire natural system, with consequences for all the organisms and cycles of matter and energy in it. See the original paper here.


Examining the ecosystem consequences of a keystone species, the ant Formica podzolica

While the “Big Data” revolution is totally overhyped, I think that there is some truth to the idea that individual investigators acting on their own curiosity to test a hypothesis, gathering all the data from the ground up, cannot do as much world-changing science as a huge collaborative enterprise in which data are shared and the individual scale is transcended. With the increasing availability of global data that span huge scales of space and time, we really do seem to be entering a new paradigm of scientific inquiry, if we haven’t already entered it a few decades ago. Of course, it is tougher for individual scientists to get individual acclaim and recognition in such a socialistic, top-down system, Too much cooperation, if it overshadows individual achievement, is anathema in the market-driven way science is currently being done. I think that ultimately, that perspective may impede science. The solutions that will drive policy and that will make a positive impact on the problems facing society can only come out of large cooperative enterprises. There is still a place for manipulative experiments within this framework. In fact, the Sanders-Classen lab group is working on an experiment that is exploring the effect of global change and changes to plant species communities, replicated identically across many sites with the help of collaborators around the world. I admit this isn’t perfect, and it still has its problems, but those are the types of experiments that can make a real contribution.

A disclaimer to what I’ve just written: I am speaking from a very early-career perspective, and I still haven’t figured out the best way for me to use my skills and knowledge in a way that will benefit society (which is my ultimate goal). I don’t think my future is in doing fieldwork or in manipulative experiments, but working on them in grad school has taught me a lot and I would not give that experience up. For now, I will just end this by saying that fieldwork makes for much better photo opportunities than me sitting here at my computer desk analyzing data . . . so I’ve provided you, dear readers, with some fun pictures from this past week.


Piloting a drone, the latest and greatest in tools for field data collection


Ground-truthing for the drone flight at Almont


A drone photographing our field site


Field experiment in Maxfield Meadow, Gothic, Colorado


Not fieldwork but a snapshot from a birthday hike I took

A brief, unsolicited opinion

I am dismayed, heartbroken, and saddened at the recent events going on in the world. Part of me feels that it is a little pointless and self-serving to add to the general social media knee-jerk reaction of posting something heartfelt right after a tragedy to solidify my credentials as “someone who cares,” but I also have to express myself somehow. So I decided to just write this on this blog, which very few people will read anyhow.

I want to express grief for the human tragedies that the Black population in the United States have experienced, and continue to experience. This also goes for Muslim and immigrant populations in other parts ofthe world. In a way, it is hypocritical for me, as a White male who is in some way complicit in, and benefits from, the “plunder” (as Ta-Nehisi Coates puts it) of black people by white people in this country. What good is it to complain about inequality when I’m sitting here parked on top of the pinnacle of society, with all the unequal benefits and resources that entails? It’s still important to me that I put this in writing. I don’t want to spend too much time going over the problems in society, or the sad fact that many people, in the USA, Europe and the Middle East, are grappling with these problems by resorting to violent, divisive tribalism.

Instead, I wanted to talk about a conversation my friend Tom and I just had. We were discussing ways that deep-seated problems like inequality and environmental degradation could be solved. We decided that it is pointless to focus on the biggest problems head-on, which would only lead to fatalism. The solution, in my opinion, is first to tackle smaller issues that can work towards the bigger goal piecemeal (this is why people who speak out against microaggressions and small manifestations of privilege are doing the right thing). The other part of the solution is to exploit people’s tendency to want to identify with a group—the trick is to make the group encompass as much of humanity as possible. If the use of social media and smartphones spread around the world in a few years, boosted by the increased social status that users gain, shouldn’t it be possible to enact positive changes in the same way? I would welcome anyone’s opinion on this.