The unBalanced ecoLOGist: Preprints, Open Science, and the Muddy Road Ahead (Part 1)

LeMondeBioRXiv
Monthly submissions of preprints to bioRxiv. Figure from Le Monde March 20, 2018.

While browsing my twitter feed this morning, I came across a tweet from ScienceOpen about a new article “In praise of preprints” by Norman Fry, Helina Marhsall, and Tasha Mellins-Cohen (published open access in Microbial Genomics; doi: 10.1099/mgen.0.000259). This article re-asserts familiar advantages (credit, visibility, pre-submission and prepublication review) and disadvantages (no peer review, novelty not required, financially unsustainable, and obscuring priority), and ends with a reinforced commitment to preprints (and smoothed workflow via bioRxiv) and a position statement in support of preprints from the Microbiology Society.

At ±5am EDT, there was already one response to this, from Lonni Besançon, who wrote:

can only be helpful in the dissemination of research results. I wonder whether someone has looked at whether they could actually be enough. could happen directly on preprint platforms and could be done massively and in a totally open fashion

which prompted me to wonder (and reply) whether any of the preprints I’ve posted have received any comments…

The answer: No. Not a one. In five years of posting preprints.

And, as today is a holiday here in the US, I had plenty of time to burrow further down this rabbit-hole…

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Dispatches from Abroad: In Search of the Perfect Crème Brûlèe

As readers of this blog know, I do enjoy a good (or at least innovative or weird) meal. And foodies know that a good dessert can make or break the overall dining experience. In fact, I rarely order desserts – my waistline doesn’t need it, the options are rarely interesting, and eating anything with chocolate after about two in the afternoon inevitably keeps me up at night. But I do have a soft spot for crème brûlèes. Anytime I see one on a menu, I’ll order it. And then I’ll extol its virtues or decry its vices, either way driving my dinner companions deep into their digestifs.

One’s first interaction with a crème brûlèe is always the brûlèe – the topping of gently torched sugar that always reminds me of isinglass. Everyone has their own ideal brûlèe. Mine is one that is not too thick but breaks into bite-sizes shards with a single tap of the spoon. It should have just a hint of carbonization, but not be overburned. And it should dissolve on the tongue. Beneath the brûlèe is the custard. A traditional crème brûlèe has a vanilla custard that should be creamy, not grainy, and never a pudding. It is rare to find a simple vanilla crème brûlèe on a menu anymore. More commonly, dessert chefs are adding various accoutrements; I have had crème brûlèes with maple syrup, rum, cinnamon, ginger, and coconut. It is difficult to get any of these just right, as just the right touch is needed to maintain the integrity of the vanilla custard as it interacts with any of these additional ingredients. Finally, a crème brûlèe should never have a crust. It should be nestled in the confines of a small ramekin. The well-cooked custard should be just set and neither stick nor ooze away from the sides of the dish.

While continuing a heavy travel schedule in the last year, I started keeping track of the crème brûlèes I had around the world. This is the what I hope will be the first installment in occasional postings from my never-ending quest for the holy grail of desserts: the prefect crème brûlèe. And because good meals are only part of a broader contextual experience, some background is provided with each entry.

January 13, 2018

Flossie and I were in Burlington, Vermont for a few days while Nick Gotelli and I were working on our current book project. On a snowy and icy night (are there any other kinds in mid-winter in Vermont?), we three, along with Nick’s wife Maryanne, and our friends Aimée Classen and Nate Sanders met in nearby Richmond at the Kitchen Table Bistro. After an excellent and varied meal, I ordered their Cinnamon Stick Crème Brûlée with Sea Salted Shortbread Cookies.

kitchen-table-richmond-vt-cb-20180113_200621The brûlèe was slightly overburnt, but of reasonable thickness. The custard was very good with subtle cinnamon imparting a good flavor. Memorable more for the company than for the dessert itself.

January 19, 2018

Our comfort-food destination at home in Boston is the Island Creek Oyster Bar in Kenmore Square. We’ve learned through experience that the appetizers, and of course, the diversity of oysters on the menu, are far better than the main courses, and we usually fill up on the former and rarely have room for desserts. But on this visit, there was on the menu a Vanilla Bean Crème Brûlée with Gingersnaps and Pear Sorbet.

island-creek-cb-boston-20180119_181152The perfect brûlèe overtopped a vanilla custard unadulterated by extraneous flavors. Rather than add ginger to the custard, this crème brûlèe was complemented with a small ginger candy, a gingerbread cookie, and just-right-sweet pear sorbet. This crème brûlèe was one of two for the year that approached perfection.

February 5, 2018

Just a few weeks later, Flossie and I had emptied the refrigerator prior to our (Chinese) New Year’s trip to Singapore, and so in search of dinner, we walked into La Voile, on Boston’s Newbury Street. I completed this otherwise excellent French Bistro meal with their Vanilla Bean Crème Brûlée.

lavoile-vanilla-cb-20180205_192859Although the brûlèe was perfect, the custard tilted towards a disappointing pudding, and the strawberries were from far away. ‘Nuf said.

February 14, 2018

Ten days later, we were in Singapore for Chinese New Year. Singapore is justifiably famous for the high quality and diversity of its food, but it is rare that among all the different ethnic and fusion restaurants one gets classic “Singaporean” food. But on this evening, we went with my in-laws to Folklore, which serves traditional Singaporean dishes. Although I wasn’t expecting it to be a crème brûlèe, the Baked Custard with Gula Melaka (coconut-palm sugar) suggested it might be a southeast Asian close-equivalent.

folklore-singapore-cb-20180214_201810Indeed, this was more like a classic Latin American flan (coconut custard), albeit with a brûléed palm-sugar topping, than a crème brûlée. The brûlée was good, if a bit thick and unevenly torched. The coconut flakes were a nice touch, but they couldn’t save the grainy custard.

April 30, 2018

In April, I was in Melbourne, Australia, working with colleagues at the Independent Schools Victoria and presenting some workshops for schools on the intersection of art and science. Like Singapore, Melbourne is renowned for its innovative restaurants. One night, we went to Gazi Restaurant, a Hellenic-fusion restaurant in downtown Melbourne. After a delicious meal marred only by the seemingly 100-decibel volume of music and conversations in the restaurant, I ordered the Krema Kataifi (Crème Brûlée, Crispy Kataifi, Pistachia).

gazi-melbourne-cb-20180430_201337Like the rest of the items on menu, this Krema Kataifi was a fusion of styles and flavors. The classic crème brûlée custard – here nothing but a basic vanilla pudding – was topped with an Arabic-Turkish-Hellenic bird’s nest pastry (kataifi), raspberries, mint leaves, and flower petals. There was no opportunity to brûlée the topping, which would have left just a residue of charred kataifi. Overall, this was much more enjoyable to look at than to eat.

July 3, 2018

Back home for the summer, we found ourselves at a dinner party at Harvest Restaurant in Cambridge, wrapping up this summer’s session of Leading Learning that Matters with Independent Schools Victoria. Harvest is well-known and praised for its creative uses of local ingredients in delectable dishes. For dessert, I had the Choux à la Crème Brûlée (Pistachio, Vanilla Bean Mousseline, Elderflower & Apricot Sorbet).

harvest-boston-cb-20180703_182544This was another attempt at fusion of styles, which rarely is successful with a crème brûlèe. And unfortunately, this was no exception. The brûlèe was overburnt and too thick to break easily. The custard was pudding-like and grainy (not as hoped with the promised mousseline), but not too sweet. The unexpected (only because I had missed the “Choux” in the dessert’s title) pastry shell was tasty but rubbery. This desert was saved by the sorbet.

September 28, 2018

nan thai atlanta thai tea creme brulee 20180928_190208In September, Flossie and I went to Atlanta, where we visited the Atlanta Botanical Garden and had a behind-the-scenes tour of the greenhouses and the carnivorous plant collection. I gave a talk about carnivorous plants and the large book I’ve edited on them (Carnivorous Plants: Physiology, Ecology, and Evolution). On our last night in Atlanta, we went to a justifiably highly-rated Thai restaurant, Nan Fine Dining. This restaurant, a bit outside the main downtown area, surprised us with its innovative Thai dishes. None was more surprising than seeing a Thai Tea Crème Brûlée on the dessert menu.

Of all the year’s crème brûlèes, this one was my hands-down favorite in terms of its presentation. It came in a long, thin ramekin reminiscent of an áo dài. Although the brûlèe was very fine, the Thai tea custard was less than perfect and a little grainy. And while I prefer my custard less sweet, this one actually could have been sweeter. The flower of whipped cream was a very nice touch.

 

 

November 17, 2018

This mid-November weekend found me shuttling between New Haven, Connecticut, where I gave the keynote talk at this year’s final event week of the World Scholar’s Cup, and the ginormous temple to excess consumption that is the Woodbury Common premium outlets mall, where Flossie, my in-laws, my parents, and sister, brother-in-law, and niece were engaging in America’s favorite past-time (no, not baseball, the other one). After a long day talking and driving (for me) and shopping (for them), we had an outstanding Italian dinner at La Vera Cucina, in nearby Monroe, NY.

la vera cucina-monroe-ny-cb-20181117_191605Their no-frills, home-cooked crème brûlée was well above-average. The brûlèe was excellent and just the right thickness. The custard was very creamy and not at all grainy, marred only by being just a little too sweet for my taste.

December 17, 2018

December found us in the UK for the annual meeting of the British Ecological Society in Birmingham. Although Birmingham doesn’t have the foodie reputation of the larger city to its southeast (that would be London, for the geographically impaired), we did find a number of excellent restaurants. For one of my birthday dinners we went to Opus, where we had an incredibly innovative meal topped off with their Rum and Cinnamon Crème Brûlée.

rum-creme-brulee-opus-20181217-ame-212820This birthday crème brûlée was the only other one of the year to come close to perfection. The brûlée was just a little thick but was just the right degree of carmelized. The custard was creamy and excellent, the rum and cinnamon combined in smoothly, and their flavors complemented the vanilla without overpowering it.

January 19, 2019

A year and five continents after I started this crème brûlée odyssey, I spent a weekend in Santiago after a week working with my colleague Ronny Vallejos on spatial statistics at the Universidad Técnica Federico Santa María in one of my favorite cities in the world, beautiful Valparaíso, Chile. Just a short distance from my hotel, I found Le Bistrot Việt. After an outstanding vegan stir-fry and a pot of fresh green tea, I indulged in their Crème Brûlée avec lait de coco et fruit de saison.

bistro viet santiago cb 20190119_132451_resizedThis surprising crème brûlée was really a classic coconut custard (flan) that had been gently brûléed on top. Dressed up with fresh strawberries and mint, passionfruit and raspberry emulsions, and dollops of whipped cream, it was delightful to look at and had just the right degree of sweetness. It got a happy face in my notes, and I left the meal, and my 12 months of searching for the perfect crème brûlée, pleasantly sated.

The quest continues…

the unBalanced ecoLOGist: Still Blogging for Others

I guess it’s a good sign that I’m writing for other blogs and outlets for nontechnical writing. Here are some new pieces:

Today on the Methods.blog, the Official Blog of Methods in Ecology and Evolution, I talk about my new role as one of the team of Senior Editors for the journal.

Last week, two of my essays were published back-to-back in the April 2018 issue of the Bulletin of the Ecological Society of America (and yes, that is a photograph of mine from my December trip to Antarctica on the cover):

Cover_Scale

  1. A sense of scale (solo effort)
  2. Art/science collaborations: new explorations of ecological systems, values, and their feedbacks (a team effort with Carri LeRoy, Kim Landsbergen, Emily Bosanquet, David Buckley Borden, Paul CaraDonna, Katherine Cheney, Robert Crystal-Ornelas, Ardis DeFreece, Lissy Goralnik, Ellie Irons, Bethann Garramon Merkle, Kari O’Connell, Clint Penick, Lindsey Rustad, Mark Schulze, Nickolas Waser, and Linda Wysong)

I’ve also published three book reviews in the last 16 months, and have four more in the works, including one for Quarterly Review of Biology, two for Biotropica, and one for Myrmecological News.

More soon, so stay tuned!

The unBalanced ecoLogist: Blogging for Others

Well, it’s been three-and-a-half months since I last managed to post here, but that doesn’t mean I haven’t been blogging. It’s just that those posts have appeared elsewhere.

So while you’re waiting for me to fulfill my Chinese New Year’s resolution (which, fortunately, was only resolved 3 weeks ago), check out these recent posts:

On OUPblog

  1. The ‘most wonderful plants in the world’ are also some of the most useful ones (February 21, 2018)

On The Revelator:

  1. Don’t believe the hype: giant pandas are still endangered (January 11, 2018)
  2.  Climate: riding the chaotic wave (August 28, 2017)
  3. 5/9: the day we passed the climate tipping point (August 14, 2017)

On The Hill

  1. Pesticides, Pruitt and a plea for biodiversity (June 15, 2017)

And if you want to see what else I’ve been up to while I’ve been stateside (in the last three months, I’ve been to Antarctica, New Mexico, Singapore for Chinese New Year, and Germany), check these out:

  1. Hemlock Hospice lecture tour, press coverage (ongoing since October 7, 2017), and a fabulous podcast for The Native Plant Podcast (February 20, 2018)
  2. New sculpture created for the Shifting Sites group exhibition in the Department of Landscape Architecture at the Rhode Island School of Design (March 5-19, 2018)
  3. New book published: Carnivorous Plants: Physiology, Ecology, and Evolution by Oxford University Press (January 21, 2018 in Europe; February 21, 2018 in USA)
  4. Paper on reproducibility in ecological research published in Nature Ecology and Evolution (January 16, 2018)

Meanwhile, it’s still winter here in Massachusetts, so I need to shovel out!

Red Oak
A magnificent red oak, Royalston, Massachusetts

The unBalanced ecoLOGist: Hemlock Hospice [III]

Since my last post on our Hemlock Hospice installation and exhibition, we had a very successful opening event (October 7) that brought more than 150 people to Harvard Forest, many of who had never been here before; the 18+ outdoor sculptures have successfull weathered torrential rains, howling winds, and the season’s first three snowfalls; and, in the past 6 weeks, over 400 more visitors have signed into the log book, leaving comments there and on ribbons tied to the Exchange Tree.

HemlockHospice-October2017--20171017-AME-3192
“Exchange Tree” Installation at Harvard Forest, 8×10×12.5 feet, wood and acrylic paing, 2017. Collaborators: David Buckley Borden, Aaron M. Ellison, Salvador Jiménez-Flores, and Salua Rivero. Photograph © 2017 Aaron M. Ellison

Lead artist and designer David Buckley Borden and I have given many tours of the exhibition to groups both large and small, and to visiting journalists who have written or are writing pieces about it for a range of audiences. All of these individuals have asked interesting and provocative questions that have spurred us to continue to think ever more deeply about the pieces and their broader meaning and context.

In this essay, I reflect on “invasive species”, how we conceptualize and contextualize them, and how we relate to them. My focus here is on the hemlock woolly adelgid (“HWA”), which is the non-native insect that is killing eastern hemlock throughout the range of this magnificent, late successional tree, but the ideas are, I hope, applicable to other invasive species.

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The unBalanced ecoLOGist: On Tipping Points, Regime Shifts, and the Balance of Nature

While washed up in Manaus, I’ve taken a few hours to catch up on some recent papers in the (technical) ecological literature. A new paper by Egbert van Nes et al. in the most recent issue of Trends in Ecology and Evolution caught my attention. Entitled “What do you mean, ‘tipping point’?“, van Nes et al. encapsulate well the competing ideas and definitions of tipping points in the ecological and broader literature, but then end up arguing for a broad definition: “any situation where accelerating change caused by positive feedback drives the system to a new state.” But they then go on to say that their “proposed definition essentially boils down to the necessary conditions for [Malcom] Gladwell’s examples where a small initial change makes a big difference.”

I think this is unfortunate. They give too much credence to Gladwell’s sloppy handling of tipping points in his book, their  broad definition will lead to a proliferation of “tipping points,” and such vagueness can only result in so much watering down of the term as to render it meaningless.

So with that in mind, I offer up for today’s posting an essay I wrote three years ago but never published. I post it here, unedited from 11 September 2013 (albeit with a few [editorial clarifications]). Perhaps an updated version could find a broader audience somewhere; suggestions welcome!


On tipping points, regime shifts, and the balance of nature

“Five-nine” doesn’t have quite the cadence as “nine-eleven,” but when we look back on the early 21st century, May 9, 2013—the day that the concentration of carbon dioxide (CO2) in the atmosphere exceeded 400 parts per million (ppm) for the first time in recorded history—may be seen as a far more important date than September 11, 2001. If the scenario described in the Scientific Consensus on Maintaining Humanity’s Life Support Systems in the 21st Century by Anthony Barnowsky and his colleagues at Berkeley[1], along with more than 500 other scientists, including Nobel laureates, members of the National Academies of Sciences, and other luminaries is true, Five-nine will be seen as the long-anticipated tipping point whereby human impacts have caused irrevocable harm to our planet. Or perhaps not. Perhaps there is still time to take the concrete, immediate actions Barnowsky et al. suggest—suggestions echoed by President Barack Obama in his June 25 [2013] speech at Georgetown University—that would ensure a sustainable, high-quality future. Or maybe we’ll just keep muddling along, slowly and steadily acclimating to our new lives on a now unfamiliar world, which, to distinguish it from our familiar “Earth,” Bill McKibben christened “Planet Eaarth”: durably, sturdily, stably, hardily, and robustly.

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Dispatches from Abroad: Reflections on the 2016 Election (I)—An Elegy for my Home

I’ve been traveling and working outside of the US since the beginning of August, and watched the evolution, media/twitter/blog coverage, and eventual vote count of the US presidential election unfold from abroad—passing through degrees of disbelief, astonishment, and horror—but also seeing it with the perspectives of physical distance and those gained through the eyes of citizens of other countries. During the two weeks leading up to the election, I was simultaneously engrossed in developing new mathematical statistics and depressed by what I could clearly see, from an overseas vantage point, was going to go down on November 8. And although I voted in Massachusetts (the first person on the first day of early voting in my small rural town—which, contra the Commonwealth overall, went for Trump by a small margin ) while I was in transit between Tokyo and Valparaiso, I suffered no illusion that my vote for Hillary would make a difference, either statewide (Massachusetts is, of course, the bluest of the blue states, notable for being the only state to vote for McGovern against Nixon in 1972) or nationally (the writing was on the wall for anyone who could read it).

As I expect many travelers and ex-pats also did, I stayed up all of election night watching the returns, until the election was called for Trump at close to 2am Valparaiso time. The next day, I watched the sunrise over the docks of Valparaiso harbor, did my daily 45-minute walk up (northeast) the esplanade, past the omnipresent graffiti, murals, stray dogs, seagulls, sea lions, and pelicans, paused to dip my feet in the icy-cold Pacific Ocean, climbed up the daily 108 stairs to the mathematics quad, and then walked up the last three flights of stairs to my temporary office at the Universidad Técnica Federico Santa María (USM), where I skyped my fiancée and had a good cry – for my country, for my family and loved ones, for myself, and for the future.

I spent a lot of that day talking about the election with Flossie and with my three friends—Ronny Vallejos, a statistician at USM, and Hannah Buckley and Brad Case, ecologists from Lincoln University in New Zealand—with whom I was working at USM for the two weeks I was there. And I thought it would be worth setting down here the common themes and ideas that emerged in those conversations, filtered through another few days of reading, thinking, walking, and flying.

These reflections come in two parts. This one, entitled “An Elegy for my Home”, and the next one, entitled “The Politics of Identity and the Destructiveness of Identity Politics”. I emphasize that these are personal reflections and opinions set down as stream-of-consciousness with little editing. The writing is rough and the ideas incomplete. But I needed to start somewhere, as the run-up to the election, the election itself, and the few days aftermath have made it hard to focus coherently. I welcome constructive engagement, discussion, and dialogue about them; please post comments here, on Twitter, or send me email.

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The unBalanced ecoLOGist: Science meets Art at ESA 2017 (II)

Last month, I wrote about a session Carri LeRoy (Evergreen State College) and I are organizing for next summer’s meeting of the Ecological Society of America in Portland, Oregon.

The clock is running, and slots are filling, so if you’re interested in talking about how making art/music/creative writing has influenced your science, seeing art/listening to music/reading creative writing has changed your science, or how a collaboration with an artist has influenced your science, now’s the time to volunteer to present (and since it will be an ignite session, the talk doesn’t count towards the one-talk limit at the meeting!).

Join the fun! Contact us today: Twitter @AMaxEll17 or @CarriLeRoy or email: aellison@fas.harvard.edu or leroyc@evergreen.edu

Dispatches from Abroad: The unBalanced ecoLOGist Noshes in Nanjing

On Sunday (that’s right, Sunday), Eryuan Liang and I took the morning high-speed train 1200 km in under 4 hours, and on time to the minute, from Beijing to Nanjing to give afternoon seminars at Nanjing Forestry University (established 1902). I was on tap to talk about forest foundation species, while Eryuan was set to talk about dresses (actually alpine treelines, but without any sense or irony, the “p” was lost in translation). Sundays are great days to give seminars; attendance is always good because the students don’t have classes and the faculty don’t have meetings. The seminars were fine, but the banquet afterwards …

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The unBalanced ecoLOGist: On the Silk Road

Silk Road

 The 千里1 concrete ribbon slashes the Gobi,

a stale cliché whose 皕公尺2 pullouts double as rest stops sans picnic tables,
but where still-damp tissues mound amply in crevices,

white cumuli cocooning empty bottles tossed haphazardly
by the wind fanning the coals of a smoldering ashcan,

while the selfsame wind,
on the steel strings crossing the ranks of high-voltage towers,
strums a dirge for the lost camel trains.

tibet-4-5-panos-20160914-ame

15/16 September 2016
Poem and photographs © Aaron M. Ellison, all rights reserved


1Read: qiān lĭ (idiomatically: a long distance, lit: 1000 miles or 500 km)
2Read: bì gōng chĭ (200 meters)