Brown Food Web Friday–in praise of litter ants

January 26, 2007



How’re y’all doing this fine Friday? I’m slogging through a cold once thought vanquished. Now seems intent on hanging over me like a stale chain mail party dress. Bleah.

    In today’s BFWF we contemplate one of the great biological systems on earth–the litter ant nest. Litter ants live on the forest floor in small hollow twigs, empty acorns, or even between leaves. The whole colony may consist of only 100 or so ants, just enough to cover the tip of your pinky. This small size allows litter ants to be incredibly abundant: in a tropical rainforest there may be 5-10 species living together in a meter square plot. Yes, I will admit it, litter ants changed my life.

Every scientist has the occasional “aha!” moment. Mine came sitting on my butt on the forest floor at La Selva, cracking twigs with Margaret Byrne, a graduate student at the University of Florida at the time. I was in the middle of a PhD project happily placing bits of seed and bird poop across the forest floor to see what ants arrived, who consumed what, and if they preferred some bits of habitat and climate more than others. I only saw the ants when they emerged from the leaf litter to crawl on my baits, but that was fine. I was getting my data, and every night at the microscope I would empty my vials and see the biodiversity.

Margaret was collecting litter ant colonies for her research and she offered to show me how. Turns out, it wasn’t hard. Read the rest of this entry »

5 ways to minimize Stuff part I: Email

January 25, 2007

stuff.jpgWe’ve spent some time talking about the big goals for a developing academic, developing the “uber-skills” of scholarship, creativity, communication and time management. These four (and the other parts of your life) underlie your strategic vision, your basic roadmap. But while having a map is an essential part of reaching a destination, you still need a detailed set of steps to get there.

One psychological barrier, as outlined by David Allen’s Getting Things Done, is “stuff”. The central idea is that much of our day to day anxiety arises from unresolved, ambiguous list of expectations. Allen defines stuff as

anything you have allowed into your psychological or physical world that doesn’t belong where it is, but for which you haven’t yet determined the desired outcome and the next action step.

In other words, only by dealing with “stuff” can you feel on top of things. Furthermore, as you proceed through graduate school you will find, without active preemption of “stuff”, this will be harder and harder to do. This is because you will accumulate projects as a natural result of being an active productive scientist. The insight of GTD is that nothing drives away the desire to tackle hard, creative, and worthwhile tasks like the nagging feeling that you should be doing something else.

Stuff comes in various flavors (and we’ll address many of them) but the kind that is easiest to deal with, and with the least effort (i.e., more “stuff for the buck”) is email. Read the rest of this entry »

5 steps to writing an effective paragraph

January 21, 2007

hemingway.jpgWe have already discussed why writing an effective title is the key to getting your paper read. But the title of a paper is paint and trim on your house. The paragraph is its bricks and mortar. Each paragraph is a self-contained logical argument, crafted to stand on its own (like an abstract, or a letter to the editor of Nature) or to be strung together to form a larger thing of persuasive beauty: a well-written scientific manuscript. All the best writers in science write gorgeous, tight paragraphs. Most of the good science writers I know personally take great pride in the fact that they write well. Furthermore, they are constantly on the lookout for ways to hone their style. Here are some key principles toward making your paragraphs sparkle. Read the rest of this entry »

What worked and what didn’t in GTD (one scientist’s perspective)

January 21, 2007

Life of Brian, Crowd Scene, The goal of time management is to implement a set of tools and practices that let you achieve you’re life goals. That said, we are all different, a mosaic of strengths and weaknesses that makes a “one-size fits all” approach downright loony.

This is why posts like this one from Fumbling towards Geekdom are so valuable. It reviews the productivity tools that worked in  2006 for this academic with a parrot fixation. A short summary: Read the rest of this entry »

Ignorance, bliss, and why we stare at the tray table when landing

January 20, 2007

One of the fantastic things about field biology is the opportunity to travel. All the same, I think there’s a reason we don’t get a “pilot-cam” showing, second, by second, the process of taking a 20 ton winged aluminum tube from a state of high to low kinetic energy.


Visualizing Pi

January 20, 2007


Simple, concise, elegant.

An animated image showing the definition of pi. A number line is marked off by a circle of unit diameter. Starting from zero, the circle “unrolls” its circumference. At one full turn, the unrolled circumference has extended to the point we call π. This number is real but irrational, transcendental, and cannot be constructed with compass and straightedge.

5 things an academic can learn from Steven Colbert

January 19, 2007

1) Smart is sexy.

2) Words rule.

3) A large chunk of your classroom doesn’t believe (2).

4) Humor is a way to work on the folks from (3).

5) TV ain’t all bad.

Congrats to Colbert on his 200th show this week. This is The Word that started it all.

Brown Food Web Friday–great green globs

January 19, 2007

The author on BCI, bathed in salineSeptember found me on Barro Colorado Island, Panama, tromping daily down the Fairchild trail to harvest some experiments. BCI is in the middle of Lake Gatun, a forested valley flooded during the creation of the Panama canal. BCI is thus a former hilltop, isolated by water.

Now, trails at BCI are of two kinds–those that follow ridge tops and catch what little breeze exists 30 m below a forested canopy (good), and those that cut across the topography, allowing you to get a good sense of how hilly this place once was (not so good). The best one can say about the cross country trails is that they clean out your pores and are every bit as effective as a rubber suit in sheddng a few pounds of unwanted water (see left).

Fairchild is a cross-country trail . Also it was the rainy season, meaning that the trails were actually little gushing rivulets. Also, many of you have already discerned that Barro Colorado means “red clay”: very slippery, clingy, red clay. Finally, there are the black palms that strew their 4 meter long fronds–covered with 5 cm needle sharp spikes– on this muddy, nightmarish, stairmaster trail from hell.


About halfway up one of the most wretched stretches on Fairchild was a newly fallen palm trunk suspended half a meter off the ground. It required a bit of finesse, as it was surrounded by aforementioned needle sharp spikes and required one to balance on one leg on a 45 degree pitch while swinging a mud-clogged boot to the other side. Needless to say, I really looked forward to this log every morning.

Over the course of the week, however, I noticed it began to, well, ooze. And drip. Slowly. Somehow, it just seemed to add to the ambience and became a signature memory of this field trip.


Turns out these kind of jelly-like secretions are not all that uncommon in tropical forests where the brown food web is as busy taking wood, leaves, and tapirs apart as the trees and tapirs are at putting themselves together. I sent the latter two photos (not the first one) to Betsy Arnold, a tropical mycologist at the University of Arizona, who replied:

Photo is very cool. From here, looks like a canker-causing pathogen in the early stages of attack. Those pathogens are likely fungal (most likely Asco or Basid) or fungus-like (could be Phytophthora). Early symptoms, as for sudden oak death disease in CA, can include bleeding wounds.

From this we can tentatively conclude that said palm may have fallen in part because it was being dismantled from the inside by a beastie from one of two kingdoms whose niches are approximately the same: Kill palms and convert their biomass into new Ascomycetes, Basidiomycetes, and/or Phytophthora spores. The fact that they do it in such a colorful way is just gravy on the biscuit.


Post script:

In the process of adding linky goodness, Google suggested this one:


Ever the empiricist, I googled “ax murderer”.
And no, eBay ain’t trafficking in them. Yet.

Keep it short redux

January 18, 2007

Sometimes less is more.  Don’t have time to pick up Pynchon’s latest, but want to be edified, sanctified, deepfatfried?  Check out Middle Zone Musings‘s 6 word story contest.

The entries from GTDA:

“Tangerines….seemed like a good idea.” (note clever use of italics and ellipses)

and the old favorite

“Ants. Ants! Omigod, thousands of ants!”

Say goodbye to the Greenland Ice Shelf

January 18, 2007

Photos are powerful teaching tools.
This one from NASA is making the rounds . The money quote:

 New measurements show that the flow of ice in the Greenland ice sheet has been accelerating since 1996 during the summer melt season. The results suggest that the ice sheet may be responding more quickly to the warming climate than previously thought.


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