Dog Days of Summer

Ice cream at Tulmeadow Farms in West Simsbury, CT

It’s hard to believe, but summer is almost over. I no longer debate whether the house stays cooler with the windows open or closed. There is almost a chill in the air when I wake up in the morning. Yes, at the height of the day the sun still shines warm and bright but there’s no mistaking it setting earlier in the evening. Hear that, tomatoes and melons? Your days are numbered! Get ripening!

The garden got a late start this year (June) so we only started harvesting a few weeks ago, mostly cucumbers and squash. Some of our tomatoes are starting to set but the big ones not so much. Corn, too. A few rattlesnake beans from the two vines that made it (still holding out hope for the one yard long bean vine that’s flowering now). The everlasting chard from last summer is still going strong, but more as chicken food as I pinch off leaves every few days stricken by leafminers. The one crop that exceeded expectations was the one we didn’t have to do anything for — nectarines, lots of delicious, bright red nectarines. I think I ate at least two a day for two weeks straight.

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Tycho: The First Eight Weeks

Photo by Jonathan Lambert

Well, we finally did it. We got a dog!! (Ok, we got engaged and married, too, but back to the exciting stuff…)

I’ve been pining for a dog for at least a couple years now, with a precipitous moment last summer when I chanced upon an adoption fair in a downtown street market coming out of the optometrist’s. His name was Monty (short for Monterey), and he was perfect: a black Lab mixed with enough other things to give him the tuxedo chest, the barest of white points, and that je ne sais quois. It helped that despite being 14 weeks old he was friendly without being excitable — a good personality for a dog.

We didn’t adopt Monty because the circumstances weren’t right, but it got the gears turning with fresh vigor. For the next few weeks I stalked the rescue organization’s website for dog listings and tried to coerce my dog-loving co-workers to adopt Monty in my stead (so I could visit him, or maybe steal him from them later).

Then nearly a year later we had another chance dog meeting. Read more of this post

A quintessential California weekend

After some weeks of cooler weather and intermittent rain, Chris and I wholeheartedly embraced a weekend of warm sunshine to spend outdoors with friends. Ben and Lisa had flown down from Seattle for Heather and Vinny’s wedding and we hosted a barbecue at our house Friday evening so they could see folks. The portable fire pit came in handy as the temperature dropped and we roasted marshmallows well into the night.
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Three months later

I haven’t been very active in my usual online spheres lately. No blog posts in three months, only the occasional jaunt into FriendFeed, and random peeks at the ever-growing Twitter stream.  Here are some random bits of what I’ve been up to.
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A visit to the “bird farm”

If you think having a pair of doves nesting on your front porch is cool, imagine living with a herd of goats and alpacas, a flock of chickens, dozens of parrots and other exotic birds, and some lizards. These are the denizens of Simon Field’s “bird farm”, which I visited about a month ago, right after SciFoo. I loved it, and knew I’d want to revisit to share it with friends.
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Role models

Over the last month and a half I’ve had the pleasure of hosting two stand-out examples of responsible parenting. These role models, however, happen to be doves.

At first I was skeptical why a pair of birds would want to build a nest on my front porch, given that we go in and out fairly frequently. To be fair, the rose vines framing the entryway are thick and strong as well as stylish, and few bad guys (except us) would even think of going up in there. They spent a couple of days scoping out the place – I like to think that they were comparison shopping – but in the end, convenience, location, and that je ne sais quoi won out. A few sticks and pieces of dried grass started showing up, and eventually there was a nest.

After a couple weeks I saw a scraggly little chick, but then we went on vacation and it was gone when we came back. I thought maybe I’d imagined it, but the doves were still there, and a couple weeks later there were definitely two chicks. Apparently, doves can have multiple broods in a single mating season, and usually use the same nest. They may even use the same nesting site year after year. So now I knew I was looking at the second brood.

Since I was actually home this time, I watched these guys grow from little pin-feathered ugly ducklings into… well, still kind of ugly but at least full feathered young doves (they had gangly awkward tweenager written all over them). The parents still took turns on the nest but switched more frequently, now that they had two hungry mouths to feed. To eat, the chicks basically stick their beaks inside the parent’s and gobble up whatever pre-processed yumness is there. Though interesting, it’s really not that pleasant to watch.

The nest soon got a bit crowded as the chicks were almost as big as the adults and would flap their wings haphazardly from time to time. I could sense the parent doves getting a little frustrated and sometimes the male would perch on the branch outside the nest to get some fresh air. The more adventurous chick joined him once (I think he also got most of the food; he was the bigger one). I noticed yesterday that the parents would sometimes both leave the nest, and the chicks would get restless and hop about in the vines.

This morning, I opened the door to find the nest empty. I guess it was time! Maybe the parents will come back and have another brood. If not, maybe next year.

Photos (from left to right and top to bottom):
1. The female parent, I think. It was slimmer and smaller than the other one.
2. The male parent, I think. Bigger and slightly more colorful.
3. The male on the nest, with one chick visible.
4. The male again, with both chicks getting a little too big for the nest.
5. The big chick sitting with Dad on the branch. The other chick is behind them to the right.
6. Both chicks out of the nest, wondering where Mom and Dad are.

Life after grad school…

… isn’t all that different. Yet. I’m sure it will change a lot once I actually start work in The Real World, but for now, I’m still going to be spending most of my days in the lab doing a lot of the same things. Only now, people occasionally call me “Dr.”, which is strange because it’s true.

With my parents and my advisor after receiving my diploma

With my parents and my advisor post-diploma

I consider myself very fortunate to have a fantastic job lined up, but not everyone is so lucky:

It's a tough time to graduate

It's a tough time to graduate

Still, everyone seemed happy:

w00t! Graduation!!

w00t! Graduation!!

I’m not much for presents, but I’m very excited about the two very useful graduation gifts I received – a snazzy Canon SD 1200 from Chris (I’ve been camera-less for a couple years; expect to see many more photos on this blog starting now) and a KitchenAid stand mixer from some pretty awesome friends (no more blisters from mixing dough by hand!):

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Then, as expected, I took the next week off. My family was in town, so we went on a hike in Purisima Creek Redwoods Open Space Preserve, which is nestled on the west side of the Santa Cruz mountains between Hwy 92, Hwy 1, and Skyline. We took the Whittemore Gulch trail up to the North Ridge trail because it sounded like it would offer diverse terrain along with great views in a reasonable hike (~ 4.5 mi roundtrip), and, indeed, it did not disappoint.

View towards the Pacific from the North Ridge trail

View towards the Pacific from the North Ridge trail

My mom especially wanted to see banana slugs. Well, it must have been just after spawning season, because we saw more banana slugs than we could count, from babies an inch long to adults almost as long as my forearm. We even saw one actively chomping away at some green leaves. There were also a couple snakes, mice, butterflies, and plenty of wildflowers to keep our senses engaged.

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On Tuesday, we drove up to Napa for an afternoon of wine tasting, visiting Folie a Deux/Napa Cellars, Saddleback Cellars, and Mumm Napa, where we bought two bottles of a unique sparkling Pinot Noir. Despite having lived here for 5 years, I’d never gone to Napa before this trip.

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Chris and I headed off to visit his parents in Ashland (just over the border in Oregon) the next day. We took the scenic route out of Napa but spent most of the drive on I-5. I’d driven north on I-5 once before (to Seattle) but for some reason didn’t remember Mt. Shasta. I must have been sleeping because Shasta isn’t a mountain you quickly forget!

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We spent two and a half days in Ashland, walking around town, chilling with some furry friends, hiking, and watching a lot of shows. Ashland is known for its lively theater scene, and we saw no fewer than three shows while we were there, each at a different venue: “Don Quixote”, “The Music Man”, and “The 25th Annual Putnam County Spelling Bee”. All were quite good, and each was funnier than the last. “Spelling Bee” was at the Cabaret; being a dinner theater in a converted church, it was a very intimate setting with the tiny stage right up against the first row of tables and a lot of engagement with the audience. “Don Quixote” was held in the Elizabethan theater, which recalls the theaters from Shakespeare’s time.

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On our last full day there, we hiked to the summit of Pilot Rock with Chris’s parents. Despite being in their 60’s, they outhiked and outclimbed me both to the top and back to the bottom, scrambling up and down over the rocks like mountain goats. I hope I have half that energy and courage when I’m their age!

View of the summit from the trailhead

View of Pilot Rock from the trailhead

The view over the valley from near the top

The view from near the top

At the base of the summit

The base of the summit

Not for the faint of heart

Not for the faint of heart

On top of the world

On top of the world

Stopping to smell the flowers

Stopping to smell the flowers...

Lots of flowers

... lots of flowers


And there it is — the thrill of victory and the view from the top is why we risk life and limb (ok, maybe only I felt that way…) to get up there.

Now it’s back to the grind for another week, and then I’m off for another week for a tournament near Boston, visiting friends in Boston and on Bainbridge Island, WA, and then another tournament near Seattle. Expect copious photodocumentation now that I have a camera I can take with me everywhere!

Kangaroo rats go high-tech – and help inform environmental policy

Photo by mariozama on Flickr

Photo by mariozama on Flickr

If you need a cute, unique posterchild for conservation, look no further than the kangaroo rat. Imagine a gerbil rendered in the anime style – huge eyes, disproportionate body, and super talents. Not only can it leap a meter or more in a single bound, it also has special adaptions for thriving in its desert habitat, including highly efficient kidneys and the ability to extract all the water it needs from the seeds it eats. They hop around on their hind legs like kangaroos, using their tails – which can be up to twice as long as their bodies – for balance. Freakish and adorable, what’s not to like?

Turns out that kangaroo rats are also a key component of the desert ecosystem. They clip grass like little lawnmowers and leave the clippings in circular rings surrounding their burrows so that the seeds can cure in the sun. These clippings act as mini-compost piles, enriching the soil beneath them. Their behavior also creates the preferred, low-profile habitat for other desert animals.

Photo by runneralan on Flickr

Now add this to their list of assets: because of their crucial role as a “keystone” species, they help scientists in the Carrizo Plain National Monument area make important land management decisions. To do this, researchers attempt to estimate the size and distribution of the kangaroo rat population. In the old days, they tried physically trapping the animals, or conducting aerial surveys. Neither of these methods was effective or cheap enough to make good management decisions.

Kangaroo rat burrows are visible from space

Kangaroo rat burrows are visible from space

Recently, The Nature Conservancy began working with researchers at the University of California – Berkeley to count kangaroo rat populations using satellite data. The new technology allows them to create accurate, reproducible maps of kangaroo rat “precincts”, taking advantage of the fact that the nearly perfect circles of clippings the animals create are visible from the air. With the better data, scientists can more closely monitor environmental changes through the kangaroo rat population.

Kangaroo rats aren’t the only species going high tech – sheep are sustainably grazing in Argentina with the help of satellite imagery, and weeds can’t hide from satellite sensing in Hells Canyon.

Before I learned about the kangaroo rats, I hadn’t realized how cool “the other Nature” – – is. They’re doing a lot of interesting things not just in conservation, but also in science education, outreach, and policy. As the satellite example shows, they also value technology. So, of course, they have a blog. :) Check them out!

(Hat tip: Dan O)

I was lost but cows might help here

Let’s say I’m lost in the woods, and this time I don’t feel like improving my predicament by building a house, this time I want to find my way out of there. What’s a directionally challenged girl to do? If the findings of Hynek Burda, Sabine Begall, and colleagues are accurate, I might want to find some cows*.

In 2008, Begall et al published a fairly controversial paper where they used images from Google Earth (cows) and field observations (deer) to determine that cattle and deer preferentially align in a north-south direction:


Figure 1. Distribution of body orientations for cows (A), roe deer (B), and red deer (C), with arrows representing the mean alignment vector. The inner circles represent the threshold for statistical significance. Triangles on the outer edge represent mean alignment orientation for different continents.

Naturally, I had two reactions to this paper: “People can publish stuff like this!?” (that’s awesome!) and “Did they control for all the possible factors?” Perusing the comment thread below the Nature news article reporting on the paper, I saw that many others had the same thoughts. Of course, 99% of people who comment on the interwebs do so without doing their research, not even reading the article on which they’re commenting, let alone following up on any links provided in the article. (Also, 90% of statistics are made up.) So while I read the paper with some skepticism, I ended up fairly satisfied that the authors conducted a rigorous study. To their credit, they also responded to comments in that thread, stating not only that most people who took issue with their paper didn’t actually read the paper (oh snap), but also addressing all of the concerns in detail, so kudos to them!

Risk-free cow-tipping. Photo by blue-moose on Flickr.

Figure 2. Risk-free cow-tipping. Photo by blue-moose on Flickr.

Note that the authors don’t claim that cows and deer face a particular direction – say, north, or south (so maybe I’m still hosed even if I do find a deer in the woods) – but that they orient along the north-south axis. They didn’t make the distinction because “The resolution of most satellite images in Google Earth did not allow clear and fast distinction between the individuals’ head and rear…”. Let’s just say… I’ve wanted to say that many times, but not in such polite terms. (^_-)

Prevailing wisdom says that cows tend to orient perpendicular to the sun to maximize heat absorption, or orient with the direction of the wind to avoid heat loss, so sun and wind are obvious confounding factors. The authors took care to rule out both of these factors. With sun, they looked for evidence of behavior related to basking or heat stress, and found none. They also ruled out avoidance of “dazzling” since most images were taken near noon, when the sun is more or less directly above the animals. With wind, they note that there being windy conditions with the wind blowing in a north-south direction in most of their sample is highly improbable. Especially given the prevailing winds in each hemisphere, the animals should align themselves east-west rather than north-south. If their samples consisted of mostly windless conditions, and wind was the dominant orienting factor, then they should have observed a random distribution of body orientations, not the significant north-south orientation.

With deer, they found an even stronger association with a north-south orientation (Figure 1 B and C), again ruling out wind and sun as potential factors. Without wind and sun, the authors posit that the earth’s magnetic field may be the cause. They point out other examples of magnetic alignment in animals, including insects and fish as support for this explanation.

“But what about cow magnets?!” cried some. Never fear – the authors also address this in their response to comments, saying that the use of cow magnets (which are inserted into some cattle when they’re young to catch all the barbed wire, nails and staples these hardcore grazers ingest) is not common, especially in most of the areas where the images came from. They also note that none of the deer would be expected to have magnets in their stomachs, and the north-south effect was even greater for them.

Figure 3. Cows and power lines - whos the boss? Photo by chris_hunnicutt on Flickr.

Figure 3. Cows and power lines - who's the boss? Photo by chris_hunnicutt on Flickr.

Earlier this week, the same authors published a follow-up study that bolstered their previous findings that ruminants may be aligning themselves relative to magnetic fields. Here, they investigate the orientation of cattle and deer in the proximity of power lines, again using images from Google Earth for cattle and field observations for deer. They demonstrate that the significant north-south tendency they observed previously is severely reduced when power lines enter the picture, with animals adopting essentially random orientations.

When they stratified the data by the orientation of the power lines themselves, they found that animals may tend to orient themselves roughly parallel to them, but most of the observations were not statistically significant. An obvious factor here is the use of the power lines as a visual cue. So the authors plotted the orientation of animals at increasing distances from the power lines and found that for E-W power lines, the animals as a whole progressively oriented themselves more and more N-S, and for N-S power lines, the orientation of the animals went from random to more and more significant along the N-S axis. The opposite would be expected if the animals were using the power lines as a visual cue.

Figure 4. Orientation becomes increasingly north-south with increasing distance from power lines.

Figure 4. Orientation becomes increasingly north-south with increasing distance from power lines.

If you’re like me, you’re also intrigued by the way they visualized their data. Maybe these circle diagrams are typical in animal alignment studies but this was the first time I’d seen one, and I’m a fan. A lot of information in a small space, intuitive to interpret once told the underlying concept, and no unnecessary embellishments. So bravo on the data viz front! But how did they make these diagrams, you ask? I would never have guessed it, but they apparently used Powerpoint:

“Screenshots of the chosen pastures were copied from Google Earth and pasted into Microsoft Powerpoint. … We marked the cattle’s longitudinal axis by drawing a straight line with the Powerpoint drawing tools and estimated for each animal separately its direction to the nearest 5° by overlaying a circular scale with 10° steps.”

That’s not to say that they didn’t redraw the diagrams in a different drawing program for publication, but yeah. Powerpoint. Granted, I used Keynote to mock up logos so maybe it’s just because these programs offer a blank canvas and simple drawing tools.

So what can we conclude? Perhaps cows and deer do preferentially align themselves north-south when not under the influence. The use of Google Earth, while cool, does take a bit of environmental control out of the hands of the researcher, though. Could there be artifacts introduced by their data source? Next time I’m in the woods and I happen upon a herd of resting or grazing deer, maybe I’ll make an observation and send it to them. Heck, they should set up a “MagneticRuminantZoo” type thing, where people can enter individual observations of grazing and resting ruminants. Let’s settle this with the awesome power of crowdsourcing!

*Actually, I’m pretty sure deer are probably more common in the woods than cows, but cows worked better with the title. Good thing the phenomenon seems to be even stronger in deer than in cows!


Burda H, Begall S, Cerveny J, Neef J, Nemec P. Extremely low-frequency electromagnetic fields disrupt magnetic alignment of ruminants. Proc Natl Acad Sci (Epub ahead of print)

Begall S, Cerveny J, Neef J, Vojtech O, Nemec P. Magnetic alignment in grazing and resting cattle and deer. Proc Natl Acad Sci. 105(36):13451-13455.

Cressey D. ‘Magnetic cows’ are visible from space. Nature News, August 25, 2008.

Respecting food, respecting ourselves; or Put down that Hot Pocket before you regret it

Photo by wonderfullyrich on Flickr

Photo by wonderfullyrich on Flickr

Regret what, you wonder? No, not the searing pain that accompanies biting into the microwaved pastry filled with molten lava. No, no. To those who are passionate about wholly sustainable agriculture like Joel Salatin, processed foods like Hot Pockets and Cocoa Puffs are the gastronomic equivalent of a one night stand with a stranger, what he calls, “prostitution food.” A self-proclaimed “Christian libertarian environmentalist capitalist lunatic”, he says that eating is the most intimate act we do outside of marriage, and should be given the same respect and consideration. What modern industry has done, however, is distance people from their food and break that intimate connection, such that few people these days give any thought to what they’re actually eating and where it comes from. But for food, which we put daily into our bodies, there should be a courtship, a relationship – and a romance.

Photo by roboppy on Flickr

Photo by roboppy on Flickr

To this end, Joel has spent the last few decades continuing what his parents and grandparents started: emotionally, economically, and environmentally-sustainable farming. Their farm is called Polyface, and it is built around the concept of polyculture – emulating natural diversity and ecosystems to produce food. The traditional way of doing this is through planting multiple crops in the same space. Polyface does it by controlling symbiotic interactions between different food animals and their environment in a way that more closely resembles their natural relationships. This results in healthier, happier animals and habitats, and healthier and environmentally-friendly food.

Michael Pollan’s excellent book, The Omnivore’s Dilemma, highlights Polyface Farm and catapulted Salatin into the public awareness, such that Salatin now keeps a busy speaking schedule. He spoke with gusto at Stanford tonight to a packed auditorium riveted by his passion for sustainable farming and the eloquence with which he told the farm’s story. Nuggets of wisdom interspersed throughout his talk went hand in hand with irreverent illustrations of concepts and unrepentant jibes at the various evils of the status quo, including the “US-Duh” (USDA). A few of the more thought-provoking portions of the talk included:

The importance of multipurposing. Portable, easily adaptable tools that are still highly tuned to their specific environment but derived from multi-use components. This has corollaries to web-based and computational tool development.

The importance of community. Specifically a return of crafting, such as lumber milling and butchering, to the community and the consequent return of awareness, accountability, and appreciation for the products we consume that our industrialized society has lost. Like above, this also has corollaries to tool development, namely that transparency and an invested community are good.

Photo by wonderfullyrich on Flickr

Photo by wonderfullyrich on Flickr

The importance of disturbance for progress. Polyface does this by using the natural habits of animals to stimulate new plant growth. “Two steps forward, one step back” might be one way to encapsulate it; another might be the acknowledgment that things usually have to get worse before they get better. But it’s really that short term disruption is a good way to jump-start progress, whether it be ecological or social.

The importance of creating value. Salatin is all for preserving the environment, but he believes that the way to steward resources is to create value. He does this, for example, with wood by harvesting some of it (sustainably) for firewood which he sells to local customers who come by to pick it up.

Your users are your greatest allies. The way things are done at Polyface are still a minority viewpoint, even (or especially) in their local area. The neighboring farms don’t tend to approve of their practices, and so the Polyface community consists mostly of their customers, who believe in its mission and are invested in its success. This translates to any company or group providing a service or a product – build a good relationship with your consumers, because it’s going to be your users who are your friends, and likely not your peers.

The significance of group behavior. Cows act and interact differently with their environment and each other when in a group. So do people. We can use this fact to our advantage, and we have.

The folly of industrialized goals. “Bigger, fatter, faster, cheaper” are not necessarily noble, and are not always the traits you want.

Acknowledging all the steps in the cycle gives you better appreciation for the end product. Salatin illustrated this in two ways: one, by showing absolutely adorable pictures of baby bunnies – which elicited oohs and awws from the audience – followed by pictures of rabbits being dressed and cleaned, and two, by unapologetically stating that a favorite activity of theirs is to cook and give homemade sausages to the children of vegetarians at their food festivals. He says that they’ve actually converted a lot of vegetarians back to eating meat by convincing them that their philosophy of farming is sustainable and responsible.

Photo by questa on Flickr

Photo by questa on Flickr

In addition to these overarching concepts were a couple choice statements, such as:

“When your neck is bigger than your head, you’re a freak! And Nature weeds you out!” – qualifying a statement he made saying that the average age of death for NFL players is 57 years, which itself was said in regards to his statement against “bigger, fatter, faster, cheaper.”

“It’s a one night stand – it’s prostitution food!” – as explained in the first paragraph, in regards to modern processed food.

“Our pigs have a great life and one bad day.” – apparently how Michael Pollan sums up the life of a Polyface pig in his book.

“It’s how we respect and treat the least of us that determines how we respect and honor the greatest of us.” – commenting that we cannot truly respect ourselves until we respect the earth and the organisms that sustain us.

This is the gospel that Joel Salatin preaches, and it speaks to a growing hunger many of us have for meaningful and socially responsible living. It is still a minority viewpoint, but Joel’s hope is that a new generation of holistic, environmentally-conscious farmers will arise, elevate the once respectable vocation from the “redneck hillbilly” reputation it has come to wield, and bring romance back into people’s relationship with food. As I learned today, he’s a man on a mission, he does not shy away from controversy, and even if you don’t agree with everything he says, you can at least respect him for his respect for all of nature’s facets, no matter how ordinary they seem to us at first glance.

Photo by wonderfullyrich on Flickr

Photo by wonderfullyrich on Flickr