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.

Read more of this post

Trail of Tears VII – Portola Redwoods to Castle Rock

IMG_0737A group of my friends and teammates organizes a mostly annual backpacking trip known as “Trail of Tears”. One year it was Yosemite, climbing every major landmark in the park in 4 days (6 all told), another year it was the Emigrant Wilderness where they put in a 25 mile day because the map didn’t have distance markings. (Those trips would definitely make me cry.) They’ve also done Skyline-to-the-Sea, a 30 mile trip, a couple of times, as it’s close and relatively convenient to plan.

Two years ago, I went on my first real backpacking trip with these guys. Billed as “Trail of Leisure”, it was a 3 day affair in and out of Sykes hot springs in the Ventana Wilderness in Big Sur. Day 1 would involve hiking in 10-12 miles from the inner valley, Day 2 would be spent lazing about in the river and hot springs, and Day 3 would consist of hiking out 8-10 miles to the coast. Sounded pretty leisurely, until we discovered that the trail in from the valley was unmaintained and required a fair amount of plowing through shoulder high bushes in the high desert, and the two dogs who were with us fell into bad shape from the blisters and fatigue, so that their owner had to carry them in addition to his pack. Oh, and someone left most of the hot cocoa packets we’d assigned to him at home, thinking “how can we possibly need this much hot cocoa!?” (Note: when the organizers of a backpacking trip tell you to bring something, bring that exact something. Summer sausage is not a substitute for beef jerky. All that hot cocoa isn’t just for you. Jus’ sayin’.)


This year’s Trail of Tears was very local – just 45 minutes away in the Santa Cruz mountains – and seemed like it would be fairly straightforward. What was originally going to be another rendition of Skyline-to-the-Sea turned into a creative road-less-traveled hike from Portola Redwoods State Park to the Castle Rock trailhead. After shuttling some cars around, the 7 of us – me, Chris, Paul, Andrew, Jimmy, my brother Wayne, and his girlfriend Stella – set off from Portola HQ towards Butano Peak via the Ridge trail. We picked up the Basin trail which brought us across park lines into Big Basin but also put us off the available maps for a while. The terrain changed from redwood forest to chaparral as we ascended Butano ridge with views out to the Pacific ocean. Around mile 7 we started gradually descending through tan oak forest, passed remote Lane trail camp, and finally came upon the Skyline-to-the-sea trail and a marker for our first day’s destination – Waterman Gap trail camp. By the time we saw that trail marker, most of us were already ready to call it a day, so when we learned that it was 5 more miles it was kind of a slap in the face. Fortunately, the going was shady and padded – if not easy – through rolling redwood forest along Hwy 236. Getting into camp was a welcome relief for everyone!

Half the group went on ahead to set up camp while the other half hopped in the car that had been left at the intersection to procure water and refreshments. During dinner at the campsite, a park ranger stopped by on a routine check and informed us that we’d basically broken every rule in the book: killing trees (by tying up a slackline), occupying multiple camp sites (we only had a permit for one), having too many people in one camp site (the limit was 6, but 4 were leaving after dinner), and having glass bottles in a state park (our victory beer). He seemed very confused that our camping permit was from Portola Redwoods, and when we told him that we’d hiked in from there, he said incredulously, “you’re the first group I’ve ever heard of to hike that route, you must have done 20 miles today!” Actually, it was probably closer to 15, but still, it made our utter exhaustion feel somewhat justified. At any rate, the ranger let us off pretty easy.

After the day hikers left, darkness descended pretty quickly and we soon turned in for the night. Earlier, when we’d gone to the store for water, we’d passed some signs on Hwy 9 that read, “Night racers, we have” “your plates” “calling CHP”. Sure enough, sometime around 1 or 2 AM we heard the vroom of engines and squealing of tires echoing loudly through the mountains as several cars and motorcycles raced up and down the curves of Hwy 9 less than half a mile away. I could see how it might get tiresome if it happened regularly.

IMG_0734We got a late start the next morning, emerging from our tents around 9:30. After breakfast and breaking down camp, we set out around 11AM for Castle Rock trail head some 9.5 miles distant. Following Skyline-to-the-Sea to Saratoga Gap trail, we crossed into Castle Rock SP and picked up Travertine Springs trail to Castle Rock trail camp. We crossed several springs and streams along the way and stopped for lunch at Travertine Springs proper, though all we could see of the springs were thick stands of reeds.

After lunch, we ascended steadily through tan oak forest to the chaparral and manzanita of Castle Rock’s southwestern slopes. Once we passed Castle Rock trail camp (where we saw our friend the park ranger again), we were afforded the best views of the weekend from the rocky outcroppings of the Saratoga Gap trail over Big Basin, Ben Lomond, and the Santa Cruz bay.


Castle Rock really has it all – rivers and waterfalls, redwoods and madrones, shady forests, exposed rock formations, climbing and hiking, and some of the best vistas in the bay area – so it was great to end the hike there. Once we passed Castle Rock Falls, it was a short 1.5 miles to the main parking lot, where we were picked up by Andrew and a Jamba Juice for everyone.

IMG_0738 IMG_0736

All in all, it was a great, sweaty weekend far away from civilization and yet right in our own backyard. That’s the beauty of living here. There’s talk of doing Yosemite again for next year’s trip, which would be awesome since I’ve never actually hiked there. And maybe some day Joshua Tree, and Lassen, and all the other amazing places in California…


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!):

IMG_0239 IMG_0139

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.

IMG_0141 IMG_0143 IMG_0149 IMG_0150 IMG_0146 IMG_0154

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.

IMG_0176 IMG_0182 IMG_0196

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!

IMG_0212 IMG_0220 IMG_0225 IMG_0235c

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.

IMG_0251 IMG_0256

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!

Banana slugs 27, newts 11

dsc01862No, the title isn’t the score between two Bay Area school teams – I went for a hike yesterday in Big Basin, which is California’s oldest state park. Only an hour away from most locations in the mid-peninsula, the short journey there is a trip in itself. Winding mountain roads take you by the horse pastures and villas of Silicon Valley’s elite up to Skyline Blvd, where expansive views of the bay and rolling hills leading to the Pacific Ocean alternate with stately groves of redwood trees. Skyline hits Hwy 9 at Castle Rock, and you take Hwy 9 down to Rte 236, treated to more stunning vistas of lush tree topped mountains. Rte 236 takes you “straight” into Big Basin, where over 80 miles of trails await.

For our hike, we chose an 8 mile loop that led us through mostly redwood forest along numerous creeks. Being “winter”, the forest was very damp, but the trails had held up surprisingly well, and the weather that day was sunny and mild. The air smelled fresh and sweet and the undergrowth vibrant with new green.

img_0081e img_0087e1
img_0088e img_0104e

It wasn’t long before we encountered our first banana slug. For someone who grew up with the tiny, nondescript black slugs that are common on the east coast, banana slugs never cease to astound me with their sheer out-of-this-worldness. The large, bright yellow slug (genus Ariolimax) is practically ubiquitous in this area, however, and is the mascot for UC-Santa Cruz. The ones I’ve seen have all been a solid yellow color, and are either California or Pacific banana slugs. On this particular hike, we saw 27 banana slugs, some up to 8 inches long. It seemed to me that whenever we saw a profusion of mushrooms we tended to see a slug soon after, and this makes sense given that they are fond of eating fungi, in addition to rotting plants.

img_0066e img_0121

As we descended and traversed the various creeks at the valley bottom, I noticed my first rough-skinned newt (Taricha granulosa). The first one was a baby, as it was only a few inches long and lighter in color. We eventually saw a total of 11 newts, most of them mature adults, between 6-8 inches long. Their backs are dark and roughly mottled, while their bellies are smoother and a bright orangey yellow. I was struck by their well formed hands and feet, their seeming obliviousness to us, and their relative clumsiness. They moved almost mechanically despite interruption but when placed on a slight incline they more often than not simply fell over. I’d never seen a newt before so that surprised me – I expected all lizard-types to be, if not “sticky”, then climbers in some way.

Another group of organisms that fascinates me is fungi. There was no shortage of species encountered on our hike, many I’d never seen before. Again, the suburbs of the east coast don’t really expose you to the myriad of shapes, colors, and textures found in the forest during the rainy season, so each encounter was like discovering a treasure. Below is a gallery of most of the fungi we saw.




Some kind of polypore

A species of Ramaria fungus

Pinkish coral mushroom

Mycena osmundicola

Mycena osmundicola? growing from the side of a tree

Possibly some kind of chanterelle, but non-terrestrial

Possibly some kind of chanterelle, non-terrestrial

Probably either a dye-maker's polypore, or a false turkey-tail

Maybe a dye-maker's polypore or false turkey-tail

Either smoky coral or white worm coral

Either smoky coral or white worm coral

Possibly a waxy cap mushroom, or a small chanterelle

A waxy cap mushroom, or small chanterelle?

Possibly a jelly mushroom of the Dacrymyces family

Possibly a jelly mushroom of the Dacrymyces family

And this shows why I might have trouble hiking – I stop every few feet to examine a new specimen of plant, bug, or fungus. Maybe I should have been some kind of field scientist…

Notes: All photos except the first (by me) were taken by Chris Doyle. Mushroom identification attempted with the help of David Fischer’s American Mushrooms and this wonderful set of photos taken of mushrooms in Big Basin state park by Ron Wolf.

Little trouble on the Big Island: thoughts on organizing a workshop and tourist notes


View from the lobby at the Fairmont Orchid hotel

As some of you know, I helped organize a workshop on Open Science at this year’s Pacific Symposium on Bicomputing. I was grateful to have as my co-chair a certain Cameron Neylon, who has spent far longer pondering the issues we were going to discuss and has organized some similar meetings in the past. Cameron took on most of the meat work of the workshop for this reason – writing the introduction for the proceedings, giving the introduction to the session, moderating the panel discussion, and presenting the highlights to the rest of the conference. As for me, I tried my best to be useful!

Others have summarized the workshop nicely so I won’t be doing that here. (If you’re interested in viewing any of the slides or talks, you can access a full list of them from the workshop’s media page.) Instead, I’ll just reflect a bit on what it was like to organize a workshop for the first time, and how I found the Big Island of Hawai’i (hint: it’s a very unique place).

Hurry up and wait

Organizing something starting from almost a year ahead of time was an interesting exercise, marked by short bursts of furious activity followed by long stretches of inactivity. For most of the year, I wondered if I was supposed to be doing anything! But the reality is often that there simply isn’t anything to do until certain times, and then you have to get a lot of things done quickly. For us, we had about 5 flurry points: getting the proposal submitted, taking care of administrative stuff after the proposal was accepted, evaluating and responding to talk proposals, preparing the introduction for the proceedings, and running the actual workshop.

It’s all about the Benjamins

One very important task that didn’t quite fit the mold of hurry up and wait was fundraising. We started looking into this in the spring after our proposal was accepted, and didn’t really stop looking until early fall. One challenge was the nature of the workshop itself, which didn’t fit very neatly into existing categories. Most funding organizations have specific topic areas in which they will fund projects, but these tend to be domain-based, e.g. cancer or infectious disease. Others will fund individuals – minority scientists, for example – working in specific areas of research. We felt it might be difficult to obtain funding from the traditional granting agencies so we tried several companies and organizations associated with companies. Even with connections at some of them, our proposals didn’t get any consideration.

Our only successful proposal was to the Burroughs Wellcome Fund, which, ironically, is more of a traditional granting agency. I sent essentially identical proposals to two different topic areas, one of which was rejected twice – the program officer deleted it the first time thinking it was a conference invitation, and then formally rejected it the second time after I wrote again to inquire about it. (This was actually a problem I never really came up with a good solution for. What do you put as the subject line in an email so that it doesn’t sound like spam?) The other was the one that ended up getting funded. Nothing distinguished it from the other requests except where we sent it, and even here, I had to inquire more than once to make sure someone saw it.

In the end, the money had a huge impact. Not only did it allow me to go to the workshop (!) but we were able to fund several of our participants and had some money left over to cover an emergency (which happened, of course). Having even more money would have helped, because we could have used it to support Kaitlin Thaney from Science Commons. I learned several things:

  • Fundraising is one of the most important aspects of organizing an event
  • Look for funding in as many places as possible. Leverage your network but realize that it won’t always help you get money.
  • Apply to multiple places within one organization if you can. Sometimes the same proposal will get different consideration depending on whose desk it ends up on.
  • Be persistent. If you don’t hear back within a month, contact them again. Contact them at least twice, or until you get a response. If you get any leads at all, follow up – treat every lead like it’s the only one you might get. After all, it never hurts to have too much money, but you literally can’t afford not to have any.
  • (If applicable) Being a student has its pros and cons. On the one hand, you’re an unknown (and so might go straight into the trash folder); on the other hand, you present a sympathetic case. If you can actually get someone’s attention, they will probably understand that you really need the money and that you probably don’t have many other options. So again, be persistent, and emphasize the fact that you’re a student and the reason you need funds is for other students.

Murphy’s law is alive and well

img_9749Whatever can go wrong, will go wrong. And while rarely does everything go wrong, rarely does nothing go wrong. In our case, we had several of our headlining speakers, including the keynote, drop out at the last minute for various reasons and had to scramble to find a replacement. The workshop would probably have been fine even if we hadn’t found one, but we were extremely fortunate that Phil Bourne agreed to participate on 2 days notice, as he contributed a great deal of legitimacy as well as content to the workshop.

We were very lucky that 1) Phil Bourne was free, 2) plane fares dropped very temporarily, 3) we had some funds left over, and 4) there were still affordable vacancies at the nearby Hilton, despite them hosting a conference of their own.

Speaking of things going right, we had very few technical difficulties, even with the live webcasts, so maybe Murphy was too busy relaxing on the beach to bother us during the actual workshop. ;)

Lava, lava, everywhere

Mountain goats next to the road

Mountain goats next to the road

Love the contrast

Love the contrast

Mauna Loa? or maybe Mauna Kea

Mauna Loa? or maybe Mauna Kea

Lava as far as the eye can see

Lava as far as the eye can see

Waipio valley

Waipio valley

The Big Island of Hawai’i is strange, and wonderful. Bigger than all of the other islands put together, it is still very small by continental standards, as you can go from the west to the east in about an hour and north to south in probably about 2 hours. I can imagine a 7-10 day trip would be just about the right amount of time to explore the Big Island.

Given that there are five volcanoes (two of which are still active), the landscape is extremely varied. The central west coast is covered in piles of broken up lava rocks, making it look like a giant had recently tilled the ground with a huge shovel. Mountain goats almost the same color as the rocks perch on some of these piles. Along the ocean, however, the black lava rocks mingle with pure white wave-worn coral. One charming consequence of this is that instead of using spray paint to make graffiti, people use the white coral rocks to “paint” words and pictures on the dark rocky embankments along the roads.

As you go north, the rock piles give way to green swaths and rolling hills, all gently sloping down towards the ocean. In the center of the island are the high mounts of Mauna Loa and Mauna Kea, both of which sport snowy caps. In the valleys below them are broad expanses of young lava flows, shining black and rippled. When we visited this area, we alternately drove through thick fog, then bright sunshine and gusty winds, and finally rain.

On the northeast side of the island are the tropical forests and ridges, including the well-known Waipio valley. We got here too late to hike down into the valley, so we only went in about 1/3 of the way, but with a greater than 15% grade, it was still a workout!

At the southern end is Kilauea, the most active volcano on the island. Someone told me a story about how a small town was obliterated in the last big eruption, but some of the houses were completely spared. Lucky ducks, you think? Maybe not – it turns out those people couldn’t collect any insurance because there was no damage! Doesn’t matter if your house value just dropped to negative or if you can’t live there anymore because you’re surrounded by lava – the house is fine, so thanks for calling and have a nice life!

So much for volcano insurance

So much for volcano insurance

Anyway, Kilauea is still doing its thing, being hot and bothered and adding land mass to the island bit by bit. In the past, I’ve heard you could walk very close to the live lava flows, but these days the viewing areas are about half a mile from them, and so during the day all you can see is a huge column of roiling steam from the lava meeting the ocean. If you hike in close to sunset and stay after nightfall (headlamps or flashlights required), however, you can see a distinct red glow, and the occasional plume of sparks. Helicopters kept buzzing around the steam column, so if you can afford it, I bet the view from the helicopter is amazing.

Awesome column

Awesome column

img_99021 img_99474
img_99551 img_99692

There was much more to see but my stay was short and busy. If I ever go back, I’ll definitely be going up to the observatory on Mauna Kea, swimming with manta rays near Kona, snorkeling at Hapuna beach, and hiking around the northeast part of the island.