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.

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.

The big hairy ambitious haircut – finally!

It seems like ages ago that I was fretting over what big hair ambitious haircut to get… because it was, well, ages ago. But I finally went out and got it after determining that you could see my split ends from Google Earth and that brushing my hair required more shoulder flexibility than I possess.

After some back and forth with the stylist over whether I could have my short hair cake and not have to blow dry it too, I ended up with this:

While I think I might have to compromise and use some kind of “product”, it might just work. Well, except for the bits across my face, which are already starting to annoy me. Still, it’s leagues better than the $4 mullet cut I got in college, which was the only other short style I’ve had since I was a toddler.

The jury is still out on whether I can actually play sports and see at the same time.

In memoriam: Warren DeLano

 

PyMOL has starred in many journal covers

On Tuesday, November 3rd, the scientific community suffered a great loss with the passing of Warren DeLano. Most people know him as the creator of PyMOL, a popular and extremely powerful molecular visualization tool, but most – including myself, until recently – may not know all of the other unique qualities that made Warren a mentor, collaborator, inspiration and friend to many. And by making PyMOL open source, Warren demonstrated his generosity and ensured that his work would continue to help future generations of scientists.

Posts in the pipeline, and in the meantime

October’s been a busy month and so I haven’t had much time to post. But busy means interesting, and so I have lots of things to write about, it just doesn’t really get done. Some of the posts I have in the pipeline — mostly just as titles with scarce notes to remind myself what they mean:

The commenting conundrum: about where and why scientists do or don’t comment on scientific articles.

Responding to “them”: about the whos, whats, wheres, whens, whys, and hows of criticism and responding (or not) to it; mostly on the web but also off.

A detailed look into PLoS’s article-level metrics data: it’s open, so why not? And the results might just surprise you.

Thoughts from Science Commons Salon: with the amount of brainpower in that room, I’m surprised it didn’t explode. In fact, I’m surprised the whole town of Mountain View hasn’t exploded from sheer intellect yet.

So yeah, plenty to write about, sometime. I saw Pete Binfield of PLoS at the SC Salon and he joked that I was falling behind, reposting things that he’d posted a whole four days ago. Makes me want to start the Slow Blog movement…

Those posts will probably keep simmering for a little while. In the meantime, I haven’t been completely idle – in the last three weeks, I’ve written three blog posts for 23andMe‘s Spittoon on genetic association studies on glaucoma, bone mineral density, and blood-related traits. Another one is set to come out early next week. So if you haven’t been tuning in regularly to the Spittoon, now you know where else to find me!

New job and curation 101

It’s been several weeks now since I started working at 23andMe, a personal genomics company located in Mountain View, CA. Perhaps not coincidentally, it’s also been several weeks since I last blogged. The transition hasn’t been difficult, but it did take some getting used to, mentally and physically. I mean, leaving for work by 8:30am? Regular hours? Commuting??

Ok, so I really have nothing to complain about. 8:30 isn’t that early, and I could shave half an hour off each end of my commute if I didn’t choose to take advantage of bike-friendly roads, good weather, and a company-sponsored free train pass (OMG benefits!?). All in all, things are pretty much fantastic. The work environment is friendly, flexible, and laid-back; we have plenty of food and drink to keep us fueled throughout the day, and regular workouts/yoga if we need to get fired up or mellowed down (and to keep the “Free Food 15″ at bay). Plus, personal genomics is a super interesting and rapidly evolving industry, so there’s really never a dull moment.

So what is personal genomics, anyway? We’ve known for a while that genetics – the sequence of DNA inside our cells – plays an important role in our form and functioning. Many diseases are caused by changes in DNA (often in genes, parts of DNA that code for proteins) that alter the normal functioning of cells, though not all genetic differences lead to negative changes. (Genetics can also tell us about ancestry – who is related to whom and the history of populations – but I won’t be addressing that in this post.) Where it gets personal is when you apply it to individuals, such as when someone gets a genetic test to determine whether they have or are at risk of developing or passing on a particular disease. Where it gets genomics is when we use high-throughput technologies to do what is essentially thousands of genetics tests at once. Put them together, and you get personal genomics.

How do we know what genetic “pieces” correspond to what conditions or diseases? The general strategy is to compare the DNA of a whole bunch of individuals that have that condition (cases) to a whole bunch of individuals that don’t (controls). As long as both groups are similar save for their case-control status, any significant genetic differences between them should have something to do with that condition. We call this a genetic association.

It turns out that there are millions of single locations in the human genome where the exact sequence of the DNA might differ between two people, and these places, called single nucleotide polymorphisms, or SNPs, can contribute to differences we can observe, such as whether you flush when you drink alcohol or how easily you put on weight. 23andMe personal genomics kit determines what your sequence is for a representative subset of SNPs. Many are already known to be associated with certain conditions, and new research is being done every day to uncover more and more of these associations.

So what exactly do I do at 23andMe? My official job title is “Scientist, Content Curation”. Curation, I’ve found, is not very familiar to most people. Most people probably know that there is such a thing as a museum curator, but might not know what they do. Hardly anyone has ever heard of scientific curation. (And I thought explaining what I was studying as a grad student was hard! Biomedical informatics, anyone?)

But it’s really not that complicated. The essence of curation is almost always the same: the selection, acquisition, and management of content. What that content is differs depending on the field – for example, an art curator might look for and organize artwork for exhibition in a gallery, while a curator in the “Ancient Civilizations” department of a museum may be in charge of acquiring, managing, and presenting archaeological artifacts.

In science, curation involves organization of scientific knowledge and data. An area where this has been especially important is the life sciences, as the amount of information being generated by high-throughput experiments, large-scale projects, and scholarly publishing has skyrocketed. In order to manage this information and render it useful to others, the field of biocuration was born. Any database that organizes scientific knowledge – UniProt (the Universal Protein resource), FlyBase (database for that very important model organism, Drosophila), PharmGKB (a database focused on how genes and drugs interact), etc – depends on curators to keep the information up to date and easy to use.

And so it is with 23andMe. The genetic testing kit is one part of the product, but the other part is information – what knowledge is there about associations between the SNPs on our platform and health traits or conditions? What does your particular data mean? The science is far from exhausted on this subject, and in order to stay up to date with the research, 23andMe spends a lot of effort on curating the scientific literature for new genetic associations and presenting the information on our website for our customers.

Day to day, this means that we keep track of papers recently published in scientific journals, skim through to find ones that may have promising findings, and then vet these more thoroughly to see if they pass our stringent scientific standards. If they do, we extract the bits of information we need and put the bits together in reports that will eventually become part of the content on the website. It’s a job that definitely benefits from an organized system and an eye for detail – as well as a sense of curiosity.

After three weeks on the job, I think I’m starting to get the hang of the day to day work. Since my work is even more directly tied to the literature than it was as a graduate student in academia, I’m also developing an enhanced awareness of issues surrounding scientific publishing – those related to standardization and metadata, publication bias towards positive results, and closed vs. open access. The hardest aspect of transitioning from academia to industry hasn’t been the regular schedule, or the work environment, or the work itself, it’s been getting used to being on the other side of the pay-wall of scientific journals.

But that’s a rant for another time. ;)

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.

Ianni, 1996 – 2009

Thirteen years ago, we brought home to our new house a small ball of white fluff with floppy, tawny ears and dark, twinkling eyes. He was full of energy, scampering clumsily across the tile floor, and he yawned all the time. So we named him Ianni.

Since that day, he’s been our constant companion. We all grew up in the new house together – Ianni from a young pup to content dog, us kids from teenagers to self-sufficient adults, and Mom and Dad finally starting to enjoy the fruits of years of hard work with a house built just for them. When my brothers and I headed off to college and beyond, we’d come home during breaks and holidays and Ianni would always be the first to greet us at the door, tail wagging furiously. During the day, he would occasionally patrol the property’s expansive six acres, or sun himself on the deck or driveway. He’d be the last thing we saw before we headed upstairs to bed.

As the years went by, he seemed to stay the same spirited, even-tempered dog. We had a familiar play ritual involving the long hallway between the kitchen and the side door. When I picked up one of his toys – usually his bouncy orange dumbbell toy – he would immediately tense and perk up his ears. Winding up my arm, he’d steel his body, and as I threw the toy he would launch himself after it at full speed. Nevermind that the hallway, though long, went only about 25 feet before it ended in a wall. Ianni would sprint after the toy, and as it hit the wall and bounced back, he’d scrabble for a split second before also hitting the wall. On the rebound, he’d snatch up the toy and regain his footing in one movement and sprint back to me for another go. I know this behavior was not unique to Ianni, but it still always impressed me how undaunted he was in the face of that wall. When I was home over the winter holidays eight months ago, he was still playing this game like a dog half his age.

Maybe that’s why it seems so strange that he should be gone. Despite the fact that he was going on 13 (91 in dog years!), Ianni had no signs of arthritis or illness and seemed by all accounts healthy and vibrant, going out for daily walks, throwing his body around in pursuit of toys, and, apparently, chasing after girl dogs way too young for him. But there are silent killers as well as visible ones, and this time there was essentially no indication anything was wrong until it was too late. He passed away the same morning that my parents found him in pain.

That morning two weeks ago when I heard the news, I experienced a torrent of emotions. I felt the loss of knowing I would never see him again, or pet him again, or sit with him on the step again. I was upset that I wasn’t able to be there with him when he passed and despondent over how much pain it sounded like he’d been in the last hours of his life. I wish I could have comforted him and let him know that we loved him. I wish we could have known sooner about the cancer that took him from us so suddenly, and maybe done something about it. I wish he could have held on for just another two weeks until I visited, though I knew it would probably not have made me feel any better.

Last Sunday when I came home, I opened the door to find not an overjoyed dog, but an empty space. There were no excited barks as I reached for the doorknob, there was no tail wagging or flurry of ear ruffling. No more pitter patter of paws. Although the pain is a little more muted now and I knew Ianni would no longer be there, it was hard to be back in a home I’ve never known without him. His bed and crate and bowls were still in the laundry room, his leash was still hanging by the door. His bouncy orange dumbbell toy was lying in hallway. Heck, there was even a little pile of poop still in the grass near the driveway. Little things like these made it all the more surreal.

It seemed that we had only just realized how little time Ianni had left and he was already gone. A few months ago we half-joked about whether or not to buy a new collar. Maybe humor was the only way to cope with what had suddenly struck all of us: Ianni was old. But still, he seemed unchanged, and so we were lulled into optimism. When I came home, on the counter were two unopened boxes of specially formulated “senior” dog biscuits, which my mom had bought recently for the first time. “It’s never too late,” she probably thought. The irony struck me heavily, cruel and profound.

Yet I’m thankful that when I was home last winter, I spent ten minutes my last night before I went to bed sitting quietly with Ianni in his room as he settled down to sleep. I don’t think he thought anything of it, but in the back of my mind I knew that I might not get the chance to spend time with him again.

If I could, I would have told him just one more time,

“Good dog.”

Things shouldn’t be so hard by Kay Ryan

A life should leave
deep tracks:
ruts where she
went out and back
to get the mail
or move the hose
around the yard;
where she used to
stand before the sink,
a worn-out place;
beneath her hand
the china knobs
rubbed down to
white pastilles;
the switch she
used to feel for
in the dark
almost erased.
Her things should
keep her marks.
The passage
of a life should show;
it should abrade.
And when life stops,
a certain space—
however small—
should be left scarred
by the grand and
damaging parade.
Things shouldn’t
be so hard.

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 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

Still, everyone seemed happy:

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!):

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

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.

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.

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!

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.

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 Pilot Rock from the trailhead

The view from near the top

The base of the summit

Not for the faint of heart

On top of the world

Stopping to smell the 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!

A girl’s gotta do what?

I have a lot to think about after the unexpected outpouring of debate that followed my open letter. I’ve been alternately encouraged to send the letter to be published in larger news venues and to frickin’ do my research before posting anything. Admittedly, there are a lot of things I don’t know about vaccines, or about parenting, having not been in the position yet to make decisions about a child’s health. Watching the debate unfold, however, made it clear that there are some fundamental issues underlying the controversy which go deeper and broader than the discussion on vaccination. I hope to reflect on this in a later post but it will take me some time to get everything down in writing with other obligations pulling at me.

Photo by tekmagika on Flickr

For now, though, it just kind of galls me to see this. After watching a truly flabbergastingly misleading video of hers about the need to purge all toxins (including yeast, wheat and dairy, which are apparently equivalent to marijuana in McCarthy’s strange universe) in favor of “natural supplements” (cue list of commercial vendors), I was surprised to see that she blogged about getting her hair colored, extensively and often. Sure, people get their hair done. Sure, people are hypocritical. But you never want a spokesperson for a cause to do things that suggest they’re not entirely serious about that cause.

I guess this is what one might call a hypocrite. I talk about staying away from toxins, yet I bleach the hell out of my hair every month. It’s tough to avoid everything that is not good for you. Yes, I have given up a lot so far, but I don’t think I can ever let people see me with my original haircolor. Yuck.

I agree that it’s tough to avoid everything that’s not good for you. That’s  why we have priorities, so we can focus on what’s really important. That she goes on the record lambasting so-called toxins and then publicizes the fact that she willingly subjects herself to harsh chemical hair treatments (joking about it all the while) gives me some idea of what her priorities are. And that’s just one of the reasons why people should look elsewhere for medical advice.