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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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:

Photo 5 Photo 3

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

 

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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.
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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.
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Ianni, 1996 – 2009

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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.

ianni 008As 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.

ianni5That 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.”

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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.