But this post isn’t about how I secretly love PowerPoint (I don’t think I can quite go that far) or how to give a good presentation, or why PowerPoint slides with blue backgrounds should die — DIE — a slow and painful death. This post is about my new favorite use for PowerPoint:

(full res: pharmacy-sign)

When I was working on my dissertation, I learned that you can make pretty elaborate line drawings in PowerPoint and export them as PDFs. This creates a vector-based image file that can be enlarged or shrunk without loss in image quality. And it’s simple (at least on a Mac): select all the objects in the drawing, group as one object, copy, create a new document in Preview (this automatically pastes what’s on the clipboard), save.

I used this to make many of the diagrams and figures in my dissertation, and have continued to use it at work to make quick, high-quality vector-based images. So when my parents asked me last week to create a sketch from a photo of a building for a plaque engraving, I decided that rather than find a copy of Adobe Illustrator or installing Inkscape, I’d give that old nugget PowerPoint a try.

It required some creativity in adapting PowerPoint’s drawing tools, and I wouldn’t say PowerPoint is ideal for this purpose, but I’d say it worked pretty well!

Here is the original photo for reference:

You may have already heard the rumors floating around and they’re all true: 23andMe is having another sale — the whole thing for $99!

Edit: No discount codes are needed. There’s an instant discount of $400 off due to the Black Friday+ sale, which will go until Christmas Monday 11/29 or while supplies last. Head on over to the store, or read on for a bit more info.

Use discount code UA3XJH at checkout to get $400 off the regular price. (This code is only valid until Friday, 11/26.)

Even if you saw another discount code somewhere, make sure to use this one (and distribute this one to everyone you know!) because only then will I be able to prove that I have more and cooler friends. :)

Some things to note are that there are no longer different editions of the product and purchase now requires a 1 year subscription at $5/mo, billed monthly once you get your results back (or up-front if you’re buying it as a gift). At a total cost of $159 after one year, it’s still a rad deal!

Feel free to ask questions but I can’t guarantee I am allowed to answer all of them… if you are generally curious about the product though (like “Wow, what a great deal! But what the heck is this thing?”), I am happy to give you more info, or you can browse 23andMe’s website to learn more (FAQs, product descriptions, sign up for a free demo account, etc).

Now go take advantage of this deal and get a really cool gift for that genetics geek, genealogy buff, or general science nerd you know (especially if it’s you)!

At bioinformatics conferences, the common theme is computational methods, applied to a wide variety of topics. At a conference like ASHG, the common theme is human genetics, probed and interpreted with a variety of methods. But even the topic is breathtakingly broad. Sessions covered complex disease, non-coding RNAs, methylation, ethical/social/legal/education issues surrounding genomic research and genetic testing, mouse models, high-throughput sequencing, population and evolutionary genetics, pharmacogenetics, cilia, computational methods, and Mendelian disorders, to name just a few.

I made my first visit to ASHG this year as part of a small contingent from 23andMe*, a direct-to-consumer genomics company. Although I missed a good portion of the conference due to my schedule, some of my colleagues took notes on sessions that I missed, and ample coverage of many of the sessions could be had by following the Twitter hashtag #ashg2010. The following summaries and reflections represent a composite of tweets, other people’s notes, and my personal notes and impressions.

The meeting kicked off with several keynote talks on Tuesday evening. The two that got the most attention were Eric Lander’s retrospective on the fruits of the Human Genome Project (HGP) and a talk about the ENCODE project by John Stamatoyannopoulos. In Lander’s retrospective, he painted a picture of our knowledge of human genetics before, during, and after the HGP:

• 20 years ago, we knew about 70 loci for Mendelian diseases. Ten years ago, we knew about 1300. Today, we know almost 3000.
• 20 years ago, we knew one locus linked to common disease (HLA). Ten years ago, we knew about 25. Today, we know of about 1100 loci linked to about 165 common diseases and traits.
• 20 years ago, we knew 12 loci associated with cancer. Ten years ago, we knew about 80. Today, we know 240.

We also know now that every person carries about 150 genetic variants across 1% of genes, unique to his or her genome, that change the amino acid sequence of a protein. (Clearly they don’t all cause dramatic problems, but it’s very likely that some of them have an impact on our individual health.)

Photo by jwhitesmith

Lander discussed the rise and fall of GWAS — genome-wide association studies — which lost some of their cachet when it became clear that the vast majority of associations resulting from such studies were for genetic variants that had very small effects on phenotype. Taken together, these associations thus far explain a relatively small amount of the variance in common diseases and traits, spawning the criticism of “missing heritability”. Alternative theories sprung up like dandelions in a field planted with the seeds of discontent, copy number variations (CNVs) and rare variants among them.

But Lander was skeptical that rare variants will account for the missing heritability, saying that the heritability explained by common variants is still increasing as we include the long tail of small effects, and that it will be challenging ever to find all of the heritability for common, complex diseases. Even if genome-wide association methods manage to find all loci involved, if there are multiple ways to develop the disease, those loci may never explain more than that fraction of the heritability, unless we learn how to detect and quantify epistatic interactions between loci on a large scale.

Stamatoyannopolos followed Lander’s talk with an overview of the ENCODE project, which is tasked with building “a comprehensive parts list of the functional elements of the human genome.” He presented some interesting statistics regarding the distribution of GWAS hits throughout the genome: 47% are intronic, 7% are in coding regions, 2% are in promoter regions, 10% are within 50 kb of a gene, and the rest are farther away. The distribution suggests that much of the effect of common variants on disease is through regulatory pathways rather than changes to proteins. The UCSC Genome Browser now supports an ENCODE track that lets you explore this data.

The rest of the conference was a bit of a whirlwind given the ridiculous number of parallel sessions. Some were so popular (“Statistical Analysis of Human Sequence Variation”) that it was standing room only and security was running crowd control. Even though I couldn’t make it to most of the sessions, I was able to get a sense of what the popular themes were in a subset of the attendees through keyword analysis of the 1,500 or so tweets associated with the conference:

* includes word variations such as singulars or plurals

Clearly, sequencing — particularly exome sequencing and the 1000 Genomes project — disease risk, rare variants, gene expression, and genetic mutations were hot topics, at least among the Twitterati. GWAS was a relatively less popular topic, and Jim Evans was the unexpected dark horse.

This word cloud excludes some core Twitter usage, though: RTs (“retweets”) and mentions of specific Twitter users. If we include them in the mix, this is what we get:

More than 1/3 of the tweets (580/1548) associated with the conference were “retweets” or repeats of original tweets. And in almost half of cases, people were retweeting @dgmacarthur (218 RTs). @larry_parnell, @lukejostins, @Genetics_Blog, and @delahar followed not that closely behind (30-50 RTs each).

How did that compare to actual tweetput? Well, @dgmacarthur generated a lot, but not the most number of tweets. That honor went to @bullymom2 (105 tweets), followed by runner-up @bachinsky (97 tweets), while @dgmacarthur got the bronze (91 tweets). As for myself, I fell solidly in the middle with 29 tweets (if you truncate the distribution at a minimum of 10 tweets per person; there is, unsurprisingly, a long tail of minimal tweeters).

Tweets are obviously a biased sample but it’s a fun window into what at least some of the ASHG attendees were interested in. And if you went to the “tweetup” — a casual meetup of mostly Twitter-savvy conference-goers — you got to see a little further (and got to connect @ to face!). It’s also interesting to compare someone’s tweetput to how often they were retweeted, to get a crude estimate of Twitter “influence” or quality of tweets. @dgmacarthur likely had the highest RT/T score (and well-deserved); I think mine was closer to 1, which is probably respectable.

The only other part of the conference I’ll comment on was the industry exhibits. To my rookie eyes, they were ridiculous. Roche basically transplanted entire lab benches complete with equipment. Others, like Genzyme and Pacific BioSciences, had their own space-age lounges set up where you could essentially be fully surrounded by their trappings and wares. Amidst all of this, the booth set up by Expression Analysis was a welcome respite. In exchange for making your mark on a communal mural, they donated $70 on your behalf to a local health organization. The finished mural will be displayed at the recipient facility for the donations. Not only was it calming to flex some artistic muscle amidst the hustle and bustle of the exhibit hall, it felt good to contribute to a good cause.

For more accounts of the conference, see Luke Jostin’s series of posts (1, 2, 3, 4, and 5), Larry Parnell’s notes (1, 2, 3, and 4), and Stephen Turner’s notes from the 1000 Genomes tutorial session.

** The content and views expressed in this post are mine alone and do not represent the views of 23andMe.

2. Microwave until it triples in volume (it burns if you leave it in too long).

3. Before it cools, use a spoon to press and stretch the now-gooey marshmallow on the parchment paper. When cool enough to handle, use your fingers to stretch and fold the sticky marshmallow until stiff.

Voila! Taffy! Just don’t leave bowls lying around crusted in marshmallow remnants — apparently it doesn’t make mom too happy. ;)

I have a special place in my heart for beef stew (from fond childhood memories of Chinese beef noodle soup) but braised short ribs are threatening to knock beef stew from its pedestal. They’re actually not that different — both involve slowly simmering tough cuts of beef until they’re falling apart tender — but since the liquid used to braise short ribs isn’t meant to be consumed in large quantities, it means some pretty intense flavors can be incorporated. The time in the oven also blackens some of the exposed meat, giving it a caramelized, grilled texture.

My friend Eugene passed along a recipe for braised short ribs to me several years ago and I only just gave it a try today. It is decidedly Asian in influence, with sake, soy sauce, sesame oil and mirin making up the majority of the braising liquid.  Several months ago we made another recipe for braised short ribs that was closer to a traditional beef stew with the blend of aromatics, herbs, and red wine. Both were delicious but I think Eugene’s recipe wins out slightly because there’s really nothing that beats the combination of soy sauce, garlic, apple juice, and sesame oil (seriously, just read the ingredients for the braise and tell me you don’t want to drink it straight right then and there). But I can leave it up to you to decide for yourself.

Asian-style Braised Short Ribs (adapted from David Chang, according to the recipe)

1 1/2 cups pear or apple juice
1 cup sake
1 cup mirin
1 cup soy sauce
1 tablespoon sesame oil
1 1/2 cups water
1/2 cup sugar
2 tablespoons chopped garlic
10 cloves crushed garlic
Freshly ground black pepper

2 tablespoons neutral oil, like corn or grapeseed
4-5 lbs beef short ribs
Coarse salt
2 large onions, peeled and coarsely chopped
1 lb carrots, peeled and coarsely chopped
8-12 small or fingerling potatoes, trimmed
2 tablespoons butter
1/2 cup scallions, chopped

1. Season the ribs liberally with salt and pepper.

2. Preheat oven to 350 degrees. In a saucepan, combine juice, sake, mirin, sugar, soy sauce, both forms of garlic, sesame oil, 20 grinds of pepper, and water. Bring to a boil, then simmer until needed.

3. Put corn or grapeseed oil in a large ovenproof braising pan or skillet over medium-high heat and add the ribs, making sure not to crowd the pan. Brown well on one side. Turn over, add the onions and half of the carrots, and brown the other side, stirring the vegetables occasionally.

4. Carefully pour the braising liquid over the meat until submerged and bake, bone side up, for 3-4 hours or until meat falls from the bones. Remove from the oven and cool ribs in the liquid for about 1 hour, then strain the liquid.

5. Remove the meat from the bones and combine with the strained braising liquid in a pot. Bring to a boil and then simmer until the liquid is reduced.

6. About 1/2 an hour before serving, melt the butter in a skillet and add the potatoes and remaining carrots. Season with salt and pepper and cook, stirring occasionally, until browned and almost tender. Add to the meat and serve garnished with scallions.

French-style Braised Short Ribs (from Smitten Kitchen)

6 beef short ribs, 14-16 oz each
1 tablespoon plus 1 teaspoon thyme leaves, and 4 whole sprigs thyme
1 tablespoon freshly ground black pepper
3 dozen pearl onions
1/2 cup extra virgin olive oil
1 cup diced onion
1/3 cup diced carrot
1/3 cup diced celery
2 bay leaves
2 tablespoons balsamic vinegar
1 1/2 cups port
2 1/2 cups hearty red wine
6 cups beef or veal stock
4 sprigs flat leaf parsley

1. Season the short ribs well with 1 tablespoon thyme and the ground black pepper, cover, and refrigerate overnight. Allow to come to room temperature (about 1 hour) before cooking.

2. Season the short ribs generously with coarse salt about 30 minutes before cooking and preheat the oven to 325 degrees.

3. Heat a large Dutch oven or oven-proof skillet, add 3 tablespoons of olive oil, and continue heating until pan is almost smoking. Sear the short ribs until nicely browned on the three meaty sides. Remove to a plate to rest.

4. Turn the heat down to medium and add the onion, carrot, celery, thyme sprigs, and bay leaves. Cook until the vegetables just begin to caramelize, about 6-8 minutes. Add balsamic vinegar, port, and red wine, turn the heat up to high, and boil until liquid is reduced by half.

5. Add the beef or veal stock and bring to a boil. Arrange the ribs in the pot bone side up in a single layer. The stock mixture should almost cover the ribs. Tuck the parsley sprigs in and around the ribs and cover tightly with aluminum foil and a lid. Braise in the oven for about 3 hours.

6. Let the ribs rest 10 minutes in the liquid and then transfer to a baking sheet. Turn the oven up to 400 degrees and brown the ribs for 10-15 minutes in the oven. Meanwhile, strain the liquid into a saucepan, skim the fat off the top, and reduce the liquid slightly.

We served both types of ribs with a side of sauteed chard but the first one was served over rice and the second one was served over a potato puree with horseradish cream, but you can substitute whatever starch or vegetable you like.

Let that be a warning to those who could care less about cooking. :)

On Sunday I finally got to do something I’ve been trying to do ever since I moved out to the bay area: a wildflower hike. Every year, the hillsides erupt in a rainbow of color as the end of the rains and the warmth of the sun coax the wildflowers out of their seeds. Every year, I’ve missed it. The show only lasts a couple months before the dry season sets in and bakes the grass into rippling seas of gold that persist until the next winter. This year, I timed it right.

Ben and Lisa joined us at the top of Skyline at Russian Ridge Open Space Preserve, one of the bay area’s top wildflower spots. We parked away from the main lot to avoid the crowds and entered the preserve across from Coal Creek. An expansive view across the valley to the Pacific greeted us.

As promised, the meadows were bursting with California poppy, lupine, scarlet pimpernel, buttercups, Johnny jump-ups, fiddlenecks, birds-foot lotus, blue-eyed grass, Ithuriel’s spear, sweet pea, larkspur, phlox, redmaids, and checkerbloom, to name just a few! We took Hawk Trail north across the ridge line, descended down into the valley and back south via Ancient Oaks Trail. We cut back east towards Borel Hill to take in the view over the bay before heading back to the cars for a total hike of about 3.5 miles at a very leisurely pace. We got a bite to eat amid the droves of motorcyclists at the iconic Alice’s down the road before bidding farewell to Ben and Lisa and heading home to enjoy the warm evening on the back porch.

Weekends like these are why I love living in the bay area. :)

The costs, in principle, are minimal. You might need to register for an account at the journal website and be logged on, but then all that’s needed is little more than what most of us already do multiple times a day with our email — type into a box and click “submit”. (In practice, there may be nonsensical, hidden costs that make you wonder what the folks at those journals were smoking.) So the perception that the cost-benefit equation doesn’t work speaks more to the lack of benefit than anything else.

Photo by jamesclay on flickr

This doesn’t mean that no one comments on scientific articles. They just don’t do it online. Instead, they might spend months slogging through a convoluted review process similar to that for full-fledged papers so that their comments are published and citable in a “traditional” form (granted, some of these “comments” are barely indistinguishable from full-fledged papers). Never mind that by the time the comment is published, the discussion may no longer be relevant. Never mind that only a narrow slice of the possible spectrum of comments is represented.

People prefer this type of commenting to the relative ease and immediacy of online commenting, and it isn’t because of any real utility. Traditionally published comments are widely accepted as contributions to the scientific record, and so might be considered part of someone’s academic record as well. That little distinction is the only reason I can fathom people suffering through even a shadow of what this individual suffered through. The perceived benefit is high enough to offset what is arguably a very high cost.

And that benefit is conspicuously absent from online commenting.

Photo by the-majestic-fool on flickr

Does that have to be the case? No, not necessarily. But that’s how it is right now, and it will remain that way as long as hiring committees, tenure committees and funding agencies rely on traditional measures of academic success and contribution. We could ask courageous, aspiring researchers to embrace online commenting merely on principle, for “openness” and “betterment of science”, but, frankly, they shouldn’t have to.

Naturally, the discussion at the PLoS Forum centered around how to make online commenting more attractive, with the assumption being that providing incentives would shift the cost-benefit equation. But the main incentive suggested — a “karma” type system reminiscent of StackOverflow — still begs the question, “who cares?” Scientists aren’t going to comment simply because they get imaginary points for it — the points would have to translate to real-world recognition.

With all of this in mind, I was struck by the description of PLoS Currents, a new offering from PLoS that is part journal, part blog. The idea is to provide a venue for “fast-breaking” research that simply can’t be delayed by the traditional peer review process. Articles are composed in Google Knol with a blog editor-style interface; after light review by an expert moderator (with typically around 24 hours turnaround time), the articles are posted on the PLoS Currents website. The finished articles are barely distinguishable from articles that might appear in a peer-reviewed journal, with familiar document structure and detailed figures and tables. And, importantly, the articles are indexed on PubMed — making them archived and citable. The costs, clearly, are lower than traditional commenting, but the benefits are arguably similar.

Photo by ubermoogle on flickr

Is this the transitional form that will successfully bring science towards more flexible modes of publishing and professional advancement? I don’t know, but I like the idea. PLoS Currents might just satisfy the ingrained compulsion to make distinct, cohesive contributions to the scientific record but has none of the arbitrariness and convolution of commenting through lengthy peer review.

Only time (and perhaps some proactive efforts from PLoS) will tell. They’ve only launched one Current so far — Influenza, spurred by the H1N1 flu crisis — but it’s not hard to see how the concept could be extended to other topic areas. PLoS has also been fairly reserved in its advertising of Currents given its experimental nature, but I’d love to see what happens when they throw more weight behind it. Maybe, just maybe, it will be contender.

I visited my friend Mark at IBM Research in Almaden for the first time and was blown away by how beautiful the campus is. It’s located in the middle of a park in the south bay foothills and after weeks of rain the hills were a glittering vibrant green. I sat in on a talk by Stephen Turner, founder and CTO of Pacific Biosciences. PacBio is doing some really amazing stuff, harnessing the natural efficiency and speed of DNA polymerase enzymes to do single molecule real-time sequencing. The highlight of the talk for me was seeing how their technology can detect methylated DNA. The possibility of exploring epigenetics in that much detail and on that scale simply boggles the mind.

Last weekend, as those following my Twitter feed might have noticed, I was hosting several friends from college. We spent a day walking around San Francisco — starting out with a sampler of beer ice cream at Humphry Slocombe as part of SF Beer Week, then heading over to Chinatown, strolling along the Embarcadero, hiking up the stairs to Coit Tower, drinks at Boudin’s sourdough factory and dinner in North Beach before ending the night at DNA Lounge for a “Valentine’s” themed Smash-Up Derby by the always flamboyant Bootie SF. The next day we took a leisurely drive along Skyline to Castle Rock State Park, one of my favorite hiking spots in the Bay Area. We celebrated Chinese New Year by making pork buns, sesame noodles, and Chinese spinach for dinner.

At some point in the last three months, a paper I submitted in July last year finally got accepted and all the final revisions and proofchecking and what-have-you is finally done. The real version should be coming out soon but here is the provisional version.

But I’m perhaps most excited by some new additions to the family. No, not that kind of new addition — we got two cats! There’s a great no-kill shelter in my town and if you’re in the Bay Area and thinking of adopting, definitely check out Nine Lives Foundation. We got an adorable little girl tabby/tortoiseshell and a goofy all-white boy who both love cuddling and purr like little motors. :)

We named the girl “Beaker” (because she often “meeps” like Beaker from the Muppets) and the boy Storm Shadow (after the white ninja).