Success and Not Success

I typically have grand plans for completing important tasks on most weekends, just as typically fail to achieve any of them. But this weekend, because Rachel was gone all day at the NATS conference (and I therefore had free reign with the car), I decided I actually had to get things done. The two main things on my agenda: get the balcony garden going, and finally get my bike ridable again. 

The Success

Fuchsia!

The balcony garden was pretty straightforward. We had bought a fuchsia in a hanging basket several week, but the basket was plastic and flimsy and it's been just sitting on the ground of the balcony since we brought it home. First order of business was getting a nice hanging basket, and get some eye-hooks from which to hang it. 

While I was at it, I got a couple of smaller baskets - not quite sure what I was planning to do with them, but thought the extra capacity would be worthwhile. I also noticed some similar horse-trough baskets, and got a couple of those. Add to that a few cubic feet of potting soil and I was ready to go. 

What do you think I should plan in these?

I've never used these coconut-shell liners, but they seem like a pretty wonderful invention. They've got a thick enough weave to hold in the soil, and they even hold some amount of water, but let the excess drain through. The advertising claims that they'll release water back into the dirt to keep the roots wet longer, but I have no idea if that's true. In any case, they look nicer (and cost less) than a lot of other alternatives, so I'm pretty happy with them. 

Eventually, the troughs will hold a few different types of herbs - I'm wading cautiously into this balcony gardening project and trying not to be overly ambitious. My first purchase was a few different varieties of mint - banana mint, apple mint, orange mint and Kentucky Colonel mint (I'm currently working on a post for Food Matters about the science behind all the different types of mint - stay tuned for that).

All kinds o' mint

Because these great-smelling bastards can quickly out-grow a lot of other plants, I decided to give them their own basket. 

All in all, this went pretty well. I spent about $100, got to get my hands in the dirt and made the front of our building look just a little bit nicer. And we'll have fresh mint (and soon a variety of other herbs) whenever we want. Excellent!

The Not Success

The bike repair was a different story. I've been struggling with this for months now. It all started with a blown tube back in March. All in all, not really a big deal, but as my thesis was due in a couple weeks, it felt much more monumental than it was - I didn't have a patch kit and had to walk several miles home - my commute that should have taken 30 minutes ended up being about 90. The first time it blew, it took me about a week to finally get new tube put in - in the mean time I was riding the bus. Then, the very next day, I had another blow-out in almost the exact same part of my commute - AAARGH!!

Long-story short, over the following several months, I didn't do any riding. I started the new job and started to dress a little nicer, and still didn't have good cycling clothes. Once I solved that problem, I tried to ride in to work and the patch I had used to solve the last flat blew. Then the weather was bad for a while. And then finally, a couple weeks ago, I decided it was finally time to get back on the saddle (so to speak). I cleaned off the grime from the winter, then noticed my chain was messed up... wait a couple days. Got a new chain, installed it, noticed my back wheel was hopelessly wobbly... wait a few days. Tried to take it into the shop, but it closed 5 minutes before i got there...

New stand - this will make my
life muuuch easier

Finally, today, I got to the bike shop with the wheel, and Wheel Works in Cambridge managed to get it repaired in like 20 min (turns out one of the spokes was busted). I also bought a bike-repair book (better than relying on youtube videos I thought), and wanted to get a bike-stand to facilitate repairs. They didn't have the model I wanted, but the Belmont store did, so I drove over there, only realizing once I arrived that I'd left the book back in Cambridge. So I drove back, got the book, and was finally ready to get my bike ridable for the first time in months. 

...I got the back wheel installed. Then I set about putting a fresh tube into the front wheel to replace the one with the blown patch. Then I put the front wheel back in the frame and noticed that it was catching a bit on the break - did this wheel need to be trued too? I thought I'd checked that. 

Upon closer inspection, I found the culprit - there's a hole in my tire! A part of the tube was bulging out and rubbing against the break pad ever so slightly. And this is almost certainly the cause of my two blow-outs, and the reason the patch didn't hold. Ugh. So I still can't bike-commute tomorrow. But I plan on getting a new tire or repairing this one before the end of the week. I need to start riding again. 

Just one more thing... I hope. 

GMO bananas and other topics with Pamela Ronald - Audiommunity Episode 6

[Repost of Food Matters post at SciAm, originally published June 5th, 2014]

Bananas are delicious. Personally, my favorite consumption methods are in oatmeal or cereal, in smoothies, or just on their own (for the record, I peel them the right way, not from the stem like some savage). But bananas aren't just some tasty delicacy, they're actually a staple crop for millions of people, just behind wheat, rice and corn in terms of importance. Which is why a banana-decimating pathogen has the potential to negatively impact millions of people in East Africa.

So what if you could cross one plant that normally resists the infection with the bananas that these farmers grow? That would be awesome right? Unfortunately, there aren't any banana varieties that are resistant, they all succumb to infection. But luckily, rice plants do have a resistance gene, and we know what it is. And it turns out, if you put that gene into bananas, they are completely resistant to infection by this banana wilt bacterium.

A few months ago, some colleagues and I started Audiommunity, a podcast about the immune system. Our goal for the podcast and for the website we're building around it, is to generate an educational resource for people at all levels of education to learn about the immune system, including current, cutting edge research. For the most recent episode, I had the pleasure of interviewing my co-blogger Pamela Ronald, the scientist who first discovered that rice resistance gene (called Xa 21) over 20 years ago, and is now working on making those awesome GMO bananas that could save millions of lives. 

On the left, a Xanthamonas-infected banana plant. On
the right, an infected plant expressing Xa21.

We know Pam as a great educator when it comes to issues of crop genetics and sustainable agriculture, but it turns out that she's also an expert on plant immunity. On the podcast, we talk about how she got interested in science, what motivated her to start studying plant immunity, and some of her lab's recent work on genetically engineering banana plants to express the Xa21 resistance gene. Check it out on emmunity.org, or find "Audiommunity" on itunes.

Adobe Illustrator for Scientists

Scientists have a number of jobs other than just doing experiments. Of those other jobs, one the most important is communicating the results of those experiments. From publishing papers to giving scientific talks, to writing grants, data has to be shown visually, preferably in a pleasing manner. As I like to say - all of your research is worthless unless you tell someone about it (and they listen).

In order to do this communicating, every scientist that I'm aware of at some point has had to approach Adobe Illustrator (or related vector-image software), which is a rat's nest of options and tools, many of which are incredibly useful, but most of which are complicated and not easy to surface. Most of my colleagues end up finding the 3 or 4 basic tools that fulfill the bare minimum of requirements for putting together a figure and leave it at that. 

This instinct is easy to understand - Illustrator is complicated, and scientists have a lot of demands on their time. It feels like a waste of that time to watch youtube tutorials that show you how to draw a strawberry* when you've got experiments to run. I've watched probably 30 hours of tutorial videos like that one, and it's incredibly frustrating since it feels like you have to watch an hour to extract 5 minutes of useful tools, but you have no idea even what those useful tools are until you seem them used.

That said, despite all of that time "wasted," being comfortable in Illustrator probably saved me hundreds of hours over the course of writing my paper and my dissertation, since making figures, displaying data, and even making cartoons for presentations has become faster and easier (not to mention better looking). A peer reviewer for a review article I wrote recently specifically praised the quality of the figures. 

Because I don't want other scientists to suffer through irrelevant tutorial videos like I did, about 6 months ago, I made a set of tutorial videos that explains how to use illustrator that's specifically targeted at scientists. The whole series is about an hour, and encompasses the most useful and time saving tools that I've found. I thought I'd throw them up here to make them a bit more discoverable - hope you find them useful. And if you run into any issues or have any questions, please don't hesitate to ask!

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*I should point out that that strawberry tutorial was the first one I watched, and actually gave me a great foundation for getting to understand the software. 

Neutrophils and Carnivals - Episode 5 of audiommunity

Electron microscopy of NETs

This podcast is just getting awesomer and awesomer. On the latest episode of audiommunity, we're talking about when neutrophils spew their genomes all over bacteria (NETs), Kate insults people who work at carnivals, and we managed to keep it under an hour.

Only episode 5, and we're already pros :-)

New Dawn, New Day, New Life

... and I'm feeling good.

Transitions are hard, but in the end, well worth it. My life has changed radically in the past month - I got a Ph.D. and turned 30 years old in April, and started two new jobs in May, both of which are fairly radical departures from anything I've done before. The rest of 2014 is no less momentous - I published a paper inCell in February, and started a podcast in March. I'm going to have two reviews I wrote come out later in the year (one in Annual Reviews Immunology), not to mention the fact that I'm getting married in November.

To be honest, it's a bit overwhelming, but I'm feeling good, and ready to start several new chapters. Not least of which is revamping my online presence. This blog is the first part of that. I'll keep my scientific american blog for the strictly science-related stuff, this space will be more for personal reflections, including, but not limited to:

• My attempts to learn programming (mostly Python and Julia for my research)
• The way(s) that I organize my digital life (most biologists including me are terrible at this... I'm getting a bit better)
• Adventures in photography and graphic design
• Any other personal crap that I manage to take the time to write about

I suspect this blog will be entirely for myself, but hopefully some of it will be of some use to someone at some point. In any case, I'm ready for the next steps.