12 March 2014

Failure, storytelling, and science.

It's been quiet around here at Princess Tradescantia lately, but I'm excited to report back with a few of my recent adventures!

In January I had an opportunity to participate in a storytelling event co-sponsored by some fantastic folks: The Monti, UNC's Morehead Planetarium, and Scientists with Stories (SwS). The event was called #ScienceFail, and each storyteller shared an experience regarding failure and our careers in science. If you're so inclined, watch this video to learn a bit more about the event and SwS's associated research.

The story I told was from my graduate career; I wrote a bit about it a few years back (I bleed for my thesis: Part I).  I met with Jeff Polish from The Monti several times to craft the details of the narrative, and found the process to be both amusing and intense. The quick version of the story is that I wrecked my truck while doing fieldwork. A longer version of the story can be heard below. The longest version of the story is one I'm still developing, as the repercussions of the events I describe still affect how I pursue my career and think about science. I could write numerous posts about how stories and science reciprocally inform each other, and I'm very grateful to have been afforded the opportunity to participate.

You can also head over to the SoundCloud page to hear the rest of the stories told that night.


12 December 2013

Knitting and Science: Molecules!

I thought it was time to take another look at geeky knitting, this time moving away from organisms and more towards molecular biology.

Chromosome hat, Ravelry project,  pattern


I think this hat would be awesome with the chromosomes knit in different colors to mimic the look of chromosome painting (fluorescent in situ hybridization). Ideally, the hat would be black, the chromosomes in blue (DAPI staining), and small dots of green/red/etc embroidered on later…








Genome socks, Ravelry project






The pattern for these socks is actually called "Genome," given the lovely cable twining up the front. I spun the yarn, too, from some lovely wool hand dyed with organic dyes (I'll be talking a  bit more about spinning and dyeing before long!).


DNA scarf,  Ravelry project,  pattern







Finally, a slightly less stylized cable interpretation of a DNA helix, this time in scarf form. There are some really beautiful projects from this same pattern that include color-coding of base pairs.
Other posts in the Knitting and Science series: 

27 November 2013

Knitting and Science: It's a knitbot, but I'm so confused!

An article about a "knitting machine powered by tweets" came across my newsfeed this morning. "How cute!" I thought. "A knitbot! Knitting, technology, and tweeting? This is relevant to my interests!"

So I clicked through the link, and down the rabbit hole I went. It's a knitting machine cranking out Christmas-themed sweaters. Sweater-knitting goodness happens when someone tweets a particular hashtag, and it's sponsored by…BUDWEISER? Seems the hashtag in question is #jumpers4des, and the goal is to remind folks to have a designated driver over the holiday season.

So the message is as follows: promote designated drivers this holiday season by tweeting and making this robot knit a sweater! I'm a proponent of intersectionality among issues near and dear to my heart, but this seemed to be a rather obfuscated message. Perhaps if knitters were more likely to drink and drive, the logical leaps might make a bit more sense?

Once I accepted the knitbot as a somewhat ill-suited marketing ploy, I let myself wallow in the glory that is this steampunk inspired knitting machine. Check out those oversized gears! The modern flat-screen monitor embedded in a frame of copper tubing! OK, perhaps it is kind of clever.




Other posts in the Knitting and Science series: 

25 November 2013

Knitting and Science: Plants!

There's a long tradition of incorporating botanical designs into knitting, including many lace patterns inspired by and named after flowers/gardens, and entire books of patterns for creating flowers. Like all other knitted objects, these range from abstractly inspired by plants to fairly realistic representations.

Flower bouquet, Ravelry project




Let's start with the most realistic flowers: in this case, calla lilies and some campanula-style bellflowers. I strove for ease in knitting and aesthetic appeal more than botanical realism, hence the calla lily's paltry spadix and the incredibly droopy, non-differentiated sex organs in the bellflower.





Elodea socks, Ravelry project
Then there are patterns which are inspired by plants. They may or may not actually resemble said plant, but I'm a sucker for inclusion of scientific names into knitting patterns.








Lace stockings with flower motif; Ravelry project






There are plant motifs which occur in lace knitting, often featuring leaves or flowers.  
My Little Flower, Ravelry project



Finally, it's not surprising there are knitters that have contrived disgustingly cute little anthropomorphic flower-people as toys for kids.
I'm looking forward to sharing other plant-related fiber art posts with you soon, including plant-derived yarns and fiber dyes made from native plants!

Other posts in the Knitting and Science series: 


21 November 2013

Knitting and Science: Animals!

Last year, I posted a picture of the giant squid I knitted for Deep Sea News. As a long-time knitter, I have lots of other projects related to science--both directly and tangentially--which I thought might be fun to showcase to a broader community. I thought I'd start with a category of projects which is both related to the squid: animal projects.

I've included a few links in the caption for each project: Ravelry is an awesome resource for fiber folks, and I've included the page on my own profile where each project is described. You can also find the Ravelry pattern page linked from there. The second link (when available) for each project is to the website where the pattern is available. Most of these patterns are freely available online.

Some of these projects aren't that unusual, as many folks like to knit animal toys and whatnot for kids:

Elephant, Ravelry project, pattern
Kitty cat,  Ravelry project, pattern 





Instead of knitting 3-D shapes, you can also make interesting animal patterns out of textured stitches, like this owl pattern made from cables:







Dolphin puppet, Ravelry project,
pattern improvised (crochet, not knitting!)


Finally, there are projects relating to animals that I've made for cosplay: the dolphin puppet was part of my costume for Pam Poovey from Archer...








Anatomical heart, 
Ravelry project
,  pattern

...and the heart was for Daenerys Targaryen from Game of Thrones. Knitting, science, AND sci-fi/fantasy? Doesn't get much better than that!



Coming up next in this series: plants, molecules, different types of yarn, and more!



08 November 2013

Rich with science.

During my graduate studies, I shared the lab with a Chinese postdoc who was an expert at fluorescent in vitro hybridization (FISH). He spent hours at the lab bench and in front of the microscope, attempting to capture the perfect images of chromosomes with important portions of the genome highlighted in glowing dyes (you can see some of his beautiful pictures here). On productive days, he would report back to our advisor by saying "I am rich with chromosomes!" 

I wasn't alone in thinking that an odd turn of phrase, but it seemed such a beautiful way to think about science. Materials which allow accumulation of data and results are indeed worthy of excitement. Lately, as I traverse the boggy grounds of job applications, I find myself sinking down into uncertainty and dissatisfaction as my own scientific bean counting fails to match up to my peers: not enough papers, not enough grants, not enough "deliverables" to show my scientific prowess. 

Occasionally, I just take a deep breath, step back, and think about my favorite parts of my personal scientific process: kicking around wacky ideas about "big picture" science, thinking up ways to tackle interesting research questions, outlining papers before buckling down to write. Those times are my happiest at work, when I feel like I make real progress. 

In reality, I am very lucky and very intellectually "wealthy." I am rich with data. I am rich with ideas. I am rich in the currency of science that is most satisfying to me.

01 November 2013

A scary specter of scientific research: When your paper has an error.

This week at work, I encountered something far more terrifying than the costumed ghouls wandering my neighborhood last night for Halloween.

My paper on transposable elements in Asparagales just came out in Genome as a part of a special issue on Genome Size Evolution. Apart from being the first bit of research from what is the main part of my research career these days, it's also the first manuscript on which I'm first author. Even scarier…I'm the only author. Suffice it to say that there is no one to blame but myself for any and all errors which occur in this piece of research and writing. Of course, just after the paper came out in print, I found some problems.

Let me preface this attempt at a self-effacing apology by saying that the NESCent journal club just read and discussed a few real humdingers of articles last week: first, the now-classic paper "Why Most Published Research Findings are False," and second, a recent article from The Economist describing the alarming inefficiency of science (more accurately, the scientific community) at self-correcting errors or misinterpretations. The two articles cited above strike fear into my scientific heart because they indicate our implemented standards for scientific research don't match our expectations as professionals.

This admonition brings me to my own sad confession: there are two problems with my paper that, while not deal breakers for any of my results or conclusions, are bothersome and irritating issues that may cause headaches for other researchers down the line. A good portion of my graduate training was spent reconciling with myself the knowledge that I would eventually be publishing research that was imperfect. It rankles me that those imperfections are going to persist beyond "lack of data" or "insufficient sampling," and perhaps affect priorities near and dear to my heart, like reproducibility and transferability to other systems.

The first issue involved me overlooking a small change while revising the manuscript. The genome size data in Table 1 is actually Mb/1C, instead of pg/1C. Oh, the humanity! Granted, the correction was made in Figure 2, and the error is obvious if you have any frame of reference about genome sizes in plants, but still…I'm quite irked at myself. The second issue is something for which I couldn't have anticipated an problem. The software I used for genome assembly, MSR-CA, has been modified and re-released since I sent back the proofs for the article. My paper includes the website from which I obtained the program, but that website is no longer functional. Moreover, the program name has changed (MaSuRCA), so trying to reproduce my methods would be a bit difficult. However, the paper describing the software is now available, so this will hopefully be less of an issue as I continue to publish.

I understand that these issues like these happen far too commonly in scientific publishing. I've read papers with legends for figures mixed up, obvious typos, and figures where you can't tell if the dot was a data point or printing error. I suppose I feel these errors in my own work more keenly because I am so early in my career. I have more at stake regarding their success, and I'm more invested in their survival and propagation through scientific literature. Are these worth contacting the journal to issue a correction? I'm not sure. It makes me feel a bit better, though, that in the meantime, this post might get picked up by someone trying to figure out what the hell I was talking about with that "MSR-CA" stuff...