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: 

Animals

Plants

Knitbot

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: 

Animals

Plants

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: 

Animals

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 

Who? hat, 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!

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.

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...

Dreary weather getting you down? Have a picture of a rose.

You're welcome.

Journal club as training for reviewing papers.

The last two posts I've written were basically leading up to this set of musings about how journal club has helped me become a better reviewer of manuscripts. Peer review is one of the most lauded aspects of science, described as the foundation of academic integrity and part of a check-and-balance system of the scientific process. However, I find this particular task of academic life to be problematic, mostly because of the mysterious nature of the process. Moreover, most academics would agree there is a great deal of subjectivity in whether manuscripts are acceptable for publication. How much do these standards vary by scientific discipline (or subdiscipline, or model organism)? What is dealbreaker for a manuscript that is a red flag to keep it from being published?  Does anonymity factor into how we criticize papers?

Part of my impetus for thinking about this topic is a desire to be more effective at reviewing papers, which will hopefully allow me to write better papers myself. Some of these topics have been discussed at length elsewhere, but I'm interested in integrating existing obligations in my weekly schedule to this realm of professional development. I argue here that participating in journal club allows us to attune to how others evaluate manuscripts. Here are a few things I've noticed from attending various journal clubs and reading groups.

1. Some people tend to like most papers, while other people tend to dislike all papers. This goes beyond the ability to critically analyze the content of their papers. Recently during a discussion, a few senior scientists actually related their method of reading papers in exactly those terms. The take home lesson on this point is that the general tone with which someone discusses your manuscript sometimes has little relation to scientific merit of the work, but rather, simply reflects how that person views scientific inquiry.
2. There are vastly different standards for how much information to include in a manuscript. This is especially true when there is an enormous amount of information in supplementary material. Judicious use of methods summary and proper citations can make a huge difference in the reader being overwhelmed by uncertainty or accepting that the facts stated are adequate. These standards also vary substantially by subdiscipline.
3. There is a bimodal distribution of acceptance for ambiguous or unknown statements. Some readers prefer to have caveats, study limitations, and generalized discussion of impacts explicitly stated outright, while others will always view such claims as a liability to the study. 
4. Communicating results from new technologies in scientific manuscripts is a moving target. I know the most about genome sequencing technologies, which are one of the fastest-growing methods in biological sciences. Clear elucidation of the limitations and benefits of these technologies in the manuscript text is essential to reconcile misconceptions other scientists may have about these methods.

Of course, there are a few other ways we receive explicit feedback which helps normalize our standards for peer review. As authors, we receive feedback on manuscripts we've written and submitted. As reviewers, editors may forward the final decision and thoughts from other reviewers of the same manuscript. As editors, we see a wide breadth of submitted articles and have the best idea of publication standards. The problem with each of these viewpoints is that they are highly sample-size dependent. As an early-career scientist, I would be hard-pressed to have a decent representation of solid paper reviews from my own publications. Even as an editor, I imagine it would be easy to fall into a myopic view of science based on the standards of a single journal. Discussion groups with peer scientists, especially from a variety of career stages and subdisciplines, can be one of the best ways to stay abreast of fluctuating standards for scientific inquiry.

How to think about research much different from your own.

As a follow up to my post last week about the value in learning about a breadth of topics, I thought it apropos to briefly describe some of the most profound ways in which my scientific thinking has been altered because of talking about disparate research.

Here's a bit of context. I was trained as an undergrad in molecular systematics of plants. I knew a lot about plant evolution and a little about molecular genetics. What did I learn when I started grad school and had to attend seminars about cellular pathways in mice, or behavior in insects? Here are a few examples.

1. Researchers trained in particular fields approach the narratives of science from different perspectives. The way we ask scientific questions, design experiments, and convey our results differs widely depending on the biological scale and phenomena we're addressing. For example, my tendency towards thinking about organismal evolution is strikingly different from a reductionist view of molecular developmental pathways. These ways of thinking are not mutually exclusive, but sometimes it seems we get stuck in thinking about science the same way. One of my current officemates was trained as a physicist, which results in some pretty eye-opening revelations about biological complexity and uncertainty.
2. You can do really cool science by applying methods from one theoretical background to a novel question from another field. There are some obvious examples of the success of these mash-ups. The modern synthesis, evolutionary development, and systems biology are all examples of uniting previously disparate fields of research. My personal favorite is the application of ecological principles to genomics (some examples are here, here and here).
3. Cross-talk assists in uniting themes in biology that are exclusive of model system. A great example of this point comes from journal club last week. Metagenomic methods borrow largely from those developed by ecologists to evaluate how diversity and abundance of organisms differs between ecosystems. It's pretty obvious to ecologists who work on macro-organisms that the average size of species can factor heavily into their influence on an ecosystem. The same argument can apply for microbes that differ widely in average size, yet biomass is rarely considered in microbial studies. Talking about vastly different study systems helps remove model-system specific bias.

Of course, those are just a few of my favorite vignettes to validate the time I spend thinking about research that isn't directly related to my own. Dare I also say that such thought experiments are also simply fun? Basically, I refuse to let myself be impatient about attending seminars or meeting with visiting scientists if their work is very different from my own. I had a great one-on-one meeting with Darwin historian Alistair Sponsel  a few weeks back when he visited NESCent. We only spoke for half an hour, but the time was constructively spent talking about visualization of different types of data as conveyed across a time scale: certainly important insight for both historians and biologists.

My last point is that understanding a breadth of research helps make your own research deliverables more appealing to a broader audience. Some practical applications are obvious: how to communicate in a seminar to a broad audience, how to convince a panel of experts your grant is worth funding. I'll continue this thought in a few days, focusing on one particular part of our job: peer review.

Journal club and breadth of research

As someone interested in research synthesis, it's not surprising I have an appreciation for a wide breadth of biological investigations. My PhD training was in a biology department which spanned the gamut of research, from neuroscience to cell/molecular to ecology/evolution. As a result, the peers with whom I interacted often possessed research which was only distantly related to my interests in plant evolution. Fellow graduate students working on mouse stem cells, molecular pathways in fungus, and katydid behavior offered some of the best insights into formation of my dissertation questions and analysis.

The result of this training is acceptance that I will often be drawn into discussions about science which does not include direct application to my personal expertise. Rather than bemoan the time "wasted" by these "distractions," I instead use them as a way to improve the overall efficacy of my scientific thinking.

Take, for example, this selection of articles, each of which was discussed at NESCent's journal club sometime during the last few months (our journal club basically invites all NESCent scientists to read a journal article prior to an hour-long meeting where we talk through the paper).

1. Dung Beetles Use the Milky Way for Orientation
2. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
3. Is there Room for Punctuated Equilibrium in Macroevolution?
4. Genomic Evolution and Transmission of Helicobacter pylori in two South African families
5. The Tragedy of the Commons

NESCentians are all evolutionary biologists, but that's where the generalities end. That sampling of articles also handily describes the variation in research from participating scientists. Molecular to organismal, animals to bacteria, theory and empiricism. While most of the papers are current (2013), the fifth article is from 1968. The really beautiful part is that some articles don't even mention evolution at all! 

Somehow, we still manage to find plenty of things to discuss (sometimes rather heatedly). This model for journal club does well to expand our brains and promote novel research questions by taking advantage of the variety of expertise here at NESCent. There's generally one person in attendance who knows something about the model system or experimental approach, who then answers basic questions about the whys and hows of the methodology. The goal is for us to not understand every nuanced detail of the paper's analysis, but to focus on the parts in which we're interested. 

The moral of the story: it's not necessary to have a super-specific focus for a discussion group to still have meaningful and interesting discourse. The particular benefits gleaned from these interactions, however, will have to wait for another post.

On science writing: Gender

An interesting little tool popped up in my newsfeed the other day which only served to fuel my preoccupation with writing style and clarity. Gender Guesser is a system which estimates the gender of a writer based on a submission of at least 300 words of text. The estimation is based on word frequencies and parts of speech. I won't talk more about the specifics of the algorithm, except to say that the original research doesn't seem to include any discussion of science writing in particular.

Being a somewhat obsessive data collector, I proceeded to submit a broad selection of my own writing to the online interface. An example of my results appears below (this result is actually from the same blog post I wrote about revising last week).

I'm not really surprised that nearly all of my writing estimates that I'm a male, often with very high (i.e., >90%) confidence for both informal and formal writing. I tested ~20 writing samples with appropriate word lengths, including posts from this blog, personal writing, and even excerpts from my last publication, for which I am sole author. At best, I am only scored as weakly female (the semantics of which are another issue altogether). The only exception is a blog post from over four years ago. 

What are the implications? The authors of the web interface for Gender Guesser note that females writing in fields which are dominated by males (of which I believe biology qualifies) will tend to score as male. Have I been trained to write in a more masculine manner? Moreover, do I really care if my writing possesses masculine characteristics? Perhaps a more important component to this discussion is what style of writing is more appealing to a wide breadth of readers, or whether readers purposely or subconsciously discern the gender of a writer from an anonymous sample. 

On science writing: The reader's perspective

I have a good excuse for this most recent unplanned, unannounced blog break. During the month of September, I attended a writing workshop from George Gopen (Writing from the Reader's Perspective) and discovered that I still have much to learn about the process of writing. A brief overview of Gopen's premise can be found in a succinct article from American Scientist, but here are a few interesting points I noted:

1. Contemporary teaching for improving writing is often focused on the unimportant parts of communication and narration.
2. Preoccupation with good grammar and punctuation hides more effective ways to improve writing and enforces inequality.
3. First person can be useful in scientific writing but is often imprecise ("We" didn't all hold hands and perform PCR) and can sound ridiculous.
4. Passive voice is perfectly fine when used in the appropriate context.
5. Just because something "sounds" good doesn't mean readers will be able to appropriately interpret your meaning (I'm especially bad about this; I read things aloud to determine clarity).

As per Gopen's recommendations at the end of the course, I selected an old blog post and checked the writing sample for several of his identified "reader expectations" (explained in the article mentioned above). My biggest problem is misplacement of old and new information, which is a very common problem among science writers.

Knowing one or more errors may be lurking in my writing has danced on the periphery of my perception for weeks, stifling my urges to put pen to paper and making me acutely aware of my failings as a professional. While this assessment may seem a bit melodramatic, I am in the midst of sending off applications for jobs, and the requisite cover letters, research statements, and teaching philosophies I've been including now appear to be suboptimal. I've begun the tedious process of revising these documents. While perfect application of my newly learned skills is impossible, I'm hoping for marked improvement...or at least the ability to write without hearing Gopen's voice chastising me.

Monocots at Monocots!

I couldn't very well travel to the 5th International Conference on Comparative Biology of Monocotyledons and not post pictures of monocots, could I? I figured most of the other conference attendees would be covering the New York Botanical Gardens, so I took the opportunity to document monocots in the gardens at The Cloisters, a portion of the Metropolitan Museum of Art.






The Cloisters' gardens feature a variety of plants relevant to the medieval theme of the annex, including a wide range of plants used for food and medicine. Not a lot was blooming at the time of my visit, but I managed to snag a few shots of particular plants of interest. Shown here: Paris (above), Hemerocallis (right), and Allium (bottom).

I appreciated the museum's transparency in which plants were poisonous (something often overlooked by horticulturists), as well as notes in some portions of the garden about which plants were new additions and how the particular cultivars grew best.

I am a data vulture.

Heather Piwowar was one of the iEvoBio keynote speakers last week. I tweeted directly after her talk that she'd lit a fire under my ass to start advocating for open access/science/data, so immediately started my own ImpactStory profile and began meticulously analyzing my professional life.

I've long been sold on open science, and have gradually implemented practices to bring my daily professional life in line with that philosophy. In her talk, Heather spent time discussing issues hindering open science. Most of these were familiar arguments, such as current or future research being "scooped" by data being publicly available. Sometimes I'm personally hindered by technology, time, preferences of collaborators, or even just my own ignorance. I acknowledge, however, that my research here at NESCent is dependent on open access to data and analytical tools, and am hoping to continue this type of research for the rest of my career.

Starting at slide 98, Heather began relating some of the more visceral reactions to scientists opposed to providing open access to their data. I was a bit shocked at the rhetoric surrounding their claims: fear of "armchair ecologists" and "data vultures" reaping the benefit of analyzing data without having to set foot in the field.

I sat back in surprise at the realization that I am a data vulture. I literally feed my research on the carrion of discarded genomic sequencing projects, digging through the trash of the repetitive genomic fraction. I've always liked the mental image of digging through genomic junk. I use pictures of Oscar the Grouch or photos of myself digging through trash cans (right) in my professional presentations. Suddenly, though, those cute metaphors were starting to seem like a betrayal of "real" science.

Heather related the words of another respondent to her questions who was disinclined to share data: "we bleed for each data point." I nearly laughed at the rhetoric, recognizing how similar it was to a post I wrote over two years back: I bleed for my thesis: Part 1. I've literally been that scientist before.

I've sat on both sides of the metaphorical data collection fence. I know how much time, money, and energy it takes to do field/lab/greenhouse work, and I appreciate the desire to make the most of that investment with thorough data analysis. I know the work of data collection isn't always rewarded in our current academic climate. However, I'm not afraid of others knowing about my research. I gladly welcome collaborators, and am happy to foist off projects on other folks. I have enough ideas for research to last several lifetimes and will gladly share them.

What to do about my existential crisis? I suppose I'd rather spend my time really owning the label "data vulture" than worry about keeping my research secret. In my mind, the benefits of sharing data and research far outweigh the potential risks. I'll tarry onward with my perhaps idealistic view of science research and think about knitting a vulture costume...because that would be an even better visual gag for presentations, right?

Monocots at Evolution 2013!

Given my tendency to stalk plants wherever I go, including conferences and college campuses, it should be no surprise that I took some time photographing the most interesting monocots (to me) here at Evolution 2013 in Snowbird, Utah. First up (right) are some lovely irises, which are likely ornamental but more petite than those I'm used to seeing in the southeast United States.

Next (left) is a (rather blurry) false Solomon's seal, featuring the characteristic spray of white flowers at the tip.

I'm not one to normally get excited about grasses and relatives, but sedges are really adorable and this small one (right) was in full bloom.

My personal favorite (left) is this lovely onion in full bloom. My old labmate, Erica Wheeler, would know the species, but I just like the magenta color.

Then finally, I have an enigma (right). These vegetative stalks stood over two feet tall, and not a single flower bud was visible. Obviously I'm not very good at western United States/Rocky Mountain flora.

Sadly, no Commelinaceae, but still plenty of monocots to keep me entertained.

Making the most of your conference experience.

I sat next to an undergrad on the shuttle from the airport to the meeting site for Evolution 2013 this afternoon. My first Evolution meeting was in 2003 in lovely Chico, California, and I've attended this meeting nearly every year since (I've been to Botany and Ecology on occasion, too). I'm acutely aware now how much my conference experience has changed over the years. It's overwhelming at times to sort through the myriad talks offered concurrently, and the undergrad with whom I spoke was appreciative to hear a few ways to think about strategizing his conference experience.

My post yesterday mentioned three basic goals for any conference as instructed by my PhD advisor. In case you're interested in more, here you go: conference philosophy and practice.

1. I spent approximately half of my first Evolution meeting running between buildings to try and catch talks in different sessions. That was a practice which quickly fell away. Now I pick one session in each time block, arrive a bit early, and sit through the whole thing (this is also in part because I knit and sometimes use my laptop to take notes, as I've mentioned before). 
2. How do you choose which sessions? Sometimes it's obvious, and sometimes it's not. If you have a few friends with similar interests, I like division of labor: go to different sessions and compare notes later.
3. Choosing sessions part 2: Go to talks given by people you know (but see #4 below). Going to someone's talk, especially if they're a new friend, can be an effective way to show interest in their research. Sometimes grad students and undergrads appreciate having friendly faces in the audience, so it is a nice show of support.
4. Choosing sessions part 3: Albert Meier, one of my undergraduate mentors, told me you shouldn't go to a talk given by someone with whom you work (or have worked in the past). Basically, you should probably already know about their research, or feel comfortable asking them about it. Use your time to seek out folks unknown to you, or people you would like to meet. (Note: I prefer this strategy to #3)
5. Pace yourself. I've dealt with social anxiety at various points of time over the last decade, and sometimes I can't handle too much socializing with new people. I make sure I can retreat to a corner of the venue, take a walk outside, visit my room, or otherwise recharge.
6. Use technology and informal events to your advantage. There are often announcements or informal gatherings organized on the fly. Also check the job/announcement bulletin boards for opportunities to score field trip/banquet tickets, etc.

There's lots more I could write, including many issues related to large-scale conventions (for an example, see this entry on con crud). As with anything, your personal preferences may vary.

I think I'm supposed to be doing something with a conference somewhere RIGHT NOW, though...

A prelude to Evolution 2013

I'm heading to Snowbird, Utah tomorrow for Evolution 2013. I've been attending these meetings for over a decade now, and always look forward to the breadth of science discussed. Here are the activities with which I'm involved this year:

1. My talk is on Saturday, 4:15 pm in Cotton D/Snowbird Center: "Genome-wide transposable element insertion frequencies change with selection for accelerated development." It's the first time I'm not talking about plants at an Evolution meeting! I'll be talking about a pretty sweet side project (collaboration with other NESCent and UC Irvine folks) about population genomics of TEs from an experimental evolution study in Drosophila.
2. My poster is on Sunday, number P240003: "Transposable element proliferation and genome size evolution in Asparagales." This is my main NESCent project and the subject of my recent paper from Genome.
3. I'm co-hosting NESCent's Evolution Film Festival on Sunday night in the Ballroom. I've watched the entries and am impressed by the variety of topics and approaches.
4. I'm participating as a mentor for the Undergraduate Diversity Program, and am looking forward to meeting with budding young scientists.
5. I'll be hanging out at the NESCent booth at various times during the conference.
6. Looking forward to attending iEvoBio on Tuesday and Wednesday!

Definitely a busy schedule, but that's the way I like it! In terms of continuing activities at the conference:

1. I'll likely be knitting during talks (the hows and whys are worthy of another post altogether, but I assure you I'm still paying attention).
2. I'll be typing furiously on my laptop and/or iPhone by tweeting (as @k8hert, using #evol2013 for the main conference and likely another for iEvoBio) and taking notes using Evernote.
3. I'll be following my PhD advisor Chris Pires' advice for conferences: "Meet someone older than you, someone younger than you, and watch a talk that changes how you think about things."

See you at the conference!

Commelinaceae haunts me...

Old habits die hard. During my dissertation I spent lots of time traveling all over the United States and Mexico collecting species in the plant family Commelinaceae (wandering jews, spiderworts). I've mentioned in passing my propensity to continuously stalk wandering jews maintained as ornamental plants inside buildings. Tradescantia pallida (picture to the left) is frequently planted as ground cover outside in the summer. Despite its perennial growth habit, it was replanted each summer back in Missouri as the winters were too harsh for it to survive freezing. This picture was taken recently on Duke's campus, where it seems to overwinter quite happily and persist in random patches.


I don't get much time with plants now that my research is exclusively computational, so it's nice when ornamentals remind me of how attractive my selected species appear (so pretty, in fact, that I obtained a tattoo of one such flower). Therefore, I'm veritably overflowing with glee when I stumble across a member of Commelinaceae in the wild. I visited a friend's farm this past weekend and came across a really nice population of Callisia graminea (right) growing quite happily in the middle of their property. I spent a summer collecting this species with the intention of looking at range expansion of polyploids compared to their diploid progenitors, and hope to get back to this project someday.

I'm even more tickled when I travel someplace I've never been and see plants unknown to me but clearly Commelinaceae. I came across a number of exemplars from Aneilema and Commelina in Kenya last spring. Even though I don't research those particular genera, I still insisted on pulling the van over so I could take a few photos.

Regardless of where I go, wandering jews follow me. I didn't purposely pick a plant family to research that grows in all sorts of exotic, tropical locations. That's just a bonus!

Accidental irises.

My boyfriend, Matt, needed to purchase a new cell phone a few weeks back, and asked if I could accompany him to a shopping mall while we ran errands one Saturday. I agreed, careful to tamp back my utter disinterest and anxiety in patronizing that bastion of teenage angst and commercialization on the busiest day of the week.

We arrived at the mall and greeted my fears: scores of teenagers, families with young children, and the occasional lone adult wandering with a shell-shocked expression on their face. We started walking towards the store possessing new phones (indeed, the ticket to my delivery from this monstrosity and ultimate salvation) and my eyes were met with a surprising vista.

A group of tables had been set up in one of the mall's open areas, on which were displayed an amazing array of irises. The Eastern North Carolina Iris Society was showing its award winning exemplars that weekend! Tall, short, bearded, and unbearded were all represented, with a stunning array of colors to boot. Matt indulged me while I wandered through the displays, pausing to examine some particularly lovely coloration or remarking on the cultivar names (botanists are never-endingly creative, see this blog post for some examples).

Looking at irises for a few moments was a welcome reprieve from what would otherwise be a tiresome shopping trip. I was gratified to experience growing excitement in...well, growing things again, as my current job doesn't include the greenhouse and field work to which I'd become accustomed during my graduate work. I was ultimately pleased I had the opportunity to accompany Matt, and was reminded that, just in like science, it's sometimes the serendipitous encounters which yield the biggest rewards.

Today's reason plants are amazing

While walking to the bus stop last week, I happened upon this lovely example of a wicked cool plant breeding system. Allium (onion) undergoes a form of vegetative apomixis (reproduction without sex) in which little plantlets form where flowers have bloomed. The picture shows an onion growing wild on a North Carolina roadside. The long squiggly line on the bottom right is the scape, or stem which supports the inflorescence (group of flowers). I'm holding the inflorescence, which has a few small and one REALLY BIG plantlet growing out of it. These can become individual plants. Remember that in the case of onion, there are bulbs growing below ground which are also producing little bulblets, which is another form of vegetative reproduction.

Bladderwort revisited: Because the fun never ends in Junk DNA Land!

I've had some feedback and read additional commentary posted elsewhere about the bladderwort news I posted about earlier this week and feel compelled to post a follow-up. I also just submitted revisions to a manuscript, which means I'm validated in indulging my whims of...continued professional development via blogging?

Anyway, I particularly like Jonathan Eisen's Twisted Tree of Life award to MSNBC's coverage of the bladderwort study. His argument is compelling and his rhetoric is golden.

Next, my friend Jared astutely pointed out in a comment on my last post that I appear to have misrepresented the research from the ENCODE project. Again, here I fell victim to a common folly among transposable element researchers. I've adopted the term "junk DNA" to refer to any non-coding sequence in a genome, whereas others use the term in a functional sense (i.e., junk DNA is a sequence to which function has not been ascribed). I've since edited the previous post to reflect my viewpoint. Simply put, a large portion of the human genome is comprised of transposable elements and other non-protein coding sequence, yet contemporary research indicates many of these sequences still perform functions necessary to organism function. I appreciate the comment, Jared, and am so grateful for folks like you who help me stay on my toes!

Finally, there was also my embarrassing gaffe in mistyping "Badderwort" in my title of the original post. It's since been corrected, but will live on in the automatically generated permanent web address. It's ok, though, because the bladderwort is definitely the baddest of the worts regardless.

Bladderwort: tiny plant, tiny genome, weird name. So what?

My dad emailed me a link this morning. Then a NESCent coworker passed along another. Then my boyfriend tagged me in a post linking a similar article on Facebook.

All those news articles refer to a recent paper (Ibarra-Laclette et al., 2013, Nature) which reports on a newly sequenced plant genome (Utricularia gibba). YAWN, we all say, it's a silly little plant and we can't even eat! What makes it news worthy?

Turns out there are a few reasons why. First, it's called badderwort, and that's just funny. Second, bladderworts are a wickedly awesome type of carnivorous plant which capture prey by rapidly sucking them into bladder-like traps (complete with a trapdoor!).

Then there are a whole slew of other (more "publishable-in-Nature") type reasons to care about bladderworts. This species has a remarkably small genome but still possesses the same number of genes as other plants surveyed. Most of the news articles linked above talk about the implications of the research for our understanding of "junk DNA," or portions of the genome which do not code for protein sequences. It's admittedly a hot topic in science news right now, following heavy on the heels of research in human genomics suggesting that a large portion of the human genome is junk (EDIT: but still functional). The repercussions of the bladderwort genome research is that junk DNA isn't really necessary for "healthy organisms," as we now have an example of one species which has managed to "throw out" junk DNA.

I find the bladderwort research interesting for a few reasons. First, my professional research interests revolve around junk DNA and how changes in genome size affect organisms. The main focus of my research here at NESCent is comparative genomics of a group of plants called Asparagales (includes agave, onion, iris, orchid, asparagus). Species in Asparagales have genomes which range from very small (i.e., a few times larger than bladderwort) to ginormous (200,000 times larger); the variation in genome size is like due at least in part to junk DNA. The conclusions from the bladderwort news articles are kind of no-brainers: OF COURSE plants can persist quite happily without tons of junk DNA. There are fungal species which entirely lack junk DNA, too.

I'm also pretty tired of the semantics surrounding the "Is junk DNA important?" argument, which has been very well described elsewhere (and there's concomitant throwback from the creationist community as well, but that's for another day). To me, junk DNA is just another source of mutation. In the context of evolutionary biology, junk DNA provides more opportunity for evolutionary innovation. That's a hypothesis which is better tested with a broad sampling of species' genomes to infer changes over time. A snapshot of a single genome at a single point in time can't tell you as much as broad comparisons. Asking about the relevance of junk DNA to an organism living today is like asking whether money is required for humans to survive. In a strict sense, currency ISN'T required for humans to persist. It IS a means to an end, though, and a mechanism through which contemporary humans purchase food, shelter, and other resources required to survive. That might be a crappy analogy.

A better question to ask from the bladderwort research is what pathways allow for regulation of junk DNA and other mechanisms of genome downsizing. It's not just about the ability of the bladderwort genome to remove sequences already present. It's also about the ability of the genome to prevent other sequences from incorporating themselves into extant sequences, since some junk DNA is derived from viruses and the genome can be continually invaded. There is also evidence the bladderwort genome has undergone whole genome duplications at least three times, but has managed to remove most of the extra genetic material (including extra genes!) after each event. Now THAT'S some cool science.

Architecture and evolution of a minute plant genome, Ibarra-Laclette et al., Nature (2013) doi:10.1038/nature12132

Spring Fling!

Today is the day everyone at NESCent talks for three minutes and we get to throw things at them if the go over time (see pic). So exciting!

New rule for students taking my classes.

When taking an exam in a large auditorium style lecture hall:

If you have a question about something on the exam, you must write it on paper, fold it into a paper airplane, and launch it successfully towards me. If your efforts are worthy, I will answer your question.

Ok, maybe not...but it would be amusing.

Just your normal azalea appreciation post.

The azalea bush planted outside my childhood home in Indiana was always in full bloom the week of my brother's birthday (in early May). The nice part about living further south is the earlier arrival of azaleas, as well as greater variety in floral morphology. I love bushes loaded with blossoms, which can almost completely obscure the leaves hiding beneath.

Shown below are three examples of lovely southern azaleas:

First, small white blossoms in full bloom today on Duke's campus.

Next, medium-sized light pink blossoms with really interesting dark pink nectar guides, also from Duke's campus,

Finally, some huge, shockingly pink blossoms I saw weeks ago while traveling for spring break. Leave it to New Orleans to have the showiest of flowers.

Today's edition of "How Nature Attacks Me" features cute little green inchworms that dive bomb from trees into my hair and clothing.

How a traumatic week for the nation affects education.

I'm supposed to be leading a review session this morning for a class of ~400 students. Sure, I would expect only a small fraction of those enrolled to show up, but their final exam is next week and I imagine there will be at least a few questions about the material on macroevolution I assigned from Monday.

The problem right now is that, for the second time this week, a bomb threat has been called into the building where I teach. This morning's emergency text comes with speculation that this one isn't serious, but that the building is still being searched. Earlier this week, the fire alarm also went off twice right before class started. There's lots of construction in the building right now (not unusual for a college campus these days), so it's difficult to determine whether alarms and sounds are actually significant, or just a disruption.

I've spent almost all of my life either taking classes or working on college campuses. Disruptions from possible or imminent disaster occur periodically, especially in science buildings. Sometimes it's a careless student leaving "suspicious white powder" out on a lab bench rather than cleaning up. Sometimes it's a bunsen burner that sets off a fire alarm. Once it was a tank of flammable gas in a research lab that exploded.

This week, I've been reminded several times over that danger exists, either from malicious people or even just accidents. As I write, normal activity in Boston has slowed to a crawl as police seek out suspected perpetrators of violence. These types of things happen all over the world everyday, but we, as Americans, largely allow it to pass by without notice. This week, though, I can't ignore a twitter newsfeed full of minute-by-minute updates of casualties and announcements of the next catastrophic event. I'm on edge, and I'm vigilant. If something happens, I'm wondering how I'll react when a classroom full of students looks to me for guidance.

The last time there was a bomb threat it took a little over an hour to clear. I just received the text that the building is clear, and it took less than half hour. Looks like class can start in half an hour as planned. Frankly, though, if I were a student and received a text when I awoke that a bomb threat had been called into the building for one of my classes, I would probably go back to sleep. This pattern doesn't bode well for a campus heading into finals next week. I can post a video online detailing the questions I planned to cover in the review session, but that doesn't work so well for exams.

I was happy to hear a cricket chirping in the bathroom earlier, as it reminded me that, despite the chaos in various parts of life, the world still keeps doing its thing.

Teaching with concept maps

One of the most challenging parts of the introductory biology (genetics and evolution) course I've been teaching this year is helping students understand how myriad biological phenomena and tools are related to each other. As a part of my macroevolution lesson on Monday, I provided students with a list of key words and instructed them to make a concept map. If you aren't familiar with these tools, I found this website to be a particularly useful introduction, although there are many others spanning a breadth of disciplines in which they may be used. 

After students had a chance to try their hand at mapping these terms on their own, I communicated a few ideas of my own for connecting different thoughts. I used the open-source software VUE, which has functionality far beyond what I've shown here. Below is one of my attempts to unite disparate ideas in a web-like format:

Of course, there are as many ways to relate these concepts as there are scientists thinking about these concepts. Part of that complexity arises from how you choose to relate the words. The example above shows quite simple relationships. Below is another example, in which the relationships are diagrammed in a much richer manner (arrows and labels on connections, color coding/nesting of ideas, concepts mapping to multiple other nodes). 

Is it perfect? Nope. Is it comprehensive? Certainly not. I've gradually learned over the course of my educational and professional career that my brain naturally builds connections between disparate content knowledge. Whereas other folks find concept mapping challenging because of misunderstanding the relationships between nodes, I find them frustrating because of an inability to exhaustively explore relationships. Concept maps are a balance between conveying information and rendering connections useless through convolution.

I'm not sure whether this exercise helped students. I'm going to provide a few examples of concept mapping schemes later this week as they prepare for their final. At the very least, some of the teaching assistants for the course found the activity interesting and useful. Minor victories!

How does anything get fertilized around here, anyway??

My obsession with pollen was reinvigorated today as I again momentarily became the weird woman photographing the ground on Duke's campus (other evidence of my geekery includes mushrooms and bursting heart).

The reason for my interest are those grass anthers wagging around in the breeze. It's not enough that the inflorescence sticks up above the plant. It's not even enough that the anthers are exerted so far out of the rest of the flower. This grass takes it even further by expanding the anther connectives (the piece of tissue connecting the two halves of the anther to each other and the rest of the filament).

With so much pollen floating around, wind pollinated species (like grasses) really need an advantage to get their gametes out there. Given how much pollen sticks to my phone as I walk outside, though, it's hard to imagine how pollen from a compatible plant ever manages to land on a receptive stigma that isn't already covered by pollen from other species.

How much pollen is out there floating around, anyway?

As a botanist, North Carolina resident and seasonal allergy sufferer, I experience a triple whammy of acute awareness when spring begins. This week marks the start of a curious natural phenomenon: the time of year when one puzzles over the greenish-yellow waft of particles covering everything, necessitating the use of windshield wipers to allow driving despite the onslaught of plant reproductive material (see right).

Indeed, North Carolina flora are spreading their gametes with a vengeance this time of year. Never before have I experienced such a visual demonstration of the prolific nature of pollen before, so I took the opportunity to perform a few "back of the envelope" calculations. How much pollen is actually being produced, anyway? I was pleased that forestry researchers have actually done enough of the hard work collecting empirical data about this topic to make discussion possible.

Loblolly pine (Pinus taeda) is the predominant species in most areas of the southeast and are widely planted for commercial timber. An adult tree (16 m) produces 81 grams of pollen a day for 2-4 weeks. Let's assume that means ~1 kg of pollen per tree per season (my sinuses are already saying "CRAP"). An estimated 3.3 million acres in North Carolina alone are planted stands of loblolly pine (although it's dominant on an estimated 29 million acres). I will assume density of planted stands is only 100 trees per acre. This is dramatically lowballing the number of trees, but this is allowing for a few considerations: 1) trees don't start producing pollen until they are 10-15 years old, and 2) stands of trees are sometimes planted at high density and later thinned to remove diseased/damaged/crowded trees.

So 3.3 million acres of trees, with 100 trees per acre, that's over 300 million trees. That means loblolly pines in North Carolina are producing 300 million kilograms of pollen each year. That's a level of scale my brain is having a tough time processing. The population of North Carolina is a little less than 10 million people. That means we each get 30 kg of loblolly pine pollen a year! Think of a large adult German shepherd. That's how much pollen. Per person.

But wait! It gets better! Because loblolly pines also occur in natural populations, and they're not the only plants producing pollen. They're not even the only pine trees producing pollen. And guess what? Pollen can travel over 41 kilometers in the air. And each gram of pollen contains over a million grains. I'm still having a tough time comprehending this level of scale, and am half hoping someone will say I've grossly miscalculated by an order of magnitude (the other scientist half of me, of course, wants to be right). Well, now that I've thoroughly discouraged myself, I think I'll get back to work.

Literature referenced:
Baker, James B. and O. Gordon Langdon. Loblolly pine. Silvics of North America. Agriculture Handbook 654. USDA Forest Service.

Biofuels Center of North Carolina. 2011. Loblolly Pine Trees. Biofuels Wiki.

Williams, Claire G. 2009. Conifer Reproductive Biology. Springer: New York. 169 pages.

Williams, Claire G. 2010. Long-distance pollen still germinates after mess-scale dispersal. American Journal of Botany 97(5): 846-855. doi: 10.3732/ajb.0900255 (research supported by NESCent!)

Discussion role call!

I spent prolific amounts of time as a student participating in competitive speech and debate. One of the categories of high school speech in Indiana was Discussion. This aptly named group placed students in a room together where they were expected to talk about a pre-assigned issue. Such a set-up, however, begs the question: how do you rank participants, given it is a competitive event? Even more fundamentally: what makes someone better than another at talking about stuff?

Such was my first introduction to the importance of the variety of roles in a group discussion setting. Here's a description of different types of discussion roles from a non-profit group; I selected this particular link over myriad others because of the breakdown into "task" and "maintenance" roles. These same principles are applied in many contexts, including education. Often, teaching resources recommend students are assigned a single role for a class period or task. In the afore mentioned competitive sense, a successful participant was one who effectively filled multiple roles during the course of the conversation.

This digression to memories from high school is brought to you by reflections on the catalysis meeting in which I participated a few weeks back. As previously discussed, catalysis meetings present interesting dynamics. Scientists at different career stages are better suited to some types of discussion roles. Everyone can make contributions, albeit in different ways. In a broader sense, I find myself tallying my own (and others') fulfillment of these roles in other settings, such as during journal club (we meet once a week here at NESCent to talk about a recently published scientific article). My observations are based partly in a desire to study communication, but mostly in an effort to enrich my interactions with professional colleagues and expand my thinking.

It's gratifying the multitude of time I spent competing in speech and debate continue to reap benefits.