Beneath The Dome

Where once ‘wilderness’ was easy to define – vast expanses of the globe untouched, at least in the modern era, by humans – we are now confronting a reality in which the impacts of humans are being felt the world over.

Humans are not distinct from the global ecological context. We seek to control where species exist, both in and outside of our cities. Foxes are welcomed into the urban landscape as beautiful, while rodents are exterminated as filthy. Endangered species are propagated and released, and sometimes we kill their predators so that the endangered might survive. We must be mindful of what we are trying to control and why.

Conservationists are, I think, aware of the blurriness of such boundaries. But most people have not abandoned an idealized notion of a ‘pure’ wild that exists outside of us. Explaining this new reality is a task for educators and artists. I’ll encourage you to take the time to listen to Steven Millhauser’s short story “The Dome” (linked below). It was brought to my attention by friend and Philospher Stefan Linquist, and it explores these themes quite effectively.

“A change is in the air. You can feeling it coming.”

Exploring Nature and Calling it Work

Just about every biologist I know started out as a kid with a disproportionate fondness for messing about outdoors. We dammed streams, climbed trees, studied carcasses of rodents our cats dragged in, and painstakingly collected live sea creatures for private (and usually temporary) aquaria. Formal lectures on freshwater hydrography, forestry, mammalogy, and marine biodiversity did not spark our interest in biology, but rather provided scaffolding on which to rest our previously developed enthusiasm for and sense of ownership of the natural world. Apparently the geologists have a saying that goes, “The best geologists are those who’ve seen the most rocks. “ It seems that we as current or future biology teachers could and should coopt this quote for ourselves. In order to produce really good biologists or even biologically literate humans, we need to show students a whole lot of real live biology.

Students who become scientifically literate are those who can connect to scientific information to their own lives. It is a fact that modern American children are spending less time outdoors than ever before (Louv 2005). There is something very troubling about increasing isolation of young people from the unplugged, unlit, unheated outdoor environment. Forget about the demonstrated health benefits of getting dirty (Yazdanbakhsh et al. 2002), we as biology teachers should be facing the challenge of Nature Deficit Disorder head on. In this time of unprecedented global change, we cannot afford to produce scientifically illiterate students who are disconnected from their environment. So before we rely on lectures to teach about the natural world, let’s go outside and expose students to real patterns in nature. Let’s allow them see for themselves the real pressures threatening our environment, and provide them with a sense of ownership of and responsibility for protecting the future of natural systems.

A transect at the Indiana Dunes to survey plants.

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Seven Minutes in Heaven of Science at Northwestern

Northwestern graduate students are giving lightning talks tonight about their research in (you guessed it) seven minutes.

Seven Minutes of Science will showcase graduate participants in Ready Set Go: Winter 2014 as they present their research in seven-minute presentations for a general, non-expert audience. The goal of this symposium is to share the great research going on at Northwestern in a way that is accessible to individuals from any field.

For more info and to register for this FREE event, check out the Ready Set Go site.

Thursday, March 20, 2014
5:00 PM – 7:00 PM

Northwestern University
2200 Campus Drive
Pancoe-ENH Building, Abbott Auditorium
Evanston, IL 60626

This looks like a cool event – I really enjoyed giving a quick talk about my science to a room full of game designers and developers back at the Science Jam, and they turned out to be really into seaweed research. More discussion between scientists and a more general audience is more fun for everyone.

On another note, this class Ready Set Go looks awesome. It was founded by Michelle Paulsen, program director for Reach for the Stars, a National Science Foundation-funded program that places Northwestern grad students in middle and high school classrooms to serve as ‘resident scientists,’ and Alex Adler, a PhD from Northwestern with a long track record with improvisation and STEM outreach. The class is just what many of us want – specific training in communications for researchers at an early stage in a scientist’s career. Way to go Northwestern!

Research Tool: Electronic Lab Notebooks

Hey researchers!

Do you have folders within folders full of files labeled things like “FINALfinal_draft-1.pdf.docx” or “Paper_v2.3_AKHedits_revisionJan2014.xls”? Tried to learn a version control program but it just didn’t stick? Would you like to have your pictures, methods, data, etc. from a single experiment all in one place? Find yourself sending the wrong attachments to collaborators, or explaining the metadata?

Perhaps you should try an online lab notebook! I’m going to talk today about closed and open online lab notebooks, specifically hosted on WikiSpaces.

I use WikiSpaces, which is a free (paid upgrades available) service that facilitates project management and collaboration. It seems to have been designed with classes and collaborative projects in mind, however, I find it useful just for keeping my own work together!

This is what a page from my WikiSpace looks like:


This particular page I’ve set up like a mini lab report. I have my excel file at the top so I can find it easily, with my Objectives and Methods listed so I can remind myself what I did (and it’s great to have it already written to make writing it up for a paper someday easier!). Adding tables is a little clunky, so I only enter data in that format if it’s simple and easier to reference. The blue text saying “Photographs” is a link to another page where I’ve uploaded photo files from my experimental setup. I can add captions and annotations on this page, like a scrapbook. The buttons at the upper right of the white part of the screen allow me to edit the page, show how many comments my post has (since mine isn’t public this is none), and how many revisions I’ve made to it. The gray toolbar allows me to jump to other pages and files, showing my most recently viewed pages. “home” is my chronological field notebook. I try to immediately transcribe field notes into the online version! It’s great while I’m waiting for the ferry.

One thing that is different about WikiSpaces from a blog like WordPress is that it acts more like a document manager than a series of discrete posts. It can handle lots of file types, and it remembers revisions, like a more hands-on and visual version control.

My electronic lab notebook is awesome because:

  1. I can access all my data from anywhere with internet.
  2. It helps me keep a chronological record of my work and keep my most recent versions of files right at the top.
  3. Within that chronology, I can link directly to pages that compile all my work relating to a single experiment or project, so it’s easy to look up when I did things.
  4. It’s more visual and intuitive than other version control resources like GitHub.
  5. I can link together multiple types of information that relate to a single experiment, such as photographs, graphs, tables, excel spreadsheets, and any other type of document (including code) with explanations/thoughts so I don’t forget what anything was.
  6. I can add my advisor or any other collaborator to the blog so that they can view and edit my resources too, which helps keep everyone updated on progress while I’m doing fieldwork.
  7. It’s searchable! Unlike a paper lab notebook, it’s easy to find every single day that I mentioned “rain” or “tanks”. Pages can be tagged too.
So what’s an open laboratory notebook?

Ph.D Models? Betabrand’s new lineup modeled by female Ph.Ds

I’m not quite sure how I feel about this. According to Adweek:

Betabrand, an online retailer of crowdsourced clothing, just launched its spring line, and the company decided to take a different approach to marketing the new looks: Each of the models would have a Ph.D.

On the one hand, it’s pretty awesome to see smart women with graduate degrees modeling clothing. I’m all for increasing visibility of women with degrees. On the other hand though, I’m running through all my fellow graduate students in my head from my Ph.D program, and we are a pretty diverse bunch visually. I’m inclined to agree with Hanna Brooks Olsen at The Stranger:

Diverse representation is cool, but this feels like theoretical diversity, rather than, you know, visual diversity.

The majority of the Ph.Ds modeling for Betabrand are white, thin and beautiful in a conventional sense.

Wow! Such PhD. Actually looks like a pretty standard model-y type to me. From Adweek.

It makes me think of the ‘white guy in a labcoat’ depiction of scientists. There’s not a whole lot of visual diversity going on there with Betabrand’s models, but at least it’s nice to see a depiction of Ph.D-holders focused on women.

Ah yes, there’s my portrait from picture day. From Wikia.

Thankfully we are getting to see a wider array of academics in more and more venues. The Field Museum of Natural History right here in Chicago has a fully functional DNA lab that doubles as an exhibit, so visitors can connect with a wider range of scientists coming from all over the world, beyond my friend Mr. Safety Goggles and Lab Coat above.

Overall though, something deep in my brain recoils a bit from the ad campaign – women are smart and (conventionally) beautiful and model-y all at once! I guess it’s a fine line, between celebrating these women and setting the bar pretty high for the rest of us – tenure’s going to get even harder if we’ve got to be models too. But then again it is just a bunch of ads for a clothing line. Maybe I’m being a downer on an interesting concept and Ph.D models are pretty sweet – I hear there is no such thing as bad publicity. What do you think?

Stand Up for Science

To highlight the importance of federally supported biological research, and to promote science more broadly, the Federation of American Societies for Experimental Biology (FASEB) recently held a contest called Stand Up for Science. Entries consisted of short, 1-4 minute videos that were meant to highlight how research funded by different government agencies (e.g. the National Science Foundation, the National Institutes of Health) has lead to important discoveries and promoted the health and welfare of society. The winners of this contest were recently announced, and their videos were posted on YouTube for all to enjoy (see below).

All the videos can be found on the FASEBopa YouTube Channel.

On a personal note, I find the story told in the grand prize-winning entry to be particularly inspiring for two main reasons. First, this group persuasively pointed out that asking fundamental question about biology can lead to both intellectually stimulating discoveries and practical applications that have contributed enormous benefits to human health (i.e. the production of human insulin to treat diabetes). Second, the video manages to accomplish this feat without getting bogged down in technical jargon. It lucidly explains both restriction endonucleases and molecular cloning without using either of those terms! For more on the history of this area of biotechnology, I highly recommend Stephen Hall’s excellent book, Invisible Frontiers: The Race to Synthesize a Human Gene.

Kudos to all the creative people who submitted entries to this contest; you are doing both science and society a great service.

A face for radio

Scientists must communicate. I mean that practically (our jobs hinge upon teaching, delivering conference talks and published papers), but I also mean that an imploring sense. The public is concerningly misinformed about many scientific issues. Solutions to problems like global climate change will require legislation, and therefore, too, an informed public. That’s why, to me at least, there’s tremendous value in a blog such as this. It is an opportunity to create a place for discourse and learning. And so, on that note, allow me to share my most recent foray into science communication…

Recently, I began working with the Groks Science Show, developing audio pieces to be broadcast on WKPH 88.5 FM Chicago (the pieces are also available online). The whole process is new to me—interviewing, editing, and producing—but I’m trying. My first show aired a few weeks ago. It covered the research of Ben Winger, graduate student of evolutionary biology here at the University of Chicago. He studies how new species form, and his work takes him to the cloud forests of Peru. I’ve posted a link to the episode below. For the readers who dare to be listeners, forgive me; the audio quality is hardly exquisite. Any and all feedback is warmly welcomed.

Discovering Bird Species — Groks Science Show 2013-11-20.


Geese bite

Ever been bitten by a goose? It hurts. One of our colleagues, Aaron Olsen, is researching just how hard geese bite and how it is even possible for animals to execute the complicated motions they do – like eating and walking.

From Aaron:

Seemingly simple tasks such as eating or walking require the complex integration of neural signals, bones, muscles and joints to create movement. How these structural components function and interact with each other are central questions in biomechanics. Birds have evolved a number of different strategies for using their beaks to get food, with beaks specialized for catching fish, for grazing on grasses, for prying food items from inside shells or for catching small, evasive prey such as insects. The bones, muscles and joints that produce these movements are also structurally diverse. By finding the structural differences between birds that move their beaks in different ways, we can better understand how musculoskeletal structure relates to movement.

Video from the IGERT poster hall.

Imagining the Post-Antibiotics Future

Oh man – required reading on antibiotic resistance over at Medium:

I had always heard Joe had been injured at work: not burned, but bruised and cut when a heavy brass hose nozzle fell on him. The article revealed what happened next. Through one of the scrapes, an infection set in. After a few days, he developed an ache in one shoulder; two days later, a fever. His wife and the neighborhood doctor struggled for two weeks to take care of him, then flagged down a taxi and drove him fifteen miles to the hospital in my grandparents’ town. He was there one more week, shaking with chills and muttering through hallucinations, and then sinking into a coma as his organs failed. Desperate to save his life, the men from his firehouse lined up to give blood. Nothing worked. He was thirty when he died, in March 1938.

The date is important. Five years after my great-uncle’s death, penicillin changed medicine forever. Infections that had been death sentences—from battlefield wounds, industrial accidents, childbirth—suddenly could be cured in a few days. So when I first read the story of his death, it lit up for me what life must have been like before antibiotics started saving us.

Lately, though, I read it differently. In Joe’s story, I see what life might become if we did not have antibiotics any more.

Apparently 80% of antibiotics sold in the U.S. by weight are used in agriculture, primarily to protect animals from infection from the conditions in which they are raised. Read the whole article Imagining the Post-Antibiotics Future at Medium.