One Year After (Not Quite) Leaving Academia

This will be a short update. It’s been a year since I accepted a full-time position as a Data Analyst for an educational software company and it’s been going great. This is why I’ve been slow to update this space for the last year. I’m not entirely done with being a biologist either. At the start of 2015, as I reflect on a year spent wrapping up my dissertation work and transitioning into a new role as a technical member of a software company, I still have a lot going on in both worlds. Just to set the stage for some future updates (I have a long one in the works about how and why I stopped seeking out a post-doc position and accepted a position as a data scientist), here are some of the things I’m currently working on:

  1. Paper Submissions to PeerJ: I’ve got two manuscripts about to be submitted to the open-access journal PeerJ. I’ll update here when those (finally) come out. 
  2. Diagnostic Protocol for the Plum Curculio: I’ve begun drafting a new diagnostic protocol for identification of Conotrachelus nenuphar (and it’s two haplogroups) for the International Plant Protection Convention. This is a super exciting opportunity but the work has been very slow because of trouble finding people to work on this project. Still, we think 2015 will finally be the year. 
  3. Teaching Biology Education at Hunter College: Once again I am teaching the Pedagogical Content Knowledge course at Hunter College as an Adjunct Assistant Professor. More on this class in  a previous post below. This will be version 2.0, so I hope my revisions of the course improve the class from last year. 
  4. Working as Data Analyst and a Project Principle on a ground-breaking K-8 digital science curriculum. I’m working on a large post about this, so more to come! 

That’s all for now. With all these changes afoot, I’ll be tweaking this website a bit. I feel like it needs an update to reflect my current work better. 

Great Lab Websites

I’m curious which ones are your favorite & WHY

What makes an academic website great? Recently Michael Eisen started collecting suggestions for great lab websites via Twitter. He's posting the suggestions at greatlabwebsites.tumblr.com. I expressed my dismay at the rather pedestrian average of these great lab websites (deemed great by the people who suggested them) and have been asked which ones are my favorite. I could have tweeted a couple quick examples, but the request emphasized my reasoning so I thought a blog post a better answer. 

Lab websites should be judged by the standards of all websites: design and function. I'm certainly one to emphasize design and aesthetic as much as function. Sadly, most lab websites are heavy on function and absolutely dreadful on design. It doesn't have to be this way. Here are some favorites and reasons why:

Design by Template
Haters gonna hate, but check out my website: samuelcrane.com (this one you're on!). I think that there are a great many ways to leverage good design without having to pay a lot of money for it. I use Squarespace and their Montauk template. I only had to make a few design layout decisions and all the rest was baked into the template. I pay a monthly fee that includes hosting. There are very good free solutions as well. These hosted solutions include professional designs, modern web technologies underneath the hood with mobile support and responsive web design, good (i.e., user friendly) fonts and colors, traffic analysis tools, social tools, and customer support (for you). Some of these things make the website better for your readers, some make the website more useful for you. Resources for template based modern designs:

Custom Design
At the end of the day though, the only true professional solution is a bespoke solution. My favorite here is the Rob Dunn lab website done by Neil Mccoy Design. I've never had the opportunity to ask Rob about their design process, but Rob has a great set of project, lab, and personal sites. The Neil McCoy studio has also done a number of other lab websites. I think these designs are great because they feel unique—giving a voice to the lab—and they are a pleasure to use. As a lab website, all the expected elements are there: research statement, pub list (time for an update Rob!), lab people (very well done here), and news items pulled in from various places including Twitter and blog posts. Probably cost a fortune (by academic standards). 

Focus on Function
Of course, design really is the extra mile. First one must have an audience in mind and then figure out how to serve that audience well. What's the purpose of the website? Scicomm? Outreach? Software and data distribution (don't do this)? Personal promotion in pursuit of a post-doc or tenure? If a mixture of different goals, how do you balance them? These are all super important questions. 

When I visit an academic website, I'm usually there for one of two reasons: (1) I want to find out more about this person's background and research or (2) I want to find their publications and collaborators. I want to know more about who they are as a researcher or I already have a grasp of that and I want to see their science products. 

My favorite example of a website that serves up these functions really well is Andrew Rambaut's lab website. There's updated news, short descriptions about research topics that lead into longer descriptions that link out to project sites, there's an updated publications list, and then an excellent list of software. I don't think this is a great example of design. It used to be—in 2008. But in 2014 the website feels dated and unprofessional even if the function is still great. 

The Apogee: Design & Function
I could point to the Dunn lab website again, but I'll provide another example. This is cheating because it's not exactly a lab website, more a project website, but I point to this as having excellent function (identifies and serves an audience well) and design (responsive web design with clean interactive features): Epidemic: Emerging Infectious Diseases, also from Andrew Rambaut. I feel like aspects of the design could be better, but I think this is truly a great academic website. If you're looking at the website on a desktop, drag the browser window to make it thinner; observe the awesome responsive design (you can do the same to this very blog). If you're looking at it on a mobile device, it already looks good. More and more web traffic is via mobile (think about how researchers visit your site when at a conference) and the mobile experience should be considered when making a Great Lab Website. 

On a similar note, any of the Zooniverse websites point to the level of function and design that I feel academic websites could aspire to. I really like Notes from Nature and The Milky Way Project. There is a complete expression of a design vision coupled with effective delivery of content and function—and damn do these websites function well. This is indeed rare in a lab website, thus the need for examples of great lab websites. If academics aren't ready yet to partner with designers and software engineers for their lab websites (which I'd love to see), then the Design by Template approach is one that more academics would be well served by.

How To Improve Science Teaching

I've been asked to teach a class at Hunter College this Spring for the New Visions-Hunter Math and Science Teacher Residency program. The class is titled Pedagogical Content Knowledge II: Biology Education. This is the second in a series and I will be running teacher workshops covering evolution and ecology. The first series covered molecular biology and genetics. The teacher learners are enrolled in the M.A. program in the Education Department at Hunter through the Teacher Education Program in Adolescent Biology (Grades 7-12). This course is designed to provide them with graduate level biological content knowledge while also serving the in-classroom fieldwork needs of the New Visions program. I've been asked to teach the class because of my background in evolutionary biology and my years of education experience. In addition to covering ecology and evolutionary biology topics at the graduate level, the class will spend a considerable amount of time exploring pedagogical approaches to teaching high school level biology. In this I will be joined by instructors from the Hunter Education Department and education professionals from the New York Hall of Science. The class will be split between pedagogy and science content. 

Reproduced by permission of the publisher, © 2012 by tpack.org

Reproduced by permission of the publisher, © 2012 by tpack.org

I'm excited about this opportunity at Hunter because I'll have the chance to test out an idea about how to improve adolescent science education. The idea is really simple: teach the science teachers more science. This is one of the ideas behind the recent MOOCs I've been involved in at AMNH (the last of which concludes this week: Evolution, A Course for Educators) and is the basis of the Pedagogical Content Knowledge (PCK) class at Hunter. The PCK approach stipulates that the teacher have a firm grasp of the science content—the better to surface prior knowledge, misconceptions, and to know what makes learning difficult in the particular. 

The key to effective science teaching (effective meaning that the students learn) is the teacher's solid knowledge of the content. While it's important to know how to make a subject comprehensible to a learner (the pedagogy), one can't even approach that goal without a solid, thorough, robust, and up-to-date understanding of the subject area. Domain knowledge is paramount. I believe everything else a teacher does in the classroom should follow from this first principle. Once the educator truly understands the content then they can effectively design approaches to teaching. Inverting the relationship dooms the learners and the teacher to rote learning and perpetuating misconceptions. 

My goals will be to: (1) get the future masters teachers up to speed on subject areas (biological evolution and ecosystems in this case) and (2) enable these educators to stay there by teaching them ways to stay current. To do this, I expect that my curriculum for the Hunter program will extend beyond PCK and into the technological knowledge sphere, teaching the educators how to use technology to stay current with evolutionary biology and ecology. What would be really great is to also see more of a commitment from active researchers to science communication with educators (not merely the public). Where is there a place that educators can informally work with, learn from, and discuss science with scientists? 

What I've Learned Helping Learners Learn

or
How Deep in the Earth Do Earthquakes Typically Occur?

During the Dynamic Earth course, one of the questions that came up was about the depth at which earthquakes typically occur. There was some confusion around a quiz question and to get to the bottom of the issue I ended up seeking out some data that would illuminate the process. I started down this path because the initial confusion arose when one learner, based in Taiwan, was confused as to why we claimed that most earthquakes happen at depths shallower than 12-15km. He was looking at some recent earthquakes that had happened around Taiwan and the majority of them were deeper than 15km. Surely we must be wrong; look at this data. 

Well, I did look at that data. The obvious answer before even looking at the data, though, was just that the sample was limited to a short time frame in a small area of the globe. But another observation this learner drew our attention to was a global dataset of 2.5 or greater magnitude earthquakes over the last 24 hours. The claim was that this dataset also showed that most earthquakes originate deeper than 15km. Again, I was suspicious that this contrary observation (that most earthquakes were happening deeper than 15km) was due to a sampling bias—only looking across a day and only looking at 2.5 or greater magnitude quakes. So I went after a bigger dataset. 

The resource linked to was the USGS Earthquake Hazards Program, which releases worldwide earthquake data. I was chiefly interested in depth and magnitude, as that was the comparison being made in the comment thread about the topic and it's also a convenient way to visualize the depth data. Another way to look at this problem would be to make a bar chart of the number of quakes at increasing depth categories. That would summarize the data nicely but I wanted to see it all, so a scatterplot it is. I could also have plotted depth against time of occurrence, but I like the plot of origin depth and magnitude because it also makes a nice comparison beyond the scope of the issue at hand. That is, do stronger earthquakes happen deeper? That's an interesting question with some reason to think (a shaky theoretical ground, if you will) that stronger quakes might happen at shallower depths since the crust is more brittle when cooler and earthquakes are an elastic phenomenon.

So I grabbed data on the last 20,000 earthquake events (USGS limits queries to 20,000 through this interface) and went to R to plot the data. I ended up plotting the natural log of depth because there was such a great number of events between the surface and 15km that seeing all the data was difficult. After sorting out some problems with negative and zero values on the log transformed variable, I have ended up with the plot you see below. The script and dataset I used to make this figure are both on GitHub. 

Turns out, about 70% of earthquakes happen at a depth of 15km or less (so we were right, but that's no surprise). And there seems to be a trend of stronger earthquakes happening at greater depths, though this is largely driven by some outliers in the dataset. I did a linear regression on the untransformed data (not shown), and the residuals errors plotted against their fitted values show a decided trend around zero, so I don't really trust the model and it's a weak signal anyway. A normal probability plot confirms that the untransformed data is very not normal.  

My guess that stronger earthquakes will occur at shallower depths is mostly driven by detection bias–we tend to notice those ones. However, this dataset shows that lots of very strong earthquakes happen deep in the earth. We don't experience them much likely because of that depth. Many of those deep earthquakes occur along subduction zones in oceanic plates, where brittle crust is being forced down deep into the earth, and these brittle rocks can still hold stress up (which ductile rocks won't do) and then break, causing deep quakes, same as at shallower depths. And sometimes those quakes are big. 

What I really learned in this whole process is the relationship between rock elasticity and temperature. So, returning to the question of the seismogenic layer, the reason that most earthquakes happen at a depth less than 15km is because the rocks aren't ductile at that range—they can't flow, they sustain pressure, crack, and snap. And that's an earthquake. But at deeper depths, rocks can flow. That's really crazy.

Coursera and NCSLET

The AMNH is offering three classes on Coursera this Fall: Genetics & Society, The Dynamic Earth, and Evolution. These courses have been organized by the National Center for Science Literacy, Education, and Technology (NCSLET) within the Museum's Education Department. This is the same group that runs the AMNH Seminar's on Science.

I'm very pleased to announce that I've been hired by NCSLET to work with them on all three Coursera classes. I'm a member of the instructional support staff and my responsibilities will include co-moderating the forums, tracking student interactions on various social media platforms (including Twitter and Facebook), responding directly to student questions about content, and identifying content areas where students are struggling to inform our just-in-time teaching responses.

AMNH.JPG

The three classes are part of Coursera's Teacher Professional Development offerings, and as such are geared towards educators. Each of the classes addresses the Next Generation Science Standards for GK-12 education. I'm excited to see how my efforts to translate research to teaching will play out on this new educational technology (MOOCs). I've taken a handful of MOOCs myself, mostly to enhance my own work in the areas of programming and statistics. So I can sympathize with teachers who will be coming to these classes looking for resources and knowledge that can they can bring back to their every day work. This, to me, is the true value of MOOCs—they lower barriers to gaining new skills and exploring new topics.

From Bill Gates' Reddit IAmA: "How do you see technology enhancing Mathematics education without actually replacing it?" And his reply: "The ability to test your knowledge and get refreshed on a topic you are making mistakes on will personalize a lot of the learning experience…. My foundation has funded a lot of MOOCs focused on community college kids or kids who have to take remedial math. I am optimistic these will make a big difference." So there you have it. I agree with Bill and I'm super excited to work with the NCSLET team to help educators test their knowledge and get refreshed on core topics. 

If you're an educator or a researcher interested in how teachers are using MOOCs to enhance their own teaching, please consider enrolling in the class. And say hi in the forums!

Samuel

Genetics & Society
by Rob DeSalle
Sep 9th 2013 (4 weeks long)

The Dynamic Earth
by Edmond Mathez and Ro Kinzler
Oct 7th 2013 (4 weeks long)

Evolution
by Joel Cracraft
Nov 4th 2013 (4 weeks long)

DNA Barcoding Summer Workshop


I just wrapped up a five day DNA barcoding workshop for high school students that was part of the Cold Spring Harbor Laboratory's series of summer enrichment programs. You can find out more about the program over at DNAbarcoding101.org. But before I get into my experience running the workshop, first a short digression about education. 

Do college students drop out of science because science is hard, or because they are unprepared for college STEM classes by their high school coursework? A recent working paper by the National Bureau of Economic Research makes the former claim based on a study of 655 students at one college. This is briefly written up by Matthew Yglesias over at Slate. There, he cautions that, "you probably either need better-prepared 18-year-olds or else you have to make the courses easier." 

The solution I'm partial to is better-preparing our high school graduates. But this is easier said than done. Chad Orzel has written up a more through take-down of the NBER paper over at ScienceBlogs. He's less convinced that the data support the claim that students in the sampled population dropped out of science majors because of a lack of innate ability or a lack of preparation. Correlation does not equal causation, yadda yadda yadda. A bigger sample size would great. 

Still, I've worked with NYC high school students and NYC college freshman for 7 years now and so I have perspective on both sides. While my experience is necessarily anecdotal, it's also highly granular and I know some of the stories that get lost in aggregate data. Students are often not prepared for college STEM classes, and they are unprepared in a (unsurprising) variety of ways. 

This is why I was so excited to participate in a summer workshop for high school students on conservation genetics and DNA barcoding. I worked with a selected group of highly motivated rising juniors and seniors on an applied research topic. The workshop had two components: a 5-day section on biodiversity conservation genetics and a 5-day section on DNA barcoding. I ran the DNA barcoding section. This workshop was organized by the Cold Spring Harbor Laboratory's DNA Learning Center and funded by the Pinkerton Foundation

In five days, my students (featured in the photograph above) were able to:

  • Extract genomic DNA from fish tissue samples
  • PCR amplify the COI marker and submit these amplicons for sequencing
  • Process raw ABI trace files—trimming, contig assembly, and quality control base calling
  • Obtain reference sequence data from GenBank and other sources
  • Construct a multiple sequence alignment of COI 
  • Make maximum likelihood gene trees
  • Communicate results to their peers in a presentation

All in five full school days. Each of these steps was a new experience for the students and even in their AP Biology classes they would not have the opportunity to do bioinformatics. Beyond providing students with the skills directly employed (which was never the point, for me anyway), the lessons have value because they provide perspective to the students—they get to experience research—and they get to interact and learn alongside a professional scientist.  

By bringing research into the classroom we can better prepare our students for the rigors of a college STEM education. This translational research can have a big impact in high school, as I have experienced through my work with CUNY's College Now program and now the CSHL Urban Barcode project. We promote professional preparation by providing these students an experience that mirrors research. And the goal isn't really the particular science skills because, I'd argue, the critical thinking and problem solving and communication skills developed when doing research are highly transferable. 

So rather than making science classes easier, I'd argue for making science classes more interesting and more engaging for students. In my anecdotal experience, this is easily accomplished by bringing research into the classroom. And the kids? They loved it. I think GenBank blew their minds. 

 

Evolution of Insect Pests Symposium Speakers

As I mentioned earlier, I'll be co-hosting a symposium at the 2013 annual meeting of the Entomological Society of America. The topic of the symposium is the evolution of insect pests in reponse to human-induced changes to the environment. This symposium will address theoretical and empirical developments in our understanding of the genetic basis of evolution in insect pests. This is a pressing topic because the species we care the most about are often pest species. Understanding the ways in which our actions drive their evolution is paramount. With new molecular technologies we have greater leverage than ever to study how insects respond rapidly to changing conditions, and we hope that this symposium will highlight novel approaches and insights into these processes.

We have the final speaker list and I'm thrilled to announce the lineup of talks. Here's the order, speakers, and talk titles. We don't have an exact day or time yet so I'll update with that information once the ESA program is announced. But if you're into insects, pests, and evolution, please consider attending the symposium. 


Evolution of Insect Pests in a Connected World:
ESA Member Symposium, November 10-13, 2013
Austin, Texas
Hosts: Samuel Crane, AMNH & Gabriel Zilnik, NCSU

Speakers: 
Ke Chung Kim
"Insect Pests and Biodiversity"

Alison A. Bockoven
“Expression of the red imported fire ant foraging gene and colony-level variation in behavior”
Blog: 6Legs2Many

Monica Poelchau
“The molecular physiology of an evolving adaptation - insights from the diapause response of Aedes albopictus

Martin M. Turcotte
“Experimental tests of rapid evolution driving pest population dynamics.”

Megan L. Fritz
“A next-generation sequencing approach to examining the evolution of Bt resistance”

Andrew Michel
“Population genomics perspective on insect biotypes related to host-plant resistance”

Jeff Fabrick
“Genetic and physiological adaptation of insect pests to insecticides”

Yves Carriére
“Landscape-based approach for sustaining efficacy of Bt crops.”


Check back here for more information as the date approaches, or follow me and Gabe on Twitter. 

Evolution of the Indoor Biome

This month I have the opportunity to participate in my first NESCent workshop. I’m excited about this workshop because it will allow me to push my research in a new direction while building collaborations with an outstanding group of researchers, and not all of them are biologists, either.

The workshop is called Evolution of the Indoor Environment. We’ll spend three days in Durham, NC discussing the built environment ecosystem—what it is, who’s in it, how it works, and how it evolves. This will hopefully be a catalyst for developing a new framework to understand the species we intimately interact with, the species in our homes.

And even though the workshop is focused on the indoor environment, we’ll also be considering the effects from outdoors. Home and community gardens, and even full-scale commercial urban farms (for example, Brooklyn Grange) are not indoors but they are a part of the built environment. I’d like to explore the possibility that urban agriculture—from the smallest window box of herbs to commercial farms—presents a unique opportunity to manage built environments and direct evolutionary and public health outcomes. How does the outdoor built environment impact the community composition of the indoor environment? Can we manipulate urban environments through agriculture and gardening to manage the evolutionary trajectory of the species within the community? And even closer to my own research interests, urban agroecosystems are likely more fragmented than their rural counterparts. How does this fragmentation impact the small populations of beneficial and harmful organisms found in urban farms and gardens? My own research questions have always been motivated by this tension between wildlife, humans, and society.

The workshop is being run by Rob Dunn (North Carolina State Univeristy), Jonathan Eisen (The Institute for Genomic Research), Kerry Kinney (University of Texas-Austin), and Craig McClain (NESCent). You can read more about the workshop and the other participants over on the Your Wild Life blog. Expect more blog posts here about my experience at the workshop and plenty of tweets while it's going on.