Inference and being wrong in a post-truth era

There’s been a confluence of recent events that have got me thinking about truth and facts. First of all, I’ve been thinking a lot about how we move forward, as scientists when there’s this steaming mess going on.  Secondly, there’s been a series of really honest blog posts where some amazing, respected scientists, talk about the times they’ve found errors in their published work. Thirdly a student member of a online community of academic women that I’m part of posted about a severe dressing down she got from her adviser for what appeared to be a few minor errors that she worried she’d undermined her professional credibility, and possibly her whole career. Finally, I’ve been preparing for another offering of my quantitative methods course, and as such, am thinking about how to best talk to students about data, inference, and what it all means.

robot

Sci, Robot.

It’s more important, now more than ever, that scientists are willing to stand up against misinformation. We are knee deep in it, and friends, we’re the ones holding the shovels. But we don’t always, because it’s exhausting and often makes us vulnerable. We live in an era where scientists are not particularly trusted. When we’re trusted, we’re seen as inhuman. And we’re certainly not understood- who can forget how our research is openly mocked with reductio ad absurdum arguments by people with political agendas to disprove our work1 or undermine science in general (a situation that, I fear, is only going to get worse over the next few years)?  Add into the mix the funding climate leading to cutthroat competition for positions2 and stir in the scientific enterprise’s (essential and important) self-criticism, and  it’s no wonder that scientists are hesitant to engage. In short, it’s soul crushing, and the stakes are high.

This puts a lot of pressure on scientists to be right.

But I believe this climate is hurting us- in a lot of ways. Toxic levels of perfectionism. In the example I mentioned above, we have a graduate student worried about her career because of a typo. I’ve often cited the times I’ve observed students I’m working with get stuck on data problems because they’re afraid to do the wrong thing. Heck, I’m struggling to get the words out right now, because I’m afraid that someone will read what I write and think I’m advocating for sloppy science.3

But how much value does science gain when its practitioners are paralyzed into inaction?  And even more pressing, how do we encourage more diverse contributions in science when people trying to join the community are are shunned when they misstep?

This whole seeing scientists as robots, expecting scientists to be robots, even from within, I believe has a much more insidious consequence as well. It sets up the expectation  that science, all science, every preliminary study, to be absolute.  And we, as practitioners, know that’s not true. And when science is seen as absolute and invariable, it sets itself up as a convenient straw-man for people with anti-science agendas. For example, anthropogenic climate change is happening.4 If you’re reading this blog, you probably agree with this statement. But there’s a controversy, and often cited by team Give-The-Planet-An-Uninvited-Sweaty-Hug5 is the so-called Antarctic cooling, as a point to ‘disprove’ global climate change.6

So, no. Obviously no. Thinking that an overwhelming body of evidence can be brought down by localized variation in trends? And this is not even to mention the role interpretation, statistics choice, even method of observation play. This is a problem, and I can’t help but feel it is up to me, at least in a small part, to fix it. My gut says this is something we can only address by helping people really understand how science is done, and by inviting more people in.

So back to my course- my corner of influence. As this is a course that advocates a open science approach, it forces students into a paradigm where they will be publicly wrong, or at least incomplete and unpolished. As I mentioned, this is something not all scientists take kindly to. But I know I’ve had a lot more luck convincing people of my sometimes controversial conclusions when I open up, show them the steps I took to get there. This is why I applaud the scientists who are open about their missteps and mistakes- these people are teaching the world more about science and process than any ‘perfect’ paper may.

In my own work, I’ve adopted something of a radical openness. The projects I’m leading right now are out there  for the world to see, from the time I create the first file and start dumping stream-of-consciousness comments in about what I intend to do, through each bump in the road.  It is my hope that through this openness and transparency, people feel invited to build on my work,  they can validate the robustness of what I conclude, and they can use these ideas to help, in a small way, understand and buffer change in the world.7

Seventeen students have chosen to join me on this journey next semester. I hope to give them what they need to save the world, too. No pressure.

  1. The blog title makes it easy for you to do this with my work. Since really transitioning to quantitative ecology full time, you might even say I use a computer to count imaginary bugs.
  2. #operationhiremeplease2017
  3. See footnote #2. I’m not. I’m meticulous.
  4. I do hope that NASA article I linked isn’t turned into an ad for a certain prominent brand of luxury hotel in newly coastal Ames, Iowa anytime soon.
  5. This was the most PG  glib nickname for this group I could muster.
  6. Incidentally, I was at a conference in South Africa in October, and Michael Gooseff presented the data from the McMurdo dry valleys that showed this apparent slight cooling trend from the 1978-1998, and then showed the rapid increase since then. I was most intrigued by the inflection point, naturally, as a person interested in breakpoint analysis would naturally be, so stay tuned for some upcoming work in that area. I’ve started a new project.🙂8
  7. And I mean this quite literally. The project I’ve linked to is developing a tool to understand when changes are occurring in dynamic populations from legacy population data. Because it’s really hard to determine when and how the factors regulating a population changed in an unbiased way- and without knowing that, it’s pretty hard to mitigate those factors.
  8. I’m being all secretive about this to create intrigue but if you’re motivated you can check out exactly what I’m doing on my github.🙂🙂
Posted in Uncategorized | 1 Comment

Back to it!

Oh, hey you! Blog. I missed you.

I’ve been busy.  Here’s, in general, what I’ve been up to, in the form of an annotated git contribution log:

git-log
I’m working on getting back into a groove, which will involve some more posts here detailing some of these previous events, and where I’m going with some new projects.

In the meantime, though, I recently recorded a 20-minute talk on my course. In case you’re one of the few people who have not been a captive audience for the live version of the talk, you can see it here:

More to come in the near future.

Posted in Uncategorized | Tagged , , , , , | Leave a comment

Some Mozilla Science Fellowship FAQ

You still have 14 days to submit your application for the Mozilla Fellows for Science! I’ve been putting the call out there on my networks, and there is lots of interest from the community. I’ve had a lot of questions, and many of them are falling into similar themes, so in the name of openess and fairness (and efficiency!) I thought I’d share them with my answers here, so everyone is working from the same information.

NB: You may also find some of my previous posts on the topic, particularly this one, useful.

Q1. So, the fellowship asks for 80% of your time, reserving only 20% for your research program. Christie, you’re a really research intensive, highly productive scientist, how the heck did you reconcile that? 

First of all, thanks for noticing- I am really into my science1, and as a person in pursuit of a research-intensive tenure track position, I know it’s important to show consitent productivity, so stopping or considerably slowing a research program is not an option. That being said, what you do with the fellowship is fairly open.

I’ve held the fellowship as a postdoc, and it worked well for me because I could adapt and shift my focus while still keeping my research program going, albeit at a slightly2 slower pace for hard publication production- but my work is in LTER data science, data synthesis etc, so it really was just a small departure to make it more about open science training. Of the other fellows, Joey is a MS student who successfully defended while on the fellowship, Richard a PhD student who is taking a break from his PhD work to go into full time open science advocacy and development work (just recently packed up and moved to Nairobi, the rest of us fellows are going to go visit him at the end of July), and Jason is an associate professor whose work has largely continued as it was, as it was open science aligned, just with the weight of Mozilla behind it now (meaning he gets invited to Very Important Parties in DC now because people listen to him🙂 ). We all did very different things for our fellowship work- Richard and Joey developed open tools for researchers and engaged in a lot of training activities, I taught a class and developed curriculum, Jason studied and wrote guidebook on how people were sharing information in participatory medical trials. For me, I spent a lot of time thinking about the gulf that exists between research and training, and how to close that up, using existing scientific infrastructure.

So what I’m saying is the 20% of your own research can mean different things, depending on what your work is now, and where you want to take it for the fellowship. For me, it meant feeling less guilty about pushing the work I was already doing in directions I wanted to see it going, but never really drawing a line between “20% postdoc Christie” and “80% fellow Christie.” It can be intense at times- there is a lot of travel expected which has been hard but also amazing (I’ve got two young kids), but it’s been super, broadening experience.

Q2. What do you even *do* as a fellow? Are you, like, full time, open science superheros?

for_science


Yep, this is the sort of thing I do. Professionally. That’s Kaitlin Thaney on the left. Photo by Joey K. Lee. Photoshopping by Richard Smith-Unna

Well. Kinda.

Sometimes, I wear a cape.

My average day as a fellow might look pretty similar to my average day from the before-time. However, I was already involved in the open science community, the data science communtiy, the open and reproducible training community before the fellowship started. See, unh, this blog, for example. I was spending an undefined portion of my time devoted to improving reproducibility in science, particularly as this relates to data and analysis. Both for the good of humanity, and my own selfish reasons3.

The fellowship dialed these activities to 11, but also took me out of my office to meet with more people, and takes me out of the academic bubble just enough to see our inefficiencies/issues with new perspective.  Fellows maintain close, if remote, working connections to the MSL staff and each other- we have a fellows chat that we basically keep open at all times- which functions like a water cooler in an office we’re all in. As a result, we’ve become as close as colleagues/friends working in a shared lab.4

I still work on papers, analyse data, help grad students with their projects, read the literature, write grant proposals, go to scientific conferences etc. I also blog, write curriculum, participate in conference calls/video chats, travel to meetings, teach classes. It is simultaneously not different and very, very different. In a good way.

Q3. Can I have the money without doing anything?

No. Well, I don’t make this call. But. No.

Q4. What’s the application process like? Where do I put my detailed sampling plan into this form? There’s no place for my 20 page research proposal. What gives?

The application form is simple. The application is not long. Don’t panic.

The reason for this is that the fellowship is fairly open and does not require you to have a completely, 100% developed idea. The first part of the fellowship is devoted to developing your idea(s), and figuring out the best way to impliment them in your community with the help of MSL staff. Think about the goals of the MSL and the fellowship program:

The Mozilla Fellowships for Science present a unique opportunity for researchers who want to influence the future of open science and data sharing within their communities.

We’re looking for researchers with a passion for open source and data sharing, already working to shift research practice to be more collaborative, iterative and open. Fellows will spend 10 months starting September 2016 as community catalysts at their institutions, mentoring the next generation of open data practitioners and researchers and building lasting change in the global open science community.

Think about how the fellowship will help you help make science a more open, more collaborative place. Think about why your community needs it. And then tell us about it.5

Good luck with your application!

1. I *am* charming.
2. 3 4 papers so far this year, but in fairness, only one of them was first authored by me.
3. People ask me to help analyse their data all the time. When their data sucks, it makes my life harder. And it significantly constipates our science. And makes me a sad panda.
4. Real talk: the community we’ve built within the MSL and with the fellows reminds me very much of my time as a(n incredibly socially awkward) teenager who just discovered the internet. Suddenly, a new community that answers to a need I was not finding in my local population. My local scientific peers are awesome, don’t get me wrong, but between postdoc nomadism and being a data geek in a biology lab, it can get lonely.
5. Pro-tip: Use simple, clear language. Avoid jargon. Part of opening up science is becoming better communicators of science. Scientists have a bad habit of excluding people from the club with jargon because it makes us feel smart and a member of the elite- another thing that hinders efforts to diversify the scientific community- makes people with diverse backgrounds feel like they don’t fit/don’t now where or how to engage and also makes established scientists take people who don’t talk like them less seriously. I could rant about this for a long time.

Posted in Uncategorized | Leave a comment

Reflections: My ride on the Mozilla Fellow Ship

2016-06-13 20.30.34

Me, Foxy, Steph and Arliss, at the opening mixer for Mozilla All Hands London 2016. Hashtag mozLondon.

I’m just shy of two months from wrapping my Mozilla Fellowship for Science. It has been an amazing ride. I’ve traveled more than I have in my life,1 met amazing people, and I got to design, build and teach the course I’ve always dreamed of. I built a network of like-minded people, been challenged fiercely for my evangelism for open science, evaluated and re-evaluated my viewpoints. I’ve looked at the problems we face in science, and reproducibility, openness and accountability, and found the many intersections between them and our systemic problems for diversity and inclusion in the academic enterprise. I’ve gotten mad as hell and been empowered to change the system from within. My work is not done- far from it- but this fellowship has given me the tools I need to help change the world- and I hope for the better.

So, the other day, I opened up my application package for the program. Because the fellowship experience has been life changing for me, though, I thought it might be interesting to talk about how my perspective has shifted in the past year- and how I feel about my answers to the application prompts.  So here’s how I’d change my application, if I was writing it today:

 

Research fields (up to 10 words)

Entomology, applied ecology, population and community ecology, invasive species, agriculture

Not too much has changed here, except I think I’ve gotten over some impostor syndrome about data science and quantitative ecology, so I’d probably add those. I’d probably switch the term “entomology” for “insect ecology” too, because I’ve been feeling more like an ecologist in the broader sense lately.

Research focus (up to 50 words)

I study long-term trends in the population and community ecology of insects that are important in agricultural systems, like pollinators, pests, and biological control agents.  My goal is to use our understanding of these interactions to help develop healthy, better functioning, and more sustainable agricultural landscapes.

Revised answer: I use compiled or unconventional data sources to study long-term trends and responses to change in the population and community ecology of organisms. My goal is to use our understanding of these interactions to help develop healthy, better functioning, and more sustainable landscapes.

Current research team (50 words)

I’m currently working as a senior postdoctoral research associate in a moderately sized, highly productive Landscape Entomology lab. The team includes the Principal Investigator, one additional postdoc, a full-time technician, two PhD students, three MS students, seven undergraduates, and numerous collaborators in the US and around the globe.

I am now a member of a community of thousands of people with a unified goal- to open the web.2  To make information, technology, and opportunity available to everyone. I’ve worked with, interacted with so many amazing, brilliant, empowering people through Mozilla and the greater open web community.

Not much has changed about my position within academia, but I am currently on the market for something new.  I’m a well-connected, productive data scientist and quantitative ecologist. Call me!🙂

 

Cover letter (up to 250 words)

To the selection committee,

I am an ideal candidate for a Mozilla Fellowship for Open Science. I’m an early career ecologist who is passionate about open science, both for improving the efficiency of my own work, and for the advancement of science as a whole. I’m positioned in a field where there is a tremendous need for open science for open science advocacy and training, and I am embedded in several well-respected, large scale projects, giving me the audience and credibility which would allow me to do so effectively.

Holy heck can open science and reproducible research techniques improve your efficiency in the long run. Say you sent your paper off for review, and reviewer 3 just hated the color scheme you used for your 12 figures. How long would it take you to change that? I could change one line of code, rerun, and bam, all the figures would be done again with the new color scheme. Could you do that?3 I can teach you. In fact, I did teach some students, and I’m working with sites within the US LTER network to get the word out on this. And the US-LTER is sending me to South Africa this fall to talk about teaching students this way to our greater international network, the iLTER.  People are hungry for this, we just need to get it to them.

The open science movement has critical implications in most disciplines, but particularly in the applied sciences. In my subfield of agricultural entomology, research often has direct implications on both environmental health and human livelihoods. It is essential for stakeholders to have access to all the available information when making recommendations. However, the entomological community tends to be fairly conservative in regards to the adoption of new practices and is, in general, wary of open science.  I’ve made significant inroads by advocating a ‘baby steps’ approach, encouraging my established colleagues to make small, meaningful changes in practice towards open science.   I believe there is an even greater opportunity in promoting open science in a formal, structured way to graduate students, establishing open practice as the default as they start their careers, and this fellowship would give me the tools to develop just such a training program.

I still believe that the only way to really reach established academics on open science is to 1) target them through their trainees and 2) meet them using established academic routes- hence a traditional course for grad students. But baby steps are not enough for real change in our lifetimes. I think radical early training efforts are what we really need. Here are the slides from a recent talk I gave on this subject. Sprinkling in pedagogical methods that are proven to improve the retention of women and people of color in the quantitative sciences, and we have something. This is a call to action. We can make science more diverse, more inclusive and more open at the same time. We just have to go about this with intention, and not accept the status quo.

Thank you for considering my application. I look forward to hearing from you!

-Christie Bahlai

You’re welcome, Christie-from-a-year-ago.

 

Describe to us how open science advances your research (100 words)

Open science practices have been both headache-saving (though increased reproducibility)  and network-building (through increased visibility and access) for me, but probably is most apparent in my work through open data. My research program relies on long-term, collaboratively generated databases of insect observations.  Data sharing (often through informal networks) is usually how I initially obtain data, and these data often come in a format that requires a significant amount of processing before it is usable.  Truly open data greatly improves the efficiency of my work because it comes in a well-documented, well formatted package- saving headaches.

Not much to change here.

 

What work are you currently involved in that’s relevant to becoming an open science leader? (100 words)

I write a blog about data management and open science that’s designed to be a friendly introduction for the beginner- targeted at the organismal ecology community.

I sit on the Open Science Advisory Panel for the International Network of Next Generation Ecologists

I am an instructor for both Software and Data Carpentry,  and played a large role in developing the teaching materials for Data Carpentry.

I am affiliated with NSF’s  Long Term Ecological Research network, a major research initiative with 26 permanent research stations in the US. I sit on the Information Management Committee at my home site of Kellogg Biological Station.

Well, that, the fellowship, and the community now.

 

How would this fellowship accelerate your work? (50 words)

This fellowship would provide me with the means to focus more time on the open science activities I’m already actively involved in, and allow me to expand and formalize my work within my institution and my network. Specifically, I am interested in developing an open science course for graduate students.

Check and check. Now, I just need to get everyone on board with teaching the course. I’m currently preparing an instructor guide with some of my amazing Mozilla colleagues, watch this space to learn how (and why!) you should teach a course like this at your institution!

 

What do you see as the opportunities for open research at your university? (up to 50 words)

The LTER network generates numerous underused, open datasets, and network-affiliated students are required to be trained in Responsible Conduct of Research.  An open science course that takes students through the process, from data to analysis to publication, using these data, would meet both institutional needs and open science training goals.

I’m currently working to leverage this infrastructure now. Will let you know how it goes.

What do you think needs to change most immediately in the system? (50 words)

Training. Despite rapidly changing open science requirements currently unfolding at the federal level (see NSF’s “Public Access Plan” 3/2015) graduate programs almost never offer formal training in open science or reproducible research.  Proper training will help researchers cope with changing requirements- making training appealing even to ‘closed’ scientists.

Training is a big part, but the incentive and ranking structure in science is another big part. But this an opportunity, really, because we need to change how we do science because in addition to being directly hostile in many cases to open science practices….well,  I’m just going to come out and say it, the incentive structure in academic science favors the established, the white, the rich and the male and systemically disadvantages people who do not belong to those groups. It resists change in practice for the good of the people because the people who make decisions succeeded in the present paradigm.  If we do not CONSCIOUSLY and DELIBERATELY re- structure how we rank scientists, how we measure success in science, nothing will change. In short, Open Science, Inclusive Science, and Reproducible Science regulations like the one I mentioned in my app are good, but they need teeth.

 

What project in the field do you find most inspiring to further science and the web? (50 words)

Software Carpentry (+ Data Carpentry)- this project is fantastic. When I encountered software development in undergrad, I was put off by the insular, competitive culture. SC fosters a community with a spirit of “Hey, let’s learn to get better at programming and reproducibility together!” which allows even novices to contribute.

Nothing but love for SWC and DC still. The course I developed builds on them to offer the students a more immersive, long-term experience through a semester-long course, to think about their own field using a data science lens- and I feel like SWC/DC are a perfect gateway to this.

Why is the open web important to you? (100 words).

Even without the benefits I’ve directly received from open science (access to data, a wider network of collaborators, a platform for promoting my own research), I believe that opening up our practices is just morally right. It democratizes access to information and allows people outside western academia to participate.  I work with conservation biologists at NGOs and scientists from developing countries – these are people who work on the front lines to improve environmental sustainability, protect endangered species, and feed the poor- they NEED access to the science so they can make the best decisions.

This. A million times this.  Worded more strongly. In academic science, we are really good at building walls and patting ourselves on the back for how smart we are when we get grants and publish papers. I’m not going to lie- I REALLY LIKE GETTING GRANTS AND PUBLISHING PAPERS BECAUSE IT MAKES ME FEEL LIKE I AM WINNING AND IT ALSO CONTRIBUTES TO MY JOB SECURITY SO THAT’S COOL.4 But are we really winning if our science doesn’t benefit humanity, if no one other than our immediate colleagues can access it? If we are training our students to use proprietary tools they won’t have access to once they’re out of school, are we really training them at all? If we’re lamenting the lack of evidence-based decision-making in the world, and then not providing open access to their papers, we’re not just part of the problem.  We are the problem. Stop being the problem. Is publishing a closed-access paper in Nature worth the cost to humanity, just because you got a paper in Nature?

So anyway, as this fellowship ends, it’s not the end for me. It’s the beginning of something bigger. I will take what I’ve learned, the friendships and collaborations, and use them to help me become a better scientist, a better human, and work towards making science better for more humans. I’m not sure exactly where I’ll be next, but you have not heard the last of me.
—-

1. In the past academic year, I’ve been to the Estes Park CO, New York,  Minneapolis, London, Berlin, Boston, Santa Barbara, when combining my standard academic and purely Moz travels. Just got back from another trip to London for the Mozilla All Hands meeting. By the end of the fellowship I will have attained Silver Medallion status with Delta. w00t w00t.

2. none of this walled garden crap that keeps not only people with cancer from being able to research their disease, but often also the doctors treating them from accessing the research too. That’s BS and I will continue to be mad about it until it stops happening.

3. In the words of eminent philosopher Chamillionaire, “Yeah, I ain’t saying it just to brag, I say it so you can be motivated to [properly script your analyses]”

4. And postdocs need to take wins where we can get them.

Posted in Uncategorized | 1 Comment

Open Sourcing my fellowship app

The call for the second class of Mozilla Fellows for Science is open! I thought it might be helpful to the community if I opened up the application I sent in last year. Richard, a fellow fellow (HA! this will never get old)  already did this– you can see we have different styles.

Without further ado- the headers I’ve included are the ones that were on the application call last year, and the word counts were the constraints on the text boxes. Here you go!

Mozilla fellows app- Christie Bahlai

Research fields (up to 10 words)

Entomology, applied ecology, population and community ecology, invasive species, agriculture

Research focus (up to 50 words)

I study long-term trends in the population and community ecology of insects that are important in agricultural systems, like pollinators, pests, and biological control agents.  My goal is to use our understanding of these interactions to help develop healthy, better functioning, and more sustainable agricultural landscapes.

Current research team (50 words)

I’m currently working as a senior postdoctoral research associate in a moderately sized, highly productive Landscape Entomology lab. The team includes the Principal Investigator, one additional postdoc, a full-time technician, two PhD students, three MS students, seven undergraduates, and numerous collaborators in the US and around the globe.

Cover letter (up to 250 words)

To the selection committee,

I am an ideal candidate for a Mozilla Fellowship for Open Science. I’m an early career ecologist who is passionate about open science, both for improving the efficiency of my own work, and for the advancement of science as a whole. I’m positioned in a field where there is a tremendous need for open science for open science advocacy and training, and I am embedded in several well-respected, large scale projects, giving me the audience and credibility which would allow me to do so effectively.

The open science movement has critical implications in most disciplines, but particularly in the applied sciences. In my subfield of agricultural entomology, research often has direct implications on both environmental health and human livelihoods. It is essential for stakeholders to have access to all the available information when making recommendations. However, the entomological community tends to be fairly conservative in regards to the adoption of new practices and is, in general, wary of open science.  I’ve made significant inroads by advocating a ‘baby steps’ approach,  encouraging my established colleagues to make small, meaningful changes in practice towards open science.   I believe there is an even greater opportunity in promoting open science in a formal, structured way to graduate students, establishing open practice as the default as they start their careers, and this fellowship would give me the tools to develop just such a training program.

Thank you for considering my application. I look forward to hearing from you!

-Christie Bahlai

Resume

(attachment)- if you really want to see it, let me know, but I am no pro at making *resumes,* I’ve been in the academic bubble for so long and I cannot understand why not everyone wants to know the precise titles of my two dozen papers. Because they’re awesome papers, yo.

Letter of support from supervisor (500 word max)

Not included here- confidential.

Describe to us how open science advances your research (100 words)

Open science practices have been both headache-saving (though increased reproducibility)  and network-building (through increased visibility and access) for me, but probably is most apparent in my work through open data. My research program relies on long-term, collaboratively generated databases of insect observations.  Data sharing (often through informal networks) is usually how I initially obtain data, and these data often come in a format that requires a significant amount of processing before it is usable.  Truly open data greatly improves the efficiency of my work because it comes in a well-documented, well formatted package- saving headaches.

What work are you currently involved in that’s relevant to becoming an open science leader? (100 words)

  • I write a blog about data management and open science that’s designed to be a friendly introduction for the beginner- targeted at the organismal ecology community.
  • I sit on the Open Science Advisory Panel for the International Network of Next Generation Ecologists
  • I am an instructor for both Software and Data Carpentry,  and played a large role in developing the teaching materials for Data Carpentry.
  • I am affiliated with NSF’s  Long Term Ecological Research network, a major research initiative with 26 permanent research stations in the US. I sit on the Information Management Committee at my home site of Kellogg Biological Station.

How would this fellowship accelerate your work? (50 words)

This fellowship would provide me with the means to focus more time on the open science activities I’m already actively involved in, and allow me to expand and formalize my work within my institution and my network. Specifically, I am interested in developing an open science course for graduate students.

What do you see as the opportunities for open research at your university? (up to 50 words)

The LTER network generates numerous underused, open datasets, and network-affiliated students are required to be trained in Responsible Conduct of Research.  An open science course that takes students through the process, from data to analysis to publication, using these data, would meet both institutional needs and open science training goals.

What do you think needs to change most immediately in the system? (50 words)

Training. Despite rapidly changing open science requirements currently unfolding at the federal level (see NSF’s “Public Access Plan” 3/2015) graduate programs almost never offer formal training in open science or reproducible research.  Proper training will help researchers cope with changing requirements- making training appealing even to ‘closed’ scientists.
What project in the field do you find most inspiring to further science and the web? (50 words)

Software Carpentry (+ Data Carpentry)- this project is fantastic. When I encountered software development in undergrad, I was put off by the insular, competitive culture. SC fosters a community with a spirit of “Hey, let’s learn to get better at programming and reproducibility together!” which allows even novices to contribute.

Why is the open web important to you? (100 words).

Even without the benefits I’ve directly received from open science (access to data, a wider network of collaborators, a platform for promoting my own research), I believe that opening up our practices is just morally right. It democratizes access to information and allows people outside western academia to participate.  I work with conservation biologists at NGOs and scientists from developing countries – these are people who work on the front lines to improve environmental sustainability, protect endangered species, and feed the poor- they NEED access to the science so they can make the best decisions.

 

Posted in Uncategorized | 6 Comments

Passive crowdsourcing- finding the data that people don’t know they’re creating

I have a new paper out! You can read it: Predicting plant attractiveness to pollinators with passive crowdsourcing.1

2016-06-01 09.19.12

Just a human engaging in a normal human leisure activity.

A while back, my colleague, Doug Landis, was searching the web for pictures of flowers for  a project about native plants, and noticed that some pictures of flowers he looked at frequently captured insect visits.  He got to wondering- do the bees we occasionally observe in this sort of photo have…meaning?

He asked me what I thought of his observation- and could we test it. Are flowers that are photographed more frequently with insects, indeed, more attractive to insects? This idea got me pretty excited. If you’ve been following me for long, you know I delight in finding data and patterns in places we don’t normally think to look. It’s kind of my *thing.*  And through the course of everyday activities, humans passively collect data about the world around them. It seems to reason that common leisure activities -like photographing and sharing pictures of flowers– could potentially capture ecological phenomena- in this case, the visitation rates of pollinators to flowers of different species.

So we developed a method to test our hypothesis.  Using a technique we termed ‘passive crowdsourcing,’ we searched Google Images for pictures of blooms of 43 common flowering plants that are native to Michigan, and identified insects that were visible visiting the flowers in the photos. We then compared these observations to visitation rates observed in controlled experimental trials using these same plants. We found that we could predict how often a flower was visited by wild bees by the number of visits we observed in the internet images, although relationships were less clear for honey bees and bee mimicking flies. Patterns were strongest for flowers that bloom in late summer, when more bees tend to be around in our area.

We’re pretty excited to see how passive crowdsourcing can be applied in the future. This method could be used by scientists to make predictions about other ecological phenomena that may be documented by human use of the web. Essentially anything that people tend to photo-document with any frequency could be capturing data, and could potentially help unlock the scientific mysteries of the future!2

1. And it’s all completely open access, because that’s how I roll. Our raw data and code is available here.
2. If anyone asks you to put down your phone and stop taking pictures of everything, you can gently explain how you’re advancing science.🙂

Posted in Uncategorized | Tagged , , , , , , , | 6 Comments

Why the heck aren’t research papers free?

2016-03-14 13.37.23

*yelling* Is this even a question? Of course they…

Should all research papers be free?

Um. Yeah. Obviously. Scientific knowledge doesn’t do much good if it’s all locked up, only accessible to the rich and/or privileged.

When I put it that way, I never get much argument.1

In fact, the majority of scientists I know tend to agree. They want their work to be readable to the most people possible. If someone is as interested as me in how overwintering soybean aphid eggs acquire heat from sunlight due to their coloration and placement on the plant good lord I don’t want anything to stand in their way because this person will, very likely, be my new best friend. But things do stand in the way (yup, my article above is paywalled  ETA: hey cool! looks like the embargo period is over! read all about my cool model, everyone!!), and it doesn’t just make scientists lonelier people.2 It keeps the science out of the hands of the farmers who may be looking to my research to figure out if she has to worry about soybean aphids next season. It keeps science out of the hands of the policy maker that is writing regulations and guidelines about how to deal with invasive species. It keeps it out of the hands of the scientists in developing countries that are trying to crack a similar problem in their landscapes with resources much more limited than what we’re privileged to have here in North America. It wastes time. It wastes brain power.

Not having open access to scientific research hurts us. It hurts people. Many have been screaming it from the rooftops. The problem is many, many papers are ‘protected’ under copyright, and these copyrights are enforced by for-profit publishers. The law is, unfortunately on their side (at least in the US), which means they can, and do take vindictive action against those seen to be in violation of the law. The long-term solution is that these laws need to change- they need to change so they protect the interests of science, scientists, and humanity. Not large corporate publishing houses.

Why haven’t scientists all gotten together to take a stand? Well, they have. We have. Scientists are increasingly choosing to publish their work in open access venues.3 This is good. This is important. But there is still a heck of a lot of human knowledge still going into closed venues. The reason? Costs. Costs, measured in money, time and professional prestige. This is how they get us, this is how they persist.

The big publishing houses are nothing if not very clever with developing their business model. They have created a market where they are the arbiters of ‘quality’ of science that is self-reinforcing. Scientists are busy people. The higher rank you achieve,  the busier you are. Publishers capitalize on that by creating exclusive journals- essentially filtering4 the scientific product for the busy scientist. These contributions that make it past these filters are valued more in this paradigm, thus the scientists authoring these contributions are valued more, are more likely to be promoted. You can see how this value system propagates itself- and thus, there’s a direct incentive to buy into the system.

I mostly fight this aspect of the system by yelling at it. It works, sometimes.

The other disincentive, though, is something I struggle with more, because no amount of yelling helps.

In a lot of cases, publishing in open access journals (or paying for the open access option in a ‘regular’ journal) is prohibitively expensive at the individual lab level. PLoS One, for example, cost $1450 last time I looked. In a discussion on Facebook this weekend, a friend cited a $640 bill from PeerJ.5 You can often publish closed access for much less, or even free in journals under the purview of the big publishers. This can be difficult to justify when you don’t have a large research budget and you need to pay an extra semester of GRA stipend for a student whose experiment took longer than expected.6

The situation is even complicated  for small-medium society journals. For example, in the journal I published in most early in my career, Environmental Entomology, there is no publication fee for members of the society for subscriber-only access, but open access fees for the same paper start at $2000USD. I love the ESA and what they do, and I know that they use the revenues they make from both subscriptions and open access fees to support society activities- our annual meeting, scholarships for students, funds to help support parents in science- things I’ve personally benefited from. This model has always worked for the society and I know they’re hesitant to change it.

There are a few outlets and workarounds. For example, Royal Society Open Science currently doesn’t have publication charges (and they cover the cost of a data submission to Dryad!). Another friend  at another large American university told me that her library has a program to help researchers offset the costs of open access publication (you just need to apply for funds VERY EARLY in the fiscal year, because the money is snapped up quickly due to high demand). We can advocate this approach to our own libraries- eventually, the budget allocated to subscription fees could be allocated to open access charges instead. I feel like this is the most likely long-term solution. But the patchwork of current availability means that, unfortunately, change to an entirely open access model is not immediately feasible for many labs. Combine that with the professional disincentives, and it’s clear we still have a lot of work to do on the road to open access to scientific information.

*sigh*

This is the kind of thing that keeps me up at night, you know. But we will get there.


1. This may be because I’m scary when I start on about the morality of open access. But…You’d tell me if I was scary. Right? RIGHT?!
2. Please, email me for a reprint, my secret friend.
3. This content better not be paywalled. It would reach a critical level of irony. The world might implode.
4. Filtering for…well that depends. Some might argue they filter for the most sensationalized, oversold, and likely irreproducible science. I’d never make that claim without data though.
5. This is even more painful when you consider exchange rates. Canadian researchers are plagued with a weak dollar right now, for example.
6. You want this student to, y’know, be able to eat and live and stuff.

Posted in Uncategorized | Tagged , , , , , | 4 Comments