Feeling Clumpy?

By Ian Vorster March 20th, 2014 at 9:07 am | Comment

Citizen scientists can help ID the progression of bacterial infection in plant cells by determining how “clumpy” plant cell images are.

Explore the microbiome around and inside you with these citizen science projects!

clumpy
The language on the Clumpy homepage might be considered a challenge for the average citizen scientist: “The model plant-pathogen system comprising the plant Arabidopsis thaliana and the pathogenic bacterium Pseudomonas syringae has been used very effectively to elucidate the nature of the pathogenic interaction.” However, once you get started on this citizen science project, you will soon get a feel for it, and perhaps even enjoy it as I did.

Clumpy is a citizen science project that tests for a bacterial infection in plants. When microbiologists found that organelles in the plant’s photosynthetic cells (i.e. chloroplasts) tended to “clump” together when subjected to bacterial infection, they saw opportunity for a citizen science experiment whereby the public could assist with help in classifying images for ‘clumpiness.’

The Clumpy project came out of observations made by Dr. Littlejohn, a postdoctoral researcher in the Bioscience Department at the University of Exeter; Dr. Murray Grant, a Professor of Plant Molecular Biology; and Dr. John Love, Associate Professor in Plant and Industrial Biotechnology at the University of Exeter. They noticed this unusual phenomenon, which might have important implications for how they understand plant-pathogen interactions. “It was through a conversation with Professor Richard Everson at an Exeter Imaging Network meeting, that the multidisciplinary team got together to set up the online experiment,” said Littlejohn.

The idea to use citizen science to annotate bacterial infections in plants came about in part due to the difficulty in using computational methods alone. Trying to characterize images using abstract notions such as ‘clumpiness’ is an area where humans can easily outperform current computational approaches. In addition, annotation of the images doesn’t require any special expertise, so the problem seemed like an ideal match for citizen science. “We also thought the images themselves were intrinsically interesting, which would help motivate people to provide a wide range of annotations,” said Hugo Hutt, a PhD student in the Department of Physics at the University of Exeter.

Dr. Littlejohn commented, “It would be great to know if it were the plant or the bacterium that initiates the ‘clumping’ of chloroplasts in the leaves. This might help us understand why the chloroplasts clump and which partner in the pathosystem is benefiting from it.” What does this do for society, you might ask? The benefit of a study like this might include fighting diseases in food crops for one.

Verifying the Data

When I first started to use the Clumpy website to classify whether an image was clumpy or not clumpy, I kept second guessing myself, and moved through the selections very deliberately, mulling each one over carefully. They all looked too similar, which got me to thinking about verification of the data. Since all science depends on accurate data, how do they know whether or not answers provided by the average Joe are accurate or not?

Hutt was involved with this aspect of Clumpy—the verification of data:

In 2013 we published an article in Computational Intelligence about this. We tested statistical methods to evaluate the accuracy and reliability of users. For example, to evaluate the accuracy we compared the user annotations with those assigned by an expert. We also measured the degree of consensus among users based on how correlated their annotations were.

The results showed a surprising level of accuracy, which my purely objective test might support—after about 15 attempts I began to recognize ‘clumpiness’ more intuitively, and after just 30 I felt I had it nailed. Hutt and colleagues hope to publish an extended version of the paper this year in a special issue of Soft Computing.

Image

With respect to obtaining a consensus score people were asked to make annotations in one of three paradigms: classification, scoring and ranking. Termed “a web-based citizen science experiment,” Clumpy tasks are evaluated in relation to the accuracy and agreement among the participants using both simulated and real-world data from the experiment. The results show a clear difference in performance between the three tasks, with the ranking task obtaining the highest accuracy and agreement among the participants. That means people like me were capable of producing accurate results when we checked in to Clumpy!

[Note: Read more on how other projects verify crowdsourced data through consensus, and read about one success story about how crowdsourced data was comparable to that produced by leading experts.]

Until now the results have been used to publish more on the computer-collection side, than on the plant biology side, but Littlejohn said, “We are looking to fit this result in with a broader biological study.”

The project has been running since August 2012 and currently houses over 10,000 annotated images. Imagine the cost, time and resources allocated to this process, if citizen scientists had not been involved!

Images: Courtesy of clumpy.ex.ac.uk


Ian Vorster has a MS in Environmental Communications and most recently served as director of communications at the Woods Hole Research Center in Massachusetts. Prior to that he worked in the health communications field. Ian has served as a designer, writer, photographer, editor and project leader in the field of science, and now works freelance in a blend of these roles. You can see more of Ian’s work at www.dragonflyec.com.

Me, Myself, and My Microbes

By Sheetal R. Modi March 19th, 2014 at 5:34 pm | Comment

Participate in American Gut to find out what bacteria live in your body and help scientists gather data on the diversity of microorganisms that affect our health.

Explore the microbiome around and inside you with these citizen science projects!

american_gut_image

Bacteria usually get a pretty bad rap. Perpetrators of strep throat, food poisoning, hospital infections, the list goes on. But not all bacteria are insidious in their intentions–in fact, many are harmless and even friendly, including the trillions that tag along in and on our bodies on a daily basis. In return for providing these microorganisms with a comfortable and long-lasting residence, they perform a number of chores for us and proactively help maintain our health.

Notably, they extract energy out of the food we eat, aid in the development of our immune system, and fend off intruding pathogens. Bacteria live in multiple areas on the human body, but bacteria in the gut have received the bulk of scientists’ attention so far. And not without good reason–these bugs amount to a whole kilogram in an average individual’s gastrointestinal tract, meaning that on a yearly basis a human adult will excrete their own weight in fecal bacteria. Recent work has shown that bacteria in the gut environment play a causative role in weight gain, obesity, and malnutrition, and that sustained changes in diet can have substantial effects on the composition of these bacterial populations. So not only do the bugs in our gut affect our health and well-being, but our diet and lifestyle modulate what bacteria live there, giving the phrase “you are what you eat” a whole new meaning.

Thus far, most scientific studies on gut-residing bacteria have focused on specific cohorts of carefully selected individuals. As a result, these studies reflect our diversity “to about the same extent that Congress does,” as a team of researchers at the University of Colorado, Boulder puts it. This team, led by microbial ecologists Rob Knight and Jeff Leach, wants to remedy current limitations by obtaining a larger set of bacterial data from a much more diverse population- basically people like you and me, or even literally you and me.

In a citizen science project called American Gut, Knight, Leach, and collaborators offer anyone living in the U.S. the opportunity to submit a biosample (from your skin, mouth, or fecal matter), and for a $99 donation they will process and analyze your sample and give you a detailed description of the microorganisms on your body, in your mouth, or in your gut (depending on the source of your sample). Additionally, the analysis offers you a relative comparison of your bacterial community to the thousands of other people who have participated in the project.

So what’s happening with all the data that’s being collected? American Gut asks participants to take a lifestyle survey and a detailed week-long dietary inventory to accompany their biosample. American Gut researchers and collaborators seek to associate different factors like smoking, veganism, or gluten intolerance to different microbial communities. ”We’re interested in whether we can pick up diet, geographical or seasonal associations. There are also some more specific projects being run through American Gut on inflammatory bowel disease, autism, and several other diseases” said Knight. Overall, scientists studying the human microbiome (or the collective genome of host-associated bacteria) want to know which of these factors make a difference in shaping our microbial populations and what that means for our health. By crowd-sourcing data from all walks of life, American Gut is amassing what’s arguably the largest and most diverse set of information on host-associated communities to start discerning this information. “It will substantially expand our knowledge of the kinds of microbiomes that are out there, will give us a better understanding of what matters and what doesn’t (in terms of factors and controls), and will perhaps allow us to start seeing similarities among different disease states (depending on how many people who are willing to share de-identified medical information sign up).”

Using a citizen science approach offers the benefit of having a large pool of data to work with, but there are some downsides. “The main challenge is cleaning up errors in the data, for example, we don’t really think we have participants who were born in 1060 or in the future (and we don’t know how they managed to bypass the web form validation either),” said Knight. In line with its citizen science goals, Knight and Leach have prioritized making the project open source and open access. The data, in the form of sequences of bacterial DNA (with no personal information), will be publically available for anyone to obtain and analyze. Most academic labs don’t have the funding to generate this type of data, so American Gut enables researchers to independently pursue their own hypotheses about the microbiome and its complex interplay with the environment and human health.

Interested in knowing what bugs are in and on your body? Perhaps you want to know how your bacteria change over time or what bacteria you share with a family member or significant other? Check out different options for your donation to American Gut. Even biosamples from dogs are welcome!

Image: Courtesy of Rob Knight at American Gut

More reading on the microbiome:

1. http://www.nytimes.com/2013/05/19/magazine/say-hello-to-the-100-trillion-bacteria-that-make-up-your-microbiome.html

2. http://www.scientificamerican.com/article/microbiome-graphic-explore-human-microbiome/


Sheetal R. Modi is a postdoctoral fellow at the Wyss Institute for Biologically Inspired Engineering at Harvard University where she studies how bacteria develop and spread antibiotic resistance. She has a PhD in Biomedical Engineering, and when she’s not growing her bacterial cultures (and repeatedly killing them), she enjoys science communication and being outside.

 

Measuring Environmental Stewardship

By Lily Bui - Executive Editor March 19th, 2014 at 12:17 pm | Comment

Cornell Lab of Ornithology’s Environmental Behaviors Project seeks help in sorting and ranking environmental stewardship.

Citizen_Science_hiking_credit_GlacierNPS

Many citizen science projects have been very successful in collecting high-quality scientific data through the participation of citizen scientists. However, less emphasis has been placed on documenting changes to citizen scientists themselves. In particular, many projects hope participants will increase their environmental stewardship practices, but few, if any projects, have been able to accurately measure or detect behavior change as a result of participation.

Beginning in 2010, our team of researchers at the Cornell Lab of Ornithology set out to create a toolkit of resources for helping project leaders measure participant outcomes. This project, titled DEVISE (Developing, Validating, and Implementing Situated Evaluation Instruments), is the parent of the Environmental Behaviors Project. In fact, the EBP is one of the final elements of the toolkit to be developed. So far, the DEVISE team has created and tested valid tools to measure interest, motivation, self-efficacy, and skills related to both science and environmental action.

When completed, the Environmental Behaviors Project will result in a tool for measuring environmental stewardship behaviors in citizen science participants. We are looking for about 75 participants to sort a variety of stewardship activities into categories, and then rank those same activities by ease and importance. What makes this tool unique is that it will have input from a variety of people and be a weighted scale, informed by the degree of ease and importance that people assign to each item.

The environmental behaviors tool will be an exciting conclusion to the DEVISE project. It is very common for citizen science projects to list behavioral change and increased stewardship as main goals – but these can be very difficult to measure accurately! Hopefully, by making this, and the other DEVISE tools available to project leaders, we can go beyond anecdotal accounts of the power of citizen science and provide evidence-based outcomes of the importance of citizen science to the people who make it possible.

Image: Glacier NPS

Co-authors:

Tina Phillips
Evaluation Program Manager
Cornell Lab of Ornithology

Marion Ferguson
DEVISE Project Assistant
Cornell Lab of Ornithology

Citizen Science in The Classroom: Monarch Migration

By Karen McDonald March 16th, 2014 at 10:16 am | Comment

Using Journey North’s Monarch Project to Meet Common Core and Next Generation Teaching Standards

Journey North 3

Journey North supports a variety of citizen science projects, including monarch migration. (Photo: Journey North)

Citizen Science and Monarch Migration as a Teaching Tool

Grades:

K-12th

Description:

Journey North (JN) is a citizen science project for the observation and tracking of seasonal weather changes and phenology or life cycle changes in animals and plants. This website is an amazing resource and interactive platform for teachers. There’s so much information that they provide that it’s almost jaw dropping. On their site you’ll find how your class can participate in tracking everything from seasonal changes in daylight to migrations of humming birds, whales, and even flower blooming. One of the most popular citizen science projects on their site is the monarch butterfly project. In this project students and teachers can learn about the life cycles of monarchs, their natural history, and migration. Students may look for monarchs in their local area and report observations of eggs, larvae, pupa, and adults. This project encompasses much more than just observations. The content provided on their site includes geography, historical and real-time data, ecological conservation, life cycles, reading comprehension and more.

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Journey North support real-time data and mapping of monarch sightings, which are useful geography tools for the classroom. (Photo: Journey North)

Materials You’ll Need:

  • A computer with internet access.
  • A printer that can print in color (preferably).
  • Optional: milkweed plants and flowers that may be conducive for monarch food, water, or shelter.

Why This Citizen Science Project is a Strong Candidate for the Classroom:

  • This project can be done either in or out of the classroom and in or out of urban areas.
  • It requires very little equipment or tools.
  • Usable data, graphs, maps, reading materials, and lesson plans, and identification tools are provided on the site.
  • You can meet almost every standard of Common Core and Next. Gen standards with this project and all the resources provided on the site.
  • Teachers can use the lessons provided even if they don’t participate in the project.
  • Students learn geography and science together.
  • Students obtain a “sense of place” by making local observations and contributing to a global observation effort that can be seen in “real-time” on the site’s maps.
  • Zero data can be useful, which teaches children about the importance of collecting all types of data.
  • Uploading data is safe and children remain anonymous, it’s put in as a class.
  • They have a free app that you can use in the field with a smart phone so you’re not tied to the classroom for uploading data. Students can put in their observations in real time.

Teaching Materials:

Supplied on Journey North’s Website you’ll find a while host of videos, reading materials, maps, slide shows, downloadable data, and more. There is also a teacher’s guide that can help you find introductory lessons and more information for your lessons. They also offer the ability to be monarch “ambassadors” and exchange cards with schools in South America through their “symbolic migration” butterfly card program.

Online Safety for Children

Teachers create one account for uploading data for their entire class so no specific student data is needed. They do ask that you put in your address and provide an e-mail. They also ask you what grade you teach and approximately how many students are in that grade.  After one initial registration you don’t need to do anything more except log in and begin recording observations. A log-in is not required to access all the free lesson support materials on the site.

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Journey North has a free mobile app for uploading your observations. (Photo: Journey North)

Read the rest of this entry »

Visionlearning: An innovative online resource for STEM education

By Carolyn Graybeal March 13th, 2014 at 8:37 pm | Comment 1

In recent years there has been a growing emphasis on improving STEM (science, technology, engineering and math) education.  A correlate of this is has been the increase in digital resources available to students and educators. An excellent example of this is Visionlearning.

http://www.visionlearning.com/

http://www.visionlearning.com/

Visionlearning is the brainchild of Dr. Anthony Carpi, professor of toxicology at John Jay College. What started as a small project for a natural science course has evolved into an open access STEM education tool for students and educators. Its mission: to provide “high-quality, accessible, educational content in the science, technology, engineering and mathematics (STEM) disciplines.”

Instead of simply being an encyclopedia of science terms and theories, Visionlearning organizes its content into a library of lesson modules. These modules are geared toward the introductory undergraduate level and are designed to be concise and engaging. Modules begin with a ‘pre-reader’ section introducing the topic, providing key terms and posing questions for the student to consider before launching into the main material. Comprehension check points and animations are embedding throughout the module to stimulate thinking and keep students engaged.

All content is written and designed by professional scientists and educators. And all content is peer reviewed for accuracy. Dr. Anne Egger, an assistant professor of geological sciences and science education at Central Washington University, is a senior contributor at Visionlearning. She shared her motivation for joining the project and the philosophy of the organization.

Being involved in Visionlearning is immensely rewarding. Early in my career, I was frustrated with the low quality and high cost of textbooks. Each year, I’d see my students purchase these subpar textbooks and only to watch them resell the books to recoup the cost. Joining Visionlearning was an opportunity to improve the reading material available to my students. Its a high quality, low cost resource that students can continue to use and refer back to again and again.

Visionlearning’s library includes modules in biology, chemistry, physics, and earth sciences as well as modules that focus on the philosophy of science and the scientific process. In each module, emphasis is placed on illustrating the nature of scientific inquiry and providing a context for scientific advancements. “We want to demystify who scientists are and how science is performed,” says Egger. “We want to show that it is a self-directed process. There is no predetermined direction.”

Currently Visionlearning is adding a series of “math in science” modules, which will be rolled out over the next six months. These modules explore the transfer and application of mathematical principles across subject matters. The goal is to encourage cross-disciplinary connections as a way to reinforce concepts and demonstrate their importance and utility.

As part of Visionlearning’s emphasis on accessibility, all lessons are available in both English and Spanish. In addition, audio files are available for streaming to assist aural learners. There is also a ‘Classroom’ feature where students can bookmark modules and glossary words for future reference and where teachers can assemble the materials into a learning management system.

Visionlearning is supported in part by grants from the National Science Foundation and the US Department of Education. The project welcomes new contributors and content reviewers. Inquiries can be made by contacting Heather Falconer at hfalconer@jjay.cuny.edu.


Dr. Carolyn Graybeal holds a PhD in neuroscience from Brown University. She is a former National Academies of Science Christine Mirzayan Science & Technology Policy Fellow during which time she worked with the Marian Koshland Science Museum. In addition the intricacies of the human brain, she is interested in the influence of education and mass media in society’s understanding of science.

Categories: Citizen Science