Thursday, September 29, 2011

Citizen Science Watches the Waters with the EPA

Photo Courtesy: U.S.
Environmental Protection Agency
Last week I posted an opinion piece about the use of bounties in citizen science and how citizen scientists could be rewarded for performing certain data collection tasks.  For example, earning a small amount of money for analyzing pollution in a set number of streams.   Depending on how financially valuable the data is, companies such as mining companies or home developers could afford to pay for this data as part of their environmental permitting or remediation duties.  Sadly that day is not yet here despite our efforts to create it.  However, there are models for how they can be put together and today we look at an important one, the EPA's Volunteer Environmental Monitoring Programs.

To quote the EPA's web site, "Volunteer water monitors build community awareness of pollution problems, help identify and restore problem sites, become advocates for their watersheds and increase the amount of needed water quality information available on our waters."  They receive training in pollution prevention,  provide data for waters that may otherwise be unassessed, and increase the amount of water quality information available to decision makers at all levels of government. Additionally, "Among the uses of volunteer data are delineating and characterizing watersheds, screening for water quality problems, and measuring baseline conditions and trends."  So it is the perfect opportunity for citizen scientists concerned about local water quality and the ecology of their neighborhoods.  Training and equipment are provided by many of the chapters, as well as a full organizational infrastructure to coordinate everyone's work, ensure high quality data, and keep everyone motivated to see the project through.

If this sounds familiar it should; it is very similar to the Skywarn program run by the National Weather Service(which we'll be talking about much more next week). Like the Skywarn program, this is not just a single project but  a collection of projects across the country. Large and small, each is devoted to monitoring wetlands and bodies of water in a certain geographic area. Technical and organizational assistance is sometimes provided by the government but the passion, and work, all come from a concerned citizen scientists. Many projects are also done in close coordination with State and local government agencies though this isn't always the case. These others evolve from the concerns of public citizens, interests of local firms, and mission of local non-profit organizations.

Getting Started is Easy:
That's all there is to it!  I admit this one has less detail than other project descriptions, but that's only because every local project is different.  Some are concerned with pH monitoring, some with tracing individual chemicals or harmful microbes, while others are concerned with fish surveys or remediation work.  And the good view is there's something for everyone.  So pull out your best galoshes, find a local group, get involved, make new friends, and be sure to have fun!

Tuesday, September 27, 2011

Earn Citizen Science Merit Badges with Project NOAH

Welcome to the first week of Fall and the continuing saga of Tuesday's Citizen Science "Tools of the Trade" profiles.  This week we look at Project Noah, another in the line of mobile field guides available for most popular cell phones and tablets.

Project NOAH (Networked Organisms And Habitats) is not a citizen science project in and of itself, instead it is a tool for citizen scientists to store information on any animals they spot and make that data available to researchers regardless of the project.  So users take pictures of specific animals, provide notes on the species along with the habitat they were found in and the geographic location, and upload to the central system.  If you can't identify the species you've spotted you can also ask the citizen science community to help classify it for you.  Once properly classified the system also links to both Wikipedia and the Encyclopedia of Life where you can learn much more about that animal and its habitat.

This data is not just available to individual users.  It also made freely available to other users and independent researchers to work with as they please.  So projects that track certain species or the biodiversity of a certain geographic area can use the information made available to them through the project.  Researchers can also design their own project (such as tracking squirrels in a certain area) and work with the Project NOAH team to create a "Mission" requesting users specifically look for and upload information on any squirrels they spot. 

This emphasis on missions is one area the helps Project NOAH differentiate itself from the many other citizen science tools and projects already out there.  To encourage participation users are awarded "Mission Badges" for completing certain animal spotting goals.  Similar to the badges used by FourSquare and other social networking companies, these can be created for reaching a certain quota of animal spottings, for successfully participating in a mission organized by an independent research team, or by proving a certain number of spottings in a geographic area (or areas).  So you can win awards for submitting data from three different countries, participating in a butterfly sighting program, or uploading pictures of ten different animal species.  The badges can reward almost any activity that the system can track.

Getting Started is Easy:
  • Visit the Project NOAH web site and click on Mobile to access the Android Store or iTunes Store to download the application.  The app is available on the iPhone and adaptable to the iPad, but there is no dedicated iPad app yet.
  • Once installed open the application and sign in by either creating a new account or by logging in through an existing social network account, such as those through Google, Yahoo, Facebook or Twitter.
  • Once logged in, take a long walk and find an animal of interest you wish to record.  Click on the "New Spotting" button and then "Take a New Photo" (you can also take a photo separately and just access it through the application, but let's try it the fun way first).  This will bring up your device's camera mode...just get as close as the animal will let you safely approach and take the picture.
  • Identify the basic type of animal (e.g., mammal, bird, fish, invertebrate, etc) with the spinning wheel and click "Go".  If you have location tagging on, make sure the map shows your correct position and click "Done".
  • You will now see your specimen sheet like the one shown below (a cute rabbit I found in the front yard).  It will have the picture you took in the top corner and categories for notes below.  Add as much information as you know.  If you don't know the species type click on "Help me ID this species" for assistance from your fellow citizen scientists in the Project NOAH community.
  • Click "Submit".  That's all there is to it!  You've created a record for you and everyone else to access.

Photo Courtesy:
Of course that's just how you get started.  There are now many more things to do once your first spotting is complete.  Go back to the home page and check out some available missions to participate in.  View the badges you've received.  Or look around the map for other users in your neighborhood and the wildlife they've seen.  But most of all, just have fun with it.

Oh yeah...and let me know about your fun in the comments below too!

    Monday, September 26, 2011

    Coming Soon: Exciting Improvements for OpenScientist

    Wow. Its hard to believe I've published over 80 posts and discussed over 70 different citizen science projects and tools on this blog already. It's been a lot of fun and just the beginning as I look forward to many more posts. But it's time to start entering the next phase.

    One of the best things is knowing that I've already discussed a large number of different important projects. Certainly not every project available but a wide variety of the most popular, highest quality, and most accessible projects developed so far. This is the critical mass I hope to build upon in this next phase. You can see the benefits in some of commentary and analysis pieces I've posted recently. Discussions of what citizen science is, different classifications of citizen science, whether these should include distributed computing, and my call for more bounty projects have sparked many great discussions and inspired me to emphasize these thought-provoking types of posts in the future.

    I'm also committing to a more regular schedule of updates. So expect new posts at least twice a week every Tuesday and Friday morning. Of course I hope to have many more outside that schedule. But I wanted to make at least that commitment for you.

    Another change you may have already noticed is the web address changing to be much easier to find. So instead of the long blogspot address you can reach this blog directly at All my posts have also been moved to the new address but don't worry, all the old links (along with your bookmarks and blog links) will still reach the same place.

    Finally, what about content? Expect more compilation pages organizing the projects we've talked about in one easy-to-find place. Expect commentaries on reasons for private businesses to invest in citizen science, ways for workers to expand their employability with citizen science, and secrets to designing a successful citizen science project. Expect more of the citizen science projects you love.

    And continue to expect my favorite saying...Getting Started is Easy.

    Friday, September 23, 2011

    Searching for Citizen Science Bounties

    Photo Courtesy: AMagill
    Two weeks ago we had a great discussion after my Finalizing a Definition of Citizen Science post where I first mentioned the concept of bounty projects that could benefit from distributed computing. I also briefly touched on the concept when asking Is Distributed Computing Really Citizen Science?  But I haven't had a chance to describe it further until now.

    What I'm thinking of is very similar to, but distinct from, some of the innovation awards that groups like the Ansari XPrize and NASA Centennial challenges have offered.  Those are all focused on achieving a specific technical goal or development of a process.  And they are also quite large endeavors with precise rules on how the goal should be accomplished.  They may be somewhat loose rules, but they are still somewhat prescriptive in how to accomplish the goal. 

    The bounties I'm thinking of are different by focusing on discovery, not creation.  They reward accomplishment of a specific tangible goal but are usually smaller in nature or more precise.  The example is an award to people who can find examples of a particular rare bird, sight the first flower of a certain type to bud in spring, or discover an asteroid that will pass within a certain distance of Earth.  So it rewards a very specific discovery that is not a technical feat in and of itself, though building of tools to aid the discovery (such as building the proper telescopes of automating bird call identifications) may involve significant technical work.

    Historically people have used these types of bounty prizes to accomplish scientific goals but they haven't been popular recently.   The most recent example of this type of "pure" bounty prize I've seen are the Electronic Frontier Foundation Cooperative Computing Awards for finding the largest prime numbers.  The group offered prizes of up to $250,000 to the first person to discover a certain type of prime number.  There were no rules on how to do it, or what should be done with the number.  All the group required was someone to prove that the number was a Mersenne Prime and of the certain length.  This type of bounty-hunting is well-suited for distributed computing approaches that could crunch huge sets of numbers by brute force until the sought-after number was found.  And that's exactly what the GIMPS distributed computing project did to win the two most recent EFF bounties.

    As a side-note they are still looking to win more all about it in my GIMPS blog posting.

    There are also other uses for bounties that do not involve distributed computing but which could also benefit greatly from the approach.  One example is understanding protein folding...there are millions of potential solutions but only one correct one, so why not offer a reward to the person discovering the shape of certain important proteins from their component molecular structure?  In other words, researchers would provide the components of a key Malaria protein and offer $1,000 to the first person that identifies it's shape.  Or provide the shape of an important AIDS protein and provide $5,000 to the person discovering a structure that will fit around the protein. In other fields I can even imagine prizes to the first person that spots a comet directly crossing Earth's orbit.  The possibilities are endless.

    On a similar note, there is another concept that I also put into the bounties category.  These again focus on meeting a simple, tangible goal, but are used to reward progress or effort on a per-unit basis.  Again, nothing is being created here.  Instead we are rewarding someone who performs a scientific analysis task ten times, or collects three samples of a certain specimen, devotes 100 hours of computing time, identifies 200 uncharted Mars craters, or tracks the pollution in ten different streams.

    Looking around I've seen a few examples of this so far but nothing major, and nothing active right now.  The closest I've found is the Cosmology@Home, a distributed computing project trying to model the current universe from various hypothetical starting points.  To encourage participation researchers offered a prize to the person whose computer model came closest to reality by a certain date; there was not a monetary prize but the winner would be mentioned in scientific articles about the work.  The most widely-known version may be's Mechanical Turk project.  Although not necessarily Citizen Science, it did provide bounties on a piecework basis for crowdsourced activities.  So people could be paid for writing ten web reviews, or transcribing a certain number of podcsts.  The private sector QMULUS Cloud Computing Platform also used this approach to encourage participation in an actual Citizen Science appplication.  Each month the company gave away gift certificates and free merchandise through a raffle to users of the system.  As a commercial entity they could afford to invest in these give-aways but there's no reason non-profit organizations couldn't do the same thing.   There could also be many variations in the raffle entry for every work unit performed, or for per person using the system per month, or per participant in general.  There are many possibilities that could fit depending on the nature of the particular project.

    So these are my initial thoughts on bounties.  Not much has happened in this area recently but I believe there's a strong potential for it to really take off.

    But what are your thoughts?  Is this a legitimate subset of Prize Projects in general or have I made an artificial distinction?  Are there other projects currently utilizing bounties that I've missed? Are there existing Citizen Science projects this idea could be adapted to?  There's much more to write but I'd love to hear your thoughts in the comments below first.

    Tuesday, September 20, 2011

    Identifying Trees in a Snap!

    Fall is here again. A time when the seasons change and nature shows her full color in the leaves of Autumn.  It's also the perfect time to introduce our new Fall "Tuesday Tools of the Trade" postings for citizen scientists.   These are tools that people can use in their own scientific endeavors or to get more from existing projects put together by others.  But these tools aren't exactly projects in and of themselves, they just help you perform your citizen science job better.  So we'll be highlighting a new one each Tuesday for the next few months and showing ways they can help in a wide variety of projects and other uses.

    Fall is also the perfect time to talk about LeafSnap, a tree identification and marking program that is first up in our "Tools of the Trade" lineup.  This free iPad application let's you take pictures of leaves and have the tree they came from automatically identified by the program.  It also tags the tree's type and location for use by anyone looking for the data.  So I can use it to figure out the types of trees we have in my backyard, along with information on their flowering ability and species names.  I can also see the trees my neighbors have assuming they use the program too.

    The program is built on the power of facial-recognition software initially written at Columbia University and the University of Maryland, and utilizes the botanical collection information of the Smithsonian Institution.  So it's another great example of combining forces to create a field guide that can be used by anyone to advance citizen science.  Currently the program can only identify trees in the Northeastern U.S. (e.g., New York and Washingon, DC areas) but they are looking to expand nationwide.  It is also not yet available for either Android (or even the iPhone) but additional versions are promised soon.  But let's now wait any longer...let's dive right in!

    Getting Started is Easy!
    • Go to the LeafSnap web site to learn more about the program, or just go straight to the iPad App Store to download the program.  Just search for "LeafSnapHD" and install it for free.
    • Find a tree in your backyard and (gently) remove a leaf that appears typical to that tree.
    • Place the leaf flat on top of white piece of paper making sure it is in a reasonably well-lit area.
    • Open the iPad Leafsnap App and once it loads click on the "Snap It!" icon.  This will start the iPads camera function. 
    • Center the leaf in the center of the white-framed area, being sure to get as close as possible so the leaf fills the white-framed screen.  Click "Snap It" to take the picture.
    • Once the picture is taken your iPad will analyze the photo by connecting to the internet and comparing it to known shapes in it's database.  If you don't have an internet connection you can always upload it for identification at a later time.
    • If this is your first time using the program, uploading the first leaf sample will trigger the app requesting a username and password to set up an account.  You can also determine if you want the location tagged on your data.
    • That's all there is to it!  Now that you know the species open your web browser and learn more about the trees around you.

    In the picture above you can see I've tried the program with a Japanese Maple tree from my own backyard.  It's a beautiful specimen with strong green leaves that also have a solid red tinge to them.  They turn a lovely bright red in the fall (which is a sight to behold) so I've always been curious to learn more about them.  Thanks to Leafsnap, now I have my chance.

    So what can you do with the program?  Well, for one the data is now available to see what neighbors around you have and to see what the local ecology is like.  For birders, you can use LeafSnap to see where the birds you hear are residing and if there are any preferences to those you follow most often.  For participants in Project Budburst or other phenology projects, this will help you identify the flowering plants you are reporting on.  But it's also just a great way to learn more about your local environment. 

    So have fun with LeafSnap, and let me know what interesting uses you are putting it to!

    Monday, September 19, 2011

    If One Citizen Science Project Doesn't Succeed...Try Another!

    Photo Courtesy:
    Iván Martínez / Wikimedia Commons
    Over the weekend ran an interesting article about the citizen science fight against AIDS.  Summarizing a recently published article in Nature Structural and Molecular Biology, it describes how the protein-folding game FoldIt has helped solve the structure of an enzyme important to understanding AIDS and similar diseases.  The protein, a protease in the Mason-Pfizer monkey virus  that plays a key role in it's replication process, works in a similar way to HIV-1 proteases and understanding this structure may be key to understanding HIV replication as well.

    The most newsworthy part of this article is obviously the scientific breakthrough.  But there's also a very interesting citizen science story here as two different projects have combined to provide an answer that neither could on its own.

    To investigate the protein's structure researchers initially looked to the Rosetta@Home program for an answer.  This distributed computing project takes data about the molecular make-up of proteins and uses the donated time of distributed computing participants to derive the protein's actual structure.  After much effort the program actually did not came close and provided some key insights into the structure, but an ultimate solution was not found.

    That's when the researchers turned to FoldIT.  Starting with five potential solutions from the Rosetta program, they asked volunteers to use their own creativity to finish determining the structure.  This is a key strength of the FoldIt project which turns deriving protein-strucutres into a video game and allows close collaboration between players working on each puzzle.  And so the players solved it in less than ten days.  The credit goes to a team of volunteers who work on each structure independently and then share their results (and insights) with the rest of the team to continue with.  In this case a key insight on the looping structure was made by one member with another following up by incorporating it into another near-solution of their own.  And that's when it all came together.

    All this goes to show not just the power of citizen science, but also the importance of using different techniques and the power of individuals working together on a problem.  No one project or volunteer ever identified the structure.  But two projects, the research group, thousands of volunteer computers, and a devoted team of creative game-players, all came together with the answer.

    But enough of my take on the article.  Read the article or head straight to the scientific paper itself.  I think you'll find them both very intriguing.

    Wednesday, September 14, 2011

    Filling Out Our Distributed Computing Collection

    Now that we've shown the Distributed computing projects really do belong in the realm of Citizen Science (see our earlier blog post), let's add a few more to our growing list. 

    All of the projects below are available for new participants and ready to download.  But one difference from my previous lists is that we are starting to add a few independent projects not directly linked to the BOINC or World Computing Grid networks.  So while there is a VERY MINOR additional set-up required don't let that scare you.  It will literally take less than a minute and you'll be up and running.  Not only that, but as independent projects outside the scope of the larger groups your participation is appreciated that much more.  In many cases these are citizen scientists just like you creating their own programs, so let's do what we can to help.

    • Simulate Particle Accelerator Designs: Muon1 ( is trying to design better particle accelerators by simulating how particles would actually flow in various configurations.  In this case, the project is experimenting with the pion-to-muon decay channel, adding different components (such as a muon "cooling ring") in successive versions.  Don't worry if this is a little over your head...suffice it to say this is an important problem for physicists to understand.  To get started, visit the Muon1 project site and click on the downloadable zip file of the software appropriate to your computer.  Save it in its own folder and open the "muon1.exe" file.  The program may then need to extract additional files before running (click on "extract" if requested) and then run "Muon1.exe" again to run the full program.  That's all there is to it.  If you want to play around a bit more, view the "readme.txt" file for directions on making it your standard screensaver or running it continuously in the background.
    • Model our Galaxy's Formation: The MilkyWay@Home ( project is trying to understand how our Galaxy was formed and whether it collided with smaller galaxies in the past. To test this theory, researchers are modeling the Sagittarius galaxy (a nearby companion galaxy to ours) to identify the path it may have taken through our galaxy and whether it would  look the same way it does today after such a collision.  Click on our BOINC blog post for easy directions on getting started.
    • Model our Universe's Formation: The Cosmology@Home ( project is trying to understand the conditions present when the universe began and simulate it's development over billions of years.  Researchers will then compare the resulting value of certain physical values (such as the cosmic microwave background, rate of expansion, distribution of galaxies, etc.) against their current known values.  Click on our BOINC blog post for easy directions on getting started.
    • Roll the Dice on Quantum Mechanics: Quantum Monte Carlo ( is trying to better understand the solutions to certain problems in quantum mechanics.  Current solutions only describe the simplest of situations so distributed computing is the next hope for moving the field forward.  This project differs from others by using a Monte Carlo simulation heavily reliant on random numbers (thus the dice analogy).  Click on our BOINC blog post for easy directions on getting started.
    • Stabilize Nanaotchnology: Magnetism@Home ( hopes to understand the magnetic properties of nano-scale compounds.  These effects are not normally seen for macro-scale technology but are vitally important at the molecular and sub-atomic levels.  Click on our BOINC blog post for easy directions on getting started.

    As always, these are also available on our Distributed Computing Projects Open for You page.  So check these out or any of the others we've been listing.  It's not a 100% complete list yet but a large number of the most active projects are included.  I've also tried to maintain the list by keeping off those projects which have completed or no longer seem active.  But if there are ones you'd like me to add just let me know in the comments.  I'll be happy to include them!

    Monday, September 12, 2011

    Is Distributed Computing Really Citizen Science?

    For the past two weeks we've been working on a definition for citizen science.  After much research and many good reader comments we came up with a pretty good definition last week.  It covers the large range of activities performed by citizen scientists while still providing room for "professional" scientists to be involved as well. 

    Most people were very happy with this answer, but there is one issue a commenter brought up that is worth a much greater discussion.  He noted that he considers "...citizen scientists to be providing either brute force observation or brute force analysis. I think this would (rightly) exclude someone, for example, who installs SETI@home (or similar application) as they are not providing a service that couldn't be provided by a super computer."  My initial reaction was to disagree as this blog has considered SETI@Home and other Distributed Computing projects as Citizen Science.  But it definitely merits further discussion.

    First of all, there are a few reasons weighing against Distributed Computing as part of Citizen Science.
    • Lack of Scientific Involvement: This argument can be made in two ways.
      • In the first, citizen users are not actively participating in science by running these programs. They are just observers donating resources to the cause. They do not perform any independent research, develop hypotheses, make predictions, design the program, or analyze the results of the program.  Basically, they are not involved with any part of the scientific method.  This is the argument our commenter initially made.
      • There is also the related argument that the algorithms being run are not scientific, or at least are not part of the scientific method. The computer program itself is not engaged in research, hypothesis development, or analysis. It is just running numbers in the exact same way it does to to run an accounting spreadsheet or even play a YouTube video. When it comes down to it, all those videos are just computer calculations displayed as cute videos. So unless the Distributed Computing program performed some other tasks besides number-crunching, it would not be scientific in nature.
    • Non-Scientific Purpose: Many Distributed Computing projects do not have a scientific focus. When used for data mining stock tables to find a hot tip, or to crack a heavily-encrypted message, it is not being used to understand natural phenomena and is thus not scientific. So it is tool useful for science, but it not it's own field or branch of (Citizen) science. This views distributed computing like spreadsheet analysis...useful for science but not a science itself.

    Then there are a number of reasons I've included it so far and that merit continuing consideration of Distributed Computing as a part of Citizen Science.
    • Historical: Over the last 15 years distributed computing projects have been some of the most-cited examples of Citizen Science in both scientific journals and mainstream media.  Much of the credit goes to SETI@Home which re-invigorated the field when it began in 1999.  Their development of an easy-to-use and simple-to-understand project gained the project rapid public recognition.  Writers build upon this recognition as an effective way to describe the Citizen Science concept.  So despite being eleven years old it is still one of the first examples writers use when describing Citizen Science.  Rghtly or wrongly, the common convention has become including Distributed Computing as part of the field.
    • Common Uses:  A quick look at lists of distributed computing projects show a large number, (usually over a majority) are utilized for "traditionally" scientific projects.  These chemistry, biology, pharmacology, and physics projects are designed to explore and test hypotheses according to the scientific method.  Distributed computing can be applied to many other fields too, such as computer science, mathematics, cryptology and economics that many people consider part of the sciences (and I'm not getting into that argument here).  But even taking a highly conservative approach that doesn't include these as sciences, distributed computing is clearly an important scientific tool in the more "traditional" areas.
    • Ladder to Increased Citizen Invovlement:  The lack of personal involvement that some see as a negative can also be considered a strength.  Looking at the Citizen Science field there are many ways to get involved and many different levels of involvement.  The highest level of involvement usually requires large amounts of time, energy, dedication ,and knowledge, and it takes a while to get to that point.  Many users instead play around with many different projects until they find the ones that are most interesting, then spending most of their time on just those few.  So we need to see Distributed Computing projects as part of a ladder to increasing involvement.  Even if it's just the first rung, we shouldn't discount this starting point for public scientific involvement.
    • Potential for Expanded Uses:  Some of the criticisms of Citizen Science revolve around it's lack of involvement by users.  Once a program is downloaded the computer does all the work...there is no intervention by the user.  Although that's the current model I don't believe it will remain that way.    There's no reason the Distributed Computing can't utilize more involve the user and combine the best aspects of human creativity with the brute-force calculations of computers.  In this scenario a problem is presented that requires a user to make certain assumptions, hypothesize the starting value of certain variables, or do independent research that sets the project's initial state.  Once that is done then a computer can run a series of time-consuming algorithms, presenting both the initial conditions and results to a central server.  For example, this could work well for developing a global climate model.  The computer program can crunch numbers and provide 50 years worth of temperature projections but it still requires input of initial temperatures of the relative impact of variables on each other.  So a person can guess that humidity is twice as important as cloud cover, or can do independent research to set better starting points for current temperatures.  Then the computer can run the program based on those conditions.  Or once the computation finishes the user can analyze the final product and modify assumptions in case the results seem faulty.  All of these future implementations would allow Distributed Computing models to include much more significant user involvment is currently provided.

    Looking over these arguments I'm still strongly swayed that Distributed Computing does belong as an important aspect of Citizen Science.  Some of the strongest arguments are for areas where the field may lead and the potential it has.  Just because we are in the field's (relatively) early stages is no reason to discount it as a science.  Just writing this post the answer became increasingly undeniable to me (hopefully that didn't introduce a bias in my arguments).  I'm also loathe to go against the many experts who also agree that it's a science, though that's not my ultimate argument.  At the end of the day Citizen Science is all about incorporating unlikely elements into scientific research, and recognizing the scientific value of including everyday people.  So it seems disingenuous to deny Distributed Computing fans the title of Citizen Scientist.  There efforts deserve recognition too.

    So those are my thoughts.  But does anyone out there disagree?  I've tried to provide some arguments on both sides though there may be many more I've missed.  Or I may have misconstrued some arguments already out there.  So let me know about it in the comments below.  I'd love to see the conversation continue.

    Saturday, September 10, 2011

    More on Mary Anning...The Fossil Hunter

    Photo Courtesy: Palgrave Macmillan
    Our latest Book of the Month features another tale of Mary Anning and her friend Elizabeth Philpot, two Victorian women who helped change the world's view on evolution, dinosaurs, and even a woman's role in science.  We previously talked about them in the fictional book "Remarkable Creatures", but now we get the true story in "The Fossil Hunter: Dinosaurs, Evolution, and the Woman Whose Discoveries Changed the World" by author Shelley Emling.

    Many of the themes from Remarkable Creatures carry through to the Fossil Hunter as well, such as the second-class role of women in both social as well as scientific circles .  Despite Mary's singular ability to discover fossils other could not, and despite her providing the very data being used by male researchers to build their own fame, she was not allowed into their meetings and did not receive public credit for most of her work.

    What we see more in this book, however, are many of the class issues that also came to influence her life.  She was a poor girl raised for many years by a single mother who collected fossils for money and sustenance, not pride or curiosity.    As we can see early in the book's Prologue:
    By birthright, Mary should never have grown up to be a famous fossil hunter and geologist.  In addition to being dirt poor, Mary Anning was also marginalized by odds clearly not stacked in her favor: her sex, regional dialect, lack of formal eduction, and adherence to the Dissenter faith, a religious strain that didn't conform to the teachings of the established Church of England. But she enjoyed one powerhouse advantage: the very good fortune of having been born in exactly the right place at the right time, in 1799 in an unassuming town called Lyme Regis alongside some of the most geologically unstable coastline in the world.  Unbeknownst to anyone at the time, its wobbly cliffs held the remains of a baffling array of ancient reptiles, reptiles that used to roam the land and inhabit the seas hundreds of millions of years in the past.
    We also learn more about her father and how he provided her all the tools she'd need for fossil-hunting, both literally and figuratively.  It began when was she only five or six years old when he'd take her for long walks on the nearby beach looking for "curios" -- the former name for fossils.  An avid fossil-hunter and and shopkeeper himself, he taught Mary how to identify interesting specimens, clean away the stone surrounding the fossil, display them in attractive cases, and smooth talk  souvenir hunters into paying a proper price for the piece.  He even crafted special tools for her child-size hands.  So even if she could not be apprenticed into a trade like her brother, she would always be able to support herself and her mother.

    Sadly, her father would pass away when she was only eleven years old.  After her father's death life was not easy for the Anning family.  Constantly in debt it was all Mary could do to help with her mother's laundry business, collect fossils, and sell them in her small shop just to make ends meet.  It was up to Mary to keep the family going, although it often wasn't enough.
    It is likely that living on parish relief for five years had caused Mary to focus her efforts even when she might have preferred to do otherwise.  Often the family faced the real threat of starvation, and fossil hunting was the concrete means by which they knew how to earn a living.  In addition, Mary likely continued her pursuits in an effort to honor her father's memory.  His dream had been to open a proper fossil shop, one with a glass-fronted window through which he could show off his wares.
    Fortunately her discovery of complete Pleisosaur and Icthyosaur skeletons, along with countless other high quality fossils, allowed her to eventually collect enough money to purchase a quaint little house of their own complete with an attractive storefront for the "Anning Fossil Depot".  But this was small payment for all she was providing to the world of science.  As contemporary Anna Maria Pinney once wrote, "...these men of learning have sucked her brains, and made a great deal by publishing works of which she furnished the contents, while she derived none of the advantages."

    We also learn a bit more about the scientific debate of the time over evolution, and even a story with an American twist. We are reminded that fossils weren't considered new in Mary's time; they had been discovered for years in many parts of the world. But the idea that these creatures didn't exist never entered peoples minds. If the creatures seemed strange, it's just because they no longer lived in a certain area but still lived elsewhere. The idea that God would create animals he didn't need was inconceivable to most. But in 1796, famed French naturalist Georges Cuvier first pronounced the theory of extinction, theorizing that mammoth fossils previously found were significantly different than African and Indian elephants, and that since nobody had ever seen these giant creatures in the wild (weighing up to six tons), they must be extinct.
    One person closely watching Cuvier's work was U.S. president Thomas Jefferson. A longtime fossil enthusiast and also a devout churchgoer, Jefferson felt certain that the giants described by Cuvier were hiding somewhere in the vast wilderness of the American West. He even implored Lewis and Clark to seek out the creatures during their trek in 1803 and was certain they would return with tidings of mastodons, dead or alive. By this time debate over extinction was also stirring in America, where huge bones and teeth, weathered our of farmers's fields, were initially described as belonging to giant animals drowned in the biblical flood.
    There are other, smaller discoveries that are no less important to our understanding of the ancient world.  She was the first to notice that when adding water to the tiny chambers in some marine fossils, she could create an ink that could be used for either painting or drawing.  These would turn out to be the very ink sacs ancient creatures used to avoid predators.  Just like a modern-day squid. 

    Eventually the world slowly began to recognize the value of all Mary's works.  When the King of Saxony came to visit her home town, he visited her shop to look at the fossils they'd heard so much about. As she reportedly told his personal physician while purchasing some of her fossils, "I am well known throughout the whole of Europe."  She also had a few fossils named after herself, the Acrodus anningiae  and Belenostomus anningiae ifish.  But while the Royal Societies had paid small amounts for her discoveries and might even place her name on the skeleton when mounting them in the museum collections, this was tiny compared to the amount being made off of her work.  Only after much turmoil and many years of waiting, two prominent scientists did provide some repayment for her trouble.  One, fossil collector and retired British officer Thomas Birch, sold off nearly his entire fossil collection with the proceeds going straight to Mary.  Another, famed paleontologist William Buckland, arranged for Mary to receive an annual Civil List Pension of 25 pounds per year from the British Association for the Advancement of Science.  Not a princely sum but enough to keep the family comfortable in their later years.

    As always her recognition would not come until later in life, and even then her fame did not last long.  Sadly she is more often remembered today as the purported inspiration for the tongue-twister "She sells sea shells by the sea shore." Given the very real contributions she made as a scientist when her age, rank, and gender would normally not let her, we hope these books keep her well known for her more illustrious achievements.   And we will always have her legacy.
    There is no question that the fossil-hunting craze that started when Mary was alive is still going strong today. Every weekend, hordes of fossil hunters flock to the cliffs of Southern England, a 95-mile stretch of shoreline now called the Jurassic Coast that was declared a UNESCO World Heritage site in 2001. When a huge landslip occurred late in the evening of May 6, 2008 -- the worst in 100 years, destroying 1,300 feet of coast, crowds of fossil hunters gathered at the scene, just as Mary and William Buckland and so many others had nearly two centuries ago. And, like Mary, they were all looking for something special hidden amid fallen boulders, uprooted trees, and mounds of earth.

    Sometimes fossil hunters risk their personal safety in their constant hope to make the discovery of a lifetime. Like Mary, they never give up.

    Wednesday, September 7, 2011

    More Distributed Computing Projects for You

    It's been a while since we last talked about the many distributed computing projects looking for volunteers. But in just those few months many new projects have popped up while others have gone away after successfully completing their goals.  All good news, especially for us who are always looking for a new project to learn about.  So here are a few more to add to our ongoing list.  Won't you give them a look?  You'll see these on the dedicated OpenScientist Distributed Computing Web Page too.

    • Cure Tropical Diseases: The Drug Search for Leishmaniasis ( project is looking for a cure to a tropical disease that infects over two million people in 97 countries each year.  Although there are treatments to this often-neglected disease, they aren't completely effective and can cause many negative side effects.  This project will use participant computers to comb through a vast library of potential drug compounds to find just the perfect one to treat the disease.  Click on our World Community Grid blog post for easy directions on getting started.
    • Spot Incoming Asteroids: Orbit@Home ( is developing statistical models to identify the best places to identify near-Earth asteroids and most accurately determine their likelihood of hitting our planet. The program does not look at individual asteroids but finds the best way to use valuable telescope time. Click on our BOINC blog post for easy directions on getting started.
    • Predict Weather 100 Years from Now: wants to improve climate models that project up to 100 years in the future by better understanding how small changes in assumptions can impact the forecasts. By tweaking these assumptions ever so slightly, the program runs a global climate simulation and analyzes the final results in comparison to simulations run by thousands of other useres. This is important to better understanding global warming and quanitfying the amount of error in current models.
    • Turn Genes On and Off: The DNA@Home project ( is trying to better understand gene regulation and transcription, or how cells turn on and off their genes.  Using home computers to collectively examine the genome of a small bacteria, researchers hope to figure out what sets of DNA base pairs control transcription.  Once we understand transcription it becomes easier to turn on beneficial genes and turn off those that cause deadly diseases.  Click on our BOINC blog post for easy directions on getting started.
    • Fold Proteins: POEM@Home, or Protein Optimization with Energy Method (, is a protein-folding project taking advantage of networked computers to run these computationally-intense tasks. The difference for POEM is the use of some novel new approaches that provide quicker results and allow researchers to investigate the characteristics of each protein shape. Click on our BOINC blog post for easy directions on getting started.
    • Investigate How Genes Become Proteins: RNAWorld ( is a collection of projects looking at how these molecules read the DNA code and perform their work in the cell.  Some of the projects are purely basic research while others focus on specific disease-causing aspects of RNA activity.  Click on our BOINC blog post for easy directions on getting started.
    • Dabble in Many Projects: The Lattice Project ( is not just a single project but a method for allowing multiple projects to all share the power of distributed computing networks.  In a nutshell, researchers can add their projects to the Lattice, and the system will distribute the work for all those projects to the networked projects.  This benefits smaller projects that may not want to create their own, free-standing applications but want to take advantage of existing networks instead.  Click on our BOINC blog post for easy directions on getting started.

    If you have time take a look at some of these for me and let me know your thoughts.  I'm particularly interested in how you think these projects fit within the definition of citizen science we've been working on.  Some people think this should not be considered true citizen science while others disagre.  Before considering that question more I'd like to hear your informed opinions first.

    Tuesday, September 6, 2011

    Time to Shake, Rattle, and Roll...for Science

    Photo Courtesy:
    Quake Catcher Network
    Last week a rare strong earthquake hit the U.S. eastern seaboard.  Although damage was minimal the shaking reminded us easterners that the Earth is always in motion.  That's not news for anyone from California or Japan, and especially not for the Stanford Geology Department or the Quake Catcher Network of citizen scientist seismologists (citizen sci-esmologists?).  They've been tracking geologic activity across the country with low-cost seismometers and built-in laptop accelerometers.  This network is contributing to better understanding of active quakes and helping understand how future quakes will impact individual areas at the very local level.

    One citizen scientists member in particular, Carolyn McPherson of Charlottesville, Virginia, had the closest sensor to last week's Virginia earthquake and was highlighted in a Washington Post article (summarized here on OpenScientist).  A $50 Christmas gift of a Quake Catcher Network (QCN) seismometer was all it took for her to get started, and though this area had to wait a while for a large enough quake to be interesting, her patience paid off as she gets to see her data be used to better understand this recent event.

    Stepping back a bit, the Quake Catcher Network started as Stanford researchers wanted a method to augment the existing network of seismographs without spending huge amounts of money.  They were working on theories about how earthquakes travel over different types of terrain, including differences from city to city and even block to block.  Developing a large network was vital to their research, but they could not afford to set up hundreds of sensors costing up to $100,000 each.  There had to be a better way.  So they devised a cheaper version that could be made for under $50, and though each would not be as sensitive the value of having a pervasive network was much more important than finely detailed data.  They could also take advantage of existing accelerometers many laptop makers have been recently including in their devices.  They just had to repurpose the internal sensors and collect the data.

    Now that they've made literally thousands of devices, how to distribute them?  Well, for those people in the most earthquake-prone areas such as those near the San Andreas fault in parts of California or the New Madrid fault (in parts of Tennessee, Missouri, Arkansas, and Kentucky), sensors are free to individuals willing to set them up and keep them running.  Low-cost ($5) sensors are also available for classrooms across the county: not just for data collection but also as a learning tool for students.  For the rest of us (like me), sensors can be shipped fora low fee of $49.  A small price to pay for the fun of understanding earthquakes (if you ask me).  They also make sensors available through their Rapid Aftershock Mobilization Program to capture data on local aftershocks taking place after major earthquakes hit.

     So check out the Quake Catcher Network web site, and sign up for a sensor!

    Getting Started is Easy:
    • We can't do much without the actual sensors.  So head to the Quake Catcher and click here to order one for $49 (or enter your zip code here to qualify for a free one).  Alternatively teachers in K-12 schools can click here for nearly-free ($5) sensors to use in the classroom.  Based on my experience they will arrive in 2-3 days.
    • Before the sensor arrives scout out a good place to install it.  The program requests it be placed flat on the lowest level of your building, and it will need access to your computer through a USB connection.  So find a place near a downstairs computer, or find a way to link it up to a wireless USB connection (I hope to provide more on this step in future posts).  It should also be a place the sensor can sit accurately measure earthquakes it needs to be stable when the rumbling starts.  So it will need to be glued or strapped into place.
    • Once the sensor arrives secure it in place, making sure it is on a flat surface and the compass is compass on top is pointing North.  Don't worry about being exact...the alignment can be off by a few degrees and still provide very accurate data.
    • Install the QCN-Live program on your computer.  If you have already installed the BOINC distributed computing software it's just a simple download from the Quake Catcher Network. All you should need to do is click on the appropriate software for your computer here (review the full user manual if you have any trouble).  If you do not have BOINC installed already, click on the BOINC Installer and then upload the QCN software.  You may also want to review the OpenScientist Distributed Computing page to learn about the many other citizen science projects that use the BOINC system software.
    • For laptop users, many of you already have sensors installed that can provide data too.  Just click on the Laptop Network page to see if yours qualifies, and to download the QCNLive software for you machine.
    • Once all the software is installed it's time to let the fun begin. Just attach the USB cable to both the sensor and your own computer.If you see the following earthquake map, you're in the right place.
    • Click through the interface and you should see a seismograph reading like this:
    Photo Courtesy: Quake Catcher Network
    That's all there is to it. The computer will record data automatically in the background and submit it to QCN-Central on a regular basis. Of course it can't record unless the system is left running but keeping your machine on low power while not in use should help conserve energy while still providing important data.

    With all of this data project scientists are looking to validate their own micro-zoning theories they also want everyday citizen scientists to have access and manipulate it also as they desire.  The data is not yet available online yet, but check their Data site frequently for updates.

    Finally, I can't let this post end without mentioning the project's need for continued money donations to support the discounted sensor project for classrooms.  They only cost the schools $5 but that only covers shipping and costs the project even more to make the device available in the first place.  So won't you help them out?  Donate a sensor or two to a school and help this worthwhile project continue.

    Photo Courtesy: Quake Catcher Network

    Sunday, September 4, 2011

    More Citizen Scientists in the News

    Photo Courtesy:
    Iván Martínez / Wikimedia Commons
    It's been a big week for citizen scientists.  The media is taking notice of the everyday people contributing to science on a daily basis, and highlighting their achievements for everyone to learn from.

    Yesterday I stumbled across a recent Washington Post article about the work of high school student Alexa Kenzler.  She asked a very simple question: "How much dry cleaning fluid remains on clothing after it is cleaned"?  Given the environmental and personal health ramifications this question should have been answered years ago.  When she discovered nobody ever had, she contacted Georgetown University professor Paul Roepe and they began working the problem together.  As the Post describes it:
    ...what started out as something to “sponsor the kid’s curiosity” prompted a chain reaction in the university lab: an e-mail exchange, an invitation to collaborate and, this week, a paper published online in a peer-reviewed environmental journal. The paper gives new details about the amount of a toxic chemical that lingers in wool, cotton and polyester clothing after it is dry-cleaned.

    “At the end of the day, nobody, I mean nobody, has previously done this simple thing — gone out there to several different dry cleaners and tested different types of cloth” to see how much of the chemical persists, said Roepe, who supervised the study.
    Since then what started out as a school research paper (Grade - 100 out of 100) also won her first place in Chemistry at the Arlington County Science Fair, and she hopes to compete in the much larger Intel International and Engineering Science Fair next year. 

    Beyond academics and and feel-good story about a local kid rising to the top, this is important data necessary to understand the impacts of the nearly 15,000 dry cleaners nationwide using perchloroethylene as the main cleaning solvent.  It also underscores importance of everyday people getting involved and asking questions about the world they live in.  "Professional" scientists can teach us much and government can protect public health when it understands the dangers.  But people need to keep asking the questions, whether they are tenured professors, government regulators, or bright 15-year-olds who just want to make a difference.

    Saturday, September 3, 2011

    Finalizing a Definition of "Citizen Science" and "Citizen Scientists"

    Photo Courtesy: Booksworm
    Over the last two weeks I've been thinking a lot more about our question of "What is a Citizen Scientist?"  On the one hand the various definitions we've already talked about seem even stronger than they did on first glance; incorporating many of the thoughts I presumed would be missing.  But yet there are still some holes we need to fill.  So let's look more closely at some of the proposed definitions.

    There are two definitions that come closest, so let's examine each one in turn.  The first is from Silvertown:

    "A citizen scientist is a volunteer who collects and/or processes data as part of a scientific enquiry."

    The main issue I have with this entry is the use of the term "volunteer".  Certainly there is a hobby or avocational aspect of citizen science, but making money from scientific contributions should not be ruled out.  For starters, many of the Challenge-type projects (such as the Innocentive project or the Ansari X Prizes) rely on profit motives to encourage participation and to inspire innovation.  Even further, they recognize that key insights to problems may come from outside the established scientific community (or at least from outside the targeted discipline).  There are also projects that rely on profit motives for the collection of data...I term these "Bounty" projects.  These would also be excluded from a volunteer-based definition.

    I haven't talked much about Bounty projects on this site since there haven't been many good examples of them developed so far.  But I expect to see them in the future and think this is an exciting area for future development in the field.  Not only will it help science generally but it will also help overcome the monetization problem needed to make citizen science increasingly mainstream and incorporate citizen scientists more firmly in the corporate science environment.  Similar to Challenge projects they use profit as a motive, but don't use it to spur innovation.  Instead rewards are used to incentivize the collection of data that may not be a goal in and of itself, but which is needed for others to fulfill the scientific goal.  Examples are data collection projects that base raffle-style drawings based on the amount of data each user collects, or which offers prizes for hitting certain levels of participation.  I'll have much more on this in future posts (after doing some more research) as it's an exciting new area for potential growth.

    The second definition is more of a description, and comes from the Po Ve Sham blog of Muki Haklay (who is apparently writing a book chapter on citizen science in GIS - Geographic Information Sciences):

    "[Citizen Science is defined as]...scientific activities in which non-professional scientists volunteer to participate in data collection, analysis and dissemination of a scientific project..."

    What I like about this one is that it includes the a brief, but concise and encompassing range of activities citizen scientists perform.  It even adds dissemination, which I had not initially included but which may be appropriate.  In my understanding dissemination involves teaching others about science and the scientific process, and activity performed by our most illustrious professional scientists as well.  But the distinction between "professional" and "non-professional" scientists in this description does cause some problems for me.  It neglects the many scientists who are active in one field "professionally" but whose love of scientific inquiry in general leads them to become involved in citizen science projects outside their current discipline.  Anecdotally I'd say this describes the majority of currently active citizen scientists since these people are most likely to have both the general tools and personality to be interested in this research.  So we have to make sure they are included too.

    Another problem with this description is it's circularity that defines citizen scientists as performing scientific activities in a scientific project.  Instead I'd prefer a definition that describes the nature of science without using that term, such as dictionary definitions involving systematic explorations/discoveries of natural phenomena.  Or we could just use synonymous terms such as "Investigator" or "Researcher". It's admittedly a minor point, and possibly a bit pedantic, but we should keep it in mind.

    Looking at everything said over the last few blog posts (here, here and here),  any definition needs to capture professional scientists working outside their discipline.  And it can't be relegated to just certain disciplines currently popular in citizen science such as ecology or astronomy.  So I'm offering the following alternatives for people to comment on.

    Citizen Scientist: Researcher who participates in the systematic collection and analysis of data; development of technology; testing of natural phenomena; and the dissemination of these activities on an avocational basis.

    Citizen Science:  The systematic collection and analysis of data; development of technology; testing of natural phenomena; and the dissemination of these activities by researchers on a primarily avocational basis.

    So what do you think?  Does this go to far?  Is there anything missing?  Should dissemination be included?  Is it too wordy or even just not very poetic?  Leave me your comments below and we can come up with the most definitive (no pun intended) version we can.