Archive for the ‘Biology’ Category

Digital Fishers: Data from the Deep, Judgment from the Crowd

By June 24th, 2014 at 10:44 am | Comment

Save the sablefish (also known as black cod) and help scientists by counting the fish in video clips.

Want more marine-themed citizen science projects? We’ve got you covered!

Sablefish on soft bottom habitat.

Sablefish on soft bottom habitat.

Scientists call it Anoplopoma fimbria, fishers might know it as the sablefish, while some chefs call it the Black Cod. Found hovering just above the muddy North Pacific seabed, you may have enjoyed one down at the Moby Dick restaurant or whatever your favorite seafood restaurant is called. The sablefish—a yummy opportunistic feeder known for its buttery taste has been harvested from US waters since the late 1800s.

In Alaska, heavy foreign fishing depleted the sablefish stocks through the seventies until the US took control of the waters in 1976 and phased out foreign fishing. After that, the fishing season began to shorten and the number of fishers actually increased. When this happens a fishery produces a lot of poor quality fish—the outcome is an unstable stock. In 1995, conservation managers implemented a program that sought to more strictly regulate the Alaska commercial fishery; it set limits for each fisher, but within a longer season. This decreased the harvest of immature fish, which meant those fish had a good chance to reproduce at least once.

Now a citizen science program called Project Digital Fishers needs your help, and it may keep the sablefish on the table at the Moby Dick. It is a project that enlists public support to run a second trial for researchers, and for computer scientists as well. For the latter, an undergraduate student at the University of Victoria has developed an algorithm that can “count” fish. He will use this campaign to ground truth his software. This video on YouTube shows this in action.

As researchers continue to monitor the resource, they hope to inform careful management of the stock. Jodie Walsh, the research coordinator for the Center for Global Studies at the University of Victoria in Canada, says, “A research group at the Marine Science Institute (Institut de Ciènces del Mar) in Barcelona, Spain, investigates biological rhythms in various species around the world.  By better understanding species behavior they hope to help in marine resource management and provide advice to improve fishing practices. And Carolina Doya, a PhD student working with Dr. Jacopo Aguzzi, uses NEPTUNE Canada cameras to study biological rhythms of fish in Barkley Canyon.” Counting fish in the field of view of the camera, and using specialized statistical tools, will enable her to see if fish movements and/or behavior can be predicted in relation to known natural cycles.

When an experiment returns a broad variety of results, researchers typically have to run the numbers again, which in this instance means they have to review the film footage of a submarine transect once more, while counting the number of Black Cod seen in a specified time. The result will be punched into a formula and extrapolated out for a region or field—which produces an accurate estimate of the number of fish in a population. So now you can contribute to real science—compare apples to apples (or in this case sablefish to sablefish) by counting the sablefish exactly as the research crew is doing in their labs. This will save an enormous amount of time and money, and it will contribute to both computer and environmental research.

Screenshot of Digital Fishers page.

Screenshot of Digital Fishers page.

You have to create an account, and the controls of the digital interface take a bit of getting used to.  After a few awkward attempts, I got the hang of it, had learned to identify the species and was counting for the A team. The website says you only have to count for 15 seconds, but each video clip runs for almost a minute. After those first few attempts I settled down and actually began to anticipate seeing a sablefish—I counted as many as six in a 60 second clip, and sometimes none appeared. To beat the first level you have to complete 10 ‘annotations’ or views, but to advance to the third level you have to complete 24!

Digital Fishers is currently counting sablefish, but Walsh says, “We have also looked at crabs, Mapping Seafloor, Trawling, thornyhead rockfish and deep-sea ecosystems, or sometimes we just show some of the video that has been collected and ‘digital fishers’ annotate many other species in our general campaigns.” Digital fishers hail from Canada, US, Spain, France, Germany, South Africa, Oman, Switzerland, Colombia, Czech Republic, Australia, Iceland, Italy, so anyone can compete. (The sablefish is found in UK waters as well—there it is called the blue cod, bluefish, candlefish or coal cod, and in Canada it’s known as the coalfish, beshow or skil.) The sablefish project will likely run through July.

Resources:
How to measure a count
NOAA FishWatch

Top Image: NOAA Photo Library
Bottom Image: Digital Fishers/University of Victoria


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 dragonflyec.com.

Ocean Sampling Day – Cataloging the Diversity of Microbes in Our Oceans

By June 18th, 2014 at 9:15 pm | Comment

Sampling the ocean. Source: OSD-Micro 3B

Sampling the ocean.

This Saturday June 21st, collect samples from bodies of water to catalog the ocean’s microbial biodiversity.

Want more marine-themed citizen science projects? We’ve got you covered!

 

This Saturday June 21st, citizen scientists will be able to take part in MyOSD (official site) the citizen science component to this year’s Ocean Sampling Day (OSD). The event is organized by Micro B3 (Microbial Biodiversity, Bioinformatics and Biotechnology) a European cross-disciplinary multi-institute collaborative aimed at developing large-scale research efforts to forward marine biodiversity research. On OSD, scientists around the world will collect water samples in an effort to catalog the ocean’s microbial biodiversity. On the same day, citizen scientists will gather environmental and contextual data. Organizers say that this ‘snap shot’ of the Earth’s waters might be the ‘biggest data set in marine research that has been taken on one single day.’[1]

Scientists are interested in marine microbes because of the role they played and continue to play in shaping our global environment. Microbes were critical to the evolution of life on the Earth. “Microbes were the first organisms evolving on Earth. When microbes developed the ability to photosynthesize, they began producing oxygen. This transformed the Earth’s early environment, making it hospitable to life,” explains Julia Schnetzer a graduate student at the Jacobs University and Max Planck Institute and the MyOSD coordinator.

“Today, marine microbes still produce more than fifty percent of the oxygen we need to breathe and consume fifty percent of the world’s carbon dioxide. In addition they are involved in key biological processes in the ocean system such as nitrogen fixation and the carbon pump.” Nitrogen fixation increases the availability of biologically accessible nitrogen by transforming atmospheric nitrogen into ammonium. The ocean’s carbon pump is a biological cycle which removes atmospheric carbon and sequesters it into organic materials deep inside the ocean. Several gigatons of atmospheric carbon are cycled into the oceans each year.[2] “Their participation in these processes make microbes critical in shaping the climate of the planet and thus are essential to the health of our environment.”

OSD will help scientists understand microbe biodiversity and how microbes affect the environment. On the 21st of June, teams of scientists will take water samples at various locations and identify microbial content via DNA sequencing. Marine microbes are particularly challenging to raise in culture, which has hindered their study in the laboratory. However advances in high through-put DNA sequencing technology have made it more practical and cost effective to study marine microbes directly from their natural habitat. In addition to analyzing microbe content, scientists will be taking environmental and contextual data such as water salinity, mineral content, air and water temperature.

There are 168 sampling locations. Source https://mb3is.megx.net/osd

There are 168 sampling locations.

“The results from OSD will produce two sets of data especially useful for marine scientists. The data about microbial biodiversity will help us understand which species are present and what they are doing. The environmental parameters will give us an idea on how the microbes influence their environment and how the environment influences them,” says Schnetzer. All the collected data will go into a publicly available open source repository. Researchers and citizens can visit the OSD map to see the locations and the genomic, environmental, and contextual data from the sampled sites. The website provides a helpful tutorial on farming the data.

More areas sampled mean better resolution of our ocean’s picture. OSD organizers need citizen scientists to help fill in the gaps. If you live near a body of water, you can help collect environmental information such as location, time, and temperature. Even if it is just a small nearby stream, OSD organizers still want your data. If you own water sampling devices, or are willing to build your own like a simple Secchi Disk, you will be able to provide additional useful information such as water pH or transparency. Download the free OSD app (Android and iPhone compatible) to make submitting your measurements easier. Don’t have a phone? Just save the data and submit it later online. Find out details about contributing to the project, data gathering instructions and analysis kits here.

Organizers hope that by engaging citizen scientists it will provide a better understanding of the value of our oceans and the need to protect them. “The more citizen scientists support there is for MyOSD the better the event will become and the more emphasis can be placed on the importance of education and outreach in marine science in future OSDs,” says Schnetzer.

So this Saturday, go out, get wet and get some data!

References:
[1] My OSD-OSD Citizen Science
[2] National Oceanography Centre – Biological Carbon Pump

Top Image: OSD-Micro B3
Bottom Image: megx 


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.

Ahoy, Citizen Scientists!

By June 9th, 2014 at 10:25 pm | Comment

We’ve waded through our database and come up with a boatload of marine-themed citizen science projects! Dive in!

Also, don’t forget to stop by DISCOVER Magazine and SciStarter’s online Citizen Science Salon; look for our new collaboration in the pages of Discover; or listen to beautifully produced citizen science stories from our partners at WHYY radio!

MyOSD-Ocean Sampling Day
On June 21st, during the summer solstice (the longest day in the northern hemisphere) join a local marine research team to collect data for an open-access data set to be used by marine scientists and others. Get started!

 

iSeahorse
Whether you’re a diver, a fisher, a scientist, a seahorse enthusiast, or just on a beach holiday, you can help improve understanding of these animals by sharing your photos of seahorses!  Get started!

 

Horseshoe Crabs as Homes
Horseshoe crabs play a key role in coastal ecosystems but they might also serve as substrate for many invertebrate species. Let’s find out what lives on Horseshoe crabs.Take and share pictures when you see them on the beach and aid research in the process!  Get started!

 

Secchi App
The phytoplankton underpin the marine food chain, so we need to know a lot about them. To participate in this project to advance research about them, you’ll need to build a Secchi Disk, a tool that measures water turbidity, and use the free iPhone or Android ‘Secchi’ application to share data you collect.  Get started!

Digital Fishers
Digital Fisher needs people to help analyze deep-sea videos — 15 seconds at a time. You’ll watch a short video of ocean life and click on simple responses to help identify what you are seeing.  Get started!


Check out “Exploring a Culture of Health,” a citizen science series brought to you by Discover Magazine, SciStarter and the Robert Wood Johnson Foundation, serving as an ally to help Americans work together to build a national Culture of Health that enables everyone to lead healthier lives now and for generations to come.

Want your project featured in our newsletter? Contact jenna@scistarter.com

How Many Can You Spot with Celebrate Urban Birds

By May 29th, 2014 at 9:36 am | Comment

In ten minutes, record the number of urban birds you observe in your neighborhood; your observations can improve the bird habitat in your community.

Want more birds and bees citizen science projects? We’ve got you covered!

Baltimore Oriole  (Photo: David Brezinski)

Baltimore Oriole
Photo: David Brezinski, for the US Fish and Wildlife Service

Spotting birds in an urban environment not uncommon and these feathered friends have certainly found a place for them in the city. But how are they coping with an environment that is less green and more concrete? This is exactly what a citizen science project from Cornell’s Lab of Ornithology is set out to find out.

The project — Celebrate Urban Birds – started in 2007, after consultations with community organizations across the US, as well as scientists and educators. From the start, the objective has always been to develop rigorous protocols to provide reliable scientific data, but also to encourage a strong educational and engagement component to make it happen in communities which citizen science wouldn’t normally reach.

Participation is simple: all you have to do is see how many birds from a list of 16 you can spot in 10 minutes and submit your results online. Not surprisingly, the team has been inundated with submissions across the country and beyond, from Canada to Mexico, and from Boston to Portland.

Despite this overwhelming response, the team has so far been a bit shy about showing their results, as they feel the project needs enough data to allow a reliable analysis. The good news is that, according to ornithologist Karen Purcell, the driving force behind the project, they are currently deep in analysis and we should expect some news in the upcoming months. “This is an exciting year” says Purcell, “because of the fact that we can take a look at the data and we’re going to be able to really understand what’s going on”.

The interesting part is that they’re not just looking at birds. “We’re looking at both the people factor and the community factor, in addition to the bird factor”, says Purcell. This is exactly what differentiates this project from other citizen science projects, as it is as much about the science as it is about the participants and their communities. In fact, although participants can join as individuals, it is through the links with community partners that the project thrives. “We work a lot with organizations that have community events, and that engage participants in the citizen science component, so that’s a big way in which we reach out”, says Purcell.

Very generously, “Celebrate Urban Birds” awards mini-grants to participating organizations, not only to help them develop ways for their members to learn about bird identification and submit their observations, but ultimately to improve bird habitat in the community. This approach “lets us reach a big variety of ages, people that have not participated in this kind of thing before, and the idea in terms of making it appealing towards that audience, is to create something that is useful in the community”, says Purcell.

Ruby-throated hummingbird.

Ruby-throated hummingbird.

Nothing was left to chance and this community focus is also strongly reflected in the list of 16 focal species which participants need to spot. They’re characterized by a strong urban presence throughout the US and further afield, but most importantly as the project deals with novice bird spotters, it includes some species people are likely to see, allowing them to engage with the project.

The list also contains some species chosen for conservational reasons, such as orioles and brown-headed cowbirds, and the team hopes to add more to the list. Top of the wish list at the moment is the hummingbird, which is both a great urban bird to get people to fall in love with bird spotting, and it’s also an important species due to their impact as pollinators.

The project is ongoing, and you can submit your results at any time. So, why not grab your binoculars and see how many birds you can spot in your neighborhood?

Resources: Celebrate Urban Birds Official Site

Images: Wikimedia Commons (Baltimore Oriole, Hummingbird)


Dr. Alex Reis is a freelance science writer, with a particular expertise in the field of biology and genetics. She holds a degree and MSc in Animal Science, topped up with a PhD in Embryology. In a ‘previous life’ as a researcher, she worked in the field of cell and molecular biosciences and published various scientific manuscripts including in Nature. Nowadays, however, she spends most of her time reading and writing science articles for several news outlets. Recent work includes articles published in The Munich Eye, Decoded Science, United Academics Magazine, BitesizeBio and Science NOW. After moving around the UK for a while, she now lives in the Highlands of Scotland. When not working, she can be found trying to get friendly with the ‘locals,’ from deer to seals, otters or even sea eagles.

Learn how climate change affects plant life with AMC Mountain Watch

By May 19th, 2014 at 2:47 pm | Comment 1

Track phenology events in Appalachian mountains and contribute to climate change research with Mountain Watch!

Want more spring citizen science? We’ve got you covered through April showers and May flowers.

There is nothing more rewarding than taking in the view from above tree-line. A challenging hike always seems like a distant memory after gazing upon the landscape below, especially if it’s the White Mountains of NH. Now, the Appalachian Mountain Club (AMC) is calling on visitors of these Northeastern peaks to help them observe plant life through the Mountain Watch program. This citizen science initiative aims to investigate how the life cycles of alpine plants are affected by climate change.

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View from the Franconia Ridge Trail, one of the alpine sites on the Mountain Watch list.

To do this, Mountain Watch asks participants to record plant phenology, which is the study of how plant life cycle events, such as flowering or producing fruit, are affected by changes in environmental conditions, including temperature and precipitation. Plant life cycles are very sensitive to small variations, so even subtle changes across seasons can be observed. For example, a dry summer might cause the leaves on trees to change color earlier in the fall. When recorded over many years, these phenology records can start to uncover long term trends in the climate and help scientists to model the effects of climate change in a certain region.

Diapensia, one of the sensitive alpine flowers being monitored.

Since the AMC is based in the Northeastern portion of the Appalachian Mountains, the focus of Mountain Watch is on alpine plants that are found exclusively at high elevations in the north. The program is targeting these alpine species specifically because they have adapted to survive only in harsh, low temperature conditions and cannot thrive in warmer climates. As such, they are especially sensitive to climate change. Georgia Murray, a scientist a the AMC, describes that the Mountain Watch observations help to make up “really rich mountain data sets” that, paired with temperature observations from the Mt. Washington observatory, help to understand how climate change has affected the environment in the Northeast.

This year, the Mountain Watch program is joining an exciting new collaboration called A.T. Seasons (A.T. for Appalachian Trail), which is working to develop sites for citizen scientists to collect plant phenology data all along the Appalachian Trail. Mountain Watch joined this project to get more people involved, and as Georgia explains, to “utilize the A.T. as a north-south corridor in understanding phenology in climate change.” The goal of A.T. Seasons is to monitor the same type of plants along the whole Appalachian Trail to better understand the interplay of climate and phenology across geographical regions, as well as in relation to climate change. As alpine species only grow on the northern section of the A.T., they will not be included in this portion of the program; however, Georgia notes that Mountain Watch will still maintain the “alpine focus that is unique to the AMC and our region in the northeast” in addition to the A.T. Seasons plant list.

The incorporation of A.T. Seasons into the Mountain Watch program allows more citizen scientists to be involved, as the new initiative provides options for different levels of commitment – there is an Android app for easily making one-time measurements and more in-depth training courses for people who want to make long-term observations. The alpine flower portion of the Mountain Watch program does require more “dedicated volunteers,” as Georgia says, who can commit to regularly visiting the remote mountain sites, but there are many educational tools on the website for those who just want to learn more.

So grab those hiking boots and get outdoors! Spring and summer are the best times to observe plant phenology, and the sweeping views of the White Mountains await.

Top image: Sean O’Brien via Flickr

Bottom image: AMC Mountain Watch 


Emily Lewis is a PhD candidate in chemistry at Tufts University, where she analyzes industrially important catalysts on the nanoscale. She received her BS and MS degrees from Northeastern University, and her thesis work examined fuel cell catalysts under real operating conditions. She loves learning about energy and the environment, exploring science communication, and investigating the intersection of these topics with the policy world. When she’s not writing or in the lab, you’ll probably spot Emily at the summit of one of the White Mountains in NH. Follow her: @lewisbase, emilyannelewis.com