Despite much of the San Francisco Bay Area being generally urbanized today, that wasn’t always the case. This expedition looks into the past with newly imaged plant specimens from our collections that were collected between 1800 and 1935. It is called: 1800-1935: Bay Area Collections. In this expedition you can also see collections made by prominent early Bay Area botanists, including Alice Eastwood, William Dudley,  Albert Kellog, S.B Parish, Katherine Brandegee and more. Today more than 1200 plant species can be found in the greater Golden Gate Recreation Area, and the San Francisco Bay Area to this day boasts a level of access to nature and open space that surpasses most metropolitan areas in the United States. Bay Area habitats occupy a wide range , including coastal redwood forests, chaparral, deciduous forests , rocky serpentine outcrops  and coastal scrubland and more. Here are a few species you can find in this expedition and around the Bay Area:

Penstemon heterophyllus: Sometimes known as bunch leaf penstemon , is a member of the family Plantaginaceae. This species of plant is a California native, and is an excellent drought resistant addition to native plant gardens. It is known to grow in California chaparral habitats as well as alongside live oak forests.

Plagiobothrys nothofulvus: Also called rusty popcornflower , is a member of the family Boraginaceae. Versatile, it can be found in coastal sage scrub, woodlands , meadows and wetland habitats. This species serves as food for many species of insect and mammal who eat the seeds and flowers as well as being a source of nectar for bees and butterflies.

Castilleja densiflora: Sometimes known as owlclover is native to california and can be found up and down the California coast. It is a member of the family Orobanchaceae and in the genus Castilleja alongside other familiar flowering plants like Indian Paintbrush – Castilleja coccinea. Several subspecies of Castilleja densiflora exist including ssp. Obispoensis, only found in San Luis Obispo County.

And to put some faces to the names of early Bay Area Botanists …

Alice Eastwood:  b. 1859 – d. 1953: Born in Toronto Canada, Alice Eastwood was a self-taught botanist who first started collecting in Colorado after immigrating to the United States with her family. She first worked as a teacher in Denver, but her botany collections caught the attention of Katherine Brandegee at the California Academy of Sciences who hired her to work in San Francisco in 1891. By 1892 she was promoted to joint curator and by 1894 appointed as head of Botany where she served a long tenure until 1949. She was responsible for extensive collections in California and for saving important specimens during the 1906 earthquake and fire. She published more than 310 articles in her career , served as editor for the journal Zoe, and collected in many states and traveled to partner institutions around the world to expand her work.

William Dudley: b. 1849 – d. 1911: Born in New Guilford Connecticut, William Dudley studied and received a bachelor’s in 1874 and master’s degree in 1876 from Cornell University. He later went on to teach at Cornell and various other universities on the east coast until being hired to Stanford University in 1892 as head of systematic biology. William Dudley was an environmental activist key in preserving the coastal redwood and advised the establishment of the national forest system in California. William Dudley later died in 1911 from sicknesses caught while conducting research in Iran and Egypt.

Katherine Brandegee: b. 1844 – d. 1920 Was born in Tennessee as Katherine Layne but moved to California with her family during the California gold rush of 1849. After the death of her first husband in 1874 from alcoholism, she enrolled soon after in U.C Berkeley, becoming the third ever woman to attend medical school there. In 1878 she received her M.D. and became a doctor, although chose to pursue Botany instead in 1879. She became a member of the California Academy sciences and became curator of botany in 1883. She later met her second husband Townshend Brandegee who shared her love of botany in 1889. The two later collaborated for many years while she served as botany curator. She was responsible for the co-founding of the academic journal Zoe which allowed academic independence from east coast universities. She went on to hire her successor as curator, Alice Eastwood in 1892 . She and her husband later donated 76,000 specimens to U.C Berkeley before her death in 1920.

Albert Kellogg: b. 1813 – d. 1887 Born in New Hartford Connecticut, Albert Kellogg first studied medicine and received an M.D from Transylvania University in Lexington Kentucky. Through the 1840s he practiced medicine and collected and illustrated plants as an amateur botanist in New England and the South East before moving to california in 1848. He later continued to practice medicine and run a pharmacy in San Francisco until he later refocused his career on botany and was one of the founding members of the California Academy of Sciences in 1852. He went on to describe more than 200 species of plants, and wrote extensively on california forests. He was hired as surgeon and botanist by the US government to survey Alaska in 1867. Albert Kellogg was one of the first members of the academy to advocate for opening membership to women in 1853, later on hiring Catherine Brandegee to succeed him as curator of Botany.

Visit the 1800-1935: Bay Area Collections expedition on the CAS Plants to Pixels project.

October 10-13 marked the 15th time Notes from Nature has participated in WeDigBio. The, now twice a year, event is great time to learn more about what the natural history museum community is doing by participating in a symposium, interacting with volunteers and generally supporting our data providers with expeditions and special events.

For the October 2024 event, Notes from Nature recorded over 21,700 classifications. We are so honored and appreciative of all the support. There is still lots of expeditions to work on, so please stop by anytime and help us spread the word!

Stay tuned for the the exact dates of the next WeDigBio which will take place in April 2025.

— The Notes from Nature team

Many thanks to all that have been participating in WeDigBio. We are in awe of your contributions! Over 12,600 classifications have been recorded so far. Capture the Collections had another huge day with over 2,300 classifications. We are also very excited to see all the interest in our newest project Ranges Mammal Traits from western North America .

We are excited to see what Day 3 brings.

With gratitude,

– The Notes from Nature Team

It was a fun and exciting first day of WeDigBio. In total Notes from Nature received over 7,000 classifications! We so appreciated everyone that contributed.

Our symposium titled How is AI Being Used in Biodiversity Efforts? was very well attended with over 100 registered participants. Many thanks to the organizers and speakers.

Please visit Notes from Nature today and help us spread the word about this important event.

— The Notes from Nature team

We wanted to remind you that WeDigBio starts in one week on October 10th and continues through October 13. WeDigBio or Worldwide Engagement for Digitizing Biocollections, is a global data campaign, virtual science festival, and local outreach opportunity, all rolled into one. The annual, 4-day WeDigBio events mobilize participants to create digital data about biodiversity specimens. You can learn more at https://wedigbio.org/

Notes from Nature will be hosting lots of expeditions that you can work on from anywhere. Just head over to Notes from Nature select a project of interest and then choose one of the expeditions to work on. Every record you enter makes a huge difference!

Lastly, please see out previous post about a special WeDigBio symposium being held on October 10th at 2pm central

Thanks,

The Notes from Nature Team

How is AI Being Used in Biodiversity Efforts?

The WeDigBio board is pleased to announce a one-hour symposium, “How is AI Being Used in Biodiversity Efforts? on October 10 from 2-3pm Central Time (3-4pm Eastern Time). This session will include three different examples of how AI can be used in service of digitization and conservation efforts, and how its use is being monitored. As the presence of AI in all walks of life becomes more common, the use of AI (both the why and the how) is not always clear. In this session, three researchers will share how they use AI in their work, why it is useful for them, and the methods they have in place to ensure data quality.

Schedule

2:00–2:05 Welcome! by Samantha Blickhan (Zooniverse)

2:05–2:20 The evolution of AI as a tool for conservation, by Sarah Huebner (Smithsonian National Zoo and Conservation Biology Institute)

2:20–2:35 Phenobase: a central global database of plant phenology by integrating in situ observatory and image-derived phenology data, by Daijiang Li (University of Arizona)

2:35–2:50 Leveraging ground truth Smithsonian data to evaluate AI tools (Smithsonian OCIO Data Science Lab and Office of Digital Transformation)

2:50–3:00 Panel Discussion

The 4-day WeDigBio event runs from October 10-13. WeDigBio stands for Worldwide Engagement for Digitizing Biocollections. To learn more about WeDigBio, visit wedigbio.org.

Register to get a Zoom link: https://www.eventbrite.com/e/how-is-ai-being-used-in-biodiversity-efforts-tickets-1033701638427

We are looking forward to the next WeDigBio, which is less than 3 weeks away! The event takes place April 18-21, 2024. There is still time to get involved, so please reach out if you are interested or have any questions at all about the event.

If you are interested in hosting an event, please check out https://wedigbio.org/content/register-event-tour-or-campaign.

The WeDigBio symposium for this event will focus on Artificial Intelligence. More details to come soon.

Looking forward to it,

The Notes from Nature Team

California’s deserts are far from wastelands, but bursting with biodiversity and plant life. Each of California’s desert habitats, the Mojave, Colorado and Great Basin deserts each have their own distinct landscapes and ecology. The Mojave is a high desert with winter snowfall and low overall rainfall, while in contrast the colorado desert is a low desert with monsoon-like seasonal rains. The Great Basin desert begins in the shadow of the Sierra Nevada Mountains in California and spans across much of Nevada and Utah. The great basin has even higher altitude conditions than the mojave and is subdivided by several ranges of mountains. Each of the desert habitats is home to thousands of plant species with hundreds of unique species that are endemic to California. While this expedition will only contain a selection of the wide breadth of flowering desert plants native in California, we hope you enjoy it and learn something new.

Please give it a try https://bit.ly/4cBICKK!

Here is a highlight of some interesting desert-dwelling plant species that you can find in this expedition:
Eramalche Rotundifolia also known as the desert five spot is native to the Mojave , Colorado and Great Basin deserts of California and neighboring states. It is a special sight in Death Valley National Park or Anza Borrego Desert State Park during the spring blooms.

Chylismia Munzii or the Death Valley Suncup is native to California and Nevada, and can also be found in its name-sake national park Death Valley. Chylismia Munzii is in Onagraceae or the evening primrose family.

Larrea tridentata commonly known as the creosote bush or La Gobernadora in Mexico, is widespread across the Mojave, Colorado in the United States and the Chihuahuan desert in Mexico. This hardy plant can go up to two years without water. Larrea tridentata has a long lifespan and the interesting ability to clone itself asexually. Single individuals can be found to live up to 500 years with clonal colonies ( colonies of genetically identical clones from a single ancestor) able to live up to 11,000 years. You can read more about Larrea tridentata at nps.gov here.

Plants of the Mojave, Colorado and Great Basin deserts: https://bit.ly/4cBICKK!

Have you ever wondered why bugs are the colors they are? From the bright hues of butterflies to the earthy tones of ants, these natural colors serve many important roles. These roles include attracting mates, warding off predators, and staying warm.

In dragonflies, a 300-million-year-old group intimately connected to freshwater ecosystems on Earth, the uses of their vibrant body colors are almost entirely unknown. This is because of an unfortunate problem – color fade. We would normally turn to specimens in museum collections for data on the colors of species, but because their pigments naturally degrade over time their vivid colors disappear in weeks to months. 

For this reason we turn to iNaturalist, a citizen science platform where users upload photo observations of organisms. Since it contains photos of live organisms, color fade is no issue. But it also presents many challenges because of how incredibly variable these images can be. Think of all the different viewing angles, lighting conditions, and cameras that many thousands of observers use across the 2 million dragonfly images on iNaturalist. All of these affect the color we see.

We have developed an approach that uses computer vision and AI to deal with these issues. We are able to pull the dragonfly out of each image, filter bad or weird ones out, then discover what colors are present. This data will allow us to finally answer questions about the colors of the 2000 dragonfly species on iNaturalist globally. For example we think that dark body colors might be used to help warm dragonflies in cold environments, and that vibrant patterns are used for species recognition during mating.

An essential part of trying a new method in science is you make sure it works. Our approach to getting color data is really complex and novel, and we want to compare it to the common standard of having human observers code colors – and for that we need your help! If the colors you choose for an image match up to what our computational approach detects for that same image, we’re golden. Otherwise, I have more work to do! 

Thanks for considering joining the Big Dragonfly Color team!

Link to our expedition:

https://www.zooniverse.org/projects/md68135/notes-from-nature-labs

Be sure to choose “Big Dragonfly Color” on the right side of the page!

The Notes from Nature team is thrilled to announce the launch of a new project called CAS Plants to Pixels! We currently have two live expeditions and a demo that shows off some of the capabilities that we’ll be using for the project in the future. Please give them a try and let us know what you think.

The main goal of this project is to digitize California collected herbarium specimens housed at the California Academy of Sciences. You can learn more about the exciting high throughput method being used for imaging and the resulting research involved in this project on the project Research page.

We’ve got a lot more to share in the coming weeks and months. You can get involved now by give the project a try — visit: https://www.zooniverse.org/projects/md68135/notes-from-nature-cas-plants-to-pixels