Methods | Big, old data about plants

Some people might associate big data with information about humans, but humans compile all kinds of big databases, such as the data that supports articles in scientific journals. Plant communities generate plenty of information that humans curate online: plants have been leaving traces in the fossil record for over 1.5 billion years. Our team will publish the redwood cuticle descriptions from this study in the Paleobotanical Database (PBot), a much-needed platform currently in beta testing. In this note, we will cover big old plant data, why scientists made PBot, what this project of non-fossilized species contributes to that database, and what PBot contributes to human social networks and the larger living world.

Analysts generally define big data by three V's: its volume, variety, and velocity. Never mind PBot for now, the Looy Lab alone meets criterion for big data. According to Oracle, the definition of big volume varies with the setting: "For some organizations, this might be tens of terabytes of data. For others, it may be hundreds of petabytes." Looy's collections utilize more space in the campus cloud than nearly any other lab. Earlier this year, Cindy passed Meriel a copy of the complete data for this project that was comfortably nested on its own terabyte harddrive. As for variety, the lab collections include photographs, maps, videos, spreadsheets, articles, and a few jokes. With respect to velocity, along with the community of studious Looy labfolk, a microscope with an automated robotic arm that Cindy helped the department acquire for collective use swiftly outputs data. So what about PBot as big data? The Looy Lab is just one of many, many labs in the world. Plus, beyond a lab's typical activity scaled to the globe, PBot might absorb a unique influx: so-called dark data that has been piling up around the world in museums, suddenly coming "to light."

Plant fossils generally pose more of a challenge to classify into Linnean species than animal fossils do. They are underrepresented in the widely popular Paleobiology Database in large part because samples must be identified in a way that's compatible with the Paleobiology Database's design in order to be logged. Paelobotanists use an informal technique called morphotyping to categorize plant fossil complexity. Morphotyping doesn't work on that database. Samples have been accumulating for centuries in physical museums and have remained offline during digital revolutions. A former Looy Lab doctoral student, Dr. Dori Contreras helped found PBot to meet that need for plants. The Looy Lab is participating in beta testing the design. By the way, the platform isn't just for professionals. It's built for students and citizen scientists, too. Jump in. (Bruch 2021)

As we've mentioned in our Experiment introduction, information from living species helps to classify extinct ones. Living species are the terminal buds on the branches of the metaphorical tree of life. Logging a collection of California redwood cuticles to PBot makes that information easily accessible to the nearly global community where Sequoioideae fossils have been found. It also helps with developing the functional user interface along the way.

Digitizing paleobotanical information improves human-community access to information about past plant-communities. All this data tells a huge part of the story about the evolution—and coevolution—of life on Earth. Facebook might have photos of what your friends were doing yesterday, last month, or last year; PBot has photos of what plants were doing for the past few epochs, periods, and eras. Your contribution to this project supports a tiny part of that growing network.

References:

Bruch, Kimberly Mann. (2021) “Paleobotany Database" EarthCube, https://www.earthcube.org/paleobotany-database. Accessed 25 Nov. 2022.

PBot Integrative Paleobotany Portal: The community gateway to fossil plant research and education, https://pbotportal.weebly.com/