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Maureen O’Leary

Maureen O’Leary. Photo courtesy of SBU

By Daniel Dunaief

Like the great white shark that needs to keep swimming to stay alive, scientific databases that provide resources to researchers from all over the world can’t stay still or they risk losing their usefulness and reliability.

The directors of these resources need to find funds that will ensure that the data remains accessible and that users, who range from high school students conducting work for a class to the chairman of research departments at colleges, can benefit from the availability of information.

Maureen O’Leary. Photo from SBU

Maureen O’Leary, a Professor and Graduate Program Director at the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook University, is looking to ensure that Morphobank, a web application and database that allows scientists around the world to share raw data on the structure of various organisms to help determine their evolutionary links, receives funds that sustain its mission.

O’Leary helped start MorphoBank in 2000 to encourage researchers to share data and propel science forward and is currently the director. By making observations of the structures of organisms available in one place online, she hoped to help advance the field of phylogenetics — the relationships among organisms in a family tree — while cutting down on the need to reproduce data from the same fossils at museums or other sites.

Up to this point, O’Leary has found financial support for the effort through grants from the National Science Foundation, the American Museum of Natural History and the National Oceanographic and Atmospheric Administration.

Looking to the future, however, O’Leary wanted to create a financial plan that would ensure ongoing funding for a database that has not only helped researchers explore data, but has also enabled collaborators to share information privately in a non-public area of MorphoBank.

O’Leary has been working with Phoenix Bioinformatics, a nonprofit group based in Fremont, California that has developed funding models for databases. Phoenix started its operations in 2013 after the staff of TAIR, a curated database for plant genome information, lost its grant funding.

The business is in the early stages of helping O’Leary with Morphobank, said Eva Huala, the Executive Director of Phoenix and a founding member of TAIR.

Phoenix has helped construct a financial model that is similar to the way university libraries and scientists pay for subscriptions to journals. The prices vary depending on the database the library subscribes to and the amount of usage of that database from the university. 

Huala said Phoenix is providing software that helps recruit members. The company is also enabling users to see whether their institution is supporting MorphoBank. So far, the Executive Director is “encouraged by the response. We know that this often takes several months or longer for libraries to decide” to lend financial support, she said.

The cost of running MorphoBank is connected to the time people spend curating as well as fixing bugs or managing computer-related challenges. Without software patches and fixes, the databases can run into problems.

Universities often require their researchers to make sure the data they collect is available to the scientific community, Huala explained, adding that MorphoBank can give scientists a way to “demonstrate the impact of their research” by offering download and viewing statistics for their data.

Mike D’Emic, an Assistant Professor in Biology at Adelphi University and a member of the Executive Committee of MorphoBank, has used the database for over seven years.

D’Emic suggested that MorphoBank “saves people from reinventing the wheel in doing science” by providing free, raw data. Scientists don’t have to travel to museums or other sites to gather the same information.

An early career researcher or student might have a small grant to visit three or four museums. These scientists can “supplement that data set with information from MorphoBank that’s multiple times the value of a grant they would have gotten,” D’Emic noted.

Scientists can freely use data from MorphoBank that would have taken tens of thousands of dollars to acquire. This includes photographs of a dinosaur skull from distant countries or CT scans that can be expensive to produce.

D’Emic, who helped convince the Adelphi library to provide financial support for the database, said MorphoBank addresses bug reports quickly, fixing problems with a few days.

Prior to O’Leary’s effort to start MorphoBank, a researcher might need to search through the appendices or the published reports from other scientists in their field to access raw data for tree building, sometimes retyping by hand large spreadsheets of numerical scores.

MorphoBank has been “invaluable and transformative in terms of the way people access and replicate science,” D’Emic said.

Some journals have started urging authors to publish their data online. The Journal of Vertebrate Paleontology strongly recommends uploading dataset, character descriptions and images to an online repository.

“For not too much money, MorphoBank has a huge impact on science,” D’Emic said, who said it was a cost effective boost to evolutionary biology and related fields

Scientists have changed significantly in their approach to sharing information. Around 30 years ago, some researchers wouldn’t always share their raw data. Other scientists would then have to spend thousands of dollars to travel to places like Thailand, Australian and Madagascar.

“People have come around” and are more comfortable exchanging data, sometimes as they produce it, D’Emic said. “MorphoBank has been an integral venue for convincing people you should share.”

O’Leary believes researchers have evolved in the way they think about the information they collect as a part of their studies.“We have reached a social transition where scientists get used to not only writing a paper and walking away, but making sure the data content is in a digitally reusable format,” she said.

O’Leary feels fortunate to have received funding for over two decades for MorphoBank. She plans to remain the director when MorphoBank moves to Phoenix. It’s an “important and dynamic tool” and she feels a “responsibility to allow its continuity.”

 

Maureen O’Leary wraps fossils during an expedition in Mali. Photo by Eric Roberts

By Daniel Dunaief

Mali is filled with challenges, from its scorching hot 125 degree temperatures, to its sudden rainstorms, to its dangers from militant and terrorist-sponsored groups.

The current environment in the landlocked country in West Africa makes it extraordinarily difficult to explore the past in a region that includes parts of the Sahara Desert, but that, at one point millions of years ago, was part of a waterway called the Trans-Saharan Seaway.

Maureen O’Leary, professor of anatomical sciences at the Renaissance School of Medicine at Stony Brook University, led three expeditions to Mali, in 1999, 2003 and 2008, collecting a wide array of fossils and geological samples from areas that transitioned from an inland seaway that was about 50 meters deep on average to its current condition as a desiccated desert.

Maureen O’Leary and Eric Roberts with Mali guards. Photo from Maureen O’Leary

On her third trip, O’Leary quickly left because she decided the trip was too dangerous for her and the scientific team. Rather than rue the lack of ongoing access to the region, however, O’Leary pulled together an international team of researchers from Australia, the United States and Mali to look more closely and categorize the information the research teams had already collected from the region.

“We made the most of a bad situation,” O’Leary said. “It is a silver lining, to some degree.”

Indeed, O’Leary and her collaborators put together a paper for the June 28 issue of the Bulletin of the American Museum of Natural History that is over 170 pages and contains numerous images of fossils, as well as recreations of a compelling region during a period from 100 million to 50 million years ago. This time period coincided with one of the five great prehistoric extinction events, during the Cretaceous-Paleogene boundary.

O’Leary characterized some of the more exciting fossil finds from the region, which include the first reconstruction of ancient elephant relatives and large predators such as sharks, crocodiles and sea snakes.

The size of some of these creatures far exceeds their modern relatives. For example, O’Leary’s scientific colleagues estimate that a freshwater catfish was about 160 centimeters in length, which is four times the total size of a modern catfish. The larger catfish dovetails with similar observations the researchers had made about sea snakes in 2016 and 2017. They started to knit this trend into a preliminary hypothesis in which a phenomenon known as island gigantism may have played a role in selecting for these unusually large creatures.

“Species become bigger in these environments,” O’Leary said, suggesting that other scientists have made similar observations. “It’s not clear what causes that kind of selection.”

Above, some of the species that lived in and around the TransSaharan Seaway, including an extinct species of crocodile. Illustrated by Lucille Betti-Nash/ Department of Anatomical Sciences, Stony Brook University.

 

In addition to studying vertebrate and invertebrate fossils, scientists including Eric Roberts at James Cook University in Australia looked at the geology of the region. Roberts helped name and describe many of the formations in the area. This provides context for the lives of creatures who survived in an environment distinctly different from the modern milieu of the Sahara Desert.

Roberts, who is a part of the Sedimentary Geology & Paleontology Research Group that has nicknamed themselves Gravelmonkeys, explained that his initial efforts in Mali came from the fieldwork over a course of weeks when he explored the rock sequences and took copious notes on them.

He suggested that the region still represents a geoscience frontier, in part because it is so difficult to get to, takes serious logistics to do fieldwork and is hard to maintain research.“Over many years, I have worked with collaborators on the project to analyze the samples in many different ways and especially to compare our notes and analytical results with descriptions of rocks and geological formations in other parts of the Sahara and further afield in Africa to understand how they are different and how they correlate,” he said.

O’Leary suggested that the paper provides some context for climate and sea level changes that can and have occurred. During the period she studied, the Earth was considerably warmer, with over 40 percent of today’s exposed land covered by water. Sea levels were about 300 meters higher than current levels, although the Earth wasn’t home to billions of humans yet or to many of the modern day species that share the planet’s resources.

Robert Voss, the editor-in-chief of the series at the American Museum of Natural History, praised the work for its breadth. “This was an unusually large and multidisciplinary author team, as appropriate for the broad scope of the report,” he explained .

“Seldom is such a large geographic area so poorly known paleontologically, so there was a unique opportunity here to break new ground and establish a broad framework for future work,” he added.

Voss described O’Leary as a “force of nature” who “responds constructively to peer reviews.” Roberts, too, appreciated the effort O’Leary put into this work.

O’Leary “drove the entire process and product,” which was only possible with someone of her “vision to wrangle so much science from so many different scientists into one place,” he offered in an email.

Roberts is very pleased with the finished product and added that it is “something that I will be proud of for the rest of my career. This took a lot of effort over the years and it great to see the end product.”

O’Leary said that much of the literature for the science in Mali was in French, which had kept it a bit below the radar for scientific discourse, which tends to be in English.

Indeed, O’Leary was able to facilitate conversations among the many people involved in this project because French was the common denominator language. She studied French at the Holton-Arms School in Bethesda, Maryland. “When I was sitting in my high school French class, I didn’t think it would come in so handy to be fluent in French” in her career, O’Leary said. “It was helpful as a female leader in this situation to be able to speak for [myself], whether speaking to other Americans or collaborating or working with guards.”

O’Leary plans to look at different projects in the United States, including in Puerto Rico, and in Saudi Arabia next. “We now have this synthetic story for Mali [and will be] building out from this to other areas. I anticipate a large time to ramp up to study areas like deposits in Nevada.”