Bacteria naming method relies on DNA
A controversial new system for naming bacteria and other prokaryotes relies only on their DNA, rather than laboratory cultures, to identify them. The approach, dubbed SeqCode and described this week in Nature Microbiology, promises to relieve a backlog created because so many microbial species are being revealed through DNA analyses. Under an existing protocol, the scientific community accepts a bacterium, or a prokaryote known as an archaeon, as real only if microbiologists grow the species in the lab and submit a pure “type” culture to at least two of the world’s facilities that keep microbes in perpetuity. Instead, SeqCode accepts a full or comprehensive set of a bacterium’s genome sequence data as its “type” material and outlines a protocol for assigning a Latin name. SeqCode software checks to make sure the DNA sequence is unique, and scientists evaluate whether the name was chosen according to guidelines. But it’s unclear whether the method will take hold. Some microbiologists refuse to accept a genome as sufficient evidence of a species’ existence.
Disputed botany paper stands
The journal BMC Medicine announced this month that it will not retract an influential but controversial 2013 paper by botanist Steven Newmaster of the University of Guelph (UG) that questioned the purity of herbal remedies. In 2021, eight scientists signed a complaint alleging that Newmaster was responsible for “missing, fraudulent, or plagiarized data” in three papers, including this one, which helped make him a sought-after expert and industry consultant. Independent specialists supported those concerns, as detailed in a Science investigation. A UG investigation cleared Newmaster of misconduct in June, although it cited his failure “to apply the standards reasonably expected in research” for his work supporting the BMC Medicine article and others, including one that was retracted. Despite not retracting the herbal remedies paper, BMC Medicine retained a note posted in February alerting readers that doubts had arisen about the reliability of the paper’s data. Newmaster did not respond to a request for comment.
You’re counting votes. Many of us are just counting bodies.
- Yale University epidemiologist Gregg Gonsalves
- tweeting about President Joe Biden’s remark that the pandemic “is over,” although about 400 Americans continue to die from the disease daily.
Math professor given probation
An applied math professor at Southern Illinois University (SIU), Carbondale, will avoid prison and instead serve 1 year of probation in the most recent resolution of a case involving the U.S. government’s controversial China Initiative, which targeted U.S. academics, most of them of Chinese ancestry. In May, a jury found Mingqing Xiao not guilty of making a false statement to the government regarding his ties to Chinese institutions on a grant application. But Xiao was found guilty of filing incorrect tax returns and failing to report a foreign bank account, charges added to his original indictment. At Xiao’s sentencing this week, District Court Judge Staci Yandle said no purpose would be served by incarcerating him and that he posed no threat of reoffending. Xiao, who has been on paid administrative leave since his arrest in April 2021, told the judge he hopes to be reinstated by SIU and resume teaching and research. In February, the U.S. Department of Justice dropped the name China Initiative after concluding that the phrase has “fueled a narrative of intolerance and bias.” The department has announced no new indictments of academic researchers since the name change.
King of the hill: 20 quadrillion ants
Ants were already estimated to be the most numerous insects. Now, a research team has developed the most comprehensive estimate to date of the number of individual ants, one that puts a new perspective on “teeming anthill.” By combining data from 489 studies from around the world, the team pegged that figure at 20 quadrillion, or 20 followed by 15 zeroes. Although individual ants are light, that astronomical figure translates to a collective dry weight—the weight with all the fluids removed, which constitutes the total biomass of carbon—of 12 megatons, more than all wild birds and wild mammals combined, the team reports this week in the Proceedings of the National Academy of Sciences. The estimate is two to 20 times higher than previous ones, which varied because many were extrapolated from studies of ants in just one place or calculated based on an estimated percentage of ants relative to all insects. The new study relied on actual tallies of ants caught above ground but may be incomplete because it included no studies covering ants hidden in nests and lacked surveys from boreal forests, much of central Africa, and parts of Asia.
Europe protects more sea floor
To prevent damage to sensitive marine habitats, the European Commission will next month close more than 16,000 square kilometers of shallow coastal waters in the northeastern Atlantic Ocean to bottom trawling. When fishing boats drag heavy nets along the sea floor to catch bottom dwellers, such as rose shrimp, they also kill other species and cloud the water with sediment. In 2016, the Commission banned bottom trawling below 800 meters in an area covering more than 4.9 million square kilometers to protect cold water coral reefs and the ecosystems where they live. The Commission’s announcement last week extends the protections to EU waters between 400 and 800 meters off the coasts of four member states: France, Ireland, Portugal, and Spain. Scientists working on behalf of the International Council for the Exploration of the Sea drew on existing data to predict areas likely to contain vulnerable species, such as glass sponges and tube-dwelling anemones. Environmental groups welcomed the announcement, but fishing groups warned it would cost jobs.
Bringing your kids to the field
Yale University paleoanthropologist Jessica Thompson has been towing her three children with her to field sites in Malawi for years. Her experiences—both challenging and rewarding—have led her to reflect on how fieldwork-intensive disciplines raise unique questions for researchers, especially mothers, with families. Should you bring kids with you? What if they trample fragile fossils or fall sick? She and colleagues have been surveying fellow scientists about professional imperatives to do fieldwork and their decisions about child care. She hopes the answers will support changes in practices to make fieldwork more manageable for researchers with families.
Q: How have child care issues affected your ability to do fieldwork?
A: When I was just starting, my oldest son was 1, and my parents would take him for me during the summer so I could focus on what I needed to do. Without that family support, there’s just no way I could ever have done that. Because my partner works in the field with me, it means either my parents help out, or we bring [the children]. There’s no other option. … The most obvious obstacle is financial. The airfare costs of bringing multiple kids to Central Africa, where I work, rapidly add up. … The local community loves the fact that we bring our kids. It opens doors in ways that would otherwise be completely closed to you, because it humanizes this group of scientists coming in.
Q: How do kids on site affect the work?
A: I worry about the morale of the other people at the field site. If there’s this kid who’s annoying them for some reason, are they going to feel like they don’t want to be there? Or that they’re not part of this family unit? … If everyone is living in the field camp sharing housing and food, and your research grant is paying for all of that, how do you separate out people’s personal expenses [for the children]?
Q: How are these challenges affecting your area of science?
A: We think being mothers is one of the reasons why women don’t have a lot of representation among leadership in our field. I think it’s pulling a lot of people out of the pipeline of field research and directing them instead to lab-based work.