A note on apartments and bubbles

As Aotearoa enters week two of lockdown, it’s clear we’re all still working out what our “bubbles” look like and how to stay in them to stop the spread of Covid-19. New to the government’s Covid-19 website is some good guidance for people living in apartment blocks. Recent decades have seen New Zealanders in increasing […]

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Captive apes’ gut microbiomes are a lot like some people’s

A gorilla looks at the camera over its shoulder, surrounded by green leaves

Apes in US zoos have gut microbiomes that are more similar to those of people who eat a non-Western diet than to the gut makeup of their wild ape cousins, according to a new study.

Further, even wild apes that have never encountered antibiotics harbor microbes with antibiotic resistance genes.

The findings, which appear in the ISME Journal, suggest that contact with people shapes the gut microbial communities, or microbiomes, of gorillas and chimpanzees.

The findings also indicate that the gut microbiomes of wild apes provide clues to human-ape interactions that could inform efforts to protect the endangered species.

Finally, the research highlights a way to identify new antibiotic resistance genes before they become widely established in bacteria in people, giving researchers time to develop tools to counter them before they threaten human health.

Pre-antibiotic humans

The gut microbiome supplies us with vitamins, helps digest food, regulates inflammation, and keeps disease-causing microbes in check. Antibiotics can change the makeup of the gut microbiome in lasting ways.

“It’s difficult to figure out exactly how antibiotics affect the human gut microbiome when almost everyone is born with bugs that already have antibiotic resistance genes,” says senior author Gautam Dantas, professor of pathology and immunology, of molecular microbiology, and of biomedical engineering at Washington University School of Medicine.

“Wild apes are the closest thing we have to pre-antibiotics humans. Luckily, we got the opportunity to work with two highly respected primatologists.”

Coauthors Crickette Sanz, associate professor of biological anthropology and David Morgan, a research fellow at the Lester E. Fisher Center for the Study and Conservation of Apes at Lincoln Park Zoo in Chicago and an honorary research scientist at Washington University, study wild chimpanzees and gorillas in a remote area of Nouabalé-Ndoki National Park in the Republic of Congo.

The Wildlife Conservation Society and the Congolese government manage the park. To learn about the apes’ gut microbiomes, Sanz, Morgan, and their field teams followed apes in known groups and discreetly collected fecal samples from 18 wild chimpanzees and 28 wild gorillas. The noninvasive sampling method allowed researchers to collect data on the apes without disturbing them.

Chimps, gorillas, and people

The researchers stored the samples in liquid nitrogen, carried them to the park headquarters, and then transported them in a dugout canoe down the Sangha River and then in a truck to Brazzaville, the capital of the Republic of Congo, where they stayed in a freezer until they shipped them to Dantas’ lab.

The researchers also collected and shipped fecal samples from 81 people who lived on the outskirts of the park.

Meanwhile, Dantas and first author Tayte Campbell—then a graduate student in Dantas’ lab—arranged to obtain fecal samples from 18 chimpanzees and 15 gorillas living at either the Saint Louis Zoo or the Lincoln Park Zoo.

The researchers identified the kinds of bacteria and the antibiotic genes present in the gorilla, chimpanzee, and human samples, and compared the results to publicly available data on people who live in the US, Peru, El Salvador, Malawi, Tanzania, or Venezuela and follow hunter-gatherer, rural agriculturalist, or urban lifestyles.

The gut microbiomes of people whose data the study included, fell into two groups.

One group included hunter-gatherers and rural agriculturalists who typically eat a diet heavy in vegetables and light in meat and fat; this group included the people from the outskirts of the national park in the Republic of Congo.

The second group included urban people who eat a meat-rich Western diet. Wild gorillas and chimpanzees formed a third group distinct from both human groups. But captive apes fell into the first group; they were most similar to people who ate non-Western diets.

“Chimpanzees are endangered, and Western lowland gorillas are critically endangered; their main threats are habitat destruction, poaching, and disease,” Sanz says.

“Measuring the gut microbiome could be a way to monitor apes’ exposure to anthropogenic threats so we can identify areas of concern and develop effective, evidence-based mitigation strategies.”

Antibiotic resistance genes

The researchers also identified several previously unknown antibiotic resistance genes in the wild apes and people from the Republic of Congo, including one that confers resistance to colistin, an antibiotic of last resort.

For now, the genes reside in bacteria harmless to humans. But bacteria have the ability to share genes, so any antibiotic resistance gene could find its way into a more dangerous species of bacteria.

“Rare sampling opportunities of wild apes like in this study gives us a look into the future,” Campbell says. “When we find these novel antibiotic resistance genes in the environment, we can study them and possibly find ways to inhibit them before they show up in human pathogens and make infections very difficult to treat.”

“It would be very interesting to expand this research across a broader range of conservation contexts, such as commercial logging zones and tourist operations,” Morgan adds.

“With the arrival of human activities and associated anthropogenic disturbances, wild apes may be exposed to antibiotic resistance genes. We don’t know much about how antibiotic resistance spreads through natural environments, so that could have implications for human public health that we don’t yet understand. That’s something we’d like to investigate.”

The National Institutes of Health, the National Institute of Diabetes and Digestive and Kidney Diseases, the National Institute of Allergy and Infectious Diseases, the Edward Mallinckrodt Jr. Foundation, and the International Center for Energy, Environment, and Sustainability at Washington University in St Louis funded the work.

Source: Washington University in St. Louis

The post Captive apes’ gut microbiomes are a lot like some people’s appeared first on Futurity.

Oysters and clams do just fine when farmed together

tractor and oyster farm from above

Eastern oysters and three species of clams can flourish when farmed together, potentially boosting profits of shellfish growers, a new study shows.

Though diverse groups of species often outperform single-species groups, most bivalve farms in the US and around the world grow their crops as monocultures, researchers say.

“Farming multiple species together can sustain the economic viability of farm operations and increase profitability by allowing shellfish growers to more easily navigate market forces if the price of each individual crop fluctuates,” says lead author Michael P. Acquafredda, a doctoral student based at Rutgers University’s Haskin Shellfish Research Laboratory and lead author of the paper in the journal Marine Ecology Progress Series.

Farming mollusks such as clams, oysters, and scallops contributes billions of dollars annually to the world’s economy. In the United States, farmers harvested more than 47 million pounds of clam, oyster, and mussel meat worth more than $340 million in 2016.

The study, which took place in a laboratory setting at Rutgers’ New Jersey Aquaculture Innovation Center tested the feasibility of farming multiple bivalve species in close proximity to each another.

Mimicking farm conditions, the study examined the filtration rate, growth, and survival of four economically and ecologically important bivalve species native to the northeastern United States: the Eastern oyster (Crassostrea virginica); Atlantic surfclam (Spisula solidissima); hard clam (Mercenaria mercenaria); and softshell clam (Mya arenaria).

When supplied with seawater containing naturally occurring algal particles, the groups that contained all four species removed significantly more particles than most monocultures. This suggests that each species prefers to filter a particular set of algal food particles.

“This shows that, to some degree, these bivalve species complement each other,” says coauthor Daphne Munroe, an associate professor in the marine and coastal sciences department in the School of Environmental and Biological Sciences.

The scientists also found virtually no differences in growth or survival for any of the four species, suggesting that when food is not an issue, farmers can raise these bivalves together and not worry about them outcompeting each another.

“This study illustrates the benefits of diversifying crops on shellfish farms,” Acquafredda says. “Crop diversification gives aquaculture farmers protection from any individual crop failure, whether it’s due to disease, predation or fluctuating environmental conditions.

“In future studies, the feasibility of bivalve polyculture should be tested on commercial bivalve farms.”

Source: Rutgers University

The post Oysters and clams do just fine when farmed together appeared first on Futurity.

At Aeon: Dark matter search derailed by dogma?

Question: Have we found more dark matter than fairies all this time?

The issues at stake are huge. Acceptance of dark matter has influenced scientific thinking about the birth of the Universe, the evolution of galaxies and black holes, and the fundamental laws of physics. Yet even within academic circles, there is a lot of confusion about dark matter, with evidence and interpretation often conflated in misleading and unproductive ways …

This is how I stumbled into the field in the late 1990s. I was studying the dynamics of small satellite galaxies as they orbit our galaxy, the Milky Way. From observation, we expected that these satellite galaxies must contain a lot of dark matter, from 10 to 1,000 times as much as their visible, normal matter. During my calculations, I made a perplexing discovery. My simulations produced satellite galaxies that look much like the ones actually observed, but they contained no dark matter. It seemed that observers had made wrong assumptions about the way the stars move within the satellite galaxies; dark matter was not required to explain their structures.

Pavel Kroupa, “Has dogma derailed the scientific search for dark matter?” at Aeon

It’s a lot like Darwinian evolution except that, in this case, people are willing to talk about it.

See also: Are dark matter and dark energy scientific?

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Eric Holloway: The Turing test is unscientific

Eric Holloway points out that the assumption that the human mind can be reduced to a computer program has never really been tested:

This test for intelligence, the Turing Test, was invented by and named after the mid-twentieth century computer pioneer Alan Turing. It is a subjective test in that it depends on whether an artificial intelligence is capable of convincing human testers that it is a human. But fooling humans, while impressive, is not really the same thing as actually possessing human-level intelligence. In any event, some judges may be biased in favor of the AI passing the Turing test and may thus be easier to persuade than skeptical ones.

In 2014, an AI chatbot named Eugene Goostman passed one Turing test competition, organized by the UK’s Reading University.The chatbot was developed to give the impression of a 13-year-old Ukrainian boy, so that errors and manipulation of conversation could be overlooked. Quantum physicist Scott Aaronson showed just how unconvincing this chatbot was in a short conversation.

Eric Holloway, “Current artificial intelligence research is unscientific” at Mind Matters News

See also: Math shows why the mind can’t be reduced to a formula. The Liar’s Paradox shows that even mathematics cannot be reduced to a fixed set of axioms. Gödel’s discovery brought back a sense of wonder to mathematics and to the rest of human knowledge. His incompleteness theorem underlies the fact that human investigation can never exhaust all that can be known. Every discovery builds a path to a new discovery.

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