“Most people recognise we need clean water,” says microbiologist Jo Handelsman, but nearly all of us underestimate the importance of a less glamorous material: soil. “Soil is often called dirt, and it’s not very well respected in this world. It is probably the most critical resource right now that we are losing at a very high clip.”

Handelsman’s primary mission is antibiotics. She finds new ones and is part of the global battle to counter antibiotic resistance. She is also on a crusade to tackle gender bias in science. And she says all scientists, driven by data and evidence, must challenge US president Donald Trump’s “anti-science”.

But soil is her current obsession. The disappearance of soils rather than disease is the biggest threat to the world, she predicts. It will exacerbate global starvation and shut off the main channel for generating new antibiotics.

“Agriculture and the environment are the things that will really devastate the human condition; much worse than human disease,” says the former scientific adviser to former US president Barack Obama, now director of Wisconsin Institutes for Discovery at the University of Wisconsin-Madison.

“If we can’t grow crops, which is the direction we are all going, by losing our soil just washing away across the world, then disease isn’t going to be the problem, starvation is.”

During a recent visit to Dublin, she cites projections from her time in the White House. The US will have hardly any soil by the end of this century, she says, even though areas of the US midwest have the richest and deepest soils in the world, outside Ukraine.

“There are areas where we have used up all our top soil and we are right down to subsoil and bedrock. We can’t continue that way, and still have a food supply. We need to build an appreciation of our natural resources, and in particular soil.”

Antibiotics and probiotics

Some 75 per cent of our antibiotics in current use have come from soil, she notes. If we found more, perhaps there would be a greater appreciation for soils, suggests Handelsman.

On new sources of antibiotics, she says: “I think we are going to be in trouble. One of the problems with humankind is that we don’t anticipate problems far enough in advance...There has to be a crisis before they are taken seriously. The problem with new antibiotics is it’s usually a 10-year lead-in time. So we can’t be in a crisis and have a solution tomorrow.”

The solution, however, is multifaceted. It should include managing the antibiotics we have in a better way, faster and harder work on discovery of new antibiotics, and alternatives to antibiotics. Avoiding disease in the first place through hygiene and good health has to be in the mix, through management of both humans and animals. Consuming probiotics using bacteria to fight other bacteria is beginning to emerge as an option.

She believes probiotics could be beneficial but says “we don’t have the knowledge yet”. “There are some good studies that show they can have beneficial effects in the case of colic in children, gut ailments, ulcers, and immune disorders.”

Probiotics, none the less, are “getting more play in real research studies”. But right now, “there’s kind of a mixture of ‘snake oil’ and selling people a product that may or may not do something.”

On current antibiotic use, she says there is a tremendous overuse in animals and to some degree in humans too. “We have to take responsibility for that in medicine as well as in veterinary treatments.”

In animal production they are used not only for treating disease but also in preventing disease “and even worse, for stimulating growth”.

Giving pigs antibiotics in feed stimulates growth and makes them put on weight faster. “We don’t understand why. If we did, we might find other solutions to the problem – food additives other than antibiotics that have the same effect.

“The result is just devastating in terms of introducing antibiotics into the ecosystem.” Resistance to antibiotics in the human population builds as a result.

Handelsman suspects enforcement of antibiotic use in Europe is not sufficient. In the US it’s not good because so much hinges on individual farmers, and there’s insufficient staff to check every farm’s practices.

Ireland’s “interesting model”, whereby pharmacists dispense veterinary drugs, may have good sides and some negative aspects. Overall, she says, “there isn’t sufficient training of pharmacists and doctors about veterinary medicine, and so a lot of mistakes are made just out of ignorance.”

President Obama totally understood the difference between fact and fiction, and fact and opinion

She highlights the case of the antibiotic Colistin being using in animals. The irony is that it works in humans but it was being saved as the “antibiotic of last resort”. Its use in veterinary settings was due to a lack of communication through the fields.

Handelsman is interested in the concept of “one health”, bringing human and animal health into a common structure and even adding environment aspects of antibiotic resistance and sending a whole ecosystem message.

Donald Trump

On Trump, she notes a dispiriting difference from the previous administration, which was deeply committed to not just science but to evidence.

“President Obama thought about every issue in terms of what the evidence was, what the data predicted would happen ... He totally understood the difference between fact and fiction, and fact and opinion.”

In the current administration, Handelsman adds, there seems to be a blurring of lines “between what a belief is and what a fact is, and what knowledge is. That’s very damaging to science. Because, for example, climate change isn’t something we believe in or not. It’s an evidence-based assertion about the future. It’s very discouraging.”

There’s no indication, however, that scientists doing important work are leaving the US, rather “they’re holding on...sticking it out”. The view from outside the US is that the country is dominated by Trump, but Congress controls budgets and always has been strong supporter of biomedical science – and in a bipartisan way, she says.

Scientists have maintained their focus on key agencies such as the National Institutes of Health and the National Science Foundation. “They haven’t lost their funding – yet,” she notes with a tinge of irony.

Being pro medical research is “selfishly smart” because we are all going to be affected by disease. While Congress is not going to abandon its decades-long support for bio-medical science because of one president, she wishes there was a broader understanding of what science can do and of what issues are important.

She would like if there was more commitment to agriculture.

When she first went into the White House as associate director for science at the Office of Science and Technology Policy in 2011 scientists would often talk about what the White House should be doing for them or seek funding for a project, which isn’t exactly its role. After election night on November 8th, 2016, “it was really fascinating. I started getting calls from scientists asking, ‘what could I do to make a difference? How can I change public opinion about science?’ How can I teach science?’ ”

They were recognising their obligation to society, which is “a very positive side to Trump’s election”. She sees “more activism among young scientists than I have ever seen in my career”.

Her lesson for younger scientists in such uncertain times when anti-science asserts itself: “Learn to teach and to communicate.”

In Handelsman’s institute, graduate students have formed Catalysts for Science Policy, which seeks to change science policy; question how we spend on science, and seek to inform the public. “If that’s an outcome of having an anti-science presidency, it’s a very good one – especially if it goes beyond this president.”

Science’s gender bias

Handelsman has a particular interest in gender bias in science. In 2012, the leading journal Nature named her one of “10 people who mattered this year” for her research on the issue.

She acknowledges it’s a persistent issue but was heartened by the recent conference she attended at Maynooth University, where the majority of speakers were women, and the top research prizes for poster presentations went to women. She was headline speaker.

The biggest issues, Handelsman believes, “are the unconscious biases that we bring to decision-making and evaluations that we don’t realise we are applying, that we don’t mean to apply”.

They’re cultural norms and habits that go way back in our individual development. “Apparently these biases emerge when kids are less than two years old,” she adds.

Her own institute’s study some years ago provided an illustration of that reality, she recalls. Her group sent a resumé of a student with questions to professors of biology, chemistry and physics around the US. Half got the resumé with the name Jennifer on it; half got the resume with John on it – the student’s credentials were exactly the same.

The answers to the questions were radically different: “They were much more likely to hire John. They would pay him more. They were more likely to mentor him. They thought he was more confident.”

“And I’m sure these were are all the same people, that if you asked them they would say the opposite – ‘of course we’ll hire them’. It’s unintended but there it is.”