Breathomics: Looking Into Breath Analysis for Medical Diagnostics

Hello! Who are you and what are you working on?

I’m Paul Monks, and I’m currently the Chief Scientific Advisor to one of the UK government’s departments, the Department of Business, Energy, and Industrial Strategy. I’m responsible for the role that science plays in supporting development and delivery in policy across quite a wide range of areas in business, energy, and industrial strategy. Everything from the UK science system, such as nuclear power, COP26, energy, climate, and business innovation. So it’s a very wide portfolio.

When I’m not doing that, I’m a professor at the University of Leicester one day a week. Where we are currently working on air pollution and climate change.

What sort of projects are you working on at the moment at the university?

Much of my research is focused on breath analysis/medical diagnostics. So as a tech transfer, I guess, from my work in air quality, I got very interested in how you could measure the composition of the atmosphere in real-time. Then I began looking at how you could apply that in different areas. One of the areas that we started looking at was measuring the molecules in the atmosphere (the organic molecules in the atmosphere) and then measuring the organic molecules on your breath. So we got into breath analysis as a medical diagnostic, or metabolome/breathomics which is another phrase for it.

So, we’re working on a very large clinical study, looking at breathlessness, and whether that’s because you’ve got respiratory tract infections, or asthma and inflammation, or you’re having a heart attack, in order to have a look at the different markers that come from that. It’s a massively interesting and varied area.

Please let us know more about your background and your backstory.

I did an undergraduate chemistry degree at the University of Warwick before going on to do a Ph.D. at the University of Oxford on nighttime chemistry. That involved simulating the chemistry in the laboratory that goes on in the real atmosphere, particularly the chemistry of something called the nitrate radical, which is a nighttime oxidant.

From there, I went to use the same sort of techniques that I’d learned in my Ph.D., and I went to work for NASA in the US at the Goddard Space Flight Center. To look at planetary atmospheres, and spent a lot of time looking at the atmospheres of Titan, Neptune, Jupiter, Uranus. I really got into what the origins of life are, working on studies using Voyager data (some of the early seventies probes of the solar system).

Were you involved in that project? That’s amazing.

Well, I was using the data, using the data from the composition of Titan, in particular, to look at something called nitrile formation, which is fundamentally the bonds of carbon and nitrogen, which are the building blocks of amino acids: the building blocks of life. So how do you go from an atmosphere, which is methane and nitrogen, to begin to form those molecules that form the building blocks of life.

I also worked on ozone chemistry, and ozone hole chemistry as well. You might think there’s not a relationship between the two, but the techniques I used did connect the two of them. It was all about simulating atmospheres in the laboratory at NASA.

I then came back to the UK, a place called the University of East Anglia in Norwich, and what I did was I transferred from measuring in the lab to measuring in the real atmosphere. The first place I went to was a place called Cape Grim in Tasmania, which is 41 degrees south in the roaring forties, to essentially begin to do some of what work. At that time, the landmarks studies were about the chemistry that goes on when there’s no pollution.

Cape Grim is one of the cleanest places in the world. The air doesn’t touch land for 10 days and whisks around the bottom of the earth quite quickly. So you can really understand the fundamental chemistry of the atmosphere, and it’s essentially the pollution chemistry. But if there’s no pollution, what does that chemistry look like?

So we worked at Cape Grim in Tasmania and then went on to do field studies at Jungfraujoch, in Switzerland, looking at the free troposphere. We also went to Mace Head in Ireland looking at the chemistry as it comes off the Atlantic Ocean, the Atlantic storm tracks, and then went on to work at other places, such as the rainforests in Malaysia, looking at the rainforest chemistry where you’ve got a lot of biogenic species (a lot of all species from the trees). It was very interesting.

From the University of East Anglia, I then went to join the University of Leicester, which I did 25 years ago. This is where I did a lot of atmospheric chemistry air pollution studies, which I will not rattle off the list of them.

Lastly, becoming quite interested, five or ten years ago in coming out of this interest in atmospheric chemistry, essentially inventing some technology, we then applied it in forensic science, smelling dead bodies.

Yes, I remember that study.

We’ve used it on fruit and fruit rotting, to see whether you can tell that, as well as the breath stuff latterly as well. So yeah, I mean, a huge range of stuff over the years.

I wrote all this up in a brief presentation when I joined my current job, which I could probably find and send to you as a sort of very high-level thing, which might be of some use to you.

Yes, of course! How about the project you are working on now with air pollution? How did you come up with the idea?

Yeah, I guess I have a phrase which is: “ideas are cheap, and achieving them is expensive”. Because often to go from an idea is to really get a really good outcome, particularly if you work in areas of science where you need to build instrumentation or develop instrumentation or using instrumentation, can take you five years or more. So that’s kind of what I mean by ideas are cheap.

Actually, the ability of a good scientist is to spot which of the many ideas that they have are good ones, and which ones are bad ones. Now, the danger, what you’re always trying to do as a scientist is a balance of the element of increments. Wouldn’t it be great, if I’m doing something, that I could see what the next step is? Versus something which is transformational.

Also, you’ve got to factor serendipity into that as well. That you just find things and you go “wow, that’s really weird, why is that?” And don’t dismiss it instantly, you have a look at it. That’s played a lot in my career. I mean, I’ve always been quite lucky to be well-funded enough to be able to deliver the projects that I’ve been funded to deliver. But at the same time, being able to explore around the edges, to develop the next sort of idea.

I’ve also been very lucky that I’ve worked in teams with some absolutely wonderful people. When I made that transition from a postdoc to a lecturer, I was able to hit the ground running because, Di, who I was then working for, supported me essentially to carry on doing the stuff I was doing for him, at my new university, and begin to work flying on an aircraft. I used to fly an aircraft at 250 feet over the sea at 500 miles an hour, which was quite thrilling.

Just out of interest, could you talk about what policies in the government you are also involved in?

At the moment, I’m working on a whole range of different things. I work in a department that’s responsible for the delivery of net-zero, which is essentially the de-carbonization of the system. The government has made a pledge to have reduced its carbon usage to net-zero by 2050 compared to 1990 levels.

That means a massive de-carbonization of the transport sector, of the industrial emissions of energy, of buildings, and the like. So I do a lot around the science of that. I’m working on three big themes at the moment, concerning sustainable net-zero:
1) How do you make that sustainable in terms of materials that you use?
2) How do you make it resilient?
3) How do you make net-zero resilient? Which is, how did you make it stick?
So you make some choices on the way to 2050 which won’t stick.

For instance, you will plant trees, because you want to plant trees because that’s a way of drawing down carbon dioxide and creating renewable carbon, but you can’t just carry on planting trees. So what do you need to do in order to accomplish that? And how do you measure progress towards net-zero?

Because the way that we do it currently is a slightly artificial construct. Can we actually measure real progress? That’s just a flavor of all the sciences that I’m working on. I also spend a huge amount of my time doing COVID-19 science. There’s a huge effort going into supporting science.

This week, I’m working on something called the events research program, which is a science-led program to think about underpinning and putting a safety net around opening events in the UK to reduce and mitigate the risk of COVID transmission at those events.

It’s about working with people to plan the opening of nightclubs, and weddings, and lots of strange sort of things as well, like cinemas. I’m thinking about how to make that safe. So I’ve learned an awful lot about COVID transmission. You might go, well, what scientifically do you know about COVID transmission? Well, interestingly, it comes back to that knowledge of aerosol science, being an atmospheric science, because it’s transmitted in that way, and also back to the breath analysis stuff. I know a lot about that sort of process as well. So I’ve got a little bit of knowledge about the physical process and the environmental transmission of COVID.

But again, it’s using that translational knowledge, as a scientist in governments, a chief scientist in the government, it’s often also knowing what you don’t know and going out and asking people to explain stuff to you. Some of the areas of energy are not familiar to me at all. But as an air quality scientist I’ve got a vague understanding of energy because of course it’s a major polluter. So it’s actually amazing how, being an atmospheric scientist by training, what a multidisciplinary science view then allows you to bring to government science.

It’s also very transferrable as well, as you said. You are an aerosol scientist, but this comes a lot into biology as well.

Yeah, as you well know from the project that you did, that came around a conversation with your then supervisor, which was, what role do, as I breathe in air pollution, what actually happens to it and what role do bacteria play in that? That serendipity, that scientific method I talked about earlier, it was a conversation between me -who had a certain set of skills and knowledge- and Judy Morrissey, who had a different view. That has created, in some senses, a whole new field of scientific discovery, hasn’t it?

Yeah, indeed.

Yeah. We don’t play it down too… I mean, it is. The journals have even created a term for it. Is it environmental academia, I can’t remember what they called it now.

I think that’s a very interesting kind of method, and we spend a lot of time in science flagellating ourselves over being able to do multidisciplinary science. But yeah, these are great examples of how to do that. It’s things like atmospheric science that are not exclusive… you’ve got to know a little bit of chemistry, a little bit of physics. Actually, if you understand the way the chemistry and the physics work, you can apply some of that to stuff like COVID-19 transmission. Know what you don’t know as much as what you do know of it as well.

Okay.  I’m going to switch gears a little bit and just ask about your routine and how you do this as a scientist. So what is your morning routine? What happens when you first get up, and so on?

Well, COVID-19 means that I do the two-minute commute to my office. Or actually 30 seconds or five-second commute to my office. I think that it’s interesting that the wider question, has varied over the years. My science has taken me all over the world. I’ve worked everywhere except on one continent, which is a bit irritating. I’ve got to find a way of getting to Antarctica.

But yeah, my morning routine is breakfast and a shower, the shower is an important place for the scientist. That place to contemplate something. Often you’ll have woken up in the middle of the night going, God, yeah, I’ve got it, that’s a really good idea, and then instantly forgotten it the moment you’re woken up, and the shower is that place where it comes back to you.

I think it says about your routine, I mean, do as I do, not do as I say, not do as I do. You’ve got to give yourself time to think. Can’t say in the current job, I’m particularly good at that. It’s a bit wall-to-wall at the moment. But that’s an important part. An important part is to listen.

The great thing about my current job is that I can ask virtually anybody to come and talk to me about any scientific thing. Just ace. I want to know about something, I can actually summon the national expert to tell me about it.

But in times of COVID, I’ve set up a home office and I’m fully plugged in with all my IT and in some senses, it’s no different for me. I do go down to London once in a while, but I haven’t had to. I talk to all my students and colleagues electronically.

Once you’ve settled down in the morning, how does the rest of the day go for you?

Currently, it’s wall-to-wall. It’s eight till seven normally continuously. Or 8:30 at the moment. This morning, I’ve done a radio interview with a radio station. I’ve met with the Chief Scientist to talk about COP. I’ve looked at critical materials. I’ve looked at the spending review. I have been on the executive committee at the department I work in. I’ve just been off looking at civil contingencies.

Then, by the end of the day, I’ll have looked at digital twins for earth carbon budget six and the events this venture research program that I talked about earlier. That’s not unusual for a day. I mean, I’ve just literally not quite read my diary, and I’ll have talked to you of course. Very importantly.

But I think that’s not an atypical day. I don’t really get to go to the lab anymore, which is a bit of a shame, but I think once supervisors get to a point…  they become more of a danger in the laboratory… more of a hindrance than a help.

Yeah, certainly. So what kind of platforms and tools would you recommend that help you in your professional life?

In a way, it’s easy, because you have what you’re given, and in the electronic era, both the university and the government department I work in, we’re using Teams. I mean, I’ve always worked with PCs. Partly because in the earlier era, when you needed to control experiments, PCs were always easier to control stuff with and program than necessarily Apples.

For me, it’s always the right IT for the right job. That’s the element. So yeah, at the moment, it’s kind of everything… But we use on a given day, Zoom and Google Meet as well. I’ve also used BlueJeans, which is pretty good. WebEx seems to have disappeared.

Do you not like WebEx, no?

Skype. WebEx, we occasionally use. Skype virtually never now. Virtually never. So actually, it all hangs together, doesn’t it? I mean, I do like it, the integration is quite nice, and that everything talks to everything else. And you can obviously see what they’re trying to do. But that’s actually really good information-wise.

Do you have any other apps and software you would suggest to people that you find very useful for your work?

It’s difficult. I’m trying not to promote software of any variety.

However, it would be Microsoft. We use Microsoft apps in both places. Yeah, and love it or loathe it, it goes a long way. I think that scientifically I’m a big fan of open-source software, so we have a rule in the lab, not to use Excel.

Excel makes you lazy, and it’s very un-automatable. So we use a lot of R and things like that. R is open source. It’s a really powerful way of being able to do it. Especially if you’re handling large data sets, you’ve got to do repetitive actions on them. We do that.

I think one of the big breakthroughs for us is the ability to operate a lot of our instrumentation remotely. So we use something called TeamViewer. This means we can operate remotely, and the people in my group can operate their instruments in the laboratory from home.

We’ve got a degree of automation, particularly around some of the analytical systems, that allow us to control them. Actually, when we’re on field work, we can be working in Germany at the moment with a German group, and we can just log into our instrument in Germany and see how it’s doing.

Yeah, that’s amazing.

That’s an amazing innovation from the days where you had to be, well, actually instruments were, we used to collect data on chart recorders. You probably don’t even know what a chart recorder is. We used to collect data on chart recorders and measure things off chart recorders. And now we can control our instruments wherever they are in the world over the internet.

So I think that it’s the power of that. I mean, I think the data analysis tools over the years, we’ve worked our way through all the major programming languages, IBL, we use Igor.

And again, on the earth observation side, the satellite side, which I’ve barely talked about, it tends to be those bigger data handling programs, object-oriented code, that are the way of doing it.

So it’s actually often the IT for the job. But I think I’m a big fan of open source as well.

Because that’s then kept up to date by the community. And I think that’s an effective way for scientists globally to work together as well.

For sure, I completely agree. I’ll try and be quick with these last few questions. Once the day is done, how do you wind down and what is your self-care regime?

In the COVID world, I’ve taken up running. I play tennis two, three times a week, hitting small, yellow balls is very therapeutic. Go for a walk with my family. So, some form of exercise I think I’ve discovered is an essential part of being able to work sometimes what can be on paper quite punishing schedules. You do have to keep a degree of fitness.

Do you listen to podcasts by any chance? Do you have anything that you would recommend?

I listen to The Life Scientific on Radio Four. I think is quite good.

I also like In Our Time with Melvin Bragg, a little bit of history. I don’t know why that is, but I do. I don’t know. Just I do quite enjoy it. I’ll always listen to The Today Program on Radio Four. I think they’re on Radio Four, if they aren’t, I didn’t realize I was Radio Four. I have another form of relaxation is watching crap television. I do enjoy watching long series of quite poor television. So I find that quite relaxing because it doesn’t take any mental capacity.

Yeah, okay, I understand. Do you have a favorite trash TV suggestion?

Favorite trash TV suggestion? I don’t know. No. I’m not going to say Bridgerton. That would be a very strange choice.

Okay, one last question. What advice would you give to other scientists that want to be in your field and have aspired to be somebody like you?

Never aspire to be like somebody else, aspire to be yourself. Because I think science rewards individuals who can work as teams, and that’s not a contradiction.

But think about that. Don’t be afraid to ask for help and mentorship. I mean, that’s quite common now. I get quite a lot of people asking me, will I mentor them. And I’m more than happy within the time constraints that I have to support people. I think that’s something I never really did. Though actually, I guess in retrospect I was mentored, I was given the opportunity, as I said earlier, by other people. So, don’t be afraid to do that and ask for help around that.

Never be afraid to be adventurous. It’s back to that point you asked earlier, don’t be afraid, a scientist should question and should be skeptical. And skepticism has sort of been hijacked by things. And a good scientist asks questions and tries to understand something. And it’s through that process that you discover what you know and what you don’t know. And there’s nothing wrong with being skeptical in the roundabout these things.