Imagine in the future, if doctors and scientists could predict who was going to get sick, before it actually happens!
In the genomic era, using genetic data from pathogens like viruses and bacteria, and integrating this with big data, we will have the ability to predict the way diseases are being transmitted, rather than playing catch up and simply relying on plotting transmissions as they occur.
This is being driven by advances in computing and Artificial Intelligence, but also by advances in the laboratory that have made generating genetic sequence data faster and cheaper. My vision of the future for disease surveillance and health system monitoring might seem like something from Star Trek, but it's closer than many of us realise!
I did a talk on this recently at the Stanton Library in North Sydney for their 'Live Science' series- and have turned my slides in to a little clip, explaining the basics of some of the science behind these advances in disease surveillance. You can watch it here:
If you want to check out any of the research I included in the above clip, see the links below:
hepatitis C virus
Hospital acquired & drug resistant infections
Byron Bay’s “Splendour in the Grass” music festival featured a “science tent” for the first time this year, and I was fortunate enough to be invited to present in it! In exchange for doing two presentations in the science tent over the course of the three day festival, the lucky scientists who were invited to present received free VIP festival tickets, so we could mingle with our 30,000 new BFFs! Having never been to Splendour before, and loving a good shin dig, for me it was a no brainer to accept this offer. The generous folks at UNSW Science kicked in some extra cash to help cover my flights and accommodation when they found out that I was the only person from UNSW who was invited to present (thanks UNSW Science, you rule! side note: UNSW is a great university kids).
The presentation I planned to do was about the work my PhD project has been based on, and I was going to have everyone in the audience play the primary school game ‘Chinese whispers’ (aka the telephone game) to explain the science behind my work (I’ll elaborate on this in another post coming soon!). I put together a slide show and collected hilarious tweets from all over the internet that I could use as the messages when we played the ‘telephone game’. I packed my gum boots, my party hat and my bubble gun, and jumped on a plane, ready to find out how well science and music festivals really go together.
I arrived the night before Splendour officially started and was shown to my pre-pitched tent, which I discovered was full of water due to heavy rain a day earlier. Not wanting to get wet so early in the piece, I ventured out in to the festival ground to find some dinner and get inebriated enough that I wouldn’t mind sleeping in a wet tent. I found that things were already heaving, despite the fact proceedings hadn’t really kicked off yet, and I quickly discovered a tiki themed karaoke bar, tucked away behind the Happy Kanye. After downing a few ‘Shaka’ cocktails and belting out two of my personal favourite karaoke tunes (‘All that she wants’ by Ace of Base and ‘Pony’ by Ginuwine) I struck up a friendship with the karaoke hosts, Svetlana and Ivanka, to whom I promised that I would be back again (and again) to do some more karaoke during the festival. Rather a lot earlier than most other punters that night, by midnight I decided I was drunk enough to fall asleep in my wet tent, so I stumbled back to get some shut eye.
The next morning, I awoke after a deep and long slumber- it was already midday! How I slept in a cold puddle till midday is still a mystery, but it wasn’t worth dwelling on, as I had a festival to slay. I bounced out of my sleeping bag and headed straight for the Glitoris tent. I had a date with Dylan the glitter man. Dylan glittered me good, so good in fact that a photo I posted to my Instagram of the two of us was later picked up by news.com.au as their number 18 ‘wackiest look at Splendour’. I decided my next stop for the day would be to check out the back stage area at the science tent and try to charge my phone. As soon as I arrived at the science tent, I was greeted by a large sign out the front that had the timetable for performances during the festival. I froze when I read my name listed at 11.30am on Friday, as it was currently 1pm on Friday. And I hadn’t done a presentation yet… woops.
There was chaos backstage as the organisers were scrambling to set up props, clear the stage between acts and just generally keep the show running. I quickly realised my earlier no show was probably a welcome break for them, and shamelessly decided I should just own being the ‘science diva’ from now own (this isn’t the first time I’ve not turned up somewhere important I was supposed to be, so I really deserve this name!). Luckily, the Future Crunch team behind the science tent had a way I could make it up to them, and I was mic’d up and sent roaming around the festival with a camera man to administer their “half glass” experiment survey. This consisted of six questions designed to gauge people’s optimism about the future of the world and correlate it with either faith or distrust in science. I had a lot of fun administering the survey and was really surprised by the results (coming soon!). In between science-ing I did some more karaoke and checked out some bands (The XX KILLED it!).
Day two of Science in the Grass saw a much anticipated event- Doctor Karl presenting in the Forum tent. But first- he had to get glittered. Doctor Karl in all his glittery glory packed out the Forum tent and it was a whirlwind of science, but really nothing could compare to what was going to happen later that night. The topic of karaoke had been bought up a few times throughout the day, probably in response to my increasingly husky voice, and it was discovered that my new BFF Doctor Karl was dying to hit the stage himself, and he knew exactly what song he wanted to sing! With only a short amount of time till he was due to be picked up from the festival, we headed to the karaoke tent. Luckily my good friends, Svetlana and Ivanka were on the mic again that night, and when I told them my ‘friend Karl’ wants to sing Doctor Doctor, by Robert Palmer, they obligingly added him to the list. But time was of the essence, so I had to name drop, “Svetlana, do you think we can bump up my friend to next in the list? It’s Doctor Karl, and he is getting picked up in ten minutes.” The universal appeal and admiration of Doctor Karl was immediately evident when Svetlana’s face lit up, “THE Doctor Karl? Of course, he’s up next!” Doctor Karl then proceeded to belt out one of the most enthusiastic and awe inspiring karaoke performances I’ve ever witnessed (and I’ve seen a few). Mumblings in the crowd began to spread “is that Doctor Karl? No, don’t be silly” and by the time the first chorus hit, everyone in the tiki bar was screaming “Doctor doctor, give me the news, I’ve gotta bad case of loving youuuu” and Doctor Karl’s Peter Garret-esque dance moves were so powerful, the whole tiki bar was shaking. If you don’t believe me, check out the video I filmed (which has since gone a little viral on Twitter and Australian media [1, 2])! We saw Queens of the Stone Age later that night, and I’m still not sure if I was more impressed by Josh Homme or Doctor Karl….
The third and final day of the festival had me hitting the stage in the Science tent at 10am to kick the final string of talks off. I have a feeling if my reputation as the ‘science diva’ was better known, I wouldn’t have been scheduled for 10am on the last day, but never the less, I was determined not to miss my final opportunity to talk about my research. Unfortunately, due to copious amounts of karaoke and screaming, my voice was almost totally gone, and after sleeping in a puddle for 3 days, I was generally feeling pretty worse for wear. But I decided to put on my floral playsuit, a sparkly hat, some glitter, and soldier on. Despite a small audience, we had a lot of fun playing Chinese whispers, with my favourite moment being the butchering of a Tweet from Donald Trump that ended up as “You idiots! My IQ is 100! You’re all idiots!” Later that night, someone who was in the audience during my presentation recognised me while I was watching Sigur Ross, and they told me how much they enjoyed my presentation, and how much they learned. So at least one person other than my mum (she watched online on the live Facebook stream) loved the presentation! Hilariously, earlier that day Doctor Karl and I were snapped by a photographer while walking through the festival (unbeknownst to us), and the photo later surfaced in the Daily Mail with the bizarre caption “Colourful printed shirts and t-shirts were the go-to attire for some of the festival-goers.” Clearly they had no idea that Doctor Karl and I both dress like this all the time:
All in all, I had a fantastic experience at Splendour and was genuinely inspired by people's enthusiasm for science and knowledge. This really drove it home for me that if we make science and knowledge accessible to people, they will consume it! The days of science and knowledge being hidden away in libraries and dark lecture theatres is over. It's time for science for the masses!
Beginning to teach at uni was pretty intimidating when I first started, even though it was only first year subjects and I clearly knew more about the subject than any of the students. But when I was an undergrad, I really looked up to the tutors, demonstrators and lecturers, and I thought "they really know stuff!"
I'm going to be completely honest here though; I've learned more while teaching these subjects than I actually did when I took them as part of my undergraduate degree! That's not a reflection on my teachers or the university I went to, it's more a reflection on the difference in maturity level between 20 year old me, and 28 year old me. But aside from the actual content and subject area knowledge that I've gained from teaching at uni, I've learnt a few really valuable lessons that I'll take with me in to all elements of my career, and I think some of them are worth sharing. So I've written a list (because who doesn't love lists!?):
1. You can't please everyone. You aren't a jar of Nutella. I got some anonymous feedback from students I was teaching a couple of weeks ago, and of the 14 comments, 13 of them were really positive. I'll give you some examples (actual comments from students):
"Great demonstrator, had some negative experience last year in chemistry labs but she's made my time in biochem so much more enjoyable and calm because I feel like I can just approach her without fear of judgement etc."
"Extremely helpful, organised and always willing to lend a hand"
Then there was this comment:
"She's kinda scary and anxie at times lol"
I was a bit flawed when I read that last one. Am I really scary? I went back through all the feedback I've received over the last two years to try and find some hints. Nothing jumped out at me, and I was confused and a bit hurt! I spoke to the subject coordinator about it to try and find out what I was doing wrong and her response was pretty blunt; "that person probably doesn't like you or was having a bad day, you can't please everyone!" That comment really struck me- I realised the subject coordinator is absolutely right and this is a really important lesson to learn, especially if you are trying really hard and pouring your heart and soul in to something. You (or I) will never be perfect, and we won't please everyone! So, if you get negative feedback or comments, sometimes you just have to take it on the chin!
2. "Young adults" aren't proper adults yet. They are "kidults". What is a kidult? They aren't kids, and they aren't adults. They are a weird hybrid in-between the two. From my observations, this period lasts roughly from 17-25 years of age.
It is characterised by a desire to not be told what to do and a simultaneous reluctance to ask for help. There is also often a total lack of knowledge about how to figure things out or where to begin. As a result, kidults frequently have no idea what they are doing, and refuse to ask for help. This can make it quite challenging to teach them very complex or difficult topics like molecular biology or biochemistry, or actually to teach them anything for that matter!
Many kidults are able to fumble their way through fine, but some need extra assistance. I have discovered that one of the most effective ways to help kidults who struggle is to give them enough freedom and respect to feel like they are independent, while providing a safety net to catch them and make sure they don't completely screw up.
3. One way of explaining something might make total sense to one person, and be completely confusing to another person. The most difficult thing about teaching is being able to explain things in MANY different ways! Whoever said 'if you can't do, teach' hasn't tried to teach biochemistry to 19 year-olds. I have gained a new level of respect for all the people who have taught me throughout my life! Baby sitting 20 kidults for 4 hours in a laboratory, putting out (actual) fires, mopping up spilled chemicals, fixing butchered calculations and doing damage control on botched experiments is physically exhausting, and I often have a sore throat at the end of the day from talking so much!
But the hardest part of all is explaining things in many different ways. This is like trying to think in a different language sometimes! Teaching biochemical calculations is a combination of algebra and chemistry, and there are multiple ways to do these types of calculations. Different people will favour different methods. When I'm explaining calculations and going through my method, there will inevitably be 2 or 3 students who tried to solve the equation in a different way, so I then need to try and solve for their method too.
And finally, the most important lesson of all...
4. People's ability to learn and do well at chemistry/maths/biology is dependent on the amount of effort they put in, not an inherent ability or natural intelligence. Interestingly, I've recently heard many other people in various fields saying they believe 'genius' should be redefined, not as talent, but a blend of passion and persistence, or “grit,” and I couldn't agree more! The realisation that your ability isn't predetermined and that you can become 'smarter' (if that is the right way to think about it?) is really empowering for some people. For me, having thought I was terrible at science and hating it for about 19 years of my life, this was a lesson I took a long time to learn. But when I eventually did learn it, I appreciated it all the more. So I strive to help my students realise this, and I really value and appreciate students who are working hard to try and improve. I will always give extra time to a student who wants to ask questions or needs another explanation after the class. If they are willing to stay behind, I am happy to help them!
If you are a teacher and any of this resonated with you, I'd love to hear what your thoughts are! Send me a message or comment below...
As I wrote in a previous post, hepatitis C virus (hep C) isn't frequently sexually transmitted (except possibly in Africa or among Men Who Have Sex With Men [MSM]) like HIV is, yet globally, there are four times as many people infected with hep C than there are with HIV. This is probably due to a combination of factors, but the major one is that hep C has most likely been spreading among humans for a LONG time, a lot longer than HIV has!
If hep C has been around for so long, why did we only discover it in 1989? And where did it originally come from? The title of this post alludes to the answer to one of these questions- hep C is a stealthy fugitive.
Hep C is so successful at spreading undetected among populations because it is stealthy from the moment it infects people. Aside from a period of illness when first infected ('acute' illness), which many people don't experience at all and is easily mistaken as a case of the flu, hep C infection is mostly asymptomatic, meaning people experience no discernable symptoms at all. So most people who become infected with hep C have no idea they have it!
Hep C is able to be so stealthy because it evades the immune system of the people who it infects. It is able to evade the immune system because it changes a little bit every time it replicates, or makes a copy of itself. Viruses like hep C replicate themselves inside the person they have infected thousands of times every day, so it's able to mutate and change itself very quickly!
If we imagine hep C as a criminal on the run, and the immune system as the police trying to catch it, then hep C would be a master of disguise. Every time the immune police have managed to get a photo of the criminal and distribute it out to all the other immune police in the area to try and catch it, hep C has changed it's appearance again, by getting a new hair do or wearing a moustache. The mutations that hep C accumulates every time it replicates itself are usually superficial, just like dying your hair. But it's enough to fool the immune police. The immune systems of some people who become infected with hep C are able to catch the virus and kill it, clearing their infection. But for most people, the virus escapes and stays permanently on the run, sometimes for decades, until their infection is finally discovered.
Because of hep C's stealthy ability to stay undetected in the people it infects for such long periods of time, it is able to spread through entire populations of people silently. After decades of infection with this virus, the liver of people who have been infected infected sustains so much damage, that many of them develop liver failure or liver cancer, both of which are almost always fatal.
The good news about hep C is that new drugs have been developed that can target and kill the virus very effectively, curing people of their infection very quickly and with limited side effects! However, because many people who are infected have no symptoms and are unaware that they are infected, finding people to give them this treatment is proving very difficult. Without getting treatment, people are at risk of transmitting the virus to others or developing long term liver damage, leading to liver failure or cancer. So being able to find the people who are infected and offering them treatment is essential to limit the damage from this stealthy fugitive!
In early 2016 I found out about the World Health Organisation (WHO) Internship program and decided to apply on a whim, thinking it was unlikely I would be selected, but filling in the application form was a useful source of procrastination at the time. The World Health Organisation had an exotic appeal, with images of field workers surveying people in rice paddies and emergency Ebola laboratories in West Africa coming to mind. The idea of doing international public health related work in a far off place was a lovely day dream to escape my thesis induced nightmares. However, the dream soon became reality when a few months later, I found out my application had been successful.
My CV was plucked from the thousands of hopefuls and I was offered a position at the WHO Office for the Western Pacific Region (WPRO) in Manila, the Philippines, starting immediately. Suddenly the idealised day dream was becoming a tricky reality. It wasn't great timing for me, as I was in the middle of a major research project and I had numerous other activities to complete relating to my PhD thesis. When I told my PhD supervisors that I had received this offer, their reactions ran the full gamut from amazement to confusion. I distinctly remember one of them saying "well yes you can take the time off... but why do you want to go there?" Fortunately I was able to negotiate with all the parties involved to let me go for 2 months over the Australian summer, which meant I would forfeit our customary long Christmas break, but this way it would cause minimal disruptions. Even more fortunately, earlier in the year I was granted a scholarship from Layne Beachley's Aim For The Stars Foundation, which allowed me to be able to pay for my flights and some other expenses while in Manila, as of course, the WHO doesn't pay interns.
I landed in Manila at the beginning of December and was placed in the Division of Communicable Diseases (DCD) with the Hepatitis, HIV and Sexually Transmitted Infections (HSI) Unit. On my first day in the office, a meeting was held to plan their impending Year End Party (YEP) performance. I soon found out it's a long standing tradition at WPRO that all divisions perform a pantomime style routine in a competition held at the annual YEP, and the theme for 2016 was "throwback to the 90's". Apparently they were having trouble recruiting Spice Girls, and my first act of service to WPRO would be to play Ginger Spice in DCD's YEP performance. Needless to say, I was happy to oblige. Sadly, we didn't win the YEP competition, but it is widely agreed that DCD was robbed this year (as it also was the year before apparently).
From then on, the actual work began. I quickly discovered that the WHO relies heavily on interns and volunteers to complete much of it's work, in large part due to a very restricted budget, but also because of a culture of donor countries supplying many personnel in-kind, through secondments and various other strategies. Interns do a lot of grunt work and are essentially the minions of WPRO. At times, one gets the distinct feeling of being 'another brick in the wall' as an intern at the WHO. My duties were split between working on HIV surveillance data and providing technical support for viral hepatitis related activities. One experience during my internship really highlighted, for me, the way viral hepatitis is often thought of both domestically in Australia and Globally. This experience was when I had lunch with the Regional Director of WPRO at the beginning of my internship. Dr Shin Young-soo, the outgoing WPRO Regional Director, regularly has lunch with visiting interns and volunteers in his (palatial) office. On this particular day, a group of 8 volunteers and interns were joining him for the obligatory lunch date, including myself. At the beginning of lunch, Dr Shin went around the group of interns one by one (with our CVs in front of him) and asked us about the projects we were working on at WPRO, our academic backgrounds and various other quips relating to either our nationality or professional backgrounds. I found this act mildly amusing and wondered what he would have to say when he inevitably came around the table to me.
When my turn arrived, I was stunned to hear him open with "Ah, Sofia, the Australian. Well viral hepatitis is almost over now in our region. We have all the amazing new drugs that cure it. What will you work on next?" I choked on my lunch for a second as my brain scrambled to process what I had heard. I thought, "surely this man knows that WPRO has the largest number of people infected with hepatitis B and C of all WHO regions, and most of these countries don't have universal health coverage, coupled with huge financial inequality and poverty? Surely he can't be serious." He was. I quickly discovered that like many other very senior public health bureaucrats, prevalence of the disease in question is usually the only thing they really pay attention to. Which is quite misleading, especially when considering countries like China.
The prevalence of hepatitis B in China is estimated to be about 5.5%, which puts it below many countries in Africa, with prevalence's above 8% in most countries on that continent. However, the total number of people in the whole of Africa estimated to be infected with hepatitis B is 75,641,609. The total number of people estimated to be infected with hepatitis B in China alone is 74,601,204 (only 1.04 million less then the WHOLE of Africa combined). I pointed this out to Dr Shin, and asked how China would be able to pay for diagnostic tests and LIFETIME therapy for hepatitis B virus for all these people? I also asked how China will implement and pay for diagnostic testing and treatment for the 9,795,000 estimated people infected with hepatitis C virus there. There is very variable quality and availability of diagnostic testing across China for both hepatitis B and hepatitis C virus, and with most people unaware that they are infected, just finding these people will be an enormous challenge. Treating them will be a whole other problem for future China to deal with. I would like to say that Dr Shin is an isolated example of this thinking, but from my experience so far, he isn't. I encounter this as the prevailing attitude among people not directly involved in viral hepatitis research. Very few people are aware of the fact that viral hepatitis kills more people globally than tuberculosis, HIV and malaria, yet this has been the case for several years. It seems viral hepatitis is the global problem everyone wants to ignore. It's just too big. Too expensive. Too difficult. It takes years for people to die from liver cancer or liver failure, unlike HIV/AIDS or tuberculosis, so no one worries now.
Thankfully, there are extremely committed individuals at WPRO, and around the world, who are prepared for the hard tasks ahead and are working tirelessly to try and eliminate viral hepatitis. But unfortunately, many, many more people will die from viral hepatitis before this happens. I don't advocate for diverting resources away from treating diseases like HIV, tuberculosis or malaria. This is a case for additional spending and additional resources. HIV transmission is far from over (case in point: the Philippines, with a 624% increase in the number of new HIV infections between 2005 and 2015!) and multiple drug resistant tuberculosis continuing to spread more and more. We need to encourage both public and private spending on these diseases, or else the chances of achieving elimination will be very low. There are still significant hurdles to clear on the journey to elimination of viral hepatitis as a public health threat by 2030, but hopefully they will get fewer and smaller along the way, thanks in part to the small but important contributions made by interns and volunteers like myself.
This blog is written by Sofia Bartlett; scientist and curious human being. Her bio can be viewed here.
© Sofia Bartlett and Rogue Transmissions, 2017. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author is strictly prohibited.