Read the Professor David Wishart section.Professor David Wishart#
Read the Jack Of All Trades section.Jack Of All Trades#
Professor David Wishart is a Professor in the Faculty of Science at the University of Alberta. He specializes in bioinformatics, algorithms, machine learning, and database systems.
He teaches BIOIN 301 and 401 at the University of Alberta.
Check out his personal website over here: https://www.wishartlab.com/
You can find out more about his research here: https://apps.ualberta.ca/directory/person/dwishart
Check out his research publications here: https://www.researchgate.net/profile/David-Wishart-4
Here are some important tidbits from the interview:
- Check out the dialogue at 0:00. Professor Wishart discusses his educational path.
Read the David Wishart 0:00 section.David Wishart 0:00#
I actually did my Undergraduate Degree in Physics. Oh, so it’s called an Honours Degree in Physics at the University of Alberta. And then after I completed my Physics degree, I did another year of biological science training, because I wanted to go into a good Bio-Physics program. So, I headed off to Graduate studies at Yale University in the States and did my PhD in Biophysics. In the United States, Bio-Physics is actually more like Biochemistry.
I ended up going from physics to biology and then doing mostly chemistry in the U.S. for my PhD. But in my PhD work, I did a lot of protein work, protein chemistry, organic chemistry. I had to learn molecular biology, microbiology, and cell biology as well.
After I finished my PhD at Yale, I came to Canada, back to the University of Alberta, and I did a postdoctoral fellowship here at the University of Alberta, with Brian Sites. And during that period, I learned a lot about spectroscopy.
So that allowed me to get back more into some of the physics I used to do. Also, I continued to do a lot of computing. Okay. And so all the computing that I ended up doing from a postdoctoral fellowship, eventually led me to positions here at the University of Alberta. My first position as a Professor of University of Alberta was with the Faculty of Pharmacy.
They wanted me to get involved with drug design, drug development, sometimes computational, but they also wanted to run their NMR spectroscopy work, peptide synthesis work as well. So these are things that I learned a little bit during my postdoctoral fellowship, but I had to learn quite a bit as a Professor.
- Check out the dialogue at 9:04. Professor Wishart discusses the technology he uses in his lab.
Read the David Wishart 9:04 section.David Wishart 9:04#
Sure. So, a lot of our work uses analytical chemistry. So that means we use nuclear magnetic resonance. NMR spectroscopy is a lot of mass spectroscopy or spectrometry. So liquid chromatography, mass spectrometry, gas chromatography, mass spectrometry, inductively coupled plasma mass spectrometry, so we have all those instruments, and some are high resolution, and some are low resolution. There’s several million dollars worth of instruments in the lab.
On the computing side, we do use a lot of artificial intelligence and machine learning. A lot of interactive visualisation tools. A lot of it is using the web, so we have a lot of web based tools with these databases. And so the software we developed is used to help predict mass spectrometry and NMR spectra in order to predicts protein structure, protein folds. There is software to identify mutations and biomarkers in blood and proteins.
So we have a lot of databases of software that’s designed to help the wet work that we do. And then a lot of the wet work that we do helps with us building the software in the databases, there’s a back and forth, as the instruments we use generate a lot of data. So it’s called big data. Having lots of data allows you to apply machine learning and artificial intelligence to learn how to analyse or predict or transform the data.
So each part of the lab helps the other, that’s been an important part of the structure.
- Check out the dialogue at 14:23. Professor Wishart discusses the importance of passion in your chosen discipline.
Read the David Wishart 14:23 section.David Wishart 14:23#
Yeah, I think that whatever you do in life, you should be passionate about it. So I tell people that my job is my hobby. And my hobby is my job. You know, I do these things because I’m really interested in them. And the fact that I get paid to do with is just kind of a bonus.
And it’s the same thing you know about a hockey player or football player. They get paid to do what they really like to do. And they just have to be really good at it. Their job is their hobby. Now only about 1 or 2% of the world actually gets to say that. But you know, the other 99% of the world still does a pretty good job at their job, because at some level, they’ve also become passionate about their job, and they want to do well, because they’re interested in it.
Now, in my case, I bring my job home, bring the job home at night, I do it on my weekends, if I have no spare time, then I just go back and do my job. Because it’s interesting.
Either people have sort of a, you know, better work life balance, and so they, you know, they’ll do their job well, at their workplace. And then when they go home, they’ll shift gears and work on something else. Maybe it’s cooking, gardening, painting, whatever it is, that’s also a hobby, that’s maybe what they’re also passionate about.
But whatever you do, try to find some passion in it. And if you feel that, you know, the rewards from doing a good job, or from discovering something about the job, discovering something about the world, something about other people, derive some pleasure from that.
Because that that sort of makes you want to do it again, and to do it better. I think a lot of people, unfortunately, especially when they’re younger, sort of, they do the thing that their parents told them or do the things that their friends are doing. But they keep on asking, why am I doing this? It’s not it’s not what really gets me excited.
And, and I think that it’s true for a lot of young people that there’s been a period where they wander around, worried that they may make the wrong decision. I think another piece of advice is that, again, often for young people, they worry that each decision they make will have repercussions that affect their lives, all the way through.
And I think, you know, my own journey is one where I’ve made many decisions that have gone in many different directions. And even though those have sort of gone left and right and up and down. Things still worked out in the end, in effect, they’ve always worked out. Because at some level, I’m still following what I was interested in, or I at least allowed myself to become interested in. And so I don’t think I had this fatalistic worry that what if I made this wrong decisions, what if I messed up? You know, there are certainly times when you’ll stumble, but you just pick yourself up, dust yourself off on it.
Some cases, you may be really interested in an area but discovered you’re not really good at it. You can give up. But in my case, I usually wasn’t very good at physics, I just wasn’t very good at chemistry. I was awful at computing. Those are all subjects that I did not do very well at. But I just kept at it. And I was interested in them. I liked to read about them. And that’s why I guess I had the passion. But when it still came to doing the subjects in High School, or even University, I wasn’t that good initially, but I just kept trying and working at it and eventually I was able to do pretty well.
Read the Full Interview: section.Full Interview:#
Read the David Wishart 0:00 section.David Wishart 0:00#
I actually did my Undergraduate Degree in Physics. Oh, so it’s called an Honours Degree in Physics at the University of Alberta. And then after I completed my Physics degree, I did another year of biological science training, because I wanted to go into a good Bio-Physics program. So, I headed off to Graduate studies at Yale University in the States and did my PhD in Biophysics. In the United States, Bio-Physics is actually more like Biochemistry.
I ended up going from physics to biology and then doing mostly chemistry in the U.S. for my PhD. But in my PhD work, I did a lot of protein work, protein chemistry, organic chemistry. I had to learn molecular biology, microbiology, and cell biology as well.
After I finished my PhD at Yale, I came to Canada, back to the University of Alberta, and I did a postdoctoral fellowship here at the University of Alberta, with Brian Sites. And during that period, I learned a lot about spectroscopy.
So that allowed me to get back more into some of the physics I used to do. Also, I continued to do a lot of computing. Okay. And so all the computing that I ended up doing from a postdoctoral fellowship, eventually led me to positions here at the University of Alberta. My first position as a Professor of University of Alberta was with the Faculty of Pharmacy.
They wanted me to get involved with drug design, drug development, sometimes computational, but they also wanted to run their NMR spectroscopy work, peptide synthesis work as well. So these are things that I learned a little bit during my postdoctoral fellowship, but I had to learn quite a bit as a Professor.
Read the Abdul-Samad Olagunju 2:50 section.Abdul-Samad Olagunju 2:50#
Okay.
Read the David Wishart 2:52 section.David Wishart 2:52#
And then, about 20 years ago, I shifted from Pharmacy into Computing science. So I became a Professor in Computing Science. So it’s been a kind of a weird journey going from Physics, Biophysics, Biochemistry, Chemistry, to Pharmacy, to you name it. But it’s given me a very broad background. And so most of my research career I have tried to combine both the whole wet bench and dry bench research by doing stuff with chemicals and computers. So in my typical lab day, it’s about 50/50.
Read the Abdul-Samad Olagunju 3:51 section.Abdul-Samad Olagunju 3:51#
So how do you balance all of that out? You have some people in your lab doing wet work and dry work? How do you have some overall idea of what you want to achieve in your lab and then tell everybody, okay, you do this, and you do this, so that you all achieve the same vision.
Read the David Wishart 4:12 section.David Wishart 4:12#
Running a lab is a bit like running a company.
You have to have revenues, the revenues we’ve worked with are grants. The grants are short term funding systems where you have very clear objectives of what has to be done. So a lab like mine is running about 15 different grants. So each of those grants has anywhere from a two year to a five year plan. And people are hired and then paid through those grants. So that helps give you, you know, a bit of your vision.
Of course, obviously, you write grants and you have to have time to think about, what would I like to do? What do I need to do? I think the challenge of running a lab is that what is fundable by a grant is often not necessarily what you really want to do?
Or some of the things that you really, really wanted to do aren’t funded. So some things that you can do aren’t the things you are most interested in. So, you know, sometimes it’s like cooking a meal from what you find in the refrigerator. Sometimes the stuff that you really want is in the refrigerator, or you just have to cook what’s available. Okay. But that’s how science is normally done. It’s funded through grants; grants represent the vision that you have for a project or goal. Those define what everyone will do, and give people specific tasks for specific periods of time.
Read the Abdul-Samad Olagunju 6:04 section.Abdul-Samad Olagunju 6:04#
Okay, so given that you’re going to have funding from these grants, when you select people to work in your lab, you obviously don’t have so much money that you can accept anybody, you have to choose specific people. So what are you looking for in a person that, you know, will be a good addition to your lab?
Read the David Wishart 6:29 section.David Wishart 6:29#
Yeah. I think, again, it’s a little bit like running a company. You have people that you’ve initially often worked with for a long time. So you initially bring them in for one task, and a new task or new grant comes in, you don’t want to fire everyone. So what you do is you try and train or retrain to work anywhere. And that sort of gives things continuity, but it’s also part of the role of professor, you’re teaching and you’re training.
So unlike a business, where yes, you could say that “I will fire everyone, because now we’ve got something else that we want to do,” and hire a brand new cohort, that’s not the model in science.
You typically will try and work with the people you have, and then either retrain them or align them with projects that are similar to the ones that they’ve been doing for a while.
I mean, normally, with grants, even though they’re short term, you will ask for renewals of grants. So in some cases, we’ve been studying the same thing for 23 years. So, you know, it still means that some of the people who’ve been around for 20 years, or you know, 15 years, they’re doing very similar things. So it’s not as if you’re jumping from one thing to another every two to three years, typically most labs will have one or two central themes that they will focus on.
I am a little different, I have probably seven or eight different themes that I work on.
The results is that the lab is quite large, around 80 people. And we have an operating budget in the millions of dollars a year. So every year, I have to try to find money in the order of about two to three million a year.
Read the Abdul-Samad Olagunju 8:38 section.Abdul-Samad Olagunju 8:38#
Wow. Yeah. Yeah. So your lab is off, obviously a very big lab. What kinds of research and cutting-edge technology are you using today? So maybe just a couple of the machines that you use regularly in your lab, or maybe some computer applications that are really cutting edge that you’re using in your lab today?
Read the David Wishart 9:04 section.David Wishart 9:04#
Sure. So, a lot of our work uses analytical chemistry. So that means we use nuclear magnetic resonance. NMR spectroscopy is a lot of mass spectroscopy or spectrometry. So liquid chromatography, mass spectrometry, gas chromatography, mass spectrometry, inductively coupled plasma mass spectrometry, so we have all those instruments, and some are high resolution, and some are low resolution. There’s several million dollars worth of instruments in the lab.
On the computing side, we do use a lot of artificial intelligence and machine learning. A lot of interactive visualisation tools. A lot of it is using the web, so we have a lot of web based tools with these databases. And so the software we developed is used to help predict mass spectrometry and NMR spectra in order to predicts protein structure, protein folds. There is software to identify mutations and biomarkers in blood and proteins.
So we have a lot of databases of software that’s designed to help the wet work that we do. And then a lot of the wet work that we do helps with us building the software in the databases, there’s a back and forth, as the instruments we use generate a lot of data. So it’s called big data. Having lots of data allows you to apply machine learning and artificial intelligence to learn how to analyse or predict or transform the data.
So each part of the lab helps the other, that’s been an important part of the structure.
Read the Abdul-Samad Olagunju 11:36 section.Abdul-Samad Olagunju 11:36#
Yeah. And also, you work in computing science as well, not just in biology, how hard is it to keep up with all the technological advances that are happening in your field?
Read the David Wishart 11:51 section.David Wishart 11:51#
Yeah. I mean, it is hard. The traditional way was that you would try and read up on journals and stay current with the literature. But the literature has exploded, it’s massive. The most effective way right now to stay current is to track what’s going on in meetings and conferences. And to access abstracting services, to summarise the latest information.
It’s also a case where you depend on your staff and your students to also help be your eyes and ears. It is important for them to stay current or on track on what’s new. So it’s an important part of staying up to date in science. But it’s also a case where, you know, if you’re trying to stay current, all you’re trying to do is basically catch up. And what we tend to do is, we’ve developed certain niches or expertise in which we know were really, really good.
In that case, we’re ahead of the curve. So that sort of like, we just have to think of our own ideas, without having to look for anyone else for inspiration. And I think that’s often where you try to get as a scientist, you’d like to be in an area where you’re not trying to catch up or play catch up. You just are really an expert in something and that way, you can see where it has to go, you know how to solve those problems. You see what problems are most important. That way you’re kind of your own boss.
Read the Abdul-Samad Olagunju 14:04 section.Abdul-Samad Olagunju 14:04#
And I also just, maybe this is more for me personally. If you were to give a piece of advice to yourself, maybe before you jumped into this field, or all these fields that you’ve jumped into, what would that piece of advice be?
Read the David Wishart 14:23 section.David Wishart 14:23#
Yeah, I think that whatever you do in life, you should be passionate about it. So I tell people that my job is my hobby. And my hobby is my job. You know, I do these things because I’m really interested in them. And the fact that I get paid to do with is just kind of a bonus.
And it’s the same thing you know about a hockey player or football player. They get paid to do what they really like to do. And they just have to be really good at it. Their job is their hobby. Now only about 1 or 2% of the world actually gets to say that. But you know, the other 99% of the world still does a pretty good job at their job, because at some level, they’ve also become passionate about their job, and they want to do well, because they’re interested in it.
Now, in my case, I bring my job home, bring the job home at night, I do it on my weekends, if I have no spare time, then I just go back and do my job. Because it’s interesting.
Either people have sort of a, you know, better work life balance, and so they, you know, they’ll do their job well, at their workplace. And then when they go home, they’ll shift gears and work on something else. Maybe it’s cooking, gardening, painting, whatever it is, that’s also a hobby, that’s maybe what they’re also passionate about.
But whatever you do, try to find some passion in it. And if you feel that, you know, the rewards from doing a good job, or from discovering something about the job, discovering something about the world, something about other people, derive some pleasure from that.
Because that that sort of makes you want to do it again, and to do it better. I think a lot of people, unfortunately, especially when they’re younger, sort of, they do the thing that their parents told them or do the things that their friends are doing. But they keep on asking, why am I doing this? It’s not it’s not what really gets me excited.
And, and I think that it’s true for a lot of young people that there’s been a period where they wander around, worried that they may make the wrong decision. I think another piece of advice is that, again, often for young people, they worry that each decision they make will have repercussions that affect their lives, all the way through.
And I think, you know, my own journey is one where I’ve made many decisions that have gone in many different directions. And even though those have sort of gone left and right and up and down. Things still worked out in the end, in effect, they’ve always worked out. Because at some level, I’m still following what I was interested in, or I at least allowed myself to become interested in. And so I don’t think I had this fatalistic worry that what if I made this wrong decisions, what if I messed up? You know, there are certainly times when you’ll stumble, but you just pick yourself up, dust yourself off on it.
Some cases, you may be really interested in an area but discovered you’re not really good at it. You can give up. But in my case, I usually wasn’t very good at physics, I just wasn’t very good at chemistry. I was awful at computing. Those are all subjects that I did not do very well at. But I just kept at it. And I was interested in them. I liked to read about them. And that’s why I guess I had the passion. But when it still came to doing the subjects in High School, or even University, I wasn’t that good initially, but I just kept trying and working at it and eventually I was able to do pretty well.
Read the Abdul-Samad Olagunju 19:07 section.Abdul-Samad Olagunju 19:07#
Yeah. Yeah, I think that’s a huge part of life. Even now in my third year, I’m starting to appreciate that too. When you really feel like you want to work at something day in and day out, that’s when the a bit of that passion starts to come through. So yeah, I think it’s extremely important that you have that. I want to thank you for taking the time to talk with me about your experiences. And I know that you’re a really busy man, so the fact that you gave me this opportunity is fantastic. I really appreciate it.
Read the David Wishart 19:43 section.David Wishart 19:43#
Well, happy to do so. Glad you decided to work on a project like this is, it’s really cool. Happy to help out with it. And I think this is something that you can develop a passion for in your experiences in education and your further career.
Read the Abdul-Samad Olagunju 20:05 section.Abdul-Samad Olagunju 20:05#
Yeah, hopefully, right now, it’s been extremely busy. Hopefully we want to get it to be more visual. So maybe start a YouTube thing, just to give young scientists, young people who want to come to university, an idea of what’s going on and what people do here.
I really thank you for giving up your time, and helping me out with this today.
Read the David Wishart 20:37 section.David Wishart 20:37#
You’re very welcome.