Natalie Kuldell (00:03):
Why don’t you start by saying where you’re calling in from.
Joshua Atkinson (00:06):
Sure. Yeah. And thank you for having me by the way. So yeah, my name’s Josh Atkinson and I’m calling in from Aarhus, Denmark where I’m a NSF postdoc fellow working at the Center for Electro microbiology.
Natalie Kuldell (00:19):
There is a lot to unpack in that one <laugh>. So I don’t know that everybody would know one, what a postdoc is or two, what an NSF fellow is, and certainly electro has a lot of interesting qualities to it. So pick and choose. What would you like to, to unpack first?
Joshua Atkinson (00:39):
Well I’ll go with postdoc because it’s a straightforward one to start with. So a postdoc is a type of position that people will oftentimes do after they finish their PhD and do graduate school. And so it allows you to kind of go work in a lab for a period of time, hone your skills or learn new skills that you didn’t have during your PhD before you go and maybe go work in industry or try to apply for faculty positions or do whatever you choose to do. Because people go down many different paths
Natalie Kuldell (01:05):
Right. No, that is, that is true. So yeah, I guess I had not, when I was young, appreciated that a postdoc was part of my training too, so. Yeah. Yeah. So cool. So what what, what are you doing there, like work-wise?
Joshua Atkinson (01:23):
Yeah, so I’m a synthetic biologist by training, but I’m here in a microbiology department studying organisms called cable bacteria. And so these are these large multicellular bacteria that live in sediments in the bottom of lakes and in the bottom of oceans. And what they do is they can oxidize sulfur down in the anoxic part of the sediment and then they can transfer electrons centimeter distances away to where there’s oxygen up near the, for water in these aqueous systems. Sorry, big words there, <laugh>. But what’s really unique about these organisms is that they’re very highly conductive. So they have these nano wires in their outer membrane that allow them to transfer these electrons really long distances. So typically when we think of bacteria, we think of short, you know, one micron cells that, you know, 10 to the the minus six meters in size. But these bacteria you can actually see with your naked eye. You can take a sediment, pull it apart and see these strings of these cable bacteria growing in there.
Natalie Kuldell (02:21):
What?!
Natalie Kuldell (02:24):
I’ve… Never heard of this. This is so amazing! So, so so they’re not microscopic and they are functioning like wires?
Joshua Atkinson (02:33):
Yeah, yeah. So they’re these kind of high voltage wires that can transfer currents that are similar to the copper wires in your household wiring but living in sediments all over the globe.
Natalie Kuldell (02:45):
Incredible. Wow. Awesome.
Joshua Atkinson (02:48):
Yeah. And so the group, Yeah, I was just gonna say the group here in Denmark are the people who discovered them. So I came out here to work with you know, founders of this field.
Natalie Kuldell (02:56):
That’s amazing. And how long will you be there?
Joshua Atkinson (02:59):
So I’ll be here for a year in total. I’m already about two months into it, so I’m gonna be here until the end of next August.
Natalie Kuldell (03:05):
That’s, that’s so cool. So I love that you introduce yourself as a synthetic biologist by training because synthetic biology has not been around all that long. So you might be among the first generation that can introduce yourself as a synthetic biologist by training. So yeah. Where, where did you get your synthetic biology training?
Joshua Atkinson (03:22):
Yeah, so I did my PhD at Rice University in as far as I know, the very first synthetic biology PhD program in the entire country. So I was in the system, synthetic and physical biology program at Rice. And I was part of the very first cohort of students to go through that. So yeah, I do think probably one of the first <laugh> people to be able to say I’m a synthetic biologist by training, yeah.
Natalie Kuldell (03:44):
That’s so cool. That’s great. And so when you were in college, did you, I mean, if you were so early in on synthetic biology, what did you study in college that led you to a PhD in synthetic biology?
Joshua Atkinson (03:55):
Yeah, no, I kind of stumbled into synthetic biology a little later. So I did my undergraduate degree in microbiology at the University of Michigan. And I started off getting interested in research, wanting to, you know, go into oncology and cancer research and try to, you know, cure cancer. But I went to go do a research program that was operated by the university and I paired with a microbiologist where I was studying these bioluminescent bacteria that live in deep sea fishes which I never had even thought of before going to college. And I learned about all these crazy things that microbes can do and just kind of became obsessed with microbiology there from and then as I was going through, you know, undergraduate, I was trying to, oh, how can we apply microbiology to make the world a better place?
Joshua Atkinson (04:39):
And synthetic biology was kind of rising rapidly at the time that I was doing my undergrad degree. And I heard about IGEM and I got really interested in that. So I joined the Michigan IGEM team and went to Boston and got to do the big jamboree and that was really a highlight of my undergraduate research career and really drove me into the synthetic biology field. So I started hunting for graduate programs that did synthetic biology and there weren’t very many, but then I saw, actually, I think I got a Google News alert about rice starting this program. I was like, okay, I gotta apply to that one. Yeah.
Natalie Kuldell (05:08):
That’s awesome. Oh, how fun. And so lots of highlights from, from synthetic biology and you have certainly like touched on some of the most charismatic of, of systems. I love that, you know, you just described very offhanded and very correctly that, you know, synthetic biology is just using biology to make the world a better place. And, and you can do that with bioluminescent bacteria or you can do it with microbes that live in sediments and carry or conduct electricity. It’s, it’s there’s a lot of biodiversity out there and to apply it to real real world challenges, that’s pretty much what synthetic biologists do. So how cool is that? That’s great. So let’s see. So I can, I’m a little torn because part of me wants to ask you about your aspirations and where you’re gonna go next. And then part of me wants to ask you about, you know, know, when did you get interested in science? So let, let’s ask where you’re gonna go next and then, or thinking about going next, and then we’ll back it up and ask how you got interested in science at all.
Joshua Atkinson (06:08):
Yeah, so I’m hoping to be able to start my own research group in the future. So I’m applying to faculty positions right now actually. So it’s a busy time at this time of year specifically I’ve been prepping, you know, research proposal documents and those kind of things and sending them out to a bunch of different schools. Yeah, so targeting some in the US and then also thinking about maybe Denmark as well. I don’t know. Yeah, it’s nice here. <Laugh>.
Natalie Kuldell (06:29):
Yeah. Yeah. Despite it getting dark at four o’clock, it’s a very nice place. <Laugh>. Yeah, for sure. So so were you always interested in science and engineering?
Joshua Atkinson (06:40):
I think so, so it’s hard to say. So I got interested in high school for sure. I had really, really good high school teachers in biology and chemistry and math. And I think just working with those brilliant teachers and their ability to engage me with these subjects really is what got me interested into them. So I’m the first student in my family to go to college. So I didn’t grow up necessarily around a lot of, you know, scientists per se. But getting to work with these people at my high school was really pivotal for me. And really I, I know my my biology teacher in high school, he’s the first person who ever really mentioned research to me because he did some research in his training and I that was like, “Wow, what is this?” And got, I was like, I need to go do something like this when I get to college.
Natalie Kuldell (07:27):
Wow. You are totally speaking our language. We, we love our high school biology teachers who are within the BioBuilder community because they really are inspiring this next generation and they, they do just impact people’s lives.
Joshua Atkinson (07:39):
Right. I met some good ones. So I was a BioBuilder mentor for the Westboro High team. So Jo-Anne Purdy, shout-our to her because she’s a really brilliant teacher.
Natalie Kuldell (07:48):
She is a brilliant teacher. She’s actually on our podcast this month, so if you wanna catch up with her and hear from her, she’s on our podcast this month. So yeah, we love our teachers and, and they do impact, they, they just open possibilities for students that hadn’t been necessarily considered before. Where did you go to high school? It’s interesting that you’re the first in your family to go to college. Where’d you go to high school?
Joshua Atkinson (08:10):
Yeah, so I grew up around Flint, Michigan. I went to Flushing High School, which is a town just kind of north of Flint. And so a lot of my family worked in General Motors in the automotive industry. A lot of them straight outta high school went and got jobs either on assembly lines or, you know, transporting parts between places. My mom worked at a hospital that was another very large part of influencing my interest in science, so I got to go visit her at the hospital and you know, I would go and see some pathologists and get to see some things on slides and kind of a little sciencey environment. And that’s really kind of got me there.
Natalie Kuldell (08:43):
I love that these little nudges towards science, right? You know, just shadowing your mom at work at a hospital and seeing a pathology slide is like, oh, you know, science is all around us. And, and you know, with synthetic biology, you know, those skills of, of taking things from a manufacturing plant and getting them out into the world and commercializing things. Yeah, we are at that position now with synthetic biology. We need, we need all kinds of folks who are interested in working in the field, so.
Joshua Atkinson (09:08):
Absolutely, yeah
Natalie Kuldell (09:09):
Yeah. That’s so cool. And so between your mentoring of the Westboro High School team and other work that I know from the EBRC with you, you clearly have an interest in education. Can I just say how much I love the slide deck you put together for EBRC and maybe have you introduce that as a, as a resource for students?
Joshua Atkinson (09:29):
Oh yeah, thank you. So this was a, a, a idea that I worked on with Michael Sheetz, who’s another member of the EBRC’s Student and postdoc Association. So we’ve developed this kind of intro to synthetic biology slide deck so that teachers who don’t necessarily have training in synthetic biology can start to teach this at all different levels. So we tried to make this really accessible and break it down into a bunch of different kind of conceptual modules that different people can use. So the idea here is to start off giving people an idea of what, what is synthetic biology? What are the things that have been done with it already to date? What is our design, build, test framework that a lot of synthetic biologists use to kind of do their business? And then what are the biomolecular tools that we use to engineer DNA and RNA and proteins and how can we use these to build metabolic circuits and genetic networks. Um and then finally, what are the different kind of organisms that we can port these into so we could, you know, go into bacteria like I love to work with, but also mammalian tissues whole animals, plants and then start actually engineering entire ecosystems at scale. So can we change the entire chemistry of a soil or a sediment to try to, you know, make more productive fields or things like that, or remediate things that are in the environment. And then finally a bunch of different industrial examples that exist in SynBio. So hopefully people find this to be a really useful tool that they can take into their classrooms. It’s all freely available and can be broken apart as needed. Yeah.
Natalie Kuldell (10:54):
Yeah, I, I think it is an incredible resource. We will, we will be teaching with it as, as part of the BioBuilderClub and we will absolutely it’s great because it, it includes so many examples and covers the range of, of opportunities within synthetic biology. So it’s amazing. Like I I I feel like I’ve gotten a whirlwind tour of synthetic biology and the impact that it can have on a, on a person’s career. I guess the last thing I’ll ask is maybe if you had any, anything you wish you had known back then that you know now that, that you would tell students in high school or, or you know, sometimes they ask about what they should be doing or thinking or learning.
Joshua Atkinson (11:34):
Yeah, that’s a, I think being really open minded is probably the best thing. So I went in, you know, with an idea of what I wanted to do, but along the way I bumped into all these different topics that have like really broken open my interests. So like I wouldn’t have been a microbiologist, hadn’t I not randomly paired with that person. I am currently a, what I would call a microbial electro-chemist. So I do a lot of electrochemistry, which was a thing that I had never even thought about before a project that I started doing late in my PhD. So now I’m constantly working with electronic devices and how we can interface cells and proteins with these devices and you know, just being willing to go with the flow as things come across your desk and like new ideas. It’s really fun to be able to explore those and I’ve really enjoyed that kind of aspect of academia because it kind of gives you the freedom to do these things to some degree.
Natalie Kuldell (12:21):
Yeah. Yeah. Wow. I mean, well you also seem very brave, right? So, so some people like get scared to try all those, you know, that, that that freedom is a little bit overwhelming to people sometimes and people start to, to sort of go through paths where the ground’s already softened and they’re aware of where, what to do and what’s expected. So one question that was asked in the Q&A is as a first gen college student do you have any advice for other first gen college students, especially if they were thinking about advanced degrees?
Joshua Atkinson (12:51):
Yeah. talk to people. So people are very friendly. So I didn’t necessarily go to a lot of office hours when I was an undergraduate and I kind of maybe regret that. I think I could have learned some subjects a little deeper than I did. Had I gone and had conversations with professors, I kind of thought, Oh, I’m gonna be a burden if I go talk to this person. I don’t need to do that. And I’ve continually had this come up throughout my career. So as a PhD student I was constantly, you know, in my advisor’s office just chatting about ideas most of the time even. And also when you’re struggling they can be really helpful resources. So just being willing to just go talk to people because you’re not a burden and people like to help.
Natalie Kuldell (13:27):
Yeah, I think that is fabulous advice. Thank you Josh. What a, what a great note to to, to open up the conversation to others now. So thank you.