00;00;06;06 – 00;00;54;14
VO Victoria
Welcome to Beyond Lab Walls, a podcast from the Salk Institute. Join hosts Isabella Davis and Nicole Mlynaryk on a journey behind the scenes of the renowned research institute in San Diego, California. We’re taking you inside the lab to hear the latest discoveries in cutting edge neuroscience, plant biology, cancer, aging, and more. Explore the fascinating world of science while listening to the stories of the brilliant minds behind it. Here at Salk, we’re unlocking the secrets of life itself and sharing them beyond lab walls.

00;00;54;17 – 00;01;26;20
Isabella
Hello, listeners, and welcome back to Beyond Lab Walls. I’m your co-host Isabella, and today I sat down with plant scientist Joseph Swift. Joseph spent the last six years as a postdoctoral researcher in another Joseph’s lab, Joe Ecker here at Salk. He’s been slowly transitioning into full time work at his very own startup, Crop Diagnostix. Joseph’s working to understand how plants genetic codes have and haven’t changed over time, and also how we can use those codes to protect plants from drought and other environmental stresses.

00;01;26;23 – 00;01;48;21
Isabella
His research has really important and interesting impacts on the world, which he’s focusing on now by pairing artificial intelligence systems with plant genome banks to see how we can optimize the agriculture of tomorrow. Let’s get started digging into his stories so we can learn all about his work at Salk and where he’s headed next. We’ll start with an easy question.

00;01;48;23 – 00;01;52;22
Isabella
Where did you grow up, and what was it like growing up there?

00;01;52;24 – 00;01;59;17
Joseph
So I’m from Australia and I grew up in Brisbane.

00;01;59;20 – 00;02;31;24
Joseph
Which is the city of, the third largest city in Australia. And growing up there was good. Adolescence, my youth there, I mean, I went to a big public school, lived in suburbia, had that kind of suburban dream. Very quiet, very easy, chill life. My parents did move overseas when I was 15, and so I went to boarding school overseas, and that was a little bit more of a journey, a good one before, before I started college back in Australia.

00;02;31;27 – 00;02;35;16
Isabella
What was your relationship like with plants and nature growing up?

00;02;35;18 – 00;03;06;11
Joseph
We did a lot of camping. My parents took my brother and I camping a lot. I wouldn’t say that we were nature lovers, but growing up in Australia, I mean, you’re always at the beach or you’re always in the bush, like it’s kind of unavoidable. So nature was always kind of front and center. I guess that really kind of inspired me then to to study biology and plant biology, as opposed to something like cancer or neuroscience, which is not as, as green or in my, my view, as beautiful.

00;03;06;13 – 00;03;14;22
Isabella
Yeah. And did you have scientists in the family, like when did you realize you wanted to do science or that that was even an option?

00;03;14;24 – 00;03;38;22
Joseph
So yeah, my father was a scientist. He was a he is a geophysicist. I wouldn’t say that that inspired me to be a scientist. I’d say my parents, if anything, encouraged me to do whatever I wanted to do. They’re kind of wild, they were always traveling around doing crazy things. And so that was a kind of a lesson to kind of embrace doing something kind of unusual or interesting or a bit risky.

00;03;38;25 – 00;04;02;26
Joseph
But science then became more of an option when I just really enjoyed learning about it at high school. That and literature. And going to college it was a kind of toss up between the two, and I decided to go for biology, which I think was a good choice. And then only after I started doing research in the lab during my master’s was I kind of really hooked on doing this full time for the rest of my life.

00;04;02;28 – 00;04;13;09
Isabella
When you first started studying biology, was it mostly plant biology or was it a mix of medical-related biology?

00;04;13;11 – 00;04;34;29
Joseph
At the college I went to, all the molecular biology and cellular biology that we learned was through the guise of the medical space, and which is great, I mean, at the molecular level, everything’s kind of beautiful and the same, right, between plants and animals. And so you can kind of learn in one sphere and then apply it to another.

00;04;35;00 – 00;05;00;09
Joseph
But once I started research and then I was doing a little bit of medical research, and I realized that the questions that I really wanted to answer were much more in the agricultural plant biology space, where I thought there was, at least to me, more interesting questions around sustainability, around climate change that could be answered. And also the spaces is less crowded.

00;05;00;09 – 00;05;07;02
Joseph
There’s just not many people working in that area. So I thought I could make a bigger contribution there.

00;05;07;04 – 00;05;09;28
Isabella
So what is plant genomics?

00;05;10;01 – 00;05;43;13
Joseph
So plant genomics is the study of the entire plant’s genome. Rather than focusing on one particular mechanism or one particular gene, which is interesting of itself, genomics tries to stitch all those mechanisms and genes together into one narrative. And when you look at it from that kind of top down approach where you’re trying to understand everything that’s going on in the cell, in the genome at once, then you can start seeing these kind of patterns.

00;05;43;13 – 00;06;12;03
Joseph
That wouldn’t be necessarily obvious if you just went piecemeal, one gene at a time. So it’s a lot of kind of computational biology, as well. Like you have to do a lot of statistics and a lot of digging around to find those patterns. But when you do, it’s really exciting because you see something that’s maybe common across all different biological systems, rather than a mechanism that is unique to one.

00;06;12;06 – 00;06;19;08
Isabella
And plant genomics was kind of something that you were interested in during graduate school, right?

00;06;19;11 – 00;06;40;09
Joseph
Yeah. Like I definitely wanted to make the switch to plant biology. And then genomics was also a kind of growing field at that time, particularly the area of systems biology. And I thought that sounded really cool. Looking back, I don’t really know if I fully understood what it was. I was, I guess, attracted to how abstract it sounded.

00;06;40;12 – 00;06;59;04
Joseph
And then once I realized that, oh man, I have to do all the statistics, I started realizing that it was maybe a little bit different than what I thought, but I really I had great mentors and yeah, I really love it.

00;06;59;06 – 00;07;07;17
Isabella
So how did you manage to get over to the States and at Salk and what attracted you to Joe Ecker’s lab?

00;07;07;19 – 00;07;40;02
Joseph
So the Salk has always been a place where you have amazing blue sky research going on and has always been one of the best, if not the best, places to do plant genomics. You have Joe Ecker and other folks here that really built that field. And so it was a dream to come, and it was a dream to be here in the sense that we could really pursue different projects that were kind of crazy.

00;07;40;04 – 00;07;43;21
Isabella
Oh, can you tell me about some of those crazy projects?

00;07;43;24 – 00;08;14;16
Joseph
So there were a few, one of them that was recently published in Nature. We wanted to understand some of the basic mechanisms behind how photosynthesis evolved. And I know that sounds kind of really kind of complicated, but it’s actually a really important question for all of us, because photosynthesis is the process in which light energy converts into sugars, and those sugars power everything.

00;08;14;18 – 00;08;47;07
Joseph
Photosynthesis is kind of the the key mechanism that provides us with energy. And what’s funny about photosynthesis is that it kind of I mean, there are different flavors to it. The main flavor is called C3 photosynthesis. And that’s where the process happens all in, in one cell, which is called the mesophyll cell. And so when you look at a leaf and you see that it’s green, it’s the mesophyll cell that’s giving that green color.

00;08;47;07 – 00;08;54;11
Joseph
And he’s the one that’s doing that conversion from light into sugar.

00;08;54;13 – 00;09;28;19
Joseph
But there are certain plants, like corn and sorghum, that are evolved or adapted to drier, hotter environments, like the savanna. And in that environment, photosynthesis doesn’t work so well. It’s too hot, too dry. And so these species evolved about a better way of photosynthesizing called C4 photosynthesis. And essentially what happens is that photosynthesis then it takes place in two cell types rather than one.

00;09;28;22 – 00;10;07;03
Joseph
And what’s kind of interesting about it is that it’s evolved more than 60 times. So it kind of keeps happening in these different plant species. And it’s not through the evolution of new genes. It’s actually just rearranging the existing blueprint to do something new. And it’s been a bit of a mystery of how that rearrangement takes place. And if we were to understand it, we could maybe engineer those enhanced photosynthetic properties into crops like rice or wheat, that may struggle in the face of climate change.

00;10;07;05 – 00;10;26;16
Joseph
Through this research, we found one of the kind of key changes in that blueprint that allows for C4 photosynthesis to happen. So we’re really excited to find that. And then our collaborators, as well as other partners are following out to see if that engineering can take place.

00;10;26;18 – 00;10;49;21
Isabella
Yeah, I’m very happy that you’re talking about that paper because I found it very interesting, especially from the perspective of thinking of science things that we take for granted, like photosynthesis is one of those words that a lot of people know. And because we learn it in grade school, you think, oh, we must understand everything about it. But that’s not true.

00;10;49;21 – 00;11;02;05
Isabella
And there are a lot of interesting questions left to ask about these seemingly basic processes. I’m curious if there are other kinds of questions that are really exciting in plant biology right now.

00;11;02;07 – 00;11;28;18
Joseph
Like, to your point about about like things that we kind of take for granted, but realize that at least at the at the molecular level, we still don’t really know what’s going on, with plants, another question that Joe Ecker and I pursued was understanding plant plasticity. In other words, when you have a houseplant at home, if you don’t water it, it doesn’t grow.

00;11;28;22 – 00;12;00;07
Joseph
But if you give it a ton of water and fertilizer, it will grow like crazy. That’s plastic, right? Compared to other systems like humans or mice, like plants can make these developmental decisions when it’s, when the environment suits them. Humans. We grow like when we’re growing from being a child to an adult. That’s a fixed trajectory. Plants can change that timing depending on their resources.

00;12;00;10 – 00;12;35;10
Joseph
And so Joe and I followed that hypothesis up in looking at how the plant leaves choose their rate of growth in response to the environment. And we found certain genomic signatures that suggested that when you don’t water your plant, when it stays kind of small, what the plant is actually doing is initiating aging responses where it’s actually kind of aging and and developing more quickly to arrest its growth, which is kind of counterintuitive, but really interesting.

00;12;35;13 – 00;12;54;12
Joseph
That may also feed into climate change and research, because in agriculture, if growers don’t receive enough irrigation, that same kind of pausing growth happens, and that ultimately affects yields and, and what we see at the supermarket.

00;12;54;14 – 00;13;23;02
Isabella
Yeah, it’s really interesting thinking about how plants have to come up with entirely different mechanisms to deal with their growth and environment, because, unlike us, they can’t really move around. And so with studies like your paper on photosynthesis, we’re learning about these really evolutionary basic properties that we could potentially use to make plants more efficient and to make crops better in the future.

00;13;23;04 – 00;13;48;27
Joseph
It’s a really tricky task, like so we know that plants have that almost magical property to be able to grow deeper roots, to forage for water or to grow longer shoots to avoid shade and to seek sunlight, like they can do all these amazing things. And the next frontier is trying to understand how we can breed or engineer for those characteristics.

00;13;48;29 – 00;14;11;20
Joseph
And it’s tricky because you’ve just got a group of plant molecular biologists out there in the world trying to tackle these really big questions, and we have to solve them in the next couple of decades. Otherwise our food systems may become much more vulnerable, more unpredictable, as well as, there’s high demands on food systems as the population continues to grow.

00;14;11;20 – 00;14;16;19
Joseph
So it’s going to be a really, really interesting time.

00;14;16;21 – 00;14;33;18
Isabella
Yeah. And on the topic of asking big questions and tackling these real world problems, I’m curious if you can talk a bit about your recent transition into working on a startup and what has inspired you to do that?

00;14;33;20 – 00;15;13;27
Joseph
Yeah, so recently I left Salk and co-founded the company with a few of my colleagues, one that was in Cambridge, one that’s now in Denver, and that we kind of came together serendipitously and realized amongst ourselves we had the expertise to develop biomarker technology for plants. And this is technology that’s sort of borrowed from the medical space. So if you if you’ve ever had a kind of biopsy, a pre-cancer biopsy where you’re basically trying to see if this tissue eventually is going to develop into a cancer.

00;15;14;00 – 00;15;41;07
Joseph
Often they’ll look at gene expression or the way the genes are behaving is an early signal of future pathology. And you can apply that same technology to plants to see if, for example, their gene expression is predictive of how they’re going to grow under, for example, do they have enough nitrogen fertilizer? Are they receiving enough water? Is there an early-onset pathogen?

00;15;41;09 – 00;16;12;18
Joseph
Those sorts of questions that growers really want to understand and know, so they can make decisions in field about whether to apply more fertilizer or to apply a pesticide, they’re currently in the dark. And so we founded a company called Crop Diagnostix that develops those gene expression biomarkers and deploy them to growers to help them both with their bottom line, but as well as to make farming more sustainable.

00;16;12;20 – 00;16;52;24
Joseph
Transition’s been really, really kind of strange in a great way. Like Salk gives this kind of space and opportunity to to to answer really big fundamental questions. And set on the cliffs and you’ve got, you’re at the ocean and it’s very majestic. And now driving out to Arizona to potato fields near the border, talking with growers, trying to understand what their problems are, and then driving back with a ton of samples in the back of my car to go and sequence them as quickly as possible, basically.

00;16;52;24 – 00;16;59;20
Joseph
And the whole motivation is very urgent and different compared to academic research.

00;16;59;23 – 00;17;12;22
Isabella
All the travel must be a huge change from going into the lab every day. Is there any major thing that you’ve learned or unexpected thing that you’ve learned in the first few months of this startup work?

00;17;12;25 – 00;17;43;20
Joseph
What’s kind of been interesting is that when you’re founding a startup, you need to have a ton of conversations with all different stakeholders in that space. So for us, we were talking to farmers, we were talking to input manufacturers, we were talking to seed companies and really understanding where the different players are at in in sustainable agriculture. And I think the I mean, the vibes were good.

00;17;43;20 – 00;18;12;24
Joseph
Everyone wants to use less nitrogen, everyone wants to use less pesticide. Everyone wants yields that are predictable and are stable. No one wants to lose their groundwater. And so we’re all on this same trajectory. And there are companies and folk out there that are basically we’re all just trying to help to make those those needs a reality in time, particularly in the face of the challenges we have in the coming decades.

00;18;12;26 – 00;18;20;25
Joseph
So that’s where it’s kind of it’s been nice to see that kind of wider picture and realize that we’re all on the same team.

00;18;20;27 – 00;18;53;05
Isabella
Okay, so correct me if I’m wrong, but artificial intelligence, AI, seems to be a huge tool that you’re using in Crop Diagnostix. And I’m curious what that integration of AI has been like as a plant biologist, kind of watching it happen in real time, it feels like it’s happened very fast and especially fast when you’re looking at genomes and big databases like that, and using AI to sort through things much faster than we could manually, and how much of that have you been able to see and benefit from?

00;18;53;07 – 00;19;27;01
Joseph
Yeah, when you study genomes, there’s so many different moving parts, and as one scientific brain it’s very easy to get lost in the data. And artificial intelligence has shown that it’s able to decode those really complicated physiologies or data sets or insights across a range of different problems. So five years ago, what we’re trying to achieve in Crop Diagnostix wouldn’t have been possible because the technology wasn’t there.

00;19;27;03 – 00;20;08;25
Joseph
And indeed, genomic technology wasn’t there either, because now the cost of omic sequencing has become a lot cheaper. So we’re at this really nice kind of cross point where sequencing is cheap enough, machine learning algorithms and AI is sophisticated enough that we can start decoding these really complicated genomic data sets and then, ideally, to provide direct benefit to growers and farmers that could use that information most readily.

00;20;08;27 – 00;20;21;02
Isabella
To go back to what you were saying about going into the field and meeting with stakeholders and farmers, could you explain how you communicate the work that you’re doing in those contexts?

00;20;21;04 – 00;21;06;15
Joseph
There’s no silver bullet in agriculture. So we need across the board different regulations, technologies, and behaviors that will get us to the sustainability targets as well as the yield targets that we made. And so plant engineering is one mechanism that will help in that journey, for sure. And particularly with traits like drought, which are inherently tricky, engineering more drought resilient lines will be necessary but not sufficient to to meet our yield goals.

00;21;06;18 – 00;21;31;15
Joseph
I think that we have to do a better job at, say, maybe saying why these technologies area beneficial in the first place. And I will say that, let’s be honest, the largest form of genetic modification in plants in this country is bt corn or bt soy. And those are products that are not for consumers. Those are products for farmers.

00;21;31;15 – 00;21;48;13
Joseph
So while farmers see the immediate benefit from those pesticide tolerant varieties, that’s not actually a benefit to the consumer. So we we can’t expect consumers to be excited about that. In fact, they feel pretty neutral about it, which I think makes a lot of sense.

00;21;48;16 – 00;22;03;21
Isabella
Has working in the field changed your perspective at all about what you were doing in the lab beforehand?

00;22;03;23 – 00;22;27;17
Joseph
I think what I’ve enjoyed learning so far is that it’s really gotten me back into thinking about seasonality. During my PhD and my postdoc in San Diego, we don’t really feel the seasons that much, but now I’m acutely aware of when crops are going into the ground, what stage potatoes are going to be at a month or two, and what stage is the corn going to be at?

00;22;27;20 – 00;23;01;27
Joseph
Learning about how there’s this cycle every year in this country around growing, planting, harvesting, all the kind of effort that goes into producing food, all the energy. And inside it’s a huge undertaking that happens every year since the dawn of human invention. And it’s also like not to get too poetic, but our interaction with plants is one of the most important and fundamental relationships we have with any organism.

00;23;01;29 – 00;23;41;00
Joseph
We, I can’t see how someone wouldn’t have joy in watching plants grow and imagine doing that for a job as a grower or a farmer or a plant biologist. I mean, you’re just so in touch with with how that system works and how it delivers for you not only the food you eat, but also the air you breathe, and and the gas you consume like it’s all there.

00;23;41;02 – 00;23;47;07
Isabella
Now, speaking of joyful human things, how do you stay busy when you’re not working?

00;23;47;10 – 00;24;15;04
Joseph
Well, I try to get to, I like ocean swimming, so I try to get to the beach at least once a week. That’s pretty beautiful. And the water’s warming up, so that’s great. And I go for lots of hikes, obviously, I try I’ve started rock climbing. I’m not very good at it, but I like it. And yeah, I try to try to read a ton of books and usually usually get around to it.

00;24;15;06 – 00;24;20;11
Isabella
What kind of books do you like reading? Fiction. Nonfiction. More science stuff?

00;24;20;14 – 00;24;39;18
Joseph
No. Always fiction. Like at the end of the day, I love a good story, learning about people’s fictional experiences. And you can read all these kind of genius authors that you can just appreciate and love without, without going any further.

00;24;39;21 – 00;24;47;24
Isabella
Joseph, thank you so much for talking with me today. Best of luck with Crop Diagnostix. I’m really excited to see where you’re headed.

00;24;47;26 – 00;24;58;00
Joseph
All right, love it. Thanks so much, Isabella.

00;24;58;02 – 00;25;22;04
Isabella
From crazy projects with Joe Ecker to shaping the future of potatoes and sustainable agriculture with friends at Crop Diagnostix, Joseph is making his mark on plant biology just like the great scientists that drew him to Salk. What I think Joseph makes very clear is that plant biology is not actually just about plants. It’s about people. It’s about the scientists working with model plants in the lab.

00;25;22;07 – 00;25;55;05
Isabella
It’s about farmers planning and laboring in the fields to grow all different kinds of crops. And it’s about every single other person on earth whose life is sustained by those crops. With modern technology like artificial intelligence and our ever growing catalog of plant genes, we’re at a really exciting spot in plant biology and human history. I’m excited to see what else Joseph learns as he wraps up his studies at Salk, and then what he accomplishes in this new chapter at Crop Diagnostix, and how his ongoing scientific story may impact the future of our planet.

00;25;55;06 – 00;26;40;18
VO Victoria
Beyond Lab Walls is a production of the Salk Office of Communications. To hear the latest science stories coming out of Salk, subscribe to our podcast, and visit Salk.edu to join our new exclusive media channel, Salk Streaming. There, you’ll find interviews with our scientists, videos on our recent studies, and public lectures by our world renowned professors. You can also explore our award winning magazine, Inside Salk, and join our monthly newsletter to stay up to date on the world within these walls.