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**Ian Lopshire:** Okay. |
**Tim Stiles:** So think of it this way... If you need to engineer a DNA construct, like these little plasmid tokens I've told you about, these little, essentially swappable functions we'd like to put into different cell types, you have to construct that. They exist in nature's bacteria, but for our purposes, we need t... |
Say you want to run a whole DNA synthesis operation - my software does that end-to-end. You can design the software, you can design the construct of interest, you can simulate how you're going to construct it, you're going to simulate these special ways of printing DNA... So DNA synthesis is a little funny, in that the... |
\[26:15\] So essentially, my focus was just on making it so you could engineer a DNA string to do what you want, and to express faithfully, and you wouldn't have problems when you send it to a DNA synthesis vendor, for them to go like, "Oh, it's not the right sequence." And so you could do it at scale, instead of like ... |
And so my software is really the only software out there that's fast and stable; it can do this reliably with high unit test coverage. There are some - I would call them predecessors, that are really impressive. And there's also really impressive GUI tools that you'll do this one at a time sort of thing too, that are o... |
My project is like the first that makes it really possible to do this at a scale where you're not looking at bad compute bills... I mean, this is the thing... Like, synthetic biology shouldn't have high compute bills. It's not like we're looking at whole genomes all the time, unless you're working on human-specific stu... |
**Ian Lopshire:** Yeah... Could I repeat that back to you and just see if -- |
**Tim Stiles:** Yeah, of course. Yeah, this is a biology lesson for everybody. I wish I was talking more about Go and my practices there... I should have done that too, but yeah... |
**Ian Lopshire:** We'll do Go right after this, I promise. |
**Tim Stiles:** Okay. |
**Ian Lopshire:** So basically, someone has engineered this like plasmid that they want to be able to produce, right? ...to do whatever X thing, make a new protein, or whatever. |
**Tim Stiles:** Yup. They've literally just whiteboarded it. It's a concept on like a napkin. |
**Ian Lopshire:** Okay. Yeah. And so they take your software - or this is one thing it can do at least, is run simulations to try to find actual DNA that we can produce... Like, synthesize in the real world. But we don't have to touch the real world, we can just simulate it, and yours can be like, "Yeah, we can make th... |
**Tim Stiles:** Yes, exactly. |
**Ian Lopshire:** Okay, that's cool. Okay. |
**Tim Stiles:** It's really valuable, because each one of those plasmids I've been talking about, the price is always going down for DNA synthesis, but right now, it's not uncommon to hear of like a $500 to $700 bill per plasmid. It's not uncommon. I have a customer who I'm working with right now, and they make DNA lib... |
Because a lot of scientists - there's a lot of prayer. I mean, if you ask a scientists what they do before they send out a sample to be sequenced, or go through \[unintelligible 00:29:56.25\] there's this false dichotomy between religion and science, but a lot of them, even if they aren't religious, do a little prayer,... |
\[30:10\] Because scientists are engineers; it's a difference in practice. Scientists are trying to discover something new, and they're doing it like the startuppy, like "Gotta do as fast as possible, plant the flag, get the research, get the data, boom!" And engineers, we can be a little slower, we can be a little bit... |
**Natalie Pistunovich:** That is really interesting. We talked about what it is, what led to that, what it is doing now... Tell us about the future of bioengineering as you see it. |
**Tim Stiles:** So this is a conversation I come into a lot. And actually, I have friends who - we are like polar opposites. It's one of those things where we both agree where the future's going, but we disagree on how the future's gonna get there, and what the practice of it is going to look like. So for me, the pract... |
But the thing is that we're gonna get to a point where hopefully there's enough software engineers with biology experience that can talk to these people that have this experience in more pointed, niche parts of the field, like immunology, or plant physiology, or these different biological topics, where they can work to... |
And then my friend - he's entirely the opposite. He thinks we should have a few software engineers writing - not GUIs, but kind of like that; you know, report generators maybe. And there's like 20 scientist analyzing them. We have entirely different outlooks on how it's going to be. So what I'm betting on is that in th... |
One of the things that's fun is that every time I rewrite an algorithm from Python into Go, it's like 25 times faster by default. We have the world's fastest DNA synthesis-fixing function by several orders of magnitude, which is kind of nuts. Like, we weren't aiming for that. That's just kind of how it happened. |
So there's a lot of work to be done there, and I think the real impetus for most software engineers is the biology is intimidating. And I think the one thing if there's a software engineer listening to this right now who's interested in biology - don't be so intimidated by the biology. Seek to learn it and be humble wh... |
My favorite is -- do you guys know the three-body problem? ...like, this classic problem of physics that's been around forever... |
**Ian Lopshire:** Yeah. |
**Tim Stiles:** ...where essentially we don't have the math to model three bodies orbiting each other, like all related to each other; we just don't have the math for it. And so that's what the protein folding problem is. That's why everyone gets excited when there's a new -- I mean, people here probably have heard of ... |
\[34:20\] That's the one piece of advice, if there's a software engineer who wants to get into like genetic engineering or DNA synthesis or anything out there, it's just - remember to be humble, because you'll learn something new literally every day, and you'll be like "Wow, this should be some basic stuff." But that's... |
**Ian Lopshire:** So you mentioned Go, and Rust, and the future there... Do you think Go has like a prominent future there? |
**Tim Stiles:** Yes, I do. |
**Ian Lopshire:** Why? |
**Tim Stiles:** Usability is the biggest thing there. And also just the DevOps tools are amazing. There's nothing that makes my life easier than writing in Go. First off, almost every tool, every DevOps tool is written in Go now. Almost every single one. For my project I regularly use -- Gitpod's a real favorite of min... |
**Natalie Pistunovich:** That's a German thing. |
**Tim Stiles:** Yeah, no, they're great. |
**Natalie Pistunovich:** Yeah. |
**Tim Stiles:** I really love them. Oh, by the way, anyone listening out there, if you haven't been to Gitpod's Discord, go. They're super-friendly. Just show them your work, with whatever you're doing. They're super-excited, supportive and ask a lot of questions. They're really, really nice. |
But when I got started, Go is like test-first; all the things you need... Like example tests are actually a great thing, where Python or a lot of other languages -- like, maybe there's a library for it, but in Go it's just standard. Whenever I write an example test, it runs every time I've run my tests, and it's an exa... |
And so I think the fact that Go has all these opinions, which if you're like a -- I guess you would call it like a gray beard or white beard software engineer... Like, maybe you have different opinions, but if you're just starting out and you don't really know where you're going DevOps-wise, Go's defaults are beautiful... |
I don't know if you've ever done like string manipulation in Rust, but it's hard. It's not something you want to teach the people coming from Python. And maybe there's a good reason for that, but I did not personally enjoy it. So when I was testing those two, it came down to Go winning on almost everything. And I think... |
One of my contributors convinced me that we need to use \[unintelligible 00:37:33.08\] is the default, and so Go's crypto library doesn't have that yet, so some guy wrote a working implementation and we just used that. Lua didn't have that, so my friend who wanted to implement it in Lua had to go and write BLAKE3 three... |
**Ian Lopshire:** Grumble-grumble... |
**Tim Stiles:** \[37:59\] That's something that -- some of my contributors are like "Why do you make us do whole words?" I'm like, "You'll thank me in six months." And Go has all these great tools for detecting like data race conditions... And that's something I learned recently. I'm still learning various things... Th... |
So a lot of scientists, they heavily rely on Docker and Jupyter Notebooks. Like super, super, super heavily. And usually, like, "What do you do to containerize your software?" I was like "Well, Docker is also written in Go, so I just do what they do, which is ship binaries if it's an application. \[unintelligible 00:38... |
And so I just think as a programming language, it's just really powerful and very suitable for people that are trying to build something stable, that may not have had that experiences, or -- you know, people in biotech have this insecurity of feeling like they're not real software engineers. That's not necessarily true... |
The stuff I've written has mostly been for DNA engineering, but next I want to get into metabolic pathway engineering, and protein engineering. That's sort of the whole reason I've gotten into this, is I want to make -- proteins, for those listening, you've probably heard this in the bodybuilder terms, of "You need eno... |
And so I'm really excited about that, but I'm also excited about the macro stuff; the stuff that we haven't touched on. Traditionally, with genetic engineering, the moneymakers are first pharma, then ag tech, and then other. And I'm really, really, really interested in the other part. I think that's the coolest part. L... |
**Natalie Pistunovich:** Like mushrooms. |
**Tim Stiles:** Yeah, like the mushroom bricks that you may have seen. Why can't we just have the mushrooms grow to house size? Is there some sort of fundamental physical limit there, or have we just not tried hard enough yet? I saw a great clip on Twitter where someone was talking to a group of kids, like "So are you ... |
\[42:08\] But with plant work, for the most part, there's a lot more to be done there with like working in morphology, and like expressing different genes... You can actually grow plants that produce medicine, which people have been working on... My personal favorite is people really want to build infrastructure, like ... |
But we also know that pharmaceuticals is super-important, and it's also a very meaningful thing, because we've all had families in hospitals before, so it's something that we all respect. And you know, if you're squeamish like me, I try to avoid it, but also, it's important. And the ag tech stuff - Monsanto ruined the ... |
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