Interviewers: Lydia Morrison, Marketing Communications Manager & Podcast Host, New England Biolabs, Inc.
Interviewee: Sam Siljee, M.D., Ph.D. candidate at Gillies McIndoe Research Institute; Ji Hyun (Sally) Kong, M.Eng., Community Project Lead at Genspace; Michael Weiner, Ph.D., Founder of Abbratech, Precision Biotools and Encodia
Lydia Morrison:
Welcome to the Lessons from Lab and Life Podcast, brought to you by New England Biolabs. I'm your host, Lydia Morrison, and I hope this episode brings you some new perspective. Today, I'm joined by three Passion in Science winners in the category of arts and creativity. These three individuals have used their knowledge of science to create some pretty incredible and unique forms of art.
With us today is Sam Siljee from the Gillies McIndoe Research Institute, located in Wellington, New Zealand. Sam has developed soundscapes by converting mass spectrometry data into sounds. Sally Kong is the creator of Mitos, a data physicalization project of hand-woven patterns generated from Sally's own mitochondrial DNA sequence. And Michael Weiner from Abbratech in Brantford, Connecticut.
I'm super excited to have all of the arts and creativity winners from the Passion in Science Awards with us. It's so exciting to see all your artwork and to hear about the process. So Sam, you take the data from mass spectrometry readings and turn it into audible noises, sounds. Where did the idea to do this come from?
Sam Siljee:
That's a good question. I have been in a process of trying to understand my data, properly understand my data and explore it fully, and it was very much like a spark of inspiration. The thought occurred to me that I've been making an assumption that graphics and visualizations is the only way to look at the data. In fact, we don't even need to look at the data per se. We can listen to it, and so that's where the first idea came from.
Lydia Morrison:
Interesting. And why did you want to use the mass spec data in this way?
Sam Siljee:
The data is really large. It is beyond the scope of human comprehension. So we talk about computer interpretable versus human interpretable, and mass spec data is very much in the realm of computer interpretable, not human interpretable. And I wanted to engage with the data directly, more tangibly, and I felt that sound is actually a much more human way to interact with it and observe it.
Lydia Morrison:
Wow. I feel like that's really enlightened. So technically, how do you translate the mass spec data into sounds?
Sam Siljee:
I'm not the first to turn scientific data into sound, and I looked a bit around. A lot of people took an approach where they took a simple string of numbers that would make a piano note go up and down with the synthesizer, and I wanted to take it a step further and have the tone and the timing and the pitch come from the data itself. So I got thinking about tones. Where do tones come from? What makes a violin sound different from a piano? And it is the shape of the waveform. So if we look at the shape of the waves, there's a difference there. And then I remembered, I don't even know where I learned this, but there's an amazing piece of math called the Fourier Theorem which describes how complex waveforms can be made by the addition of simpler waves. This is an example where seeing it graphically and visualization is actually really useful for explaining this purpose.
I took a mass spectrum, which is a set of data consisting of two dimensions. So we've got what we call peaks, and each peak has got two values to it, so it's got a mass, which is where the name mass spectrum comes from, and it's got an intensity, so how bright that mass is in the mass spectrometer. And I made a bunch of waves, pure sine waves with the mass mapped to frequency and the intensity mapped to amplitude, and then I added them together. So one spectrum has got thousands of peaks, so thousands of sine waves added together. That gives you the complex waveform which is unique to that particular spectrum.
Then my practice data set has got 58,000 spectra, so 58,000 unique tones, but the experiment has got a time course to it as well. And so I use time course to play back the tone of that spectrum at the exact time point that was observed in the experiment at the loudness of the brightness of that particular spectrum, and that's how the soundscape is composed from the raw data. The pitch, the tone, the timing, everything comes from the experiment.
Lydia Morrison:
That's incredible. Can we hear some of your soundscapes?
Sam Siljee:
Absolutely. I would love to share them.
Lydia Morrison:
So I think your music sounds, or your soundscapes sound otherworldly, like they would be a great background music for a sci-fi thriller I feel like, when you're about to come around the corner and encounter an alien being. How do you describe this soundscape?
Sam Siljee:
I've been playing around with, I even can't even think of the term, whether it's sound or tone, and I think soundscape is the best way of putting it. You're right, it is background. I play it in the lab as I do my work. In terms of the sounds themselves, I talk about air conditioning on a spaceship, so yes, sci-fi. I talk about ringing bells as well. So one of the characteristics that comes out, and one of the I think important lessons in science that we get from these tones is emergent properties from complexity.
And so this ringing quality I think comes from interference patterns of peaks with very similar masses sitting right together, and there's a phenomenon in physics where you've got two waveforms with very similar frequencies where they move in and out of phase, and I think that's where the ringing bell-like quality comes from. And what is really interesting is that I can scale these peaks so that the frequencies are well beyond what we can hear as humans, and you still get sound coming out. And I think that what we're hearing there is literally just the emergent properties, just the interference patterns that come out, so bells I would say.
Lydia Morrison:
Sam, thanks so much for being here today and for sharing your soundscapes with us. Such a cool application of data and a new way to be able to interpret results, so thank you.
Sam Siljee:
You are most welcome. Thank you.
Lydia Morrison:
Sally, thanks so much for being here.
Sally Kong:
Thank you for having me.
Lydia Morrison:
Could you tell us about your art?
Sally Kong:
So Mitos is a hand-woven series of my ancestral DNA, but at its core, it's a love letter to my mom and some of my favorite things, biology, computation and yarn.
Lydia Morrison:
That's so cool. So how is it that you translate your DNA into a pattern to be woven?
Sally Kong:
Sure. So the loom that I chose, so loom like a weaving machine, I used Schacht four shaft floor loom. So when you look at a weave, they're essentially interlaced threads or yarns of vertical and horizontal lines, and in a loom, all of these vertical lines or something we would call a warp could go through one of four shafts. So when I saw that there was four shafts in a floor loom, I thought, "Oh, well, you know what I can map into these? The ATGC of DNA." And so that's how the mapping worked. So after I got the hypervariable region of my mitochondrial DNA D-loop sequenced, I mapped the ATGC to the 1, 2, 3, 4 shafts that I have in my loom. And then essentially at that point, my loom was already programmed with my DNA, so I could do different kind of patterns such as a basket weave or a twill weave, and I would see these different patterns emerge but they all had a similar undulation to it because they were all programmed with my DNA sequence.
Lydia Morrison:
That's really incredible, and as a mother, I love the genesis of this idea, and your mother must be so proud. What made you want to focus on your mitochondrial DNA?
Sally Kong:
I remember in school learning about how the mitochondria is the powerhouse of the cell, but it was only maybe a couple of years ago when I learned about how the mitochondria is something that's in the cytoplasm and it's something that is exclusively inherited through the egg cell, and so it's something that's used to study matrilineal lineage. And I thought about that and I thought about like, "Oh, so I got this from my mom and she got it from her mom and thousands of moms." And I get very emotional when I think about the bond that I have with my mom, and I'm sure she does with her mom, thousands of moms all the way up. And when I felt this emotional, I was just like staggered I think, thinking about all these connections to my mom that I could get from my cheek swab and extracting my mitochondrial DNA, and I wanted to do something about it. I wanted to make art.
Lydia Morrison:
So I noticed that a piece you were wearing yesterday was these beautiful shades of blue and cerulean, and I heard that there was a story behind that color. Could you share that story with our listeners?
Sally Kong:
Sure, I'd love to. So in Korea, there's this concept of Taemong, which is the dream that you have when you conceive a child. And the Taemong that my mom had for me was that she was in this wide field and there was a giant blue snake that was flying, coming for her and wrapped around her, but she didn't feel scared, she felt warm. So my dad was born in the year of the snake so I think she was just thinking about my dad, but I thought that was still a very powerful imagery. And since I first made Mitos for my mom, I wanted to honor that dream that she had for me, and that's what motivated me to have these undulating shades of blue for Mitos for my mom.
Lydia Morrison:
That's so beautiful, and I can tell that this project has brought you even more joy in the celebration of your mom and your ancestry, and so what a wonderful creative way to rediscover familial ties and I think it's really beautiful. Thank you so much for being here today, Sally.
Sally Kong:
Thank you.
Lydia Morrison:
Michael, thanks so much for being here to join me today.
Michael Weiner:
Thank you.
Lydia Morrison:
Could you tell our listeners about your art?
Michael Weiner:
Yeah. I was going through a series of artwork where I was using cork bores, so the scientific cork bores. They're nested tubes, and using the different sized tubes on large four by three foot tiles of clay. And by using just the holes of different sizes could I make portraits that were realistic. And so there's an old technique called half-toning. For those of us who are older know that newspapers used to use that to put portraits in black and white because the ink was only black and white, so by changing the dot size and density of the dots, what you could do is change it to gray versus dark gray versus black versus white. And so I was interested in replicating that technique onto tiles and be able to project light through the tile. So if I mounted the six by six inch tiles, wet clay onto Lexan plexiglass, could I project light through it and make it look like a portrait?
And so I started off doing that a couple of years ago. It took me maybe a couple of years to think about how to do it, and then actual doing it didn't take that long. In fact, it's what I said. It's about the process of coming up with my artwork and not so much the art itself. Having done this, I could train somebody in 10 minutes on how the process could be applied. So the idea there was... And that worked really nice. I did Bruce Springsteen, Elvis, Marilyn Monroe, iconic figures, and the reason I chose those particular figures was that people could look at the picture and know who it was. If I had done Jennifer Doudna for example, nobody would know who it was. Not that she's not famous, but if I hung it up at work, nobody would know. But by choosing iconic figures of Einstein, Springsteen, people could appreciate what it was and then look at the technology used to do it.
And so that morphed into then walking into the lab one day and seeing this big bin of used plastic, because we do recycle it but I thought, "I wonder what I could do with this as far as artwork." And the idea there was to take then empty pipette boxes and make a square of 11 of them across and 11 deep, so 120 boxes or so as the canvas, and then be able to put the white filter tips back into various holes in the boxes to create a half-tone picture based on just a pixel, a white pixel on this four-by-four-foot canvas.
And by doing that, I was able to do a pretty decent rendition of Einstein. Again, an iconic figure. If you looked at it, you'd know it was Einstein with the white hair and the facial features. And then after having done that, which only took me two hours to do by the way and it took me a couple of years to think about how to do it, and then I walked into the lab, I paid a research associate a hundred dollars to go ahead and put tips back into these boxes because I didn't want to use new ones. Done that, figured out how to do that, I looked at it and said, "I wonder how I could do this in color." And then spent another couple of years just trying to figure out and came up with using micro-titer dishes in the same way.
The pattern of the micro-titer dish is the same as a pipette box, not eight by 12, and the spacing is actually pretty much similar. And then I thought, "Well, what could I fill in those wells that could be color?" And I swear, the first thing I thought about was thread. And I thought, "Well, that's not going to work. Let me try yarn." So thinking about putting yarn in with glue, Elmer's glue.
Lydia Morrison:
Interesting materials, huh?
Michael Weiner:
Yeah. And then I try it once or twice and I said, "This is not going to work," because there were 20,000 wells I needed to fill, and doing that would have just been impossible. And as part of a separate artwork, I was doing a project, I was using epoxy, which is the stuff if you go into a bar and there's pennies and dollar bills or whatever on the bar table, that's epoxy. They put that on and then they put this clear plastic on. It comes in A and B, mix in equal parts, forms this clear solution. So it occurred to me, if I do this using some colorant and get it to polymerize correctly, that that could be used to fill in the wells. And so that's how it evolved from being aware of half-toning, going to the pixel with Einstein, then finally doing it in color.
The first ones I focused on, I was using food colorant, just food dye that I bought in the grocery store. And the problem with that, I didn't realize when I started, was food dyes photobleached. So I made a piece, a small piece, threw it in the window in my office, and about three weeks later, it was just yellow, so it was photobleached. And in the meantime, I built this DNA that was 22 feet long, and I was thinking, "Oh my God."
Lydia Morrison:
It's a lot of work to have photobleached.
Michael Weiner:
Yeah. And then I figured out that if I just buy a UV-resistant plexiglass, I could sandwich it between the microtiter dishes and get it to work so it wouldn't photobleach.
Lydia Morrison:
Awesome. So you saved the DNA.
Michael Weiner:
Yeah, exactly. The other thing I learned was that the microtiter dishes, which I always knew dissolve in organic solvent like chloroform, and since I'm using plexiglass, if you just take a microtiter dish and just break it up and throw it in 10 or 20 mls of chloroform or isopropyl, it'll melt. It'll just form this clear liquid, a viscous solution overnight. I knew that because that's the way I used to repair gel boxes, making that as a kind of a glue.
And so to get the micro-titer dishes onto on the plexiglass is kind of interesting. I just wipe the edges around with that... You know when you buy PVC piping and you want to put it together, they have that purple solution? They sell it clear also, and the reason for that is that if I put that around the micro-titer dish, and I think it's chloroform, they don't tell you. So in big empty space, if you just briefly brush the micro-titer plate and then put it onto plexiglass, it chemically welds it to it in about seconds.
Lydia Morrison:
Cool.
Michael Weiner:
And so that was the other part of the trick. So the first one was food colorant. And then for those two pieces that I brought to New England Biolabs with me, those were done with acrylic paint because I wanted to put them against the wall. The original one was hanging in a big open space, so I want to be able to make it look like stained-glass.
Lydia Morrison:
So it's actually a super versatile material too. It can be viewed from a single side or it can be viewed from multiple sides. I noticed that the two pieces you brought, which are four-tone, right?
Michael Weiner:
Yeah.
Lydia Morrison:
To show us here at New England Biolabs, that they were Henrietta Lacks and Rosalind Franklin. How do you choose your subjects?
Michael Weiner:
So I wanted to do a series of, I'll say famous, but famous women who have contributed the most to science, or at least initially. And I think everybody's familiar with Henrietta Lacks and HeLa cells. And Rosalind Franklin of course is DNA, and so I thought of that. And then there were other ones in a series, and so I'll do a couple more. Jennifer Doudna I think is probably next, and Barbara McClintock for mobile transposons. It's a little different with them though, because like with Marilyn, Einstein, Bruce Springsteen, they're iconic, people look at that, or Elvis, they're iconic. Even when I brought the Rosalind and HeLa, I think even people at New England Biolabs were curious who they were. Somebody thought it was Eleanor Roosevelt, for example, and it's because they're not-
Lydia Morrison:
I think that was me.
Michael Weiner:
Okay, sorry.
Lydia Morrison:
That's okay.
Michael Weiner:
I think it's because they're not iconic, you're not used to seeing those pictures. Although there's only one picture of Henrietta Lacks, most people haven't yet bought the book so they're not familiar with it. So that was the other problem was she's only ever been photographed in black and white. And part of her story is she was an African-American, she was Black and she was poor, and they took advantage of her cancer, and her family and her were never paid for it. And so the question there was what was her skin tone? And so I had to go through a bunch of experimentation to get one that I thought was appropriate. It wasn't too dark so you could see some of the difference between her and shade, and not too light that she looked a different race.
Lydia Morrison:
Well, I think you did an amazing job capturing the likeness of both of them, and I think that the choice of iconic figures is telling. But I love that you're choosing female scientists to highlight now, because I think it would be great if more people did recognize them. So hopefully, you share your art widely, and thank you so much for being here today to tell us about your process.
Michael Weiner:
Yep. Thank you.
Lydia Morrison:
Thanks.
Thank you for joining us for this episode of The Lessons from Lab and Life Podcast. Please check out our show's transcript for helpful links from today's conversation, and as always, we invite you to join us for our next episode when I'm joined by Ben Kleinstiver, whose lab is located at the Center for Genomic Medicine at Mass General Hospital, and is also part of the Department of Pathology at Mass General Hospital and Harvard Medical School. Ben joins us to talk about programmable nucleases, genome editing, and the applications of this technology in the future of healthcare.
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