Episode Transcript
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(00:04):
- Welcome to the Lessons from Lab
and Life Podcast, brought toyou by New England Biolabs.
I'm your host, Lydia Morrison,
and I hope this episode bringsyou some new perspective.
Today I'm joined by three passion
and science winners in thecategory of arts and creativity.
These three individuals haveused their knowledge of science
to create some pretty incredibleand unique forms of art.
(00:28):
With us today is Sam
Siljee from the Gillies McIndoeResearch Institute located in
Wellington, New Zealand.
Sam has developed soundscapes
by converting massspectrometry data into sounds.
Sally Kong is the creator of Mitos,
a data physicalization project
of hand woven patternsgenerated from Sally's own
(00:51):
mitochondrial DNA sequence,
and Michael Weiner from Abbratechin Branford, Connecticut.
I'm super excited to have all of the arts
and creativity winners from the Passion
and 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 frommass spectrometry readings
(01:15):
and turn it into audible noises sounds.
Where did the idea to do this come from?
- That's a good question.
I have been in a process oftrying to understand my data,
like properly understand mydata and explore it fully.
(01:35):
And it was very much like, youknow, a spark of inspiration
that the thought occurred to me, that
I've been making an assumptionthat sort of graphics
and visualizations is theonly way to look at the data.
In fact, we don't even needto look at the data per se.
We can listen to it.
(01:55):
And so that's where thefirst idea came from.
- Interesting. And why did you want
to use the mass spec data in this way?
- The data is really large.
It is beyond scope of human comprehension.
So we talk about computerinterpretable versus
(02:16):
human interpretable.
And mass spec data isvery much in the realm
of computer interpretable,not human interpretable.
And I wanted to engage with thedata directly more tangibly,
and I felt that sound isactually a much more human way
to interact with it and observe it.
- Wow, I feel like that'sreally enlightened.
(02:38):
So technically,
how do you translate themass spec data into sounds?
- I'm not the first to turnscientific data into sound
and I looked a bit around, alot of people took a very sort
of approach where I tooka simple string of numbers
that would make a piano note go up
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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 violin sounddifferent from a piano?
And it is the shape of the waveform.
(03:19):
So if we look at the,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 furriertheorem, which describes how
complex waveform canbe made by the addition
of simpler waves.
This is an example whereseeing it graphically
(03:43):
and visualizations actually really useful
for explaining this purpose.
So yeah, yeah,
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
(04:04):
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 ofwaves, pure sign waves
with the mass mapped to frequency
and the intensity mapped to amplitude.
And then I added them together.
(04:25):
So one spectrum has gotthousands of peaks, so thousands
of sign waves added together
that gives you the complexwaveform, which is sort of unique
to that particular spectrum.
Then an experiment has got, you know,
then my practice data sethas got 58,000 spectra,
so 58,000 unique tones.
(04:48):
But the experiment has got aa time course to it as well.
And so I use time courseto play back the tone of
that spectrum at theexact time point that is,
was observed in the experimentat the loudness of sort
of the, the brightness ofthat particular spectrum.
And that's how the soundscapeis composed from the raw data,
(05:12):
the pitch, the tone, the timing,everything comes from the experiment.
- That's incredible. Can wehear some of your soundscapes?
- Absolutely. I would love to share them.
(05:34):
- So I think your music sounds,
or your soundscapes soundkind of otherworldly,
like they would be agreat background music
for like a sci-fi thriller.
I feel like when you're aboutto come around the corner
and encounter like an alien being,
how do you describe this? This soundscape
(05:54):
- I've been playing aroundwith the, I even, you know,
can't even think of the term,whether it's sound or tone or,
and I think soundscape isthe best way of putting it.
You're right, it is background.
I play it in the lab asI do my work in terms
of the sounds themselves, I, I talk about
(06:16):
air conditioning on a spaceship.
So yes, sci-fi, I talkabout ringing bells as well.
So one of the characteristicsthat comes out
and one of the, I think,important lessons in science
that we get from thesetones is emergent properties
from complexity.
And so this ringing quality Ithink comes from interference
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patterns of peaks
with very similar massessitting right together.
And there's a phenomenon in physics
where you've got two waveformswith very similar frequencies
where they, they move in and outta phase.
And I think that's wherethe ringing bell like
quality comes from.
And what is really interesting is
(06:59):
that I can scale these peaks so
that the frequencies arewell beyond what we can hear
as humans and you stillget sound coming out.
And I think that what we'rehearing there is literally
just the emergent properties,
just the interferencepatterns that come out.
So bells I would say.
(07:20):
- 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.
- You are most welcome. Thank you
- Sally.
Thanks so much for beinghere. Thank you for having me.
(07:41):
Could you tell us about your art?
- So Mitos is a handwovenseries of my ancestral DNA,
but at its core it's alove letter to my mom
and some of my favorite things, biology,
computation and yarn.
- That's so cool. So how is it
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that you translate your DNA into a
pattern to be woven?
- 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 verticaland horizontal lines.
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And in a loom, all of these vertical lines
or something we would calla warp could go through one
of four shafts.
So when I saw that therewas like four shafts
and a floor loom, I thought,oh well you know what?
I can map into these the ATGC of DNA.
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And so that's kind ofhow the mapping worked.
So after I got the hypervariable
region of my mitochondiral
DNA D-loop sequenced, I matched the ATGC
to the 1, 2, 3, 4 shaftsthat I have in my loom.
And then essentially at
that point my loom was alreadyprogrammed with my DNA,
(09:09):
so I could do differentkind of patterns such
as a basket weave or a tool weave,
and I would see thesedifferent patterns emerge,
but they all had asimilar undulation to it
because they were allprogrammed with my DNA sequence.
- That's really incredible.
And as a mother, I lovethe genesis of this idea
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and your mother must be so proud.
What made you want
to focus on your mitochondrial DNA?
- I remember in school learning about
how like the mitochondria isthe powerhouse of the cell,
but it was only maybe like a couple
of years ago when I learned about
how like the mitochondria is something
(09:55):
that's in the cytoplasm
and it's something thatis exclusively inherited
through the Excel.
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 hermom and thousands of moms.
(10:15):
And I, I get a very emotional,
I get very emotional whenI think about like the bond
that I have with my mom.
And I'm sure she doeswith her mom, thousands
of moms all the way up.
So, and I, when I felt this emotional,
I was just kinda like staggeredI think thinking about all
(10:35):
these like 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.
- So I noticed that a piece youwere wearing yesterday were,
was these beautiful shadesof like blue and Ilian
and I heard that there was astory behind that, that color.
(10:59):
Could you share thatstory with our listeners?
- Sure, I'd love to.
So in Korea there'sthis concept of Taemong,
which is the dream that youhave 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
(11:22):
that was flying, coming for her
and wrapped around her,
but she didn't feel scared, she felt warm.
And I thought, so my dad wasborn in the year of the snake,
so I think she was justthinking about my dad.
But I thought that was stilla very powerful imagery.
(11:44):
And since I first made mytoast for my mom, I kind
of wanted to honor thatdream that she had for me.
And that's what motivated meto have these undulating shades
of blue for mi toast for my mom.
- That's so beautiful.
And I can tell
that this project has brought you even
(12:07):
more sort of like 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 forbeing here today, Sally.
- Thank you- Michael.
Thanks so much for beinghere to join me today.
(12:29):
- Thank you. - Could you tellour listeners about your art?
- Yeah, I was goingthrough a series of artwork
where I was using cork bores, you know,
so the scientific corkbores that have, they're,
they're sort of nested tubes
and using the different sizetubes on a large, large four
by three foot tiles of clay.
And by using just theholes of different sizes,
(12:51):
could I make portraitsthat were realistic.
And so there's a, an oldtechnique called half toning
for those of us who are olderknow that newspapers used
to use that to put portraitsin black and white.
'cause the ink was only black and white.
So by changing the dot size
and density of the dots, whatyou could do is change it
to gray versus dark grayversus black versus white.
(13:13):
And so I was interested in replicating
that technique onto tiles
and be able to projectlight through the tiles.
So if I mounted the six bysix inch tiles, wet clay onto
lexan plexiglass, could Iproject light through it
and make it look like a portrait?
And so I started off doingthat a couple years ago.
(13:34):
It took me maybe a couple yearsto think about how to do it.
And then actual doing itdidn't take that long.
In fact, it's, it's what I'd said.
It's about the process ofcoming up with my artwork
and not so much the, the art itself.
Having done this, I couldtrain somebody in 10 minutes of
how the process could, could be applied.
(13:55):
So the, the idea there was,and that worked really nice.
I did Bruce Springsteen,Elvis, Marilyn Monroe,
iconic figures.
So that, and the reason I chosethose particular figures was
that people could look at thepicture and know who it was.
You know, if I had doneJennifer Doudna for example,
nobody would know who it was.
(14:15):
Not that she's not famous,
but if I hung it up at, atwork, nobody would know.
But by choosing iconic figuresof Einstein, Springsteen,
people could, could appreciate what it was
and then look at, at thetechnology used to do it.
And so that morphed into thenwalking into the lab one day
and seeing this big binof used plastic where,
(14:36):
'cause we do recycle it,
but I thought, I wonder what I could do
with this as far as artwork.
And the idea there was totake then empty pipette boxes
and make a square of 11 of 'em across
and 11 deep, so 120 boxes
or so as a, as the canvas.
And then be able to put thewhite filter tips back into
various holes in the, in the boxes
(14:58):
to create a half tone picturebased on just a pixel,
a white pixel on thisfour by four foot canvas.
And by doing that I was able to do a,
a pretty decent rendition of Einstein.
Again, iconic figure.
If you looked at it, youyou'd know it was Einstein
with the white hair and the,and the facial features.
And, and then after having done that,
(15:20):
which only took me twohours to do by the way,
and it took me a couple yearsto think about how to do it.
And then I walked into the lab,
I paid a research associatea hundred dollars to go ahead
and put tips back into these boxes.
So I didn't wanna 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 anothercouple years just trying
to figure out and came up
with using microtiter dishesin the same way the pattern
(15:44):
of the microtiter dishes thesame as a pipette box, not,
you know, eight by 12.
And the spacing's actuallypretty much similar.
And then I thought, well whatcould I fill in those wells
that could be color?
And I swear the first thingI thought about was thread.
And I thought, well that's notgonna work. Lemme try yarn.
So, you know, thinkingabout putting yarn in
with glue, elmer's glue
- Interesting materials, huh?
(16:05):
- Yeah. And then I, I try it once or twice
and I said, this is not gonna work.
'cause there were 20,000wells I needed to fill and,
and doing that would just been impossible.
And as part of a separateartwork, I was doing a project,
I was using epoxy, which isthe stuff, if you go into a bar
and there's pennies and dollar bills
or whatever on the bar table that's epoxy,
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you know, they put that on as a,
and then they put this clearplastic on comes in A and B
and mix in equal parts,forms this clear solution.
So it occur to me if I do thisusing some sort of colorant
and get it to polymerizecorrectly, that that could be used
to fill in the wells.
And so, so that's how itevolved from being aware
of half toning, going tothe pixel with Einstein,
(16:50):
then finally doing it in color.
The first ones I focused on,I was using food colorant,
just food dye that I boughtin the grocery store.
And the problem with that,
I didn't realize when I started was food
dyes photobleached.
So I made a piece and a smallpiece threw it in the window
in my, my office
and about three weekslater it was just yellow,
so it had photo bleached.
(17:11):
And in the meantime I builtthis DNA that was 22 feet long.
I, I was thinking, oh my god. So
- It's a lot of workto have photo bleached.
- Yeah. And then I figuredout that if I just buy a UV
resistant plexiglass, I could sandwich it
between the a pipe, Imean the microtiter dishes
and get it to work so itwouldn't fit with bleach.
- Awesome. So you saved the the DNA.
- Yeah, exactly. Theother thing I learned was
(17:32):
that the microtiter dishes,
which I always knew dissolve in organic
solvent like chloroform.
And since I'm using plexiglass, I mean,
if you just take a microtiterdish and just break it up
and throw it in 10 or20 mls of chloroform
or isopropynol, it'll melt, it'll,
it'll just form this clear liquid viscous
solution after overnight.
I knew that because that's the way I used
(17:52):
to repair gel boxes.
- Oh, interesting.
- Makingthat as a kind of a glue.
- Yeah.
- And, and so to getthe microtiter dishes onto the
on the plexiglass, kinda interesting.
You just, I I just wipethe edges around with that.
You know, when you buy PVC piping
and you wanna put together,they have that purple solution,
they sell it clear also.
(18:12):
And the reason for thatis that if I put that
around the Microtiter dish,
and I think it's chloroform,they don't tell you so.
So in big empty space,
if you just briefly brushthe microtiter plate
and then put it onto plexiglass,it chemically welds it
to it in, in about seconds.
- Cool.
- And, and so that wasthe other part of the trick.
(18:32):
So the first one was food colorant.
And then for those twopieces that I brought
to New England Biolabswith me, those were done
with acrylic paint.
'cause I wanted to putthem against the wall.
The original one was hangingin a, a big open space.
So I wanna be able to makeit look like stained glass.
- Yeah. So it's actually a super versatile
material too, right?
(18:52):
It can be viewed froma single side or Yeah.
Can be viewed from multiple sides.
I noticed that the two pieces you brought,
which are four tone, right?
- Yeah.- To show us here at New England Biolabs
that they were Henrietta Lacks.
Yeah. And Rosalyn Franklin.
- Yep.- How do you choose your subjects?
(19:13):
- So I wanted to do aseries of, I'll say famous,
but famous women whocontributed the most to science
or you know, at least initially.
And I think everybody's familiar
with Henrietta Lacks and HeLa cells.
And Rosalyn Franklin of course is DNA.
And so I thought of that.
And then there wereanother ones in a series.
And so I'll do a couple more.
Jennifer I think is probably next, or,
(19:35):
and Barbara McClintock forMobile Transposons.
It's a little different with them though,
because like with Marilyn, Einstein,
Bruce Springsteen, they're iconic people.
Look at that. Or Elvispeople, they're iconic.
Even when I brought the Rosalyn
and HeLa, I think even peopleat New England Biolabs were
kinda curious who they were.
Somebody thought it was Eleanor Roosevelt,
(19:55):
for example, and it's because they're not
- I think that was me.
- Oh, okay. Sorry.
- That's okay.- I think, I think it's
because they're not iconic.
You're not used to seeing those pictures.
Although there's only onepicture of Henrietta Lacks.
Most people you know,haven't yet bought the book,
so they're not familiar with it.
So that was the other problemwas she's only ever been
photographed in black and white.
And you know, part ofher story is she was,
(20:17):
she was an African American, she was black
and that she was poor and,
and they took advantage ofher, her cancer and her family
and her were never repaid for it.
And so the question there waswas what was her skin tone?
And so I had to go througha bunch of experimentation
to get one that I thought wasappropriate wasn't too dark.
So you could see some ofthe difference between her
(20:39):
and shade and not too light
that she looked a different race.
- Well, I think you did anamazing job capturing the
likeness of both of them.
And I think that the choice
of iconic figures is telling.
Right. But I love that you'rechoosing female scientists
to highlight now, because Ithink it would be great if more
(20:59):
people did recognize them.
So hopefully you shareyour art widely. Yeah.
And thank you so much for being here today
to tell us about your process.
- Yep. Thank you.- Thanks.
Thank you for joining us for this episode
of the Lessons from Lab and Life Podcast.
Please check out our show's transcript
(21:21):
for helpful links fromtoday's conversation.
And as always, we invite you to join us
for our next episode when I'mjoined by Ben Kleinstiver,
whose lab is located at the Center
for Genomic Medicine atMass General Hospital
and is also part of the Department
of Pathology at Mass General Hospital
and Harvard Medical School.
Ben joins us to talk aboutprogrammable nucleases,
(21:43):
genome editing and the applications
of this technology inthe future of healthcare.