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Wesleyan University The Honors College

Over the Falls: A Musical Exploration of the Waterfall Dace Project

by

Nicole Roman-Johnston Class of 2016

A thesis submitted to the faculty of Wesleyan University

in partial fulfillment of the requirements for the Degree of Bachelor of Arts

with Departmental Honors in Music Middletown, Connecticut April, 2016

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Introduction

I have worked in the Chernoff lab since my freshman year when my

roommate at the time, Chloe Nash, got me the job. I don’t remember being

particularly excited. I thought I would just try it out and see if I liked it because,

like most freshman, I had no idea what I wanted to study. Due to my lack of

foresight and very little guidance from my advisor at the time, registering for

courses was a free-for-all. I ended up signing up for interesting courses like

“The Art of Listening,” which opened my eyes to the world of experimental

music and changed how I thought about sound. As time passed, I grew more

and more interested in studying music and less interested in studying

science. Working in the lab became more of a campus job that I happened to

be really good at. Although I had come to master the daily lab procedures, I

had always struggled to wrap my head around some of the more complex

statistical tests and the evolutionary theory. After participating in the tutorial

with visiting artist R. Luke DuBois in the fall semester of 2015, I began to

realize that my approach to understanding the daily lab work was very

musical. Entering the three-digit microsatellite data became a percussion

piece in triple meter, the recipe for the chemical cocktails for a PCR became

an easily regurgitated sound bite, the pipettes, microwave, and the Vortexer

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became my musical instruments. I have come to the realization that finding

the forms and patterns of music in the forms and patterns of science help me

understand both a little better. My main goal in composing these three pieces

was to explore the synchronicities between how I experience scientific

research and how I experience music. Additionally, I hoped to develop the

pieces so that they could effectively and creatively communicate these

advanced scientific theories to an audience that would otherwise have a hard

time accessing them.

Chapter 1: Overview of the Research

In the Chernoff lab, our main question is: how do waterfall barriers affect

gene flow in populations of the Eastern Blacknose Dace in the Connecticut

River Valley? Previous work has shown that waterfall barriers affect orders of

larger, anadromous fish like salmonids, but little has been done to explore the

effect on smaller riffle-dwelling taxa. The Blacknose Dace, Rhyinichthys

atratalus, is a small minnow that is found in rivers on the Atlantic versant

ranging from Nova Scotia to the Roanoke River drainage in Virginia.i They

are an ideal study species because they are abundant in Connecticut and

because previous studies have been conducted in which researchers have

identified and resolved genetic markers in their genome. Our lab team

analyzes these genetic markers to test the following three hypotheses:

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1.   The waterfalls are acting as barriers or “leaky” barriers to gene flow

2.   Below the falls populations have greater genetic diversity because of

i.   In situ evolution

ii.   Migration of genes from above-falls populations

iii.   Migration from other below-falls populations

3.   Populations separated by waterfalls are more genetically divergent

than the populations that are not separated

 

While the specific hypotheses help guide our research, our overall goal is

to provide evidence that man-made barriers like dams pose a threat to river-

dwelling species by demonstrating how natural barriers can impede gene

flow. Gene flow, the movement of genetic material from individuals of one

population to another, is essential for the maintenance of genetic diversity. A

limit to gene flow can be detrimental to the resilience of a population. If a

habitat is subjected to ecological threat or to an environmental change (most

of which are caused by humans), a population with a more diverse gene pool

is expected to be more resilient than a population with less diversity. If there

is more diversity, or a greater number of genes, then there is a greater

chance that there exist some individuals with a genotype that makes them

better suited for survival. These individuals will then pass on the favorable

genotype to further promote survival within the population. Thus, we can

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determine whether or not the populations are in decline based on the amount

of gene flow between them.

To assess the diversity within these populations, we collected DNA

samples from individuals from seven different populations located above and

below waterfalls in rivers in the Connecticut River drainage basin. The seven

sites are shown below:

Roman-Johnston et al. 2015

There are three waterfalls (indicated by the red bars) that separate these

populations: Wadsworth Big Falls, Wadsworth Little Falls, and the falls at

Falls Brook. FB-B, CR-M, and CR-W are below-falls populations and CR, CR-

A, Wab, and FB-A are above-falls populations.

Over the Falls: the Effect of Waterfalls on the Genetic Structure of the Eastern Blacknose Dace, Rhinichthys atratulus, in Connecticut

Nicole Roman-Johnston1, Kayla Anatone1, Julio Angel1, Alexandra Fireman1, Abrial Meyer1, Chloe Nash1, Michelle Kraczkowski2, Barry Chernoff1

1Wesleyan University, Middletown, CT 06457, 2Middlesex Community College, Middletown, CT 06457

Waterfalls are recognized as physical barriers that isolate

fish populations. The isolated populations diverge

genetically such that populations below the falls exhibit

higher genetic diversity due to migration. These effects have

been demonstrated for salmonids (Gomez-Uchida et al.

2009, Wofford et al. 2005). Depending upon the physical

nature of the falls (height, water velocity, etc.), waterfalls can

act as either impermeable or “leaky” barriers to gene flow.

There are few studies, however, on non-migratory riffle-

dwelling taxa. One such species, the Eastern Blacknose

Dace, Rhinichthys atratulus, is found above and below

waterfalls on the Atlantic versant from Nova Scotia to the

Roanoke River drainage in Virginia (Kraczkowski and

Chernoff 2014). This small minnow is ideal for the study of

habitat fragmentation because of its ubiquity and because

microsatellite loci have been resolved for the species (Girard

and Angers 2006, Dimsoski et al. 2000, Sweeten ms.). Here

we test previously established theories about the effect of

waterfalls on the population genetic structure of R. atratulus

from populations above and below three waterfalls in the

Mattabesset River basin.

1) Barrier to Gene Flow Waterfalls act as barriers or “leaky” barriers to gene flow.

2) Greater Genetic Diversity Below Falls Below falls populations have greater genetic diversity

because of: i) in situ evolution; ii) migration of genes

from above-falls populations; and iii) migration from other

below-falls populations.

3) Genetic Divergence Populations separated by waterfalls are more genetically

divergent than the populations that are not separated.

Hypotheses

Methods

Results

Site Map Global AMOVA

1) Waterfalls are acting as either impermeable or “leaky” barriers to gene flow: i) sites separated by waterfalls are all significantly

different; and ii) sites have private and distinct alleles.

2) Genetic diversity is NOT always greater in below-falls

populations than above-falls populations: i) populations above

Big Falls are more heterozygous and have more private alleles

than below-falls populations; and ii) dace above and below Falls

Brook have similar numbers of private alleles.

3) The amount of genetic divergence among populations is

independent of waterfall barriers: i) ∆μ2 for various locations is

lower between sites that are separated by waterfalls; and ii) CR

has a significantly different genetic structure from that of CR-A

(both above Big Falls).

Conclusions

FB-A FB-B CR-M CR-W CR-A CR Wab

Falls Brook Wadsworth

Pro

bability

K=3

K=5

FB-A FB-B CR-M CR-W CR-A CR Wab

Genetic Distance Between Pairs of Populations Heterozygosity* Private* and Distinct** Alleles

Bayesian a posteriori Classification (Structure ver. 2.3.3)

Probability of group membership (color) shown as vertical bar for each individual

References: Dimsoski, P., et al. 2000. Mol. Ecol. 9: 2187-2189; Excoffier, L., et al. 2005. Evol. Bioinformatics

1:47-50; Girard, P., and B. Angers. 2006. Can. J. Fish. & Aquat. Sci. 63:1429-1438; Gomez-Uchida, D. et al. 2009. Mol. Ecol.18: 4854-4869; Kraczkowski, M. L., and B. Chernoff. 2014.

Copeia 2014(2): 325-338; Pritchard, J. K., et al. 2000. Gen. Soc. America 155: 945-959;

Wofford, J. E. B., et al. 2005. Ecol. App. 15(2): 628-637.

Collection Æ Preservation Æ Extraction Æ Microsatellite Genotyping

(Screen for 15 Microsatellites, PCR) Æ Sequencing Æ Data Analysis:

• Bayesian a posteriori classification (Stephens and Pritchard 2000)

• Analysis of Molecular Variance (Excoffier et al. 2005)

• Other population genetic parameters

Pro

bability

Location Private Alleles

Distinct Alleles

Above Falls Brook FB-A 1 4

Below Falls Brook FB-B 2 11

Above Little Falls Wab 2 6

Above Big Falls CR 17 18

CR-A 8

Below Big and Little Falls

CR-W 6 8

CR-M 2

*unique in study area; **unique in sub-basin

Comparison ∆μ2 Above vs. Above CR-A vs. FB-A 13.12

CR-A vs. CR 14.08

Below vs. Below CR-M vs. FB-B 4.45

CR-M vs. CR-W 14.17

Above vs. Below FB-A vs. FB-B 2.43

CR-A vs. CR-W 12.07

Only a sample of comparisons are represented.

Sum of Squares

Variance Components

Percentage Variation

FB-A vs. FB-B Among groups 2.551 0.026 1.618**

Among pops

within groups 0.000 -0.031 -1.944

Big Falls (CR & CR-A) vs.

Wadsworth Below (CR-W & CR-M)

Among groups 18.821 0.111 4.511**

Among pops

within groups 10.126 0.052 2.127***

Little Falls (Wab) vs.

Wadsworth Below

Among groups 14.073 0.157 6.401*

Among pops

within groups 4.318 0.065 2.653*

Falls Brook vs.

Wadsworth

Among groups 12.289 0.037 1.991

Among pops

within groups 32.248 0.086 4.588***

FB-B vs.

Wadsworth Below

Among groups 13.982 0.105 5.310

Among pops

within groups 4.111 0.078 3.930*

CR-A vs. CR Among groups 11.617 0.076 3.320***

Among pops

within groups

0.000 -0.030 -1.304

*P < 0.05, **P < 0.01, ***P < 0.001 AMOVA’s based on: i) 5 polymorphic loci within Falls Brook (FB); ii) 6 polymorphic

loci between Wadsworth and FB; and iii) 7 polymorphic loci among Wadsworth

localities.

Sample Size Hobs. Hexp.

FB-B 29 0.683 0.633

FB-A 23 0.641 0.654

CR 41 0.579 0.591

Wab 20 0.537 0.603

CR-W 38 0.596 0.637

CR-A 37 0.608 0.619

CR-M 9 0.564 0.661

Introduction

*No significant deviation from Hardy-Weinberg

Mattabesset River

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Although they are all situated within the same river valley, the physical

characteristics of these habitats like depth, width, speed of water flow,

substrate type, surrounding terrestrial ecosystems, etc. are variant. These

physical characteristics can have a profound effect on the genetic structures

of these fish populations.

According to theory, we would expect the below-falls populations, FB-B,

CR-M, CR-W, to have greater amounts of genetic diversity than the above-

falls populations CR, CR-A, Wab, and FB-A. To see if our predictions reflect

reality, we analyze DNA samples taken from individuals from each of these

populations. We wade out into the river and use a Smith-Root LR-32

electrofisher to send an electric current into the water, temporarily stunning

any fish within a three-foot radius of the current. The stunned fish are

scooped up with a net and collected in a bucket. Once twenty or so

individuals are collected, the bucket is taken to the bank of the river where a

clip from the caudal fin of each individual is taken and stored in a vial of

ethanol. The fish are released back into their habitat relatively unharmed as

there are very few nerve endings in the regenerative caudal fin tissue. We

then take the tissue samples back to the lab where we, through a chemical

lysing process, extract and store the DNA.

With this extracted DNA, we perform Polymerase Chain Reactions (PCRs)

to amplify regions that act as genetic markers. A PCR involves adding the

DNA that we extracted from each individual to cocktail of chemicals and

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exposing it to a specific set of temperatures in a specialized oven called a

Thermocycler. The cocktail of chemicals includes: primers that target the

desired region of the DNA, DNA polymerase extracted from the bacteria

Thermus aquaticus (Taq), a fluorescent color tag that sticks to the desired

region, and other pH balancing agents. These agents all work together to

amplify the desired region enough that it can be measured and even seen by

the human eye. This PCR product is then treated and sent off to Yale

University where the team at the DNA Analysis Facility processes the material

and organizes it into data files that we can access.

We use two types of genetic markers to assess the similarities and

differences in the genotypes of the fish in each of the populations. One of

these is ND2, a mitochondrial gene that codes for a protein subunit of the

NADH complex, an important component of the energy-producing electron

transport chain. The other markers are microsatellites which are small,

repeating fragments of DNA that insert themselves into larger pieces of

introns or “junk” DNA. Microsatellites are noncoding and are unaffected by

selection, making them a neutral marker that can evolve freely over time.

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ND2

The ND2 data comes back to us from Yale, in the form of a

chromatogram, but instead of outputting the sizes of gene fragments, it

outputs the fluorescent reflectance of each individual nucleotide (shown

below).

Instead of “calling peaks” as we do with the microsatellite readings, with ND2

data, we look at long strings of A’s,T’s, C’s, and G’s. When run through

Geospiza FinchTV, the software compares the novel sequence to a

consensus sequence, a sort of template of the gene that has been previously

resolved. The nucleotide substitutions are highlighted and the researcher

must sift through the sequence and verifies that the substitutions are

legitimate. The substitutions are called “single nucleotide polymorphisms,” or

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“SNPs.” If a substitution is legitimate, the novel sequence can be classified

as a unique haplotype. We then keep track of which haplotypes occur in

which populations. According to our hypothesis, we should find more

haplotypes below the falls than above.

Microsatellites

The microsatellite PCR product contains millions of copies of the

repeating fragments that are tagged with a fluorescent dye. At Yale, our PCR

product is sent through a capillary genetic analyzer. This machine sucks up

the PCR product through miniscule tubes called capillaries. Similar to the

mechanisms of gel electrophoresis, the small pieces travel faster while larger

pieces travel slower through the capillaries. Light shines on the product as it

travels through the capillaries. So, when the light hits the fluorescently tagged

fragment, a specified color of light is reflected back. This reflectance is

measured and compared to a standard sized ladder to determine the size of

the fragments in units of base pairs. These readings come back to us in the

form of a chromatogram (shown below).

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This chromatogram depicts the allele makeup of two individuals for the Ca3

locus. The top individual, #1233 is heterozygous with alleles at approximately

292 and 296 base pairs while the bottom individual #1234 is heterozygous

with alleles at 296 and 341 base pairs. The X axis represents the size of the

gene fragment (in units of base pairs) and the Y axis represents the intensity

of the fluorescent reflectance. The researcher then “calls” the colored peaks

by assigning them an official base pair size. This allows us to measure

heterozygosity. An individual is heterozygous for an allele when they inherit

two different alleles from each parent, and is homozygous when it inherits the

same allele from each parent. Heterozygosity is an indicator of diversity

because a population in which the majority of the fish have two alleles will

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have more alleles (more diversity) than a population in which the majority of

the fish have one allele. The logic is simple: greater heterozygosity = greater

diversity.

Chapter 2: Theoretical Context Prior to the advent of experimental music in the mid 20th century, the

divide between the sounds we traditionally considered to be “art” or “music”

and what we considered to be “noise” was often attributed to the divide

between humans and the surrounding environment. Traditionally, “music” has

been considered undeniably human in how it expresses our emotions and

represents our perspective. Even if natural elements were depicted, they

were anthropomorphized and represented through the human lens. For

example, the Impressionists would evoke the human emotional experience of

natural scenes like a mountainside or a summer garden instead of presenting

a literal sonic representation. However, as recording technologies became

more advanced and available for personal use, the line dividing “music” and

“sound” began to blur. Although people began to produce records of bird

songs, or of relaxing ocean soundscapes, these “natural” sounds were

inherently unnatural in how they were extracted from their environment and

tailored for human consumption. It wasn’t until John Cage revolutionized how

we thought about silence or lack thereof that the idea of any and all sounds

could be considered musical became accepted. Cage stated “Instead of

continuing, as in the past, to separate ourselves from one another, to be

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proud of pretty emotions and our opinions, we have to open ourselves up to

others and to the world in which we find ourselves”ii Cage expresses concern

about this separation in a 1970 interview: “the aspect of nature which we have

no notion today- and this notion is almost distressing-is that we, as a human

species, have placed nature in danger… So, our concern today must be to

reintegrate it into that which it is. And nature is not a separation of water and

air, of sky and of earth, etc…, but teamwork, or teamplay of these elements.”iii

Cage, by employing chance and indeterminacy, and allowing for

acknowledgment of unwanted or unintentional sounds, advocated for the

abolition of the divide between humans and nature. His iconic piece, 4’33”, is

an exercise in bringing human attention to the ambient sounds that are

normally filtered out of our perception. By surrendering to unintentional

sounds, humans relinquish creative control. So, instead of acting as creators

of an anthropocentric “art” that is narrow in scope, humans can act as an

audience and appreciate the sounds that we do not create. This appreciation

could grow into inspiration that would lead artists to accept and interact with

nature in the creation of their works. In referring to his use of the I Ching in

the compositional process, Cage says he was “imitating nature in its manner

of operation” (1993). Cage encouraged the celebration of the indeterminate

nature of the infiltration of environmental or unwanted sounds into the human

realm of perception.

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Another major advocate for the appreciation of noise is Pauline

Oliveros. She developed the concept of “sonic awareness” in her Sonic

Meditations. With the meditations, her goal was to expand the human

consciousness by encouraging attention to all sound. In her essay “Software

for People” in which she describes how technology has affected the music

world and her own perception, she states “If nothing else, music in any of its

multitudinous manifestations is a sign of life. Sound is intelligence.”iv This idea

reiterates that humans are not the most important beings and that we are not

separate from or better than another life forms that produce sound. Following

this logic, Cage’s concept of humans existing within an ecology can be

applied to our relationship with music: we are not separate from music. It can

be found within us in the form of DNA and proteins.

In recent years, as genome sequencing technologies have become

more widely available, there have been efforts to communicate data in

nontraditional ways. Prior to the accessibility of such technologies, there was

much theoretical discussion about the parallels between the nature of

genetics and music. In his 1979 book Gödel, Escher, Bach: An Eternal

Golden Braid, Douglas Hofstadter examined the relationship between the

Central Dogma and musical composition. The Central Dogma of molecular

biology, first explained by Francis Crick in 1956, describes the flow of

information from DNA à RNA à protein. The genotype; the genetic

expression of a trait, codes for the proteins that express the phenotype; the

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displayed physical characteristic or trait such as eye color or the production of

insulin. Hofstadter likens the translation of mRNA to protein to the translation

of sound waves to the organization of magnetized particles on tape: “Imagine

the mRNA to be like a long piece of magnetic recording tape, and the

ribosome to be like a tape recorder. As the tape passes through the playing

head of the recorder, it is "read" and converted into music, or other sounds.”v

In this analogy, the resulting sounds or notes, converted by the ribosomes,

are amino acids, the building blocks of proteins. This comparison drawn

between the central dogma and musical composition can be pushed further

by equating amino acids to chords. Much like how chords in Western tonal

music have unique functions and can build emotive progressions and

cadences, amino acids have unique physical and chemical properties that,

depending on how they are strung together, dictate the form and function of

the protein. Further, there are tried-and-true motifs in amino acid sequences,

similar to how certain chord progressions and motifs exist across several

genres of music. The concept of the importance of the stringing together

meaningful chunks to create a clear composite piece is essential to both

music and the central dogma. Hofstadter states:

“Music is not a mere linear sequence of notes. Our minds perceive

pieces of music on a level far higher than that. We chunk notes into

phrases, phrases into melodies, melodies into movements, and

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movements into full pieces… Proteins only make sense when they act

as chunked units” (525).vi

As technologies have continued to develop in the realms of music and

genetics, so have theories regarding the connections between the two.

Chapter 2: Creative Context: DNA and Protein Music

More concrete experiments and compositions have been performed to

realize these theoretical ruminations on the similarities between musical

composition and genetics. In 1986 Susumi Ohno and Midori Ohnovii published

a paper in which they draw informed comparisons between the two fields.

Specifically, they claim that oligomers, coding fragments of DNA, represent a

main melody or theme. To prove their theory, they went as far as to transcribe

the last exon of the largest subunit of mouse RNA polymerase II and compare

it to Chopin’s Nocturne Opus 55 no. 1. Their transcription was so similar to

the Nocturne that, when played for a test audience on the piano, they

identified the transcribed exon as the Nocturne.

They continue the exploration of the metaphor by examining it on a

meta-level, comparing the biological evolution to evolution of music

throughout history. Genetic material is highly conserved, meaning it is passed

on generation to generation for eons without much change. However, when

change occurs, it is usually very subtle and often not very influential. But,

sometimes a more dramatic change occurs that can lead to speciation, much

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like how changes in the world, like the invention of new technologies or

shifting social norms can result in a new species or genre of music.

A pioneer in this exploration was French theoretical physicist Joel

Sternheimer. He patented the practice of “Protein Music,” which describes the

use of genetic sequences to create musical compositions. This process has

been adopted by countless scientists/artists to achieve various end goals.

Such goals include education, pleasing aesthetics, theoretical exploration, or,

in the case of Sternheimer, induction of growth and disease prevention in

tomatoes!

Sternheimer’s groundbreaking 2002 publication, “Method for the

Regulation of Protein Biosynthesis,”viii outlined his discovery that the quantum

frequencies emitted by proteins could be used to affect their biosynthesis. He

posited a scientific theory illustrating why and how the old wives’ tale that

singing or playing music to a plant can increase its rate of growth. According

to Sternheimer, “The observation of protein sequences confirms that all

proteins possess musical properties in the sequence of their amino acids and

these properties are all the more developed that those proteins are, in a

general way, more epigenetically sensitive.“ix If each amino acid is

represented by a note, then each protein is a string of notes that makes a

melody. Sternheimer’s invention uses this concept by exposing the plant to

the protein melodies associated with elongation in the hopes of increasing

that protein’s rate of synthesis. So for example, the melody of cytochrome c, a

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protein essential for the energy production of the electron transport chain,

would be played back to the plant to induce its production, which would, in

theory, increase the plants energy production and growth.

Sternheimer (2002)

While Sternheimer’s compositions are practical, other

composers/geneticists use genetic sequences and proteins as the materials

to create more traditionally aesthetically pleasing pieces of music. Peter Gena

and Charles Stromx are two such composers who used the genetic

sequences of viruses and the physical properties of amino acids as

parameters for MIDI note events. Specifically, they created an algorithm to

assign a musical event to each codon, a three base-pair code corresponding

to an amino acid. The algorithm uses the amino acid’s classification to

determine the timbre, dissociation constant to determine the pitch, atomic

weight to determine the duration, and hydrogen bonding tendencies to

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determine the intensity of the MIDI note event. They created a MAX object

that ran this algorithm on a genetic sequence. The resulting sequence of

tones is pleasant to the ear and fills a niche of scientifically informed music

that is aesthetically pleasing.

Rie Takahashi and Jeffrey H. Millerxi also sought to create an

aesthetically pleasing piece informed by genetics, but with the added goal of

making the scientific concepts more accessible to the general public, children,

and the visually impaired. To accomplish this, they translated codons of

human thymidylate synthase A protein to piano notes. They were frustrated

by the limitations of previously used methods. Such limitations include: small

range of pitches, only one note at a time could sound, and a lack of continuity

in a melodic line. To avoid these limitations, they assigned a triad to each

amino acid. A triad is appropriate for representing an amino acid because

triads are made up of three notes and amino acids are made up of three

nucleotides. Much like Gena and Strom, Takahashi and Miller used the

physical properties of the amino acids to determine characteristics of the

chord. In order to preserve musicality and to avoid dramatic leaps in the chord

progression, they paired characteristically similar amino acids and assigned

them to the same chord but altered the order of pitches. For example,

tyrosine and phenylalanine, which are characteristically similar, were

assigned to G major, but tyrosine was assigned to the root position and

phenylalanine to the first inversion. This allows for some interesting motion

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and variation without compromising the sense of continuity. They determined

the rhythm by assigning one of for note durations, eighth, quarter, half, or

whole note, to each codon based on its abundance. The more abundant the

codon in the sequence, the longer the duration. What results is the creation of

a tonicization of the most abundance amino acid.

Chapter 5: ND2

As outlined in the previous chapter, there is a wealth of DNA and

protein music. However, the majority of it focuses on protein synthesis and

the functional characteristics of the DNA. The same holds true in the research

world. While the majority of microbiology, medical research, and genetics labs

are interested in determining what the genes actually code for, our lab is only

interested in how these genes are inherited.

The second piece on the program, ND2, is a MAX patch that I wrote to

translate the nucleotides in the ND2 sequences of each of the 13 haplotypes

into note events. I drew a direct comparison between the genetic data and

musical composition by translating the nucleotides A, C, and G to the note

values of A4 (440 Hz), G4 (392 Hz), and C4 (261.63). Because there is no “T”

note, I assigned T a pitch of 0, which resulted in a percussive attack.

The patch also uses Boolean logic and mathematical operations to

compare the thirteen haplotypes to the consensus sequence and bang a

button when a SNP appears. To emphasize this revelation of a novel

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haplotype marked by the appearance of a SNP, triggered presets of

parameters controlling a phase modulator would cause a change in the timbre

and rhythm of the sounding nucleotide sequence. Shown below is a boiled-

down patch that is only comparing one haplotype sequence (green) to the

consensus sequence (orange.)

(see the appendix for subpatches)

Using a Korg NanoKONTROL2 MIDI interface, I was able to perform

the piece live, triggering the change in presets whenever I saw the SNP

buttons light up. By routing the buttons on the Korg NanoKONTROL2 to the

presets, I could have creative control, and select whichever preset I thought

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would sound nice in duration of time until the next SNP appears. During the

performance, the patch was displayed in presentation mode (shown below)

on a television monitor.

I decided to incorporate a visual element for two reasons: to orient the

audience, and to portray how we actually work with this data in the lab.

The flashing of the nucleotides allows the audience to associate the note

events with each letter. I found the hypnotic effect to be aesthetically pleasing

and appropriate in how it is reminiscent of rhythmic tedium of scanning

through these 1042 nucleotides.

In addition to the translation of nucleotides into pitches, each letter

triggered a sound file that contained a collection of partials that I isolated

using SPEAR from recordings of my two friends, Elliot and Gla, speaking the

letters. As the piece progressed, more partials would be added (from higher

down to lower frequencies), increasing the clarity of speech. I included this

speech element because it reflects how, when scanning the gene sequences,

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I would recite each letter in my head or even out loud. Also, the increasing

complexity of timbres and rhythms and the increasing clarity of the speech

reflect how our analyses get more complicated while the big picture becomes

more clear as new haplotypes arise.

Chapter 6: Over the Falls

The final piece on the program, Over the Falls, combines the

sonification of microsatellite data with field recordings from each of the seven

river sites (excluding CR-M). The piece is designed to be a sound map of our

sites within the Connecticut River Valley. This idea of creating a sound map

was inspired by Annea Lockwood’s 1982 piece, “A Sound Map of the Hudson

River.” Lockwood traced the Hudson River, capturing sound from twenty-six

locations from the Adirondacks all the way down to its outlet in the Atlantic.

Not only does she capture the natural environment in beautiful way, but it

highlights the human relationship to the river by including the sounds of

human activity and interviews with fishermen and boaters.

Another piece that provides a beautiful commentary on the human-

nature relationship through field recording is Hildegard Westerkamp’s 1989

piece “Kit’s Beach Soundwalk” As she moves around the beach in

Vancouver, she narrates what she sees and hears, and directs the attention

of the listener to different aspects of the recording.

What I love most about this piece is how Westerkamp reverses the

roles of humans and nature in terms of which is perceived to produce noise

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and which is perceived to produce music. In chapter 2, I commented on the

tendency to perceive music as human and noise as environmental. In this

piece, however, it is the man-made the low roar of the nearby city that takes

on the role of unwanted noise that interferes with the delicate, “tiny clicking”

sounds of the barnacles. Westerkemp acknowledges this in her narration:

“the city is roaring around these sounds, but it is not masking them…luckily

we have band pass filters and equalizers. We can go into the studio and get

rid of the city, pretend it’s not there, pretend we are somewhere far away.”

Although I did not manipulate them as Westerkamp did in “Kit’s Beach

Soundwalk,” I made the conscious decision to include and even highlight the

human-made sounds in the field recordings, such as the siren of a fire truck

near the CR-W site and the hum of I-91 traffic near the FB sites.

I made this decision to give equal attention to the river and human-

made sounds because I wanted to present an accurate portrayal of the

soundscapes. With the exceptions of Wab, which is embedded within

Wadsworth State Park, and CR-M, which runs through the back of a tree farm

on private property, each of the sites are located where the river runs

adjacent to or is bisected by a major road. As I mentioned before, these roads

are the main sources of the ecological threats posed to the delicate river

ecosystems. Salt and sand runoff disturbs the salinity and sediment

composition. The clearing of trees disrupts the leaf cover, altering light

exposure and reducing the abundance of the minnows’ natural bird predators.

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Everything in an ecosystem is interconnected. Humans are not exempt. So,

again, by including the human-made sounds, I wanted to reiterate that

humans have a huge impact on the natural environment even though they

often feel removed from it.

Continuing with the use of mapping as an art form, the works of visual

and sound artist R. Luke DuBois provided inspiration for this piece. DuBois’

piece “A More Perfect Union” is a large-scale paper map of the United States

on which city names are replaced by the word that is most used by online

dating service users in that city and nowhere else. The main inspiration I

derived from this piece was the impact of organizing location-specific data in

a way that mirrors those locations.

With this piece in mind, I mapped each of the seven river locations to

one of seven speakers in the World Music Hall. The speaker placement and

assignments were carefully planned to reflect the locations of the river sites in

relation to one another The stage plan for the performance is shown below.

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During the performance, the audience was encouraged to leave their seats on

the stairs and to mill about the space and listen from different locations.

In addition to the field recordings, emanating from each of the

speakers was the sonification of the microsatellite data. As explained in

Chapter 1, the microsatellite data is returned to us from Yale in the form of a

chromatogram from which we determine the size of the fragments. I

translated these fragment sizes, which range from 125-370 base pairs,

directly to Hz frequencies of sine waves. The MAX patch shown below

contains an array of each of the seven microsatellite loci for each of the seven

locations.

(see appendix for subpatches)

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This piece is the most indeterminate of the three in how the only parameters

over which I had control were the duration of time for each locus to sound,

and when to play the field recordings. This indeterminacy led to the

spontaneous generation of short melodies or striking rhythmic patterns.

Chapter 6: Poster Presentation

The first piece in my recital, titled Poster Presentation, is a collage of

edited video of seven Chernoff lab researchers giving their own rendition of a

presentation of a poster that was published for the Summer 2015 Joint

Meeting of Ichthyologists and Herpetologists in Reno, Nevada. The poster

outlines the Waterfall Dace Project and is titled “Over the Falls: The Effect of

Waterfalls on the Genetic Structure of the Eastern Blacknose Dace,

Rhinichthy atratulus, in Connecticut.

With this piece, I intended to view the refined final product of

publication/presentation of findings through the lens that we view the raw

genetic data. In this way, it is a commentary on the human/nature divide that

often occurs in scientific research. Science is humankind’s way of trying to

make sense of the world. But by taking on the role of observers, we think we

are removing ourselves from the study system. In the Chernoff lab, we are

only out in the field collecting samples and experiencing the environment for

four or five days a year. The rest of the 365 days are spent on the third floor

of the Exley science center, far-removed from the river sites. So, I wanted to

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reintegrate the human element of this research into the environment by

treating the human presenter as if they were the fish being studied.

At first, I had planned on having the piece be performed live as a sort

of dance choreography in which the presenters’ gestures would accentuate

the synchronicities in the presentation. However, none of the lab workers felt

comfortable participating in such a performance. After nobody stepped up to

the plate, I gave up hope and started to dream up a new piece that would

involve the recording of the sounds that the workers and equipment make

while performing the procedures. My Zoom H1 recorder had recently broken,

so I went to the music library to check one out. All of their Zoom H1s were

checked out, so they gave me the Zoom Q3HD video recorder. This was

when I decided to use video as the medium for my original idea, or rather, it

was decided for me.

R. Luke DuBois’ film piece, Acceptance, served as a model for my

piece. Acceptance displays Obama and Romney’s acceptance speeches

from the democratic and republican party conventions of 2012 next to each

other, using language recognition to highlight the similarities in their rhetoric

despite the fact that they belong to different parties. While DuBois’ videos are

subjected to continuously running algorithms that detect the language and

synchronize the speeches whenever possible, my video was carefully

composed, edited in partnership with Ethan Oberman ’16 using Adobe

Premiere.

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The video was processed in the same way that we process the DNA:

by splicing out the important parts and disregarding the “junk.” The important

parts from each presenter are then grouped together and compared to each

other. Each presenter’s frame was situated in the same location on the

screen (shown below).

I chose to place Barry in the center because, conceptually, he

represents a human consensus sequence. Because he is the lab head, we

are constantly checking in with him, reporting our results and asking

questions. Also, over the years Barry has served as a model and has

coached us on how to give these poster presentations, so our approaches are

loosely based off of his. While the concept of the consensus sequence is

derived from ND2 analysis, the concept of synchronizing the recitation of key

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phrases falls under the realm of Microsatellite analysis. Each individual fish

possesses the seven microsatellite loci, but what varies is where in the

sequence they appear and how long the fragments are. Each presenter

touches on the many key phrases, but what varies is when in the presentation

and for how long.

Synchronicities arose in the recitation of essential phrases, and the

reading of lines directly from the text. In the editing process, I intended to

highlight these synchronicities by isolating the key phrases and organizing

them in ways that reflected the meaning of the text. For example, when

Alexandra and I say the phrase “temporarily stun,” I froze Alexandra’s frame

for a second as if she were a fish that swam into the electric field. My main

motivation for including these motifs was educational. Some of these methods

and concepts are difficult to understand when only explained and not

demonstrated. Also, I made sure to keep a continuous flow of information by

stringing together the bursts of synchronistic events with longer didactic

monologues.

It was also very intentional to keep the attitude light and comical. My

main motivation for including the few gags, like the poster falling down and

the two men interrupting Kayla by walking across the frame, was to entertain

the audience and hold their attention. In addition, these unexpected mishaps

whimsically reflect the tendency for things to go wrong when conducting

research. Progress of our research is often hindered by malfunctioning

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equipment, unexplained contamination, or running out of a particular

chemical. No offense to the lab team, but the video would not have been an

accurate portrayal of the lab atmosphere if it was dry, professional, or smooth.

When filming each of the seven researchers: Abby Meyer ’16, Chloe

Nash ’16, Julio Angel ’16, Alexandra Fireman ’16, Kayla Anatone PhD, Barry

Chernoff, and myself, I gave them no instruction on what to say or how to

structure their presentations. However, since the outline of the poster follows

the scientific method: introduction/questions, hypotheses, methods, results,

and conclusions. The presentations are structured in the same way but with

slight variation. This concept: the maintenance of the same basic structure

with slight variation from individual to individual, is the main mechanism of

evolution.

Conclusion:

While I was very intentional in editing the video and designing the

patches, carefully planning each aspect of the pieces, I could not have

foreseen the most beautiful synchronicity underlying this whole endeavor.

After the performance, I realized that the most striking synchronicity linking

my scientific and musical experiences is how my three pieces perfectly mirror

our three hypotheses. Recall that only our first hypothesis holds true, while

the second two are contradicted by the data.

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Based on the feedback I received from audience members and on my

own feelings about the performance, it became clear to me that my

expectation for ND2 and Over the Falls to be clear and informative was not

met. In fact, the opposite occurred: the audience members seemed to

experience these pieces as entertaining artistic interpretations of the scientific

processes and not as a direct representation. The audience seemed to take

away much more information from Poster Presentation than they did from the

other two pieces. This outcome, although unintentional is not negative. On the

contrary, it further supports the idea that the unintentional -whether it be

unintentional sound in music, or unintentional results in science- is as equally

important as the intentional.

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Appendix: Over the Falls Locus/location subpatch for opening data text files

Sine tone audio patch

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ND2 Entire patch, not in presentation mode

Phase modulation subpatch

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Haplotype ND2 data reader subpatch

SNP audio subpatch

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Figures:

1.   “Over  the  Falls…”  Roman-­‐Johnston  et  al.  2015  

1.   Sternheimer  2002  

Citations:

i Girard and Angers 2006, Dimsoski et al. 2000, Sweeten ms.). ii Pimenta, Emanuel Dimas De Melo., Lucrezia De Domizio Durini, and Daniel Charles. John Cage: The Silence of Music. Cinisello Balsamo: Silvana, 2003. Print. iii Pimenta 2003 iv Oliveros, Pauline. Software for People: Collected Writings 1963-80. Baltimore, MD: Smith Publications, 1984. Print. v Hofstadter, Douglas R. Gödel, Escher, Bach: An Eternal Golden Braid. New York: Basic, 1979. Print. vi Hofstadter 1979 vii Ohno, S., and M. Ohno. "The All Pervasive Principle of Repetitious Recurrence Governs Not Only Coding Sequence Construction but Also Human Endeavor in Musical Composition." PubMed (1986). Web. viii Sternheimer, Joel. "Method for the Regulation of Protein Biosynthesis." USPTO (2002). Web. ix Sternheimer, 2002 x Gena, Peter, and Charles Strom. "Musical Synthesis of DNA Sequences." School of the Art Institute of Chicago (1995). Web. xi Takahashi, Rie, and Jeffrey H. Miller. "Conversion of Amino-acid Sequence in Proteins to Classical Music: Search for Auditory Patterns." Genome Biol Genome Biology 8.5 (2007): 405. Web.