One , Two Fish, , Youfish: Embracing Traditional in a Molecular World

By ASSA ETTS I E OFOF TECHNOLGT E Lindsay Kirlin Brownell JUN 3 0 2014 B.S. Biology B.A. English LIBRARIES Davidson College, 2010

SUBMITTED TO THE PROGRAM IN COMPARATIVE MEDIA STUDIES/WRITING IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF

MASTER OF SCIENCE IN SCIENCE WRITING AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY

SEPTEMBER 2014

D 2014 Lindsay Kirlin Brownell. All rights reserved.

The author hereby grants to MIT permission to reproduce and to distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created. Signature redacted Signature of Author: Program of Comparative Media Studies/Writing May 22, 2014 Signature redacted Certified by: Alan Lightman Professor of the Practice Thesis Advisor Signature redacted I Accepted by: _ Tom Levenson Professor of Science Writing Director, Graduate Program in Science Writing

1 One Fish, Two Fish, Lungfish, Youfish: Embracing Traditional Taxonomy in a Molecular World

By

Lindsay Kirlin Brownell

Submitted to the Program in Comparative Media Studies/Writing on May 22, 2014 in Partial Fulfillment of the Requirements for the Degree of Master of Science in Science Writing

ABSTRACT

In today's increasingly digitized, data-driven world, the "old ways" of doing things, especially science, are quickly abandoned in favor of newer, ostensibly better methods. One such discipline is the ancient study of taxonomy, the discovery and organization of life on Earth. New techniques like DNA sequencing are allowing taxonomists to gain insight into the tangled web of relationships between species (among the Acanthomorph fish, for example). But is the newest, shiniest toy always the best? Are we in danger of losing vital information about the world if we abandon the thousands of years of cumulative human knowledge to gather dust in basements? This thesis explores the current crossroads at which taxonomy finds itself, and offers a solution to preserve the past while diving headlong into the future.

Thesis supervisor: Alan Lightman Title: Professor of the Practice of the Humanities

2 began in Spanish, "The other day I sent of Harvard In the basement you a barrel; inside were fifteen and a University's Museum of Natural half yards of cloth for wrapping fish..." dead fish lie History, over one million It was signed "Your daughter, Amelia." gathering dust. Some are preserved in The other million fish around me were glass jars of formaldehyde or alcohol, immediately forgotten. Who was this others are dried and mummified, and a father was whose hands had so lovingly are stuffed and mounted like few wrapped his daughter's words around trophies. Among a jumble of several this fish, preserving a slice of history and ivory-colored skeletons is one particular his own life along with its bones? That specimen of blue , question would launch me on a months- coeruleus, that's older than the museum long quest deep into the heart of itself. It arrived at Harvard in 1869 from taxonomy - the science of organizing was filed Cuba wrapped in newspaper, life. a drawer and sat there unopened away in The man was Felipe Poey, for 144 years. I happened to be exploring Cuba's most celebrated naturalist and indulging my lifelong the collection, one of the most prolific zoologists of the with fish, when I found the fascination nineteenth century. Over the course of parrotfish still sealed in its paper cocoon. his long career he catalogued thousands Intrigued, and with the somewhat of species and supplied hundreds of bemused consent of the collection's samples to Louis Agassiz, who founded I carefully began to unwrap it. curator, Harvard's museum in 1859. He had turned The newspaper employed Poey as a kind of freelance tobacco-brown with time and crumbled naturalist to help achieve his grand in my fingers like dead leaves. Diario de ambition: to acquire a sample of every la Marina was printed across the top in on Earth and classify them bold, black letters, and below that "El according to their divinely prescribed peri6dico oficial del apostadero de la order. Poey certainly delivered; some of Habana" - "the official newspaper of the his shipments contained over fifty colony of Havana," Cuba. This issue was specimens of Cuban fish, and several dated Tuesday, the 31st of August 1869. species bear his name today. briefs on the front page The news While Poey and Agassiz kept up included a London Evening Post report a cordial, professional exchange that Spain had firmly refused the United chronicled by letters, meticulous receipts States' most recent propositions and species lists, the field of taxonomy regarding Cuba's independence. The around them was in an uproar. Darwin's fragment of another article detailed the On the Origin of Species had just been most recent military offenses against the published, adding more fuel the raging Spanish forces. All had clearly not been debate over how classifying and naming quiet on this fish's home front. creatures should be done. While Poey Along with the parrotfish's carried on as he always had, carefully skeleton, I discovered a packet of its cataloging the genus and species names scales, contained in what looked like a of his samples, those categories were folded letter. I opened that, too. being jostled around, the relationships Beautiful cursive writing stretched between them coming under scrutiny. across the crinkled, time-stained page, Despite his prominence at the time, Poey dated July 13th. "My dear father," it

3 flew under the radar of history because was devoted to uncovering what he he remained committed to the old ways, thought was the natural order of the never fully engaging with the world, and he wasn't the first. Scientists evolutionary theory that eventually today continue to tackle that age-old became the basis for the new taxonomy. pursuit, but the way they go about it is Today, taxonomy is embroiled in quite different from shipping fish in another debate. The standoff now is not barrels. between evolutionists and creationists, but between those who use DNA to classify organisms and those who stick Dr. Tom Near would fit right in at to the traditional method of using a startup or tech company like Google. physical traits. The straight, black lines Large, twin Mac computer monitors on between species that we see on his desk dominate his gleaming white evolutionary trees in textbooks seem to office at Yale University. Every minute promise that this, finally, is the truth or so a new word scrolls across the about how those species came to be and glowing blue screens with its definition are related. But taxonomists are far from below, exciting my inner trivia nerd: agreeing on what arrangement is actually Hydrophobia. Tumid. Apothegm. A long correct. Even the species that we thought table against one wall of the office is we'd known for generations are being covered in neatly arranged stacks of called up for questioning. clipped papers on top of manila folders. Most of us, like Poey, would be Near himself enters from his content to ignore the debate and continue department's lounge where he has just on with life as usual. After all, it's not set a pot of coffee brewing. With his often that someone comes up to us on square, dark-framed glasses, brush-cut the street and demands to know whether dark hair and beard flecked with gray, we think the blue parrotfish belongs in and purple checked Oxford shirt, he the family Scaridae or Labridae. But we matches the stereotype of "tech junkie." use taxonomy all the time, often without Near is one of the leading experts realizing it. We classify as tame in using computer-based methods to or wild; people as friends, family or analyze DNA sequences. The only thing acquaintances; clothes as formal or that gives away exactly what kind of casual. When our inherent taxonomic DNA he studies is a large drainage map system is turned on its head, the outcome of the United States often seems ridiculous, even if it's hanging on the wall, which shows how all of the country's scientifically true (like saying that major rivers flow into one another and are descended from dinosaurs). ultimately empty into the oceans. But But that's just what modern Near isn't interested in the rivers so taxonomy is doing. It's calling into much as what they contain: fish. question our innate organizational "The group of fish I work on is system that has evolved over the called darters. They're a really millennia, beginning with our ancestors' charismatic group of North American earliest attempts to understand the world . I'll show you a picture," around them and subsequently being he says excitedly, taking down a book woven throughout art, religion, from the packed floor-to-ceiling philosophy, literature and science. Poey bookcase. It's called The of

4 Tennessee, an immense, 600+ page themselves. It was a discipline he found hardcover tome that would put a serious "very reductive and just not my thing." dent in an undergraduate's bank account. Then during his sophomore year "There's about 250 species, he took a course that would change his they're found only in eastern North life: Microbial Systematics and America. They're beautiful," he says as Diversity. It was the late 1990s and he flips through the well-worn book. He DNA sequencing, the process of reading stops on a page showing drawings of the letters that make up the genetic code, small fish with rounded, feathery fins was just starting to become easier. Now and bright, jewel-like colors. He points that scientists could look at complete to one that has a horizontal line of black genes, they could compare those genetic blotches running the length its pale body sequences in different organisms and and swaths of bright red painted along determine how closely related the its belly and on its fins. It's called a samples were. "And I realized, 'Wow, cherry darter. "They do weird stuff, you can apply this to fish!' And maybe these guys. The males defend their nest one can make a living doing this," he territories under rocks, and they have says. knobs on their fins that look like eggs. Since then Near's work has been They're thought to mimic eggs to draw largely focused on the family trees of females in; the idea is 'Oh, he knows different groups of fish, mostly the what he's doing.' darters, and trying to figure out how "The red banded darter is one of their evolutionary pasts led to the current my favorites," he says, indicating landscape of species. When he got to another fish that sports pale green and Yale, he started to become interested in orange stripes with a streak of red at the what he calls the "big picture stuff." He base of the on its back. He wanted to make his work with darters talks about these fish with the passion of more broadly applicable and beneficial a true outdoorsman who has spent a to the wider scientific community. To do good deal of time with them, so, he decided to undertake an ambitious confounding my first impression of him project: figuring out the genetic family as a computer guy. The truth is, he's tree for a much, much larger kettle of both. fish - on the order of 10,000 species. Near, a native Chicagoan, grew up in Lake Michigan with his One of the best places to see father, and at a young age became some examples of those thousands of curious about the different non- is the Giant Ocean Tank, the crown fish that they sometimes reeled in on the jewel of Boston's New England ends of their poles. That interest in Aquarium. The Tank's 67 windows glow diversity led him to enroll in Northern in the center of the dim aquarium like Illinois University, thinking he wanted to Near's computer screens. But instead of be a microbiologist and study different words, creatures of all shapes and sizes kinds of bacteria. But the labs he worked drift across them, ranging from the in mostly focused on biochemistry, majestic to the beautiful to the bizarre. analyzing individual proteins and Huge manta rays flap slowly through the enzymes rather than the bacteria clear water at the top, above the 20-foot tower of multicolored coral that

5 descends to the bottom of the tank. A same time, and take on more forms than twelve-foot long, kelly green moray eel I could possibly imagine. It's no wonder slides past at regular intervals, mouth that Tom Near got hooked. gaping open. Schools of shimmering, The vast majority of these silvery permit fish the size of dinner "endless forms most beautiful and most plates dart by, competing for food with wonderful,"' to borrow an often-used massive tarpon - torpedo-shaped, phrase from Darwin, belong to a class of muscular fish with huge underbites. I fish called Acanthomorpha. Numbering giggle as a pufferfish motors slowly 14,000-16,000 species, they comprise through the water, its fins moving one-third of all living vertebrates on comically fast at the sides of its tilt- earth; there are more of this type of fish prone, boxy body. A flounder appears than all the and reptiles swimming sideways, its body flat as a combined. The largest order of fish pancake, both bulbous eyes perched on within Acanthomorpha is one called the top side of its head, its pectoral fin Perciformes, which contains Felipe sticking straight up like a flag. Poey's blue parrotfish and Tom Near's Arranged around the Giant darters and is the largest single order of Ocean Tank are other exhibits vertebrates in the world. representing different aquatic habitats Although it means "perch-like," and the species one is likely to find Perciformes has traditionally been a kind there. One tank hosts leafy sea dragons, of "waste bucket" category for the fish their sine-curve bodies covered in thin that don't quite fit into any other groups leaf-like projections that help them blend in the fish family tree; familiar ones like in with the aquatic plants behind them. A , barracudas and snappers, and flat- thick-lipped grouper drifts forward out out weird ones like seahorses, cusk-eels, of the darkness of another tank and lumpfish, and morwongs. This is the swims along the glass, the same size as snarl of relationships that has longest the toddlers who stare at it in wonder. withstood detangling: the "bush at the The Pacific Reef Community tank top" of the evolutionary tree. Trying to houses a motley of nearly 70 different catalog and organize this hodgepodge of kinds of fish in endlessly varied colors finned creatures has plagued and shapes: long-snouted butterflyfish ichthyologists and taxonomists over the striped vivid black, white and yellow; centuries, and Tom Near is now three different kinds of angelfish; undertaking the daunting task of almond-shaped triggerfish with pointed resolving it once and for all. snouts; blue and yellow tangs and beaked parrotfish in fuchsia and azure - For most of history, fish were they all swirl around each other in a classified according to their physical glorious mess of hues and fins. traits; if it looked like a trout, swam like Their graceful, dizzying aquatic a trout, and gulped air like a trout, it was dance is hypnotic; I could park myself probably a trout. Scientists like Poey in front of one of the tank windows for painstakingly recorded even the most hours, just watching them wheel through minute variations in their specimens, the water. Compared to them I feel drab and gangly, which is also what draws me I John van Wyhe, editor. 2002. The Complete to them. They're alien and familiar at the Work of Charles Darwin Online (http://darwin- online.org.uk/).

6 sometimes down to the number of folds immediately get a sense of where it fits in their intestine, because differences in in the fish tree of life, says Near. those "characters" were used to draw the Once DNA is extracted from a line between species and group them tissue sample, molecular scientists into families. The ordering of life was isolate specific, well-known genes that and still is considered essential to are present across many species, such as understanding the world around us, tbrl, which is necessary for proper brain because it allows for quick identification development. After a gene has been of later specimens and helps scientists sequenced, scientists perform a understand how life on Earth developed. "sequence alignment," which is simply But what do you do when confronted looking at the different samples' genes with a leafy sea dragon, which almost and comparing the order of their looks more like a plant than an animal? molecules. If the two samples differ, it If you have a shiny silver fish, a mottled means there has been a mutation. DNA brown fish and a smooth, rainbow- mutations happen occasionally when colored fish that are all shaped like a cells make errors in copying their DNA trout, are they variations within one before they divide into new cells. The species of trout, or three different mistakes are usually automatically species? detected and fixed by the cell's own Many of those longstanding machinery, and never affect the questions are now being answered, organism. But sometimes they escape thanks to faster DNA sequencing and a the cell's notice and get passed down to resulting shift in the way taxonomy is later generations. done. Traditionally when scientists

discover a new species, they describe its ------4- morphology, or its collection of physical Am "k* traits, along with any behavior they've 4*4

who are experts on a given group of + - 4-

organisms will then evaluate the new Le"ar species and either confirm the new 21 W_ discovery or propose a different grouping if they feel it has been identified incorrectly, which takes time La" and a bit of politicking. Now, "more and Al more people are actually saying 'I'm C6 going to sequence a piece of DNA from Figure 1: By comparing the same genetic sequences this thing that looks like a catfish, and across different species, molecular taxonomists can compare it to these samples I've got for determine when mutations most likely occurred in the past, and by extension, when those species all these other catfishes,"' and diverged from each other.

7 Given enough time, mutations in certain inflate to several times their size by individuals can accumulate to the point filling their stomachs with water or air). where they cause physical changes that If these new families were to give rise to new traits and, eventually, hold reunions, I expect things would be a new species. little awkward. Just as a traditional taxonomist These and other results would use physical characters like the completely go against our previous number of spines or shape of the dorsal understanding of how fish are related. fin to classify fish, molecular Saying that an anglerfish and a taxonomists examine genetic characters pufferfish are close relatives is like across species. By looking at how much saying that opossums are more closely two species' genes differ from the genes related to primates than they are to other of their most recent common ancestor, marsupials. That sounds absurd, because it's possible to tell how closely they're it's clear from just looking at an related; the more genetic disparity, the opossum and a gorilla that they're very longer ago a given species probably different. Opossums have pouches and separated from the ancestor and thus the long tails, pointy snouts and big ears, less closely related it is to the other while gorillas lack all of those things. species. Yet this is the scale of disruption that Near and his team performed genetics is causing in fish. Anglerfish sequence alignments for ten genes across and pufferfish look almost nothing alike 579 different species of Acanthomorph and yet their genes say they are indeed fish, mostly within Perciformes, and kissing cousins. then used computer models to arrange all There may be a method to all this of the resulting families based on genetic taxonomic madness. Anglerfish, relationships. Some of the results were a pufferfish and are all certainly bit surprising. The genes tell us, for strange in their own, very distinctive example, that flatfish are closely related ways. "But isn't it kind of odd that those to . That means that a flounder are the ones that are involved with the (that odd, sideways-swimming fish from most dramatic taxonomic rebooting?" the New England Aquarium with both asks Near excitedly. The very fact that eyes on one side of its head) is these strange-looking fish turn out to be essentially first cousin to a swordfish (an close relatives might be telling us impressive sport fish renowned something about how extreme physical worldwide for its grace and power). And forms evolve. It may be that there was both of them are genetic second cousins some tweak in those fishes' common to the swamp eel, a long, brown, ancestor long ago that enabled it to snakelike fish that slithers through change its body shape more dramatically shallow freshwater habitats and has over the generations, giving rise to such rudimentary lungs that allow it to diverse descendents. That would mean breathe air. Another unlikely grouping that the common sense of "similar- puts anglerfish (scary-looking, deep-sea looking things are more closely related" fish with long teeth and a glowing lure might not always be true. Near thinks dangling from the tops of their heads) this is one of the most important insights into the same family as pufferfish (those from his work. "We're going to have a cube-shaped, poisonous fish which can new revolution in how people interpret

8 phenotype," the collection of an Native American bust stares at me organism's physical traits, he says. grimly from atop his Lexmark printer. More than any other animal, fish Four bookshelves are packed with have the greatest disparity between the colorful series of books that look like old old groupings based on physical traits encyclopedias: Oceanic , and the new ones that genetics is dated 1895; Resultats Campagnes revealing. Rather than being concerned Scientifiques, published in 1920. A by the mismatch, Near is excited by the stuffed armadillo perches on the enormous possibility that molecular windowsill. Old advertising signs of taxonomy has to resolve longstanding painted wood and hammered tin cover problems that have resisted traditional almost all the available wall space, methods for centuries. "That's really promoting things like Black Bass Plug interesting and super neat," he says, the chewing tobacco, a cure for typhus and a coffee he made earlier completely garage for rent. A silver boom box softly forgotten. plays 1940s music. It seems like knowing an Now in his mid-60s, Johnson has organism is no longer necessary to been at the Smithsonian for over 30 classify it - all you need is a chunk of its years. His grizzled gray hair and beard DNA. All this focus on genes and are streaked with white and his booming, computer sequencing makes me wonder gravelly voice still retains some of its what will happen to large collections of native Texas twang. Wearing a white specimens like the one sitting in and red checkered shirt and jeans, he Harvard's basement. Will they even looks like he could be sitting a eventually be closed and shuttered Lone Star saloon; all he needs is a forever, a mass tomb that would cowboy hat and some spurs. gradually be forgotten? Will their "I'm that asshole at the fish contents, along with hidden treasures market busting people who are trying to like Felipe Poey's letter from his sell Rhomboplites as red snapper," he daughter, be thrown out and erased from says, giving a characteristically history? To answer those questions, Near enthusiastic guffaw. directs me to "somebody who thinks all If anyone has spent a majority of this [molecular stuff] is going the wrong their life thinking about and looking at way:" G. David Johnson, curator of the fish, it's Johnson. He entered graduate fish collection at the Smithsonian school at the Scripps Institution of Institution. Within a month I find myself Oceanography in 1970 with "this in his office in Washington, D.C. which romantic notion that I wanted to work on is, appropriately, in the basement of the whales and porpoises." That goal National Museum of Natural History. abruptly changed when he and a group of other students decided to dig up a whale carcass from beneath the sand near San Diego. One of his professors the U.S. Navy to help If Tom Near's office is a had convinced bury the beast ten years earlier so that its minimalist, 21st-century workspace skeleton would be preserved while the centered around technology, Johnson's flesh was stripped away by microbes. looks like it was incongruously plucked Johnson shows me a picture of himself from an antiques store. A carved wooden

9 holding the whale's tongue, the only soft (the National Park Service's natural tissue that was left. The stench of history collections were transferred to decomposing whale was so the Smithsonian for curation in 2012), overpowering, says Johnson, "I still but others are simply left to languish. can't get it out of my mind to this day." The main problem is money; there That same year he took his first class in simply isn't investment in morphological fish diversity, and decided to be an taxonomy anymore. These days, it's all ichthyologist. His research has mostly about molecules and DNA. focused on identifying fish in their As we walk back to his office I juvenile, larval stage and he's discovered remark on a low, rumbling sound that his fair share of new species. He's a permeates the hallway. Johnson wryly morphologist through and through - tells me that it's the ventilation system molecular taxonomy didn't exist when "for the chemicals or whatever it is he started classifying fish. they've got up there" in the molecular The first thing Johnson does is biology labs upstairs, which took the take me down the hall to meet some of place of the Museum's fish collection his colleagues at the Department of (it's now at an offsite location about 30 Fishes' "Friday Fish Coffee Hour." minutes away). Part of the reason We're greeted in the lunch room by genetics is so appealing is, ironically, its seven scientists sitting around a large cost. If a molecular scientist is awarded a table drinking coffee out of paper cups grant that includes a $10,000 piece of and nibbling on prepackaged cookies machinery needed to sequence DNA, from colorful, fish-shaped plates. The then their lab can say that it brought in a meeting mostly consists of the heckling larger amount of money and is therefore and joking typical of groups of people more valuable to their institution or who have known each other for a long school. The Smithsonian is currently time. Many of them have; all but two of submitting grants totaling about $100 them are certainly over 60 years old, and million to do molecular "next gen" several have been in the department as research, while having reduced its staff long as Johnson has. They could have of curators from 135 to 85 over the last easily collected their Social Security few decades. Morphologists can write years ago, but all of them truly love their grants for funding too, but their required work and simply can't stay away. One of materials are much more basic: usually a the most senior, Vic Springer, proudly salary for a graduate student assistant or proclaims himself a "ROMEO" (Retired two and some collecting supplies. A Old Man Eating Out), but keeps active in single genetics machine can sometimes the department "because it's fun." cost more than a multi-year morphology This is the morphology world project. these days - a passionate but aging The result of this shift in population whose ranks aren't being investment is that fewer students are replenished with young scientists. interested in studying morphology, Museum curators' jobs are being which exacerbates the problem. eliminated after they retire, leaving "Students do not get deeply trained in collections without any caretakers. the morphology like they used to. It's Smaller museums sometimes sell or hard to sell yourself as a pure jettison their collections to larger ones morphologist. And the danger in that is

10 that you have fewer people who are Morphology itself is a fascinating giving the courses that relate to it and subject with seemingly endless give them the expertise," Johnson says. questions: Why do male seahorses That expertise represents the incubate their mates' eggs and hatch culmination of hundreds of years of their young? Why are tube-eyes' eyes human inquiry into the nature of our shaped like tubes? How does one species world; our desire to order and classify of trout evolve three different-colored the things around us. Our whole varieties that are still trout? understanding of fish (and other "The molecular stuff is organisms) so far has been based on that inherently, completely uninteresting careful attention to detail and without the morphological stuff. What is cataloguing of subtle variations. our perspective on organisms, or Morphologists use a number of traits to biology, or whatever? It's classify fish: the shape of the tail fin, the morphological. You don't have any number of spines along its back, the questions to ask unless you know the shape of its scales, whether it has an morphology. And the more you know overbite or an underbite, etc. A yellow about the morphology, the more perch and a smallmouth bass are both interesting these questions about the yellowish, oval-shaped fish that have a discrepancies or the congruences dorsal fin that's split into two, but the become," Johnson says. bass' fin has shorter spines on the front In the famously nebulous world half and the perch has distinctive black of fish relationships, those discrepancies bands on its body, which help tell the can be huge. Take, for example, Near's species apart. research and the new fish family

foik length (from wntiornost point of head) standard length (from tip of snout heed length fin spnm wfrt dorsal fin

sno nape

wcAle count below 1.1 premaxilla

length Caudid priopercle befl nafin poejduce

pet ra fin subopmer

Figure 2: Some of the common characters morphologists use to identify fish species.

11 relationships it's suggesting. "That's just in the same family. But just in case, he absolute bullshit," says Bruce Collette, went back over the morphological one of Johnson's more brusque information in greater detail. He colleagues at the Smithsonian. "They're discovered that the three samples in setting up a hypothesis based on genetics question actually were all whalefish; that is so dissimilar that we can't they were examples of the male, female, disprove it morphologically, because and larva, respectively. The three forms there are no common characters. I don't are so dramatically different that believe any of that. The only way you Johnson believes the whalefish are the can make seahorses the sister group of most extreme example of physical tunas is if you believe in creation science variation from juvenile to adulthood and and that God made them that way." between the sexes among all vertebrates. Johnson agrees, saying that many Such a scientific breakthrough would scientists write off morphological have been impossible without the input knowledge as an imperfect, outdated of both morphological and molecular interpretation of the world that needs to approaches. be shelved in favor of molecular data. Problems can arise, however, "People who don't know morphology when the results of both methods are propose groups and look for evidence to completely antithetical, because neither suggest those groups go together. And is completely infallible. If the same sometimes these people say 'We've got physical trait exists in two different the real answer, this is what God said, families, it's hard to tell without looking now it's up to the morphologists to find at DNA whether they inherited it from a the characters that support this.' I know common ancestor or developed it my animals well enough that there's independently. On the other hand, nothing to suggest that these fish are genetic analyses are only as good as the closely related." data they're using, and those data are Johnson and his colleagues aren't often incomplete given how new DNA just trouncing molecular data because studies are. There simply hasn't been it's the latest, new-fangled thing, enough time to sequence all of the genes however. They're fully aware and from all 10,000 Acanthomorph species, appreciative of the insights it can so molecular taxonomists rely on provide. In 2009, Johnson published a computer models to fill in the gaps and paper which determined that three fish predict results. that were assigned to three different Tom Near's lab is unique in that families actually all belonged in the they sequence all of the samples they use whalefish family. His collaborator rather than using others' data, and their Masaki Miya at Chiba University in sequences are 85% complete, which is Japan sequenced DNA from a whalefish nearly double the field's standards. That and from the three other specimens, and means that other scientists are making found the DNA from the fishes' claims about molecular taxonomy mitochondria to be nearly identical. despite significant knowledge gaps, Johnson originally thought Miya's data which is Johnson's primary complaint. were completely wrong, because it had It's often hard to know whether radical been accepted for years that those three genetic results indicate a previously fish were physically too different to be hidden truth or an error caused by a lack

12 of good information. Traditional One of the advantages molecules taxonomy has had hundreds of years to have over eyes and hands is the speed at develop and self-correct, and generally which analyses can be done. With produces results that can be validated by today's increased competition for the collective community. funding, producing meaningful research Not all molecular scientists think quickly can make or break entire morphology is irrelevant. Tom Near disciplines. "There's a lot of chatter makes a point of connecting the about museums closing down and firing sequences of DNA on the computer their research staff, but if you look at screen with the finned creatures from those people who are getting laid off, it's which they came. "With my students I a lot of fairly low-productivity, esoteric really emphasize developing some field stuff like cataloguing ten new species of perspective. Even to those who are lab catfishes from South America," said eggheads, I say 'Look, you have to get to Near. "As much as it would be know your critters and have those wonderful for us to fund all of this work experiences, sociological as well as of all these specialists, it's an old model biological, of being out in the field."' that just isn't sustainable." As the new, That's morphology. molecular generation is shaking things Near acknowledged that the up, the perspectives and practices of molecular data aren't infallible, because traditional taxonomy, and those who the very nature of genetic analysis have devoted their lives to it, are being involves models and assumptions that challenged. are subject to change as information and methods improve. "I think the work Over the course of my visit with we've produced [on Acanthomorph Johnson and his colleagues at the families] shows that we have something. Smithsonian, I realize that they're not Now, is that the right tree? I don't know. just worried about their job security. I'll never know, because guess what? They truly feel a deep connection to the It's an inference," he said. No matter work they do, and they fear that the how complete DNA sequences studying abandonment of a morphological them is still an attempt to look deep into approach to ordering life is a serious the past by studying the present. There's detriment to humanity at large. no way to do an experiment to see when "The molecular people always a certain fish family broke off from the talk about how morphology is important, main trunk of the evolutionary tree. but they don't do anything about it," Morphologists face exactly the same says Johnson. Despite the insights that problem, they just look for answers morphological information continues to using evidence from physical traits provide, it's falling by the wayside in the rather than genetic ones. "We're very current scientific ecosystem. "Some analogous to historians who are diving people think this is outdated, arcane, sort through archives trying to find out what of like stamp collecting. You can't get a happened in the past," said Near, Nobel prize for taxonomy, and almost no whether those archives are genetic taxonomists ever get elected to the sequences or jars of fish soaking in National Academy of Sciences. It's the formaldehyde. low end of the totem pole," adds Bruce Collette. "It's discouraging to be in a

13 field that you see crumbling when you eight high on her desk are copies of The think it's valuable and can't persuade American Historical Review, not a people with money and power that it's scientific journal like Nature or Science. really a fundamental science." She's a professor of history; specifically, I start to wonder if there's the history of natural history, focusing something more to taxonomy than just on how humans and animals relate to rearranging the branches of the family each other. It just so happens that she's tree. Why do people feel so strongly also a leading authority on the history of about a discipline that seems rather taxonomy, having written the book The mundane compared to fields like Animal Estate on the topic in 1987, and biochemical engineering and computer several others since. science? Why are scientists still trying to Taxonomy, she says, arose from resolve the minute distinctions between one of the most fundamental aspects of thousands of fish species? Fortunately, being human: communication. "The the answers to those questions happened early taxonomy largely had to do with to be just down the street from my home retrieval - simply, we need the words so in Cambridge, Massachusetts. we know what we're talking about." Our ancient hunter-gatherer ancestors had to be able to identify plants as "poisonous" or "tasty," and decide what types of Dr. Harriet Ritvo is nursing a animals were prey as opposed to predators. The transition from a nomadic Venti Starbucks coffee in her office at lifestyle to agriculture around 11,000 the Massachusetts Institute of years ago caused a shift in how Technology. "They've been doing early humans understood the world around studies for years trying to prove that it's them. They now needed to know not bad for you, but there has been only what things were, but absolutely no conclusive evidence that how they were related to each other and their caffeine has any negative effects," she environment: what kinds of plants grew says, the laugh lines at the corners of her best together, which animals were eyes crinkling. Given the trend I've domesticable, noticed with taxonomists and their etc. As civilization advanced, humans coffee, and the extra strong mug of chai probed further into the mysteries of the tea I drank earlier to make it to our natural world through disciplines like morning interview, I'm somewhat astronomy, medicine, and philosophy, relieved. The sky outside is gray-white, which were often steeped in magic and matching her short hair, and snowflakes legend; the gods caused bad weather are just beginning to swirl down into the because they were displeased Charles River; a sign that winter has by us, and strange creatures like centaurs inhabited finally arrived in New England. distant, mythical lands. Around 600 Ritvo doesn't exactly look like BCE, ancient Greek and Roman your stereotypical MIT faculty member. philosophers began studying the forces Rather than a lab coat and latex gloves, of nature in earnest, some attempting to she's wearing a dark blue flannel shirt describe natural phenomena through over a black turtleneck, a delicate silver logic that wrote the gods and other chain link necklace and navy blue sneakers. The paperback books stacked

14 mystical forces out of the equation Explorers saw many new and wonderful altogether. things in their travels, but noticeably That scientific spirit was absent were unicorns, leviathans and the abandoned when the Roman Empire like. crumbled in the sixth century and At the same time, new species of Christianity became the primary Western plants and animals were being described worldview. Religious scholars thought at an alarmingly fast rate. Whereas a the creatures of the world were arranged medieval bestiary might describe in a divine scala naturae, or "great chain between 50 and 150 animals, expeditions of being;" a fixed, hierarchical order that were returning from afar loaded with formed a continuous linkage from the several times that number of exotic "lowest," inanimate objects up through samples. It became increasingly clear the plants, animals, man, angels and that a formal system of naming and finally to God at the apex. Attempts to classification was needed, now that the organize animals according to that order world was vastly larger and its were recorded in bestiaries, an early inhabitants more wondrous than form of encyclopedia that included all previously thought. Encyclopedias and the animals known to mankind, other reference books published in the accompanied by Christian moral seventeenth and eighteenth centuries teachings. Early bestiaries didn't organized plants and animals in various discriminate between real and mythical ways: by name, by geographical creatures. "You have one article about location, by usefulness to humans, etc. lions, and another about unicorns, and But none of those systems achieved what those entries were often based on similar scholars were really after: a complete authority - someone who wrote it down and easily referenced catalog of all the in the past," says Ritvo. Far from the species. rationalism of the ancients, the medieval That all changed with the arrival Christian worldview held that if humans of the superstar of taxonomy, eighteenth- could imagine creatures like unicorns, century Swedish botanist and medical surely the superior mind of God had doctor Carl Linnaeus. Far from the already thought of them and created plodding, systematic scientist, Linnaeus them somewhere on Earth. Not to seemed to revel in flying by the seat of include one of God's creations just his pants from one wealthy "sponsor" to because it hadn't yet been seen would be the next, shirking his academic duties disrespectful and perhaps even and relying on his charisma and blasphemous. impressive knowledge of plants to eke The Renaissance movement out a living. He published the first gained traction across Europe in the edition of his landmark Systema Naturae fourteenth century and brought about a in 1735, which catalogued 6,000 species renewed interest in observing nature of plants and 4,200 species of animals. empirically. As exploration and Rather than trying to evaluate and group colonialism opened new frontiers plants by using several different physical worldwide, the range for human features, which had caused widespread imagination became smaller and smaller, confusion among his predecessors and as there were fewer uncharted places for colleagues, he organized them according fantastical creatures to hide, says Ritvo. to their sexual structures alone. He also

15 grouped the animals into kingdoms developed. "The greater the number of based on clearly defined traits: fish live traits attributed to a given group of in the water, are covered with scales, animals, the more of those traits it was have gills and swim bladders. The result likely to share with similar groups, and was a consistent, straightforward system the more difficult it became to decide that allowed anyone, not just a trained which of them were truly significant for naturalist, to look at something and classification," says Ritvo. One of the identify its place in the order of life. most famous conundrums was the Unlike the natural philosophers platypus. Taxonomists simply had no who attempted to structure the world idea what to do with it. Did it belong according to what they perceived as with the mammals, because of its fur? Or God's natural order, Linnaeus' with the birds, because it had a bill and classification scheme was blatantly webbed feet and laid eggs? Which of artificial, because he determined what those traits were more important? features were important in evaluating a Just as the confusion and tension plant or an animal's identity. It earned were threatening to collapse the field him many scholarly enemies and back into pre-Linnaean turmoil, Charles initiated taxonomy's long history of Darwin came along and swept the heated internal debate. Johann Dillenius, quarreling taxonomists' feet right out a contemporary at Oxford University, from under them. His theory of referred to Linnaeus as "the man who evolution finally revealed the natural confounds all Botany." 2 Linnaeus seems order of species, but it was completely to have been immune to the criticism, different from what anyone had once saying famously, "God created, anticipated. Rather than a scala naturae, Linnaeus organized." It may not have the "natural" groupings of organisms been the scala naturae toward which that had been observed for centuries most naturalists still strove, but his turned out to be a reflection of system was the most practical and useful evolutionary history, as one species option to date. Linnaeus helped elevate morphed into another through the taxonomy to the level of a "true" generations. "There wasn't a time that science, one that was based on someone said 'I am a Homo sapiens and systematic logic and adhered to its my parents were something else,"' says principles. Ritvo. The species weren't fixed, they Naturalists in the later eighteenth were fluid; and not only that, the process and nineteenth centuries continued to of evolution was happening all the time. classify plants and animals according to As the very last line of Darwin's Origin Linnaean taxonomy. They believed in its so eloquently puts it, the species "have ability to accurately and been, and are being, evolved." 3 That idea comprehensively describe and order the was disturbing to many people, world; they just had to carry it to especially the taxonomists. Now they not completion by cataloguing all the only had to place organisms in the right species. But as time went on, a problem niche on the tree of life, they had to understand how they had evolved into 2 Knapp, Sandra. What's In a Name? A History of Taxonomy. http://www.nhm.ac.uk/nature- John van Wyhe, editor. 2002. The Complete online/science-of-natural-history/taxonomy- Work of Charles Darwin Online (http://darwin- systematics/history-taxonomy/index.html. online.org.uk/).

16 their present form from their ancestors. disciplines. One taxonomist might The collective goal of cataloging a finite separate groups of fish based on the list of unique species was not just number of dorsal spines, while another challenging, it seemed nearly might prefer to use the shape of its jaw. impossible. It seemed to be going the way of other And yet they doggedly kept at it. defunct disciplines like phrenology Zoologists like Felipe Poey continued to (measuring the lumps and bumps on identify new species and creationist someone's skull to determine their scientists like Louis Agassiz continued mental strengths) and iridology (looking to believe in a divine natural order. Over at the iris of the eye to evaluate the course of the early twentieth century someone's health). a new movement within the naturalist That was just the beginning. community arose, as technology Over the last 60 years a number of advanced and scientific standards revolutions have attempted to bring became stricter and more analytical. taxonomy up to speed with the rest of These scientists called themselves biology. First in the 1950s was biologists, because they were strictly numerical taxonomy, which assigned focused on the study of life, rather than numbers to organisms' physical traits the broad subject of the natural world and then used computers to calculate that was typical of naturalists up to that how similar any given samples were and point (in addition to being a zoologist, construct an evolutionary tree based on Agassiz was the first to scientifically those results. Taxonomists faced with propose the idea of an ice age). the possibility that their careful Biologists didn't simply observe observations and how well they "knew" life and draw conclusions from it, they their critters would be thrown out in poked, prodded it, and examined it under favor of stark, bare numbers. Then in the microscopes. They designed experiments 1960s came molecular taxonomy, in that could produce definite answers to which scientists didn't even need to questions that naturalists had only know what an animal looked like to speculated about. How do certain classify it; they simply sequenced a physical traits get passed from one piece of its DNA and compared the same generation to the next, for example? We pieces from different samples to can thank Gregor Mendel for the determine how related they were. countless hours he spent manually A third revolution arose at almost transferring pollen between pea plants in exactly the same time: cladistics. Taking the mid-i 800s, from which he concluded its name from the Greek word "klados," the theory of genetic inheritance. which means "branch," cladistics finally As the standards of scientific solved the age-old problem of which inquiry became stricter and more traits should be used to determine analytical, biologists saw the traditional relatedness: only the ones that were taxonomists as woefully behind the unique to the descendants of one times. Taxonomy's main stumbling particular ancestor. Organisms were block was that it still largely relied on sorted into groups called "clades" that individual scientists' opinions when consisted of one ancestor and all of its classifying species, and lacked the evolutionary offspring. More than any objective rigor of other scientific other method, cladistics caused radical

17 changes to the traditional taxonomic As a historian, Ritvo sees value groupings. in the morphological perspective One of the worst insults was the because it reflects humans' innate cladists' claim that the category of "fish" fascination with the natural world and as we know it - all the smooth, scaly our desire to define our place in it. While things that swim in water - doesn't exist. each iteration of new technologies and To be a valid clade, "fish" would have to methods has revealed insights that include all of the things that evolved traditional taxonomists hadn't observed from the very first fish, like amphibians, before, "it didn't obviate the connections birds, and even humans. By that logic, they had seen," she says emphatically. we are all technically highly evolved Molecular information doesn't lungfish. It may sound absurd, but necessarily make our knowledge of evidence from both morphology and morphology obsolete, just as learning genetics supports the cladistics that the baldness gene is on the X approach. A lungfish may look more like chromosome doesn't negate the ages-old a than a human at first glance, observation that it's passed from mother but because humans and lungfish share to son. characteristics that no other related fish But there's no denying that the have (like a windpipe, the ability to newest thing always overshadows the breathe air, and similarities in the way old. Ritvo says the majority of people in their hearts are formed) cladistics the academic community view declares that we are the lungfish's closer traditional taxonomy much like they kin. view new editions of existing books. Despite all of the upheavals that "They're necessary and it's good that have threatened its relevance, someone does them, but it's not the most morphologically-based taxonomy has exciting thing," she says. While it may persisted to this day (though largely benefit humanity to chase down, name relegated to museum basements). and correctly classify every last "Current scientists say 'everything is organism on the planet, there isn't a new and completely different' in significant community of amateur today's debate between molecular naturalists who find that effort relevant methods, says Ritvo, but it's actually and interesting anymore. "Most people very similar to what's happened before. couldn't care less about taxonomy," says "When anatomy became more Ritvo, spreading her hands in resigned sophisticated and physiology emerged in demonstration of an obvious truth. the 19th century, lots of things got It's true that spending research reshuffled, just like DNA analysis has dollars trying to untangle the produced new reshufflings. When you complicated "bush" of Acanthomorpha come right down to it, cladistics in seems a bit backward when there are so taxonomy resembles what it replaces in many other fields with more tangible many ways," she says. Traditional results, like cancer treatment and taxonomy has faced a series of alternative energy. But perhaps it only opponents over the centuries, and though seems less valuable because we've lost it appears to be on a losing streak, it's touch with our innate human connection not going down without a fight. to the natural world. As scientific pursuit has become more technical and esoteric,

18 the average person understands less and Through talking with these less of it. Far fewer people are likely to experts, I realized that we need to learn how to use a computer program embrace our inner lungfish. What I mean that analyzes DNA than how to identify by that is recognizing and promoting a smallmouth bass. both molecular and morphological But just because one way of taxonomy as valid and valuable. understanding the world is more Accepting the fact that we are indeed accurate doesn't mean it's the most descendants of lungfish would affirm the useful, as Linnaeus knew when he truths that science is revealing (as created his taxonomic system for plants. illogical as they may sometimes seem) Knowing that a flounder and a swordfish and also help reconnect us to other are closely related doesn't reveal the best creatures. The more we understand our way to fish for one vs. the other. The relationship to every other living thing, fact that one of our distant ancestor was the more we can learn about ourselves; a lungfish won't tell us how to identify past, present and future. one in the wild. That's information that Hard-nosed scientists might say only taxonomy rooted in the tradition of that such an approach is silly and observing live species can provide, and promotes a blind, willful belief in things that's what's at stake in today's that just aren't real. Even though scientific world. There must be some evolution and our own genes tell us that value in that knowledge; despite there is no overall divine plan, no hundreds of years of innovations that preordained order, no scala naturae, we have repeatedly threatened to make it still see the world as being governed by obsolete, we just can't seem to shake some kind of absolute truth, regardless morphological taxonomy. of its plausibility. Ritvo sees that kind of Much as a morphologist has a knee-jerk reaction as part of our deep sense of "knowing" their animals response to the increasingly secular and understanding them at a interpretation of the modern world, "or fundamental level, we as humans the disappearance of magic or something inherently "know" nature. Ask virtually like it." When confronted with the anyone to imagine a fish, and they will overwhelming evidence that there is no think of something scaly with fins of El Dorado, no Lady of the Lake, no some sort that lives in the water - method to the madness of living things, something that any other person would we cling to any last scrap of the also identify as "fish." Our common mysterious and wonderful that we so experiences with the natural world give strongly crave. In the case of taxonomy, us a common sense for it; very few we have a hard time letting go of things people would consider an antelope or that just seem right because they are their neighbor a fish, even though woven into the fabric of our cladistics has confirmed that both are interpretation of the world. A lungfish indeed fish in an evolutionary sense. looks like it should be more closely This brings up an interesting question: is related to the salmon than to us, even the way that we interpret the world though the opposite is true. We should through science more correct or real than acknowledge that our preferred and the way that we know it through our own personal classifications might not be senses, simply by being human?

19 entirely accurate, but we shouldn't Near acknowledged that there jettison them completely. has been resistance to molecular "It's pretty clear that evolution approaches, and he's trying to change did happen," says Ritvo, as the snow that. "An ambition I have in the next few starts to fall in thicker and thicker years is to sample all 18,000 species of clumps outside and I feel my chai buzz Acanthomorphs and figure out some starting to settle down. "There's no way of getting data for all of that and try scientific argument about it. And yet to make it work. I realized this is what many people don't feel that that's I'm really interested in doing for the something that should decide their own next 20 years of my life. And I can do it, attitude toward it." Science might claim meaning it hasn't been done yet." The to hold the keys to the empirical truth more genetic information his lab can about the world, but we as a species are analyze, the more they will be able to not quick to accept them. We are all refine their Acanthomorph tree of life. humans before we are scientists. Perhaps it will turn out that flounders Morphology celebrates our collective and swordfish aren't closely related after experience and understanding of the all, and the current results are a fluke world and the organisms with whom we based on incomplete data. Or maybe share it. To sever that link completely there are even stranger relationships would be a tragedy for our species; the hiding in the as-yet unsequenced DNA loss of a fundamental aspect of being of the spotted cowfish. Only time and human. many more studies will tell. Before I left, I asked Dr. Near whether he agreed with something that Bruce Collette from the Smithsonian had told me over the phone: "the field of taxonomy is being driven to extinction." Near leaned back in his chair and looked thoughtfully toward the small collection of plastic fish and dinosaurs on his side table. One of them was a , the oldest lineage of living fish in the world. After a minute he sat up straight. "I find Figure 3: Acanthomorph diversity. it troubling that we're losing this expertise," he said, "and we're losing it Some scientists, like Tom Near, in other taxonomic already advocate a hybrid approach to groups other than the study of life. We talked until I had vertebrates too, like diatoms and algae. That's why I'm of two minds seen the word Tumid flash across the about this. I feel that you want to computer screensaver more times than I say 'Come on, get with could count, and the world outside his it' to those [morphological] people, but on the other hand, window had gone dark. But Near was you have to still as alert as ever. From the way his respect the process for the way that that eyes lit up when he talked about his information is gathered and these discoveries darters, I could tell that he isn't, in Bruce are made." Collette's words, a biologist who "can't Near also thought that while the tell one fish from another." structure of the field might be changing,

20 the science of taxonomy itself isn't said. "Everyone wants to know what's going anywhere. "We really learn a lot around them." about how evolution works and what is And it's not just fish; name a possible, in even our part of the tree of type of animal, and you're bound to find life, by understanding the evolutionary organizations of enthusiasts, scientists history of fish," he said. Immunologists and amateurs alike, who simply can't get are interested in studying anglerfish enough of them. A quick Google search because the tiny male fish permanently yields the Coleopterists Society attaches to the female's body, becoming (beetles), the Global Penguin Society, a kind of parasite in order to mate with and the Queensland Society, to her. If we can learn what genes make the name a few. "If you take a random female's body accept the male rather sampling of humans and even sample than attacking him, we might be able to randomly among cultures, you're going "fix" those faulty genes in people who to have people that want to know all the have autoimmune disorders, in which different plants and animals. You just their bodies overreact to their own cells. do. And you see this over and over There could be thousands, if not again," said Near. To him, that's a hundreds of thousands of species that reflection of the "biophilia hypothesis" still haven't been described and sampled. of the great biologist E.O. Wilson: The more we learn about what's in our there's something inherent about being world, the better we can learn to manage an organism that makes you want to and preserve it. Taxonomy is not just know other organisms. Taxonomy is one done for taxonomy's sake. "It's the of humanity's earliest and most foundational step before you can do fundamental ways of obtaining that ecology, biology, environmental science, knowledge. or management of ," Bruce Collette had told me earlier. "Step one in doing anything is to identify what organism you have. If you can't tell one As the November snow lay thing from another, you can't do white and heavy on top of Cambridge, I anything else." Near agreed, saying it's found myself making the trip to Harvard ''really important to have an to once again look at Felipe Poey's fish understanding of the biodiversity of fish samples. Their immaculately clean in some kind of historical perspective," bones and neatly printed labels make it so we can create a picture not just of clear that for Poey, taxonomy wasn't just how our world's species look today, but a profession - it was his way of life. how they got there. Every morning he rose early and Near is starting to see inklings of trundled down to the fish market in our connection to our inner lungfish in Havana, where he would chat with the his own life. "When I teach the fishermen and pick through their catches ichthyology course here at Yale, it's to see if there were any new species he getting about fifty percent non-science could record and send to Agassiz. He majors now. There's just something was paid well and respected for doing about this one half of the vertebrate tree what he loved, by his fellow Cubans and of life that attracts people's interest," he the scientific community at large. That way of doing taxonomy for a living has

21 now all but disappeared, the last few devotees clinging like anemones to slippery sea rocks as the tide of progress ebbs farther and farther away. But as the waves move away from one shore, they wash up on another. Taxonomy is now entering a molecular phase that promises advances far beyond anything Poey and his contemporaries could have imagined. And just as all of the oceans are Figure 4: A visitor at the New England Aquarium. interconnected, so taxonomy unites different aspects of what it means to be human - our impressively scientific minds and our equally powerful imaginations. What would Poey have made of the argument between morphology and molecules? He probably would have observed it with mild interest, given a little shrug of his shoulders and gone back to wrapping up his latest specimen. Taxonomy may have moved far beyond anything he would recognize were he alive today, but for Poey, the preservation of his samples in Harvard's archives probably would have been all the recognition he needed. He was "simple, direct, unaffected, but possessed of a quiet dignity, [ ... ] certainly one of the most delightful men I have ever met," wrote David S. Jordan in his 1884 biographical sketch of Poey. "Of all men I have known, he has best learned the art of growing old." Hopefully we can learn to accept with equal grace our place in the great tree of life, both that which science tells us and that which we determine for ourselves. I prefer being a human most of the time, but occasionally it's kind of neat to be a lungfish.

22 Selected Bibliography

Anderson, John G. T. Deep Things out of Darkness: A History of Natural History. Berkeley: University of California Press, 2013. Aristotle. "The History of Animals." The Internet Classics Archive 2009. Accessed 13 Dec. 2013. Badke, David. The Medieval Bestiary 2010. Accessed 13 Dec. 2013. Beckhlfer-Fialho, Aura. "Medieval Bestiaries and the Birth of Zoology." The Antlion Pit 1996. Accessed 13 Dec. 2013. Darwin, Erasmus. The Temple of Nature Or, the Origin of Society, A Poem with Philosophical Notes. Baltimore, MD: John W. Butler, 1804. Goldsmith, Oliver. An History of the Earth, and Animated Nature. Vol. 3 and 4. London: 1791. 8 vols. Grout, James. "The Medieval Bestiary." EncyclopaediaRomana 1997. Accessed 13 Dec. 2013. Johnson, Kristin. OrderingLife: Karl Jordanand the NaturalistTradition. Baltimore, MD: Johns Hopkins University Press, 2012. Knapp, Sandra. "What's in a Name? A History of Taxonomy." Natural History Museum Website, London. Accessed 12 Dec. 2013. Lucretius. "On the Order of Things." The Internet Classics Archive 2009. Accessed 13 Dec. 2013. Manktelow, Mariette. "History of Taxonomy Syllabus." Accessed 2 Mar. 2014. Martyn, William Frederic. A Dictionary of Natural History; or Compleat UniversialDisplay of Animated Nature. Vol. 1. London: Harrison, 1785. Mayr, Ernst. The Growth of Biological Thought: Diversity, Evolution and Inheritance. Cambridge, MA: Harvard University Press, 1982. "National Park Service Natural History Collections Transferred to Care of the Smithsonian." Smithsonian Science 1 May 2012. Accessed 1 Mar. 2014. Pennant, Thomas. History of Quadrupeds. Vol. 1. London: B. White, 1781. 2 vols. Rennie, James. Alphabet of Zoology for the Use of Beginners. London: Orr and Smith, 1833. Ritvo, Harriet. The Platypus and the Mermaid. Harvard University Press, 1997. Ritvo, Harriet. The Animal Estate. Harvard University Press, 1987.

23 "The Aberdeen Bestiary." The Aberdeen Bestiary. Web. Accessed 13 Dec. 2013. Van Whye, John, Ed. "The Complete Works of Charles Darwin Online." Darwin Online 2002. Accessed 12 May 2014. Winspear, Alban D. Lucretius and Scientific Thought. Montreal, QC: Harvest House, 1963. Yoon, Carol Kaesuk. Naming Nature: The Clash Between Instinct and Science. New York: W.W. Norton & Company, 2009.

Images

Figure 1: Hoegg, Simone et al. "Comparative phylogenomic analyses of fish Hox gene clusters: lessons from the cichlid fish Astatotilapiaburtoni." BMC Genomics Issue 8:317 (2007). http://www.biomedcentral.com/1471-2164/8/317. Figure 2: Strauss, R.E. and C.E. Bond. 1990. Taxonomic methods: morphology In: Methods for Fish Biology (P. Moyle and C. Schreck, eds.), pp. 109-140. American Fisheries Society, Special Publication. http://www.faculty.biol.ttu.edu/strauss/pubs/Papers/l 990StraussBond.pdf Figure 3: Copyright 2014 Lindsay Kirlin Brownell. Figure 4: Copyright 2014 Lindsay Kirlin Brownell.

24 Acknowledgements

This work would not have been possible without those people who kindly gave me a significant amount of their time and words: Tom Near, Dave Johnson, Bruce Collette and the rest of the Ichthyology staff at the Smithsonian, and Harriet Ritvo.

I would also like to thank Karsten Hartell and Andrew Williston at the Harvard Museum of Comparative Zoology for allowing me to spend hours handling centuries-old fish and papers at will.

Special thanks to:

My thesis advisor, Alan Lightman, for the constant positive feedback, excellent advice for improvements, and flexibility with deadlines.

The GPSW Class of 2014, for all the support during our many hours of writing and editing in the Briney Puddle.

My roommate Julie Duke, for solidarity through all our adventures, especially all- nighters.

Shannon Larkin, for all the perfectly-timed encouraging words, caffeine and chocolate.

Jana and Steve Brownell, for always supporting my various attempts to discover what I want to do with my life.

25 About the Author

Lindsay Brownell grew up outside of Detroit and graduated from Davidson College in 2010 with dual degrees in English and Biology. After teaching English in Switzerland, working at Google for two years and traveling as much as possible, she remembered that science writing existed and decided to attend MIT for her master's degree. She will be spending the summer of 2014 as an intern at the European Molecular Biology Laboratory in Heidelberg, Germany, traveling some more and then coming back to Boston to see what life is like outside the Science Writers' Lounge in Building E14. Her favorite movie is The Lion King and she enjoys climbing trees and dancing.

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