Evolutionary Novelty: Optical Allusions

Below is a draft of a book review I am writing on Optical Allusions by Jay Hosler. Thanks to T. Ryan Gregory of Genomicron for asking me to do this, and thereby pointing this book out to me.

Optical Allusions, by Jay Hosler. Columbus, OH: Active Synapse, 2008. Pp 127. S/b $20.00.

The stereotypical scientist is focused: Intensely focused. Imagine an aging white man with wild, graying hair, and wide eyes behind thick, dark-rimmed glasses. He is so focused that nothing matters but science. A social life? Superfluous. Hobbies? Unnecessary. Fashion? “My neon pocket protector fits squarely in my lab coat”. Stereotypes often have some basis in reality, but they over-simplify, ignoring the complexities of life. True, scientists are usually focused and driven. But they are also people; usually well-rounded, intelligent people. My scientist-colleagues are musicians, athletes, artists, and naturalists. They travel, play video games, and care for children. Yet (probably owing at least in part to my own unconscious predilection to stereotype) I am often surprised and awed when I find examples of scientists who excel in an arena decidedly different from scientific pursuits. Surprise and awe was exactly my reaction when Optical Allusions by Jay Hosler showed up in my mailbox because the book displays not only Hosler’s talent for teaching science, but also for producing art.

My favorite thing about Optical Allusions is its originality. New things often come from the combination of established entities or traditions. Examples of this abound in eye evolution, a common topic on this blog. Even inventors have fused existing things into something new, such as the lottery ticket-scratcher that is a combination of coin and key chain (another hat tip for that example to Ryan Gregory). Even the word blog is provides a etymological version of fusion. The combination of comic book and educational scientific text, which Hosler has also used in two previous books, is the fantastically novel idea explored in Optical Allusions to convey information about evolution, eyes, and vision in the context of a fun and creative comic story. Having a comic story that introduces science concepts is a great advantage for visual learners (like me). Hosler has used his comic illustrations to great effect, producing several highly memorable images that convey scientific concepts.

Combining comics and science is not the only original feature. The comic story itself is wildly inventive. The story follows the main character, Wrinkles the Wonder Brain, who is a brain without a person – no stranger than all the people walking around without a brain, as Wrinkles points out. Oh, and by the way, that is not his bottom. It is his cerebellum, thank you very much. In Chapter 1, Wrinkles quickly encounters trouble when he accidentally drops a magic eye into a vat of distilled human imagination. Armed with a bagful of newt eyes that allow him to go where and when he wants, Wrinkles plunges (ploops) into the vat to try to retrieve the lost magic eye. This is no easy task. Human imagination is vast, as Hosler demonstrates with this book.

In Chapter 2, Wrinkles meets Charles Darwin on an island, sitting behind a stand that Charles obviously acquired from Lucy van Pelt of Peanuts fame (“the doctor is IN”). Darwin teaches Wrinkles how to make an eye using evolution. This takes 364,000 years (but only one comic page), with Wrinkles and Charles acting as predators on little brains that gradually evolve complex eyes to help evade predation. Charles Darwin yelling “tuck in kid”, before playing dominant predator on a gaggle of scurrying brains is one of the unforgettable images I mentioned. This is all fine and good for Wrinkles, but after all those millennia, he gets impatient. “When do the eyes become magical?” Wrinkles asks, anxious to find his lost magic eye. Darwin replies that magic only exists in books, and suggests that Wrinkles find the mythical Cyclops of Homer’s Odyssey. With a bite on one of the magic newt eyes, Wrinkles wishes to go to the Cyclops.

Charles Darwin and Wrinkles the Wonderbrain play a friendly game of "Dominant Predator" to illustrate how natural selection can gradually produce something even as complex as an eye. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

In Chapter 3 we discover there is one problem with Wrinkles’ wish: Cyclops is not only a mythical creature, but also a giant, killer eye-bot (spelled “C.Y.K.L.O.P.S.”) built by an evil villain named “The Perfectionist” as an exact robotic replica of a human eye. The superhero Cow-boy recruits Wrinkles and together they seek to destroy the killer eye-bot who is wreaking havoc on the town of Pasteurville. The Perfectionist has created a perfect replica of a human eye that even includes perfectly replicated imperfections. This leads to one of my favorite images of the book. Wrinkles and Cow-boy make their way to the retina, and Cow-boy teaches Wrinkles about the eye-bot’s perfectly copied blind spot. Cow-boy reaches down and yanks on a “cable” (a ganglion cell axon), uprooting a rod cell as if harvesting a carrot. “Why are rods buried beneath all those cables, shouldn’t they face the light?” asks Wrinkles. Cow-boy shows Wrinkles the blind spot, where all axons are bundled together to make the optic nerve, which plunges down through the retina, leaving no place for any rods or cones in that place. These images provide an immediate understanding of why we have a blind spot.

Wrinkles the Wonderbrain ponders the imperfections of the human eye with super hero Cow-Boy. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

Another of these replicated imperfections of real human eyes becomes the eye-bot’s Achilles heel. Cow-boy and Wrinkles find and block the Canal of Schlemm (which is labeled “Do Not Block”), producing a glaucoma that explodes the eye-bot. As Cow-boy hauls him away, The Perfectionist gets the last laugh by tricking Wrinkles into wishing he were tied up on a pirate ship. This wish comes true, and Wrinkles goes on to meet some pirates. But these are no ordinary pirates.

In Chapter 4, Wrinkles finds himself tied up on the deck of a pirate ship crewed by misfit stalk-eyed flies. After teaching the human captain and his wife that acquired traits (like lost limbs) are not passed to offspring, Wrinkles learns about the plight of the crew. Where they are from, there is strong discrimination – only the males with the longest eye stalks can mate. Long stalked flies are better at fighting, and the females also prefer longer stalks, which might be an indicator of better genes. The flies’ tale of heartache is a lesson for Wrinkles on sexual selection. But Wrinkles does not win any friends by bluntly distilling the flies’ story as a description of “a bunch of wimpy, unattractive guys with bad genes”. Those wimps also own a big cannon, which they use to shoot Wrinkles off the ship. A short time later, Wrinkles finds himself on another island.

This time, Wrinkles washes up on an island inhabited by Clio, the muse of history in Greek mythology. After another brief, but still striking visual, where Wrinkles demonstrates the function of his wrinkles by inflating, showing how they allow folding more brain into a small skull, Clio introduces Wrinkles to the Cyclops. This time, it is the Cyclops that Darwin suggested, Polyphemus. He goes by “Polly”. Although Polly lost his eye in a battle with Odysseus, he has the support of a bunch of cave animals that lost their eyes naturally, over evolutionary time. Wrinkles meets a blind cave fish, and after donning a pair of X-ray specs, he learns how cavefish lens cells die during development. In other vertebrates, the lens signals to the optic cup, and without those signals, cavefish eyes do not develop properly. Wrinkles learns that mutations occurred during the evolution of cavefish favored more taste receptors at the expense of eyes and this is probably the reason why cavefish lost their eyes during evolution. Clio asks Polly to take Wrinkles to the “cerebro-expand-o-matic” (the library), so Wrinkles can devise a plan to find the lost magic eye. During his five-year sabbatical, Wrinkles the brain creates a robotic body for himself. The mildly flirtatious Clio pinches Wrinkles’ back side (the rear of his new robo-bod, not his cerebellum), revealing a fatal flaw: the butt-activated ejector seat. Wrinkles is abruptly sent into orbit.

In Chapter 6, Wrinkles meets the sun while in orbit. We learn about different kinds of radiation that the sun produces. Wrinkles apparently learned something on his five-year sabbatical in Clio’s library, because he eloquently explains how three different kinds of cone cells work together to produce color vision in humans. Wrinkles begins to feel the effects of the thin air at the edge of the atmosphere, so he bites another wish-granting newt eye, asking to be back down on Earth. When he lands, he finds that one of the Men In Black is convinced Wrinkles is an alien.

In Chapter 7, we learn that the man in black (Igor) actually works for Dr. Kleeshay, who plans to use a protein named Larry to take over the world. Larry is a self-described “ginormous rhodopsin molecule engineered by Dr. Kleeshay”. Some people call Larry the - here I can almost hear a dissonant organ chord to heighten the suspense, just before the squiggly text that reads - “Were-protein”. Larry, like any rhodopsin, can change shape. Larry’s shape changes when the retinal that is part of him is struck by light and changes itself. Next is another of my favorite set of images, simple but effective. Hosler draws a pretty standard line-representation of the chemical chromophore retinal, and Wrinkles shines a flashlight on it. In the next panel, the retinal straightens out, with motion lines and a sound effect, “ding”. Later, when light shines on Larry (the rhodopsin were-protein), the retinal makes a “clink” sound, and Larry changes shape, howling at the moon.

Larry the Were-protein is a giant rhodopsin molecule, complete with light reactive chemical, retinal. When light hits retinal, "ding", it changes shape. Below, Larry in his trans state after being exposed to light. Dr. Kleeshay wants to exploit Larry's Jeckyll and Hyde tendency to control the minds of millions. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

It turns out that Dr. Kleeshay is raising mutant zombie G-proteins, to be activated by Larry. Since a single opsin activates many G-proteins, which eventually lead to a photoreceptor sending a signal to the brain, Kleeshay plans to use Larry to turn millions into mindless zombie slaves. Luckily, Wrinkles knows that phosphates will quench rhodopsin signaling. Wrinkles adds phosphates to Larry, which happen to look like breasts in Hosler’s drawings, leading Larry to change his name to Lariette. After saving Larry(ette), Wrinkles pops another newt eye and hastily wishes to be as far away from Dr. Kleeshay and Igor as possible.

In Chapter 8, Wrinkles finds himself frustrated and sitting beneath a large shady tree. Actually, he finds out it is the tree, an idealized construct of the imagination, a Platonic type. The tree has been Yggdrasil, has dropped an apple on Newton, has eaten Charlie Brown’s kites, and has shaded the Buddha. The tree is also phylogenetic trees, and it teaches Wrinkles how phylogenies are constructed, that they are no “lower animals” living today, only evolutionary survivors, and that lineages can converge separately on similar forms during evolution. The tree also teaches Wrinkles that there is a unity to all life. For example, Pax-6 genes are involved in the development of all animal eyes. Wrinkles sees this similarity for himself when various animals spit out a ticker tape with their Pax-6 gene printed on it. All this information frustrates Wrinkles even more. He just wants to find the magic eye. But the tree inspires Wrinkles to simplify. Wrinkles has the wish-granting newt eyes, he just has to wish to go where the magic eye is. This works, but Wrinkles is alarmed to find out where the magic eye actually is. I won’t reveal here the story of the last chapter, where Wrinkles finally finds the magic eye. I will only say that there is a (somewhat) happy ending. Wrinkles again encounters the flirtatious student of history from Chapter 5. She calls his “bottom” (cerebellum) adorable. Wrinkles is ecstatic, as anyone who is proud of their intelligence would be. After all, she likes Wrinkles for his brain.

The comic story is interleaved with text and figures describing in more detail the actual science behind Wrinkles’ adventures. These cover a lot of scientific ground in a short time, using an unconventional, somewhat snarky and irreverent writing style, that I think many will find entertaining, yet informative.

I have essentially no criticisms of Optical Allusions. There were a few very minor errors of interpretation. For example, in cavefish, we do not know what is the precise mutation that causes a change in gene expression level, or if multiple mutations are involved. Also, Pax is not “the gene” that co-ordinates all eye developmental genes. But these slight oversimplifications are inconsequential for the goals of this book. Optical Allusions seeks to present the wonders of science in a new way. In some ways, it is difficult to say who exactly the target audience is. But I expect any focused person, probably high school aged or older, with thick glasses, and a neon pocket protector in their lab coat, will have a great time reading Optical Allusions. Even though my area of specialty is eye evolution, I learned some new things from this book. I was especially inspired with new teaching ideas using the drawings. I highly recommend this book for its entertainment and educational value.

Evolutionary origin of a light sensitive nerve

The origin of a light sensitive nerve was almost certainly an early step in the evolution of animal eyes, and this was thought to have happened only once, some 600 million years ago. But new open access research on the nematode C. elegans indicates a heretofore unknown instance where a nerve evolved light sensitivity.

One of the common, but incorrect, claims of anti-evolutionists is that the origin of complex features like eyes cannot be explained by evolutionary biology. As an example (although perhaps not written by an anti-evolutionist) see the comment on this post. For some history and a response to the incorrect anti-evolutionists claim, see this post.

It turns out that, as is often the case, the difficulty in understanding comes from trying to make a continuum into a dichotomy. An eye or even the genetic machinery for light sensitivity doesn't have to be all there or all not there. Instead, these features can build up gradually, by classical Darwinian evolution.

An early step in the evolution of complex eyes was almost certainly the origin of a light sensitive nerve. Darwin imagined that nerves might easily become light sensitive, but because of a lack of understanding of the molecular basis of photoreception, not to mention the molecular mechanisms of heredity, he could not even fathom a guess as to how nerves came to see the light. But just because Darwin didn't know how the machinery of light sensitivity could be built gradually by evolution doesn't mean it couldn't occur gradually.

Light sensitivity is a multi-step genetic process, where one protein signals to another. But all those proteins were not "turned on" all at once to suddenly allow for light sensitivity. Instead, light sensitivity evolved from existing "senses". Many signals are detected outside of a cell and they trigger proteins to send a signal inside a cell. Even yeast use proteins to sense pheromones outside their single cell and direct growth toward a potential mating partner. Many of these signaling genes are shared across all of our senses, and we can pinpoint by comparative study when a signaling gene became a light sensitive protein called opsin (again see this).

This brings us to the worm research. C. elegans has no visible eyes and its genome lacks light sensitive opsin genes. Yet it does display sensitivity to UV light!

Here is a link to a video showing light sensitivity.

How does it do this without opsin? It turns out that a different protein has become light sensitive. In this case, homologous proteins are known to be taste receptors (Gustatory receptors) in insects. Therefore, at some point in evolutionary history, the worm protein
gained light sensitivity, independently of the opsin "light switch"!

This is really fantastic work that suggests many new lines of research. For example, the mechanism of photoreception is unknown for the worm gustatory/light receptor. If this could be understood, we could get a specific idea about how a protein gained light sensitivity during evolution. Second, it is not known when light sensitivity was gained, which would require comparative study. These genes are present in insects - are the insect genes light sensitive? It would be great fun to put an insect gene in a worm to see if it could rescue the loss of light sensitivity due to a mutation.

Finally, I'll point out that this work is similar to another study published just last month . That workfocused not on the receptor, but on genes later in the cascade; especially on the gene responsible for "firing" (ie changing the concentration of the ions in) the light sensitive nerve. It turns out that that the "firing" gene is homologous to the "firing" gene used in vertebrate rod and cone cells - another example of how evolution often uses similar tools to produce parallel results.

Pluralism- Optimal versus non-optimal

Once people get passed the tired, unimaginative, recycled, anti-evolution claims that creationists often make (snore), there are still some common obstacles to a deeper understanding of how evolution has produced the wondrous diversity of life that we see around us every day. Primary among these misunderstandings are the monistic view that evolution produces perfectly optimal phenotypes, and the related idea that natural selection is the only process that shapes evolution.



Of course this point is also a bit tired and unimaginative of me to point out, since Gould and Lewontin famously wrote on this subject almost 30 years ago. And even then, they were not even considered original by everyone, as they were accused by some of strawmandering, of erecting a simplistic caricature of peoples' views on evolution to be argued against. But never fear, I think I do have an original contribution to offer - I think I've stumbled upon a really nifty example to help understand a pluralistic view of optimal versus non-optimal evolution. Like Gould and Lewontin's famous spandrels (architectural objects that originate because of constraint instead of optimal functionality) I provide a non-biological example. I hope to try out this example on my students in next year's Macroevolution course.



The Panglossian barriers of Joshua Tree

Somehow these examples of the struggle between optimal and non-optimal come to me while traveling. My previous best personal example illustrates how people by nature tend to think adaptively. We tend to ask what something was made for - even though many things could simply arise as by-products, not as optimal "for" anything. I found myself falling into this Panglossian trap myself while driving in Joshua Tree National Monument. This is a place I've been to often, as it marks the half way point between my home in Santa Barbara, and relatives' home in Tucson. We usually arrive late in Joshua Tree, leaving SB after 6:00pm to avoid the traffic of the Inland Empire. When we arrive, Joshua Tree is dark, and the star gazing is amazing. Driving in, our mini-van headlights are no match for the vast darkness of the desert, and so the road becomes a singular focus. Some times of the year kangaroo rats dart just out of our path, but others the monotony of the dirt road induces a hypnotic trance. It was in one of these trances that I began to wonder the function of the ridges of dirt that edged the road. Along the edges of the dirt roads in Joshua Tree, sand lays in a neat pile, sloping from a maximum of foot or two in height gradually to the surface of the road. Except for the tan color, it was as if I had just followed a plow through a fresh coat of fallen snow.



[I'll paste a picture here when I find one].



Perhaps these ridges are an attempt to keep animals off the road, serving as a barrier between the raw wilderness and these capillaries of civilization that penetrate the desert. "Wait a minute, what am I thinking??", I thought, jarred from my trance (or was I?). Why to the road ridges have to be "for" anything? It makes so much more sense if these are simply by-products of making a road in the desert. My snow analogy is probably right on. Probably to make and up-keep the roads, plows simply carve a path through the desert, resulting in a pile of desert sand on either side as a by-product. These are not adaptive barriers, these are simply by-products of a need for efficient auto travel. Yet it was so natural for me to assume there is some function, and I so easily came up with an explanation, just so. I can see how one could see the natural world in a similar and Panglossian fashion.



What's even more wondrous is that similar by-products can be later elaborated, to give an even more distinct, yet ultimately false, impression of optimality. Growing up in Wisconsin, we had one glorious winter when the long driveway of our farm house was plowed by a neighbor (as opposed to shoveled, or cleared with a snow-blower). Just like the sand in Joshua Tree, the plow of my childhood left a by-product of a flat clear path, in the form of piles of snow flanking our driveway. Through the winter, these banks piled high, and they packed tight. My brother and I soon found an outstanding use for these by-products. We created the most fantastical snow fort Germantown Wisconsin has ever seen. We spent hours tunneling through the banks, building rooms where the snow piled wide. The plow packed the snow tight enough that we could build shelves and windows in the walls and sunroofs in the ceilings. So spectacular was our fortress, it was hard for our friends not to wonder whether the banks were plowed for the express purpose of creating our winter wonderland. But similar to Gould and Lewontin's elegantly painted spandrels in the chapel of San Marco, and just like the sand banks of the Joshua Tree desert, my childhood snow bank was simply a by-product of a need for efficient car travel, no matter how optimal our resulting snow fort turned out.



The Pluralistic spires and arches Utah

It's true that some structures sometimes arise as by-products. But what I find even more appealing is a pluralistic interplay between optimality and non-optimality. Natural selection may be an optimizing force, but it is not all powerful. There are constraints on the system. Driving through Utah this week, I saw a perfect illustration of this in the inspirationally beautiful wild lands of Utah.



Water, when pulled by gravity, will find an optimal path to the lowest point. And water, when it courses over rock, gradually wears that rock away, leaving a trace of its path. If all rock were created equal, canyons would be arrow straight, as water would continually trace a single optimal path to the oceans. But canyons are complex because all rock is not created equal. As a result, water faces constraints to optimality. When softer rock lies adjacent to harder rock, the softer breaks away more quickly, producing a circuitous path to the lowest point. The harder rock constrains and controls the outcome, in combination with the optimizing pull of gravity on water. The spires, arches and canyons are stunning examples of the intricate interplay between optimization and constraint. With constraints imposed by heterogeneous rock alone, the structures do not appear. Similarly with water acting optimally on homogeneous rock, the structures do not appear. It is only through the interaction that this beauty arises.

Bryce canyon photo by James Gordon, posted on flickr.

The geology is amazing in its own right, and I am sure I have not done it justice by my oversimplification (e.g. I've ignored wind and ice erosion). But my point here is to focus one how these pluralistic ways of thinking can inform us of how evolution proceeds. Nothing in nature works without constraint, without trade-off. Only by seeing natural selection as one player in a complex (though undeniably natural) interplay of various processes, do we gain a more nuanced and pluralistic understanding of how evolution has shaped our world.



[Caveat: These are purely non-biological examples, meant as analogies to prime one's pluralistic thinking. However, where the rubber hits the road for evolution is with biological examples, but that is beyond the scope of the current post.]

Ostra-blog 3 – How we discovered chupacabra

I’m having a lot of fun with these ostra-blogs, which I started on a whim to increase awareness of my study taxon, Ostracoda (here are links to the first two posts: 1, 2). There are so many ostracods and related stories I want to share, that I hardly know where to begin. I’ve also decided to restrict myself to one ostra-blog per week, so as not to interfere with my ever-so-important other activities, like reviewing papers and sitting in on meetings. Therefore, if there are roughly 30000 ostracod species (fossil plus living), I will finish telling you about all of them by about my 600^th birthday, unless of course new species are described by then. In any event, I have reached a decision on this week’s ostra-blog. Since new species have been the subject of some recent blogs, and since I just saw chupacabra on the internet news, today, I will tell you the story of how my lab discovered and described the ostracod species Euphilomedes chupacabra. (Here is a link to the paper).

On new species

First of all, a word or two about new species: As relayed by The Other 95%, there is little academic reward for describing a species this day in age. Today, scientists are judged by their citation rate, and to a lesser but often still significant extent, by the number of grant dollars they pull in. True, in some cases describing a new species - for example by naming it after, say, Neil Young or Steven Colbert - can bring media attention. But media attention does not translate to grant dollars, and probably doesn’t usually increase citation rate.

Still, there are a few intangible perks to describing a new species. One is a certain understandability that the general public has about new species. If I tell a new acquaintance at a cocktail party (which I attend at least 8 days a week… anyway you know the figure of speech) that “we discovered a new species”, he or she seems to think it is significant. In contrast, if I say, we found a new class of vision genes in jellyfish, their eyes glaze over. Or in response, they might ask something like, “oh wow, so will that help us cure blindness, or better yet vision cancer?”). Another perk is a certain “geek cred” among those who value natural history. After all, you must be a real expert to be able to find a new species right? As I’ll discuss later, a final perk is that you get to name it!

Despite these few advantages, finding new species of ostracods for us is a bit of a hassle, honestly. It means that we really should describe the species before analyzing it (but see above regarding citation rate and grant funds – also I don’t think geek cred increases linearly with the number of species described, I think it asymptotes at about 1.1). This “hassle” of finding new ostracods is a common occurrence. In many places, roughly half of the ostracods I’ve collected are unknown to science. These are not inaccessible places. These places are beaches in the Florida Keys, where tens of tourists snorkel every day, or piers in Japan where people fish, all the time. The coral patch reefs of Australia and Belize sound exotic, and they are fantastically beautiful, but I can get there from here in a day or so in air conditioned comfort while listening to science podcasts. My best case in point for how understudied ostracods are brings me (finally!) to the story of E. chupacabra. I found this species by dipping a bucket in the water on the pier of a marine lab!

The initial discovery

A few years ago, I was visiting the University of Puerto Rico-Mayaguez marine lab, which is in Magueyes, near the famous bioluminescence bay. I was visiting my friend, who is a professor there, and we were using their ship to collect some deep sea ostracods. Before that cruise, I decided to do a bit of collecting near the pier. The marine lab is on a tiny little island. It used to be a zoo, and there are large lizards all over the island, which I’m told are descended from those that escaped from the zoo. To get to the island, one must take a boat across a small channel; they have attendants there 24 hours a day!

I’d collected in the Caribbean before, and I expected to be able to collect Skogsbergia lerneri, a species I’ve collected in Florida and Belize (and a species sure to be on a future ostra-blog). Skogsbergia come to baited traps, so I deployed a trap off the pier of the marine lab. While waiting for the animals to come to the trap, I dipped my bucket in the water. To my great surprise, I saw an ostracod buzzing around in the water like Michael Phelps on steroids. Ostracods are quite small, but they have a pretty distinctive swimming behavior (myodocopids at least). Unlike other things of their size, like copepods, ostracods swim very smoothly. I sucked it up into a pipette, and brought it back into the lab. I couldn’t believe my eyes, I suspected immediately I had a Euphilomedes!!

I was so surprised for two reasons. First, Euphilomedes is one of my favorite genera (another certain ostra-blog candidate), because the males have large compound eyes and the females do not. My lab is interested in how this strange eye dimorphism occurs developmentally and genetically. Second, Euphilomedes had never been described from the Caribbean before, so I knew I almost certainly had a new species on my hands. It turns out that it was a species unknown to science, and I had discovered it literally by dipping my bucket in the water in a place where hundreds of marine biologists, and even ostracodologists had passed; a marine lab of a major university. Still, it would be a few years before we mounted the expedition to find more individuals of this new animal, and before we’d decide on its name.

Study and description

Fast forward a couple of years. I decided it would be a good idea to describe this species I had found back at Isla Magueyes. First, we had started studying eye development of Euphilomedes from California. California water is cold, and the animals do not develop very quickly. I suspect that the new species from the warm waters of Puerto Rico might develop faster, and therefore be better suited as a lab animal. Second, I thought it would be fun to go back to Puerto Rico, and to take a couple students along to help me find out more about this species. The National Science Foundation kindly provided money for an REU (research experience for undergraduates) supplement, which would cover travel expenses for two students go to PR for a month. In addition, they would spend some time in the lab back in Santa Barbara beginning to describe the species. I think it is great to get students out doing field work, where they can gain a real appreciation for the wonder of the natural world. Our first order of business was to find more of this animal.

Why was this Euphilomedes in my bucket when I had just dipped it into the ocean? Well, ostracods usually live down in the sediment, making a living between the sand grains. But some swim, often just after sunset, usually to mate. Some ostracods are bioluminescent, the males signal with flashing lights to attract females (yet another future ostra-blog). I’ve collected some animals (mostly males) in light traps. So, I hypothesized that this Euphilomedes was being attracted to the lights at the pier. The undergrads’ first experiment was to test this hypothesis. To do this, they passed a small net through the water, the length of the pier. They put the resulting critters into a dish and counted what they had, repeating this every 15 minutes. They found that this Eupilomedes had a strong peak of activity about 2 hours after sunset. Essentially all of the Eupilomedes they collected were males, consistent with the idea that males swam around trying to find females to mate with. Females probably only mate once, and then do not swim up any more, thus the strong bias in males versus females.

The students also made many SCUBA dives to find where else this Eupilomedes lives. Another way to collect ostracods is by dragging a net across the bottom of the ocean, where the animals usually spend most of their time. We then sort the sand to keep the size class that will have ostracods, and laboriously sort sand grain from ostracod. This is another reason why it was so great to find this Eupilomedes – it is fairly rare to be able to get so many animals just by dragging a net through the water – we could get hundreds of males at a time this way, without having to sort them from sand. In the end, the students found that this Eupilomedes was living all over around the nearby patch reefs, some times very abundantly, especially in fine grained sand. Hundreds of boats, fishermen, wind surfers and SCUBA divers pass through these waters, all the time; while this unknown and fascinating species lurked inconspicuously between the sand grains below them.

Deciding on a name

A really fun part about describing a species is naming it. I took this pretty seriously, especially given some of the great names that people have come up with. Some of my favorite ostracods (again future ostra-blog candidates) are Harleya davidsoni, coined by my colleagues and motorcycle aficionados Kerry Swanson and Thomas Jellinick, and Kornickeria marleyi, named after Bob by Anne Cohen and Jim Morin. Some scientific names are pretty hard to top, like the clam formerly known as Abra cadabra or the wasp named Pison eyvae. (If you like these, you'll have fun if you check curioustaxonomy.net ). I won't go into some of the other candidate names, just suffice to say that in the end, we decided to name our new species after a mythical creature, "el chupacabra". On our first trip, I had fun joking around about the chupacabra with one of my friends who came along. Also, since the myth started in Puerto Rico, it seemed fitting to name this species after it. We simply dubbed it Euphilomedes chupacabra.

If you don’t know chupacabra already, the myth surfaced in the mid-90’s or so, when livestock, especially goats, began being found dead and ensanguinated, with puncture marks on their necks. The legend of el chupacabra (the goatsucker) has since migrated to other, especially Latin American countries. I just saw a headline today, suggesting people have captured video footage of the elusive chupacabra. Looks like a dog with a big nose to me.

So that is the story of Euphilomedes chupacabra. Perhaps one day, you too can discover a new species by dipping a bucket in the water. They are everywhere, and just think of the fun you can have at your next cocktail party. Oh, and by the way, Euphilomedes chupacabra does not suck the blood of goats, unlike the beetle Agra sasquatch, which really does have big feet. I’m not sure about its sister species, Agra yeti.

Evolve: Guts

Many evolution buffs, like myself, have been watching the History Channel Series called Evolve, which are airing here in CA at 10pm on Tuesdays. These are well produced pieces that focus each week on a particular trait (eyes last week, guts this week). Both shows have been collections of ~5 narratives, mostly showing how the focal trait works in different animals. The narratives are tied together by asserting that evolution occurred (which I am quite certain it did). As such, these are not really about the historical science of evolution, but rather they are using evolution as an organizing principle to tie together experimental science on how particular traits work in different animal groups, with a preference for charismatic vertebrates. In the end, it all works quite well, and I would recommend the series.


In honor of Guts, I thought I would post a link to some of my favorite gut science. Work by Dirk Haller and (separately) Ruth Ley lies at the interface of ecology, evolution, and medicine. They wonder, how does the composition of bacteria in the gut of humans and mice affect the host - and how does that composition of bacteria get established?

You can think of the bacteria as a community, like a forest or grassland ecosystem, living inside each of us. Communities can have different levels of diversity - they can be comprised of many of just a few species. Those species could be closely or distantly related evolutionarily. And those communities could be established from environmental sources, or established by inheritance.

I saw Dirk and Ruth talk about some of this work at last years GAFOS conference, which is a conference of about 20 Americans and 20 Germans, under the age of 40, who were invited because someone took notice of his or her work. GAFOS is funded by the National Academy of Sciences and the von Humboldt Foundation. I described it in a bit more detail in a previous post, where I linked a symposium this year on the evolution of complex adaptations.

Some of the conclusions that Ruth and her colleagues have made are that certain groups of bacteria are associated with obesity of the host. There exists an experimentally generated line of sterile mice - mice that are born and live in sterile conditions, ie with no bacteria anywhere (amazing!). Some of these sterile and genetically identical mice were seeded with different bacteria, and some combinations were more likely to result in obesity of the mice, given the same amount of food.

Another interesting result is that gut bacteria tend to be passed from mother to offspring, as opposed to being obtained from the environment. This result is based on phylogenetic trees of gut bacteria from different populations. It is heritage, not locality that determines the bulk of gut bacteria.

Dirk's presentation was a really great example of pluralism, which I like to promote. He contrasted the germ theory of disease with the genetic/inherited theory of disease. He hints at a possible link between our currently germ-o-phobic society and the increase of genetic, especially auto-immune diseases like Crohn's disease and asthma. It may be that without the insult of germs, our bodies find it more difficult to distinguish self from non-self. By just having a germ theory of disease, we lose the full picture.

(These are my memories from over a year ago, so I may have some details wrong. Check out Ruth's and Dirk's presentations on this site, to see for yourselves!)


Next week Evolve, Jaws!

Wonderful Life Part 2

Sandwalk: Science and Philosophy Book Club: <i>Wonderful Life</i>

Over at Sandwalk, Larry Moran announced a discussion forum on Gould's Wonderful Life. In part 1 of this post, I briefly presented my opinion of Wonderful Life - a deliciously audacious attempt to tell the story of how paleontology, and the Burgess Shale, changed the world. How? By showing that humans are not a pre-destined outcome of evolution, but rather lucky survivors in a world that stochastically decimates most species.

Here, I'd like to discuss a particluar comment, originally written by Dawkins and posted on Sandwalk. If true, this comment does indeed nullify most of the point of Wonderful Life.

"Gould expects us to be surprised. Why? The view that he is attacking—that evolution marches inexorably towards a pinnacle such as man—has not been believed for years. But his quixotic strawmandering, his shameless windmill-tilting, seem almost designed to encourage misunderstanding."

Is it true that it's not believed that evolution marches inexorably towards a pinnacle such as man? My take is that there is a tendancy to think of evolution as marching toward a pinnacle, especially among Gould's target audience of laypersons. First, I'll address my "target audience" argument, then I'll paste in some text from a recently submitted article on the molecular evolution of phototransduction that argues for this linear thinking (marching toward a pinnacle) even among profession biologists, a common theme of other posts here.

First, I agree in some ways with Dawkins' comment that many do not believe evolution marches toward a pinnacle such as man. These kinds of views, such as orthogenesis in its most elaborated form (the first definitions were much more modest) argued that evolution is a fully predictable developmental process, akin to ontogeny. And these view points mostly were dismissed decades ago. Evolutionists understand that there is no end goal, that evolution is a response to the here and now, influenced by past heres and nows.

But by stating this agreement, I am talking mostly about the field of evolution, the scientists doing the work. This is different from the perceptions of the general public, which is the target audience of Wonderful Life. I think chapter one makes a rather convincing case, with figure after figure, that evolution is viewed by the public as a march of progress.


Still, even among professional biologists, there is a tendency to present evolution as linear march of progress. Even though we/they know evolution doesn't proceed this way, it is difficult to stay away from such tendancies. I've collected examples, posted on this blog, from ostracods, textbooks, and even cellular phone 'evolution'. I hasten to note that I am here discussing a march of progress of traits, not species. By focusing on traits, the mis-understanding is not quite as egregious as a species march of progress, because we have a reason to choose one trait over another. We want to know how evolution could build the most complex thing we see, and so we pick that as an end point. When we are dealing with species, only ego would lead us to define humans as the most complex species, and therefore as an artificial endpoint. Still, as I recount below, in some cases this human-centric ego has led some to define the most complex eye as most human like. Furthermore, in the example below, a deep-seated assumption of a marching line of progress has led to rank eyes of living species as more or less evolved, along a scale toward human eye-ness. I think this is the march of progress that Gould points out, and Dawkins argues that no one believes.


I paste below the excerpt from a draft of "Opening the Black box: The genetic and biochemical basis of eye evolution", submitted to Evolution Education and outreach, and co-authored with MS Pankey. By way of set up, we earlier in the article define the "gradual-morphological" model of eye evolution as the idea researchers portray of eyes gradually and linearly evolving from spot to complex eye. Here is a nice video illustrating the idea:

This model is not wrong - it does help us understand how something so complex could evolve. But the model is incomplete in that it 1) makes no mention of the origins of variation (see this for more details on that idea) - and it 2) decompresses complexity into a single variable, and also ignores the branching history of all biological entities. There is no need to invoke intelligent design here, but there is a cause to do more science, and more scientific thinking.

On to the promised excerpt:

"Students of biology at all levels, but especially those less experienced, commonly have a strong tendency to view evolution as a linear series of events. What’s more, their perceived series often proceeds from simple to complex, and often equates highest perceived complexity with most human-like. This way of thinking has conceptual antecedents at least to Aristotle’s “Great Chain of Being” and to prominent biologists like Linnaeus, Lamark, and even Haeckel (Dayrat 2003), who was post-Darwinian. The biases are further re-enforced by commonplace graphics portraying evolution itself as a parade of primates, from the knuckle-walker (bringing up the rear) to the modern human (leading the way), representing an “Iconography of Expectation” of increasing complexity (Gould 1989). Such tendencies may be mired in human bias, by a deep-seated need to view humans as special, as a pinnacle of evolutionary progress (Gould 1989). Human vanity certainly seems logical, but an additional, perhaps even more fundamental impediment to tree-thinking, may be that it requires conceptions of time that are largely outside of human experience. Humans experience, imagine, understand, and communicate time as a linear phenomenon. We understand time unfolding as a process in one-dimension. Phylogenetic “time” is different because it branches, leading to multiple parallel trajectories of evolutionary history. It takes practice to learn “tree-thinking” and it is challenging for anyone to communicate precisely about phylogenies, when our every day language doesn’t have to deal with similar phenomena (see also Crisp and Cook 2005; Gregory 2008; O’Hara 1997).

The gradual-morphological model of eye evolution falls into exactly the same trap as the graphical progression of primate through proto-humans to human: these iconographies re-enforce the notion of evolution as a linear, progressive, and goal-oriented series of biological entities of increased complexity. In the case of eye evolution, Salvini-Plawen and Mayr’s figure of gastropod eyes provides an outstanding example of the linear model of evolution, especially since the figure has been copied, and elaborated. The progressive series of gastropod eyes begins with a light sensitive patch (usually with no mention of its origin), followed by eyes with an increasingly deep cup. Next, a simple lens arises, usually with no mention of how the variation originates, beyond the notion that possessing a lens is a continuous extension of morphological variation. Finally, at the end of the morphological sequence, an eye with a fully formed complex lens is illustrated (Figure 1a).

It is important to think clearly about what such models can and cannot tell us. Darwin defended his model very well, writing:

“In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition.”

In other words, Darwin was using living taxa as surrogates for unknown lineal ancestors. Darwin realized he was only testing a necessary requirement for natural selection to produce complex traits: intermediate forms of the trait must be functional and useful. Salvini-Plawen and Mayr were testing the same idea, using more closely related organisms. However, versions of Salvini-Plawen and Mayr’s gastropod eye sequence, copied later by other authors, have shoehorned additional data into a hardened gradual-linear theory. A common example of one of these extended mollusk eye series originated in Figure 3-1 (page 34) of Strickberger’s (1990) textbook Evolution. The figure uses four of the gastropods illustrated by Salvini-Plawen and Mayr, but adds two additional eyes, both from cephalopods: a nautilus and a squid (Fig. 1b). The nautilus and squid fit nicely into a gradual-linear series, intercalated between gastropods. Nautilus serves as a prime example of a pinhole eye, falling morphologically just between the pit eye of Pleurotomaria and the lens-eye of Nucella. The squid eye, often heralded as a highly complex eye, especially because of its uncanny – but convergent – similarity to vertebrate eyes, now takes the pinnacle position of the linear series. Apparently, these eyes were added to enhance the representation of intermediate stages of eye complexity. Alone, this is not a problem, as long as people remember that the goal of such collections of organs is to show that eyes of intermediate complexity are functional and useful.

Figure 1. Morphological series of eyes. A. Salvini-Plawen and Mayr (1977) illustrated five eyes of varying complexity, from different living species of gastropods. They made the implicit assumption that the eyes of living species approximate the ancestral states of a pectinate tree. This is illustrated by placing dashed lines leading to living species. B. An actual estimate of gastropod phylogeny (based on molecular data), indicates that the tree is not pectinate. Therefore, the actual history of gastropod eyes is more complicated than envisioned by a linear-gradual model of A. C. Two cephalopod eyes (*) were added to the gastropod eyes by Strickberger (1990). D. An estimate of mollusk phylogeny again shows how the actual history is more complicated that a direction march to complex eye. One interpretation is that lens eyes originated separately in gastropods and cephalopods.

However, gradual-linear series of eyes are often elevated to direct models of how evolution actually proceeded. Yet without explicit statistical phylogenetic analyses, these collections of eyes should not be taken as models of how evolution actually did happen in the groups being illustrated. Nevertheless, in some cases, the linear series are presented as actual accounts of evolution, even though they are only drawings of eyes from currently living species, unaccompanied by any phylogenetic analysis. Although the caption in Strickberger (2000) is much more balanced, the caption of Strickberger (1990) illustrates the point, calling the figure “Some stages in the evolution of eyes as found in mollusks…”. Ridley (2004) similarly, and somewhat more forcefully states “Stages in the evolution of the eye…”. The figure is again reproduced in Encyclopedia Britannica (Ayala 2008) and in Ayala (2007), with a caption stating “Steps in the evolution of eye complexity in living mollusks. The simplest eye is found in limpets (far left), consisting of only a few pigmented cells, slightly modified from typical epithelial (skin) cells…..The octopus eye (far right) is quite complex, with components similar to those of the human eye such as cornea, iris, refractive lens, and retina.”

There are at least two problems with viewing eyes of living species as an evolutionary model of how evolution actually proceeded. First, it promotes the fallacy of progress in evolution. The caption above is written as if the first mollusk eye is the same as a modern limpet, and that evolution progressed linearly to the human-like complex octopus eye. Second, a gradual-linear model ignores complexities like convergence. In particular, adding cephalopod eyes to a group of gastropod eyes ignores the phylogenetic relationships of the animals. When placed on a phylogentic tree of the animals, it becomes clear that the complex, lens eyes of gastropods and cephalopods probably originated separately (Fig. 1d)."

Wonderful Life Part 1

Sandwalk: Science and Philosophy Book Club: <i>Wonderful Life</i>

Over at Sandwalk, Larry Moran announced a discussion forum on Gould's Wonderful Life. Too bad for me the group will meet in Ontario, which is a bit too far from South Coast, California to be practical. I'd have fun hearing other people's take.

In addition to the announcement, Larry posted critiques of the book written by Dennet and Dawkins, which I hadn't seen before. In part 1 of 2 posts, I'll make a brief statement about my own opinion of Wonderful Life. (Ahh the wonder of the internet, a vehicle so flexible as to provide a venue for an obscure evolutionary biology professor to comment on a 20 year-old book...). In part 2, I will respond to one specific sentence in Dawkins' critique of the book, that I found provocative. (...and comment on 20-year old comments on a 20-year old book).

Part 1. Wonderful Book?
Even though I tend to disagree with the main thesis (but that's exactly Gould's contrarian m.o., see link here and below), Wonderful Life is perhaps my favorite popular science book ever. I re-read this book before submitting my first grant five years ago (on ostracod phylogeny) - because Gould took the subject of arthropod anatomy, and weaved a fascinating and engaging tale, without sacrificing detail. I wanted to mimic this enthusiasm for biology in my own writing. I wanted to learn from his masterful performance, and to feel again the excitement of biology that he conveyed, and to try to relay that same excitement I feel for my own work. (The grant was funded by the way).

In addition to the amazing, other worldly, impossible animals vividly described - in a time before Science Channel computer graphics - I realize now that a huge part of the inherent interest of the book is that Gould told a story about people. It's about Walcott, constrained by dogma to shoehorn ancient animals into categories of the living. It's about Whittington, and Briggs and Conway-Morris toiling away to overturn dogma through detailed and exacting reconstructions based on the fossils. We also learn details about these characters as people, I especially remember Walcott. I remember his family, the legendary story of the Burgess shale discovery (and why it is probably false) and I remember the increasing sway that administration held for Walcott as his career advanced. Some of my favorite science books are told through the eyes of the scientists themselves: The Beak of the Finch and The Altruism Equation are two examples that come to mind.

Another positive for me is the sheer brazenness of the whole undertaking of Wonderful Life. Gould concocts the thesis that his own field of paleontology has just re-written the history of life, and has changed mankind's view of the place of humans in the universe. As Copernicus and astronomy displaced Earth (and therefore humans) from the center of the universe, a quiet revolution in paleontology was displacing humans from atop an iconographic ladder of progress, just by diligently yet passionately scratching away at some shale. I guess the non-confrontationist in me finds the thought of such audacity in self-aggrandizing story telling exhilarating.

I've argued here on Evolutionary Novelties before that this audacity allowed Gould to promote pluralism within the field of evolution by taking a stand that opposes much of the field. For Wonderful Life, the question of pluralism comes down to the idea of contingency versus determinism. If we "replay the tape" of life - could we predict the outcome?



(Here, I will indulge in a Gouldian tangent, an aside that ends up being longer than the main idea, and note that this theme of contingency versus determinism is fun to lecture about and students seem to like it. They've encountered the idea before in stories and movies like Bradbury's Sound of Thunder (read the short story, I don't recommend the movie), where a time traveler changes the present by accidentally stepping on a butterfly in the distant past. They know (I assume) that Marty McFly changed his life for the better when he traveled in time and accidentally induced his dad to stand up to Biff. They know the movie Minority Report (I asked the students this year if they know that one), where the pre-cogs can predict crimes, and people are arrested before they can commit them (most students don't know the Phillip K. Dick story the movie is based on though). Even romantic comedies have played with the idea, such as when Bill Murray's character experiences Groundhog Day over and over and over; when Drew Barrymore starts afresh every morning in 50 First Dates, while Adam Sandler tries to woo her over and over.)


In Part 2, I will address the provocative criticism written by Dawkins, and quoted on Sandwalk: "Gould expects us to be surprised. Why? The view that he is attacking—that evolution marches inexorably towards a pinnacle such as man—has not been believed for years. But his quixotic strawmandering, his shamless windmill-tilting, seem almost designed to encourage misunderstanding."

Ostra-blog 2 - To e or not to e

I was happy to see that Eric at The Other 95% put up a post about Ostracoda. There, he mentioned some of the stats on the group – thousands of species, both extant and extinct, making a living in pretty much any way you can imagine (except I don’t think there are any true parasites), and living pretty much anywhere there is water. I once hiked to the top of a Santa Barbara foothill (a mountain to a Wisconsinite) and found a crevice in a boulder that had filled with water. It teemed with Ostracoda. They not only live in mountain boulders, but also deep seas, hot springs, and even pools of water that collect in bromeliads.

Eric also raised one of the central issues of ostracodology, a war that has been waged for decades, a debate that elicits passionate arguments from both sides of a fundamental divide. This fray is so contentious as to be officially banned from the Ostracoda email list (called OSTRACON). The moderator, Rosalie Maddocks wrote “We further urge that the debate not be reopened on OSTRACON. We are as unlikely to settle the issue as we are to unite all religions and stamp out all disease.”

What is this debate that so enflames the passions even the most mild-mannered scientists? To e (ostracode) or not to e (ostracod), that is the question. In other words, how to spell the common name of Ostracoda in English?

Perhaps the definitive source on the matter was published in 1981 by Dick Benson, in an article entitled “The odds on "ode" in ostracode, or the omicron and omega of chancy spelling.” Here is a link for those who can access JSTOR.

Professor Benson takes us on a wild ride through history, taking a few pit stops to enlighten us about etymology and the Greek language. He makes a fairly compelling argument that “ostracode” is more linguistically “correct” (can you guess which side of the debate he falls on?). But he is also quick to admit that “because language is based on more than logical correctness, the alternative usage is not considered wrong.”

I will not try to recount this harrowing journey through history and language in any detail. Instead, will leave you with Dr. Benson’s lyrical summary, before divulging which side of the divide I fall on:

In celebration of Oxford’s mode,
Most Americans spell it “ostracode”

The Britisher’s closer proximity to God
Causes him [or her] to spell it “ostracod”.

A German claimed Aristotle said it first,
And of the two “ostracod” is wurst;

While a Frenchman after having learned to spell it,
Said it right, by right appellate.

The Italians with gestures free,
Pronounce one “ostracod-eh” and two “ostracod-ee”

All the rest look on amused,
Most don’t care which one is used.

For now, both “ostracod” and “ostracode” survive;
The two of them very much alive.

I end this ode with a short delighter;
Both may be right, but one is righter!

(Note, Professor Benson signed his poetic summary “Anonymous”, because he “holds popular acclaim to be superfluous”)

Where, you are no doubt wondering, do I stand in this great divide? Well, I usually preach pluralism, but on this I must take a monistic stand. Although typically Americans have used “ostracode”, I favor “ostracod”, which is more typically British (despite this trend, documented by Benson, who combed journals to tabulate preferences, he also points out in an ironic reversal that the British Oxford dictionary favors “ostracode”, whereas the American Webster’s favors “ostracod”!) .

My own reasons for "ostracod" are two-fold. First, this is the word I first learned, from my advisor (typo excepted) and from a paper by Andrew Parker. Have you ever had an old friend, say "Jimmy", change his name to the more adult "James"? You still call him "Jimmy", don't you??

Second, I am a bleeding heart, linguistic liberal. Language is an evolving entity, constraining it by arbitrary rules is kinda a diss, ain’t so? Let’s let language continue to evolve! Language is decided by the masses – it’s what people use that determines its path. The only constraint should be clear communication, not ancient Greek grammar. But OMG - WTF is up with all those textisms? Even a lingustic liberal cannot keep up. ITCCTY (Is this clear communication to you?)

Chat lingo aside, I am not fully anachronistic. Eric at The Other 95% has weighed in on this issue using stunning, awe-inspiring new technology, perhaps not even conceivable in 1981 when Dr. Benson considered the question. Eric set up a GoogleBATTLE, pitting ode versus od. GoogleBATTLES scour the entire World Wide Web, tallying occurrences of one word versus another. Current usage (on the web at least) puts ‘od over twice as well used as ‘ode! Who is righter now?

So to summarize my views:

Although typical Americans might find it odd,
For me to use the Brit word, “ostracod”,
How else could I retain my nickname; “ostra-Todd”?