In books and movies, time travel is typically fraught with negative consequences. Any attempt to change the past — say, stopping the JFK assassination, or taking your mom to the Enchantment Under the Sea dance — is bound to produce ripples of change that alter the future. But what if you could safely contain a trip back in time within the boundaries of a test tube? In a new paper published in Nature, a University of Chicago geneticist used a form of “molecular time travel” to observe a crucial event in the evolutionary history of life on Earth…and extinguish a favorite argument of intelligent design advocates.

The concept of “irreducible complexity” is a favorite talking point of the forces against evolution, both today and historically. As the argument goes, the complex structures found within modern organisms — from the eye to the microscopic protein machines that conduct business in cells — are far too complicated to be the result of the random genetic mutations and selective forces at the core of Darwin’s grand theory. The argument is so old that Darwin himself addressed it in On the Origin of Species, speculating on how an accumulation of small changes could lead from a simple photoreceptor to the wondrous eye shared by many organisms today.

The best way to demonstrate how the minute changes of evolution could produce great complexity is to capture that process in action. But to happen upon such a leap live would be a biological needle in an enormous haystack. A better strategy would be to pick a historic leap in complexity from the evolutionary past, and then go back and observe how it happened. Easy, right?

To accomplish this task, Joe Thornton, a new faculty member in the Departments of Human Genetics and Ecology & Evolution, developed the method of “molecular time travel.” Instead of a Delorean, Thornton’s method uses a computational analysis of the genes from modern-day species to resurrect the genes of ancestral species that lived hundreds of millions of years ago. For the new paper, Thornton and colleagues at the University of Oregon decided to “travel” back to look at a complex molecular machine found in various species of fungus.

“Our strategy was to use ‘molecular time travel’ to reconstruct and experimentally characterize all the proteins in this molecular machine just before and after it increased in complexity,” said Thornton, professor of human genetics and evolution & ecology at the University of Chicago, professor of biology at the University of Oregon, and an Early Career Scientist of the Howard Hughes Medical Institute. “By reconstructing the machine’s components as they existed in the deep past,” Thornton said, “we were able to establish exactly how each protein’s function changed over time and identify the specific genetic mutations that caused the machine to become more elaborate.”

Their target was a molecular machine called the V-ATPase proton pump, which helps maintain the proper acidity of compartments within cells. In modern Fungi, this pump contains a six-part ring made up of three separate proteins, but that wasn’t always the case. Some 800 million years ago, that same ring was made from only two proteins, meaning some kind of event occurred around then to increase the complexity of this machine.

Thornton’s group calculated the genetic sequence of the ring proteins from that ancient ancestor using the sequences of 139 modern Fungi family members, computationally tracing their common elements back up the Tree of Life to their ancient predecessor. The researchers could then reproduce the protein before the split (called Anc.3-11) and the two proteins that came after the split (Anc.3 and Anc.11), and see how they functioned in the proton pump’s ring.

Surprisingly, the “newer” proteins were less versatile than the ancestral Anc.3-11, which could substitute for either of its descendants when transplanted into modern Fungi. The result suggests that the pump’s increase in complexity resulted not from the evolution of a new, “better-designed” function, but from an initial loss of versatility.

“It’s counter-intuitive but simple: complexity increased because protein functions were lost, not gained,” Thornton said. “Just as in society, complexity increases when individuals and institutions forget how to be generalists and come to depend on specialists with increasingly narrow capacities.”

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llustration by Meike Köhler/Journal of Vertebrate Paleontology

Just in time for Easter, a team of scientists digging on a Spanish island have discovered the fossils of a prehistoric rabbit of unusual size: 26 pounds, more than six times the size of today’s bunnies. Called Nuralagus rex - the “king of the hares” - the big guy definitely did not hop when it lived 5 million years ago. While it might resemble more of a rodent than a rabbit to the untrained eye (and its discoverers originally thought it was a tortoise?), experts in the field are convinced that it’s an ancestral figure in the line. “Really, this is a rather typical rabbit head [albeit large] stuck on an atypical rabbit body,” Brian Kraatz, an expert in rabbit evolution at the Western University of Health Sciences in Pomona, told National Geographic. (Kraatz seems like a funny guy - he also told Discovery News “It’s unclear whether their feet would have been decent good luck charms.”). Oh and before you start writing that giant bunny horror movie script, Brian Switek reminds us that it’s already been done.

Scientists in England find they can change the sexual preference of male mice by deleting genes related to the neurotransmitter serotonin. As you might expect, the study has led to some interesting headlines. For a more thoughtful take, science writer Ed Yong asks whether they are truly affecting sexual preference or whether they are merely making indiscriminately friskier mice.

Are people with strong religious beliefs at higher risk for obesity? A study by our friends at Northwestern University suggest that’s the case, finding a correlation between obesity and attendance at religious activities when other factors (such as age, race, sex, education, and more) are controlled for. One interesting take-home message from, suggested by the Medical Center’s Daniel Sulmasy in a HealthDay News article, is that religious activities might be a good place for potential anti-obesity interventions to take hold. No more donuts after Sunday services, bummer.

A scientific skirmish has erupted over a paper by co-authored by famed biologist E.O. Wilson disputing the existence of kin selection, a extension of Darwin’s theory of natural selection that has helped scientists explain the evolution of everything from homosexuality to child-rearing to altruism. Kin selection is the idea that an individual will help protect and nourish relatives beyond their direct offspring because even nieces, nephews, and cousins share some a significant portion of an individual’s genetic background. As recapped by Carl Zimmer, the current debate began with the publication of Wilson’s paper questioning the evidence of this process by Nature last August, a paper that was roundly criticized by the evolutionary biology community (my favorite quote Zimmer received for his original article: “This paper, far from showing shortcomings in inclusive fitness theory, shows the shortcomings of the authors.” Zing!). This week, Nature published several rebuttals to the original paper - one signed by 137 scientists - and the authors’ re-rebuttal. Jerry Coyne, one of the original critics of the paper on his blog, examines the latest salvos in the argument and what it says about the role of professional reputation in scientific publication.

The nuclear reactor situation in Japan appears to have fortunately become less alarming this week. But just in case you are still concerned about radiation traveling over thousands of miles of Pacific Ocean to the United States, here are reassuring comments from David Grdina, professor of radiation and cellular oncology at the Medical Center, given to Fox Chicago News. Also, to put reports on the amount of radiation being measured from Japan to O’Hare Airport into perspective, keep this awesome chart from science comic xkcd handy.

An elephant fish embryo and its yolk (courtesy Andrew Gillis)

Billions of years of evolution has produced an incredible diversity of life - “endless forms most beautiful and wonderful,” as Darwin famously put it. But a fascinating thing about evolution is it has produced such a wide variety of species with a relatively small amount of tools. Many of the roughly 23,000 human genes can be found in species as different as mice and flies, and those genes control embryonic processes that are remarkably similar despite the vastly different outcomes for an insect or a man. But sometimes, finding out just how deep this homology runs requires deep exploration.

Members of Neil Shubin’s laboratory are no strangers to adventure. The search for Tiktaalik, the famous fossil of a transitional species between fish and land-dwellers, took Shubin and his collaborators to remote stretches of the Canadian Arctic. So when J. Andrew Gillis, then a graduate student in Shubin’s laboratory, wanted to study an obscure aquatic relative of sharks with famously hard to acquire eggs, the evolutionary biologist could hardly turn him down.

“I remember when Andrew said ‘I want to get some holocephalans in the lab,’ and I thought ‘yeah, right.’ Everybody’s tried this for years; there’s a long line of people who have always wanted to get holocephalans in the laboratory,” said Shubin, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago. “It’s not like you can buy them at a store, it’s not like you can breed them easily in a lab. They breed on the bottom of the ocean, so you have to find places where the eggs are accessible.”

Holocephalan eggs are prized by evolutionary biologists because of a small but significant anatomical difference from their cousins, the sharks. Both share skeletons made of cartilage and other structural features, but split in terms of appendages called branchial rays, structures that grow outward from the skeletons’ central gill arches. While sharks form several sets of these rays, holocephalans only grow a single set near their head, which eventually forms the support for gill covers. Finding the genetic switch that triggers this anatomical difference, as Gillis, Shubin and colleagues did in a PNAS paper published yesterday, would shed light on the origins of appendage development across the animal kingdom, from fins to wings to limbs.

But first, a scientist needs to leave the safe world of their laboratory in order to find those precious eggs. Gillis’ quest for the embryos of the holocephalan species elephant fish, named for their prominent snout, led him halfway around the world and under the water, on SCUBA expeditions in Australia and New Zealand. Based on anecdotal information collected from local fisherman and marine biologists, Gillis was able to score a precious few eggs to take back to the laboratory for his experiments - but it wasn’t easy.

“Diving for elephant fish eggs was not always a pleasure trip,” said Gillis, now a postdoctoral researcher at the University of Cambridge. “Unfortunately, elephant fish like to lay their eggs in cold, muddy, shark-infested bays, so we spent months seeking out sites like this in southeastern Australia and New Zealand. When you finally find a few eggs in the muck, it feels like winning the lottery.”

Back in the comfort of the laboratory, the mood was still tense, as Gillis had to get all of his experiments working just right so as not to waste the valuable cargo from his expeditions. Previous work by Gillis and Shubin discovered that shark embryos use a gene called sonic hedgehog (Shh) to control the development of branchial arches. The next step was to test whether elephant fish embryos also use this genetic switch to mediate the growth of their less robust appendages.

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Photo by John Amend/Cornell

I’ve always been fascinated with the rock solid bags of coffee bought at the store, which have all the density of a brick until opened, when they crumble into scoopable grounds. Turns out that’s a physical concept at work, known as “jamming transition,” when separate, particulate materials are pushed so close together they act like a solid structure. It turns out jamming transitions are useful for more than just compact packaging, but can also help solve a persistent, basic problem in robotics: how can you make a robot “hand” as good as the human hand at picking up objects?

An answer was published this week in the Proceedings of the National Academy of Sciences by researchers from the University of Chicago, Cornell University, and private company iRobot. The scientists created a finger-free “universal robot gripper” by filling a balloon-like elastic bag with particulate material - such as, yes, coffee grounds - pressing the bag down on to the object, then removing the air from the bag, triggering the jamming transition and creating a perfectly shaped, tight hold. There’s video below, demonstrating some of the objects and functions the device can be used for. But when will they be installed in prize claw machines?

[Coverage from Engadget, Gizmodo, and Wired]

Resurrection of the Beagle

The HMS Beagle was the Royal Navy ship that transported a very special passenger, a naturalist named Charles Darwin, around the world in 1831. What’s left of the ship may currently lie at the bottom of a marsh, but the name has lived on as a favorite for ambitious science projects. First, the Beagle name was attached to the Mars space probe Beagle 2, and now it has been affixed to the University of Chicago Computation Institute’s newest toy: a 150-teraflop supercomputer, one of the 50 fastest supercomputers in the world. Housed at Argonne National Laboratory, this Beagle will sail the seas of data produced by researchers in physics, biology, and medicine.

As discussed previously on ScienceLife, the next wave of science will be less about collecting data and more about actually doing constructive things with it. The Beagle’s maiden voyages will be to help projects such as the Membrane Protein Structural Dynamics Consortium, the UChicago-led effort to study the shape and function of cellular machines. Other immediate uses may be for genomics projects, where scientists have struggled to keep up with analysis of the data created by cheaper and cheaper gene sequencing technology. In the Beagle’s announcement, Conrad Gilliam, UChicago’s dean of research for the biological sciences division, looks forward to a time when electronic medical records provide valuable data for the development of more effective treatments.

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Among evolution’s best tricks is the act of turning one species into two. Speciation, the foundation of a new species from an accumulation of small changes in an old one, has given birth to the incredible diversity of life on our planet. But in order for a new species to be founded, a sort of genetic restraining order must be put in place. Within a species, individual organisms can evolve extraordinary differences without spawning a new species - think dog breeds, for example. It’s only when two organisms grow so different that they lose the ability to come together and successfully reproduce, that a new speciation event can be declared - think the lion, the tiger, and the sad, sterile liger.

The nuts and bolts of speciation have given headaches to evolutionary biologists all the way back to the very first one. In his books, Charles Darwin laid out the outlines of how a new species could form from an old one, but left the dirty work of figuring out the actual mechanism to the field he created. Some of the most famed evolutionary biologists of the early 20th century took up the challenge and left the field with the DM model of hybrid dysfunction, named for Theodosius Dobzhansky and HJ Muller. For nearly 100 years, that theory stood as an explanation of how natural selection eventually produces sterile offspring, while being too technically difficult to explicitly test. But this year, in the laboratory of University of Chicago professor Jerry Coyne (and simultaneously and independently in an Indiana laboratory), the theory was finally confirmed.

With his first graduate student Allen Orr, Coyne had figured out the experiments and the mathematics that one could use to test the DM theory. The only problem was finding a set of species in which to do those experiments. Three species were necessary, and those three species had to still be closely related enough that breeding was possible, but not successful. A fast reproductive cycle would also be helpful, so the experiment wouldn’t require decades to execute, and the genetic information of those species would have to be fairly well characterized.

It wasn’t until two years ago that all those tools became available, and in a paper published in Science earlier this month, Coyne’s current graduate student Daniel Matute brings 100 years of theory and research into the end zone. Matute ran his experiments with the noble fruit fly from the Drosophila genus, and his project was made possible by the recent discovery of a new species in that genus, called Drosophila santomea. When Coyne and Matute realized that the new species finally completed the triad of closely-related species they would need to test the DM Theory, it launched Matute into a long series of breeding experiments.

Drosophia melanogaster (from Wikimedia Commons)

The central question was how quickly genes responsible for hybrid inviability accumulated. The DM Theory proposes that those genes don’t merely add up at a steady pace as two species split off from a common ancestor, they “snowball” at an exponential pace with time. To test that notion, Matute needed to count the genes responsible for inviability in two different pairs of species, with different divergence times. That meant a lot of time putting two Drosophila species together, allowing them to mate, and then counting their offspring under a microscope - essentially following the instructions Coyne and Orr had laid out 20 years prior.

Fortunately, all that work yielded exciting numbers. For Drosophila santomea and Drosphila melanogaster, estimated to have diverged 12.8 million years ago, 65 genes were found to cause inviability. For the more recently split Drosphila melanogaster and Drosophila simulans (who diverged only 5.4 million years ago), the number was far lower: only 10 genes caused inviability. Some simple math and curve-fitting later, and Matute had determined that the inviability genes were accumulating at an quadratic, faster than linear rate, confirming the central tenet of the DM Theory at long last.

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It’s traditional at the University of Chicago to invite a faculty member to deliver the convocation speech, rather than invite an outside speaker as many schools do. This year’s chosen faculty for Spring Convocation (the first campus-wide ceremony since 1929) was a well-known name from the rolls of the Biological Sciences Division: Paul Sereno, our world-famous fossil hunter. Despite being the year after the Year of Darwin, Sereno still did an excellent job of weaving the father of evolution and the theory itself into his advice for the graduating Class of 2010.

In evolutionary biology, random events with unpredictable consequences are collectively known as “historical contingency.” That randomness can be just as significant to an individual’s personal “evolution”: just as Darwin diverted from the seminary to his famous trip aboard the HMS Beagle, Sereno switched from art school to a career in paleontology. As such, Sereno advised the graduates to keep a firm hold on their liberal arts education, never knowing when it will be useful for the unforeseeable twists and turns in one’s life and career.

“I recount these life stories to extol the virtues of pathways marked by unpredictable, life-changing events small and large,” Sereno said. “Contingency is to be embraced, not feared.”

Below, watch the full video of Sereno’s convocation speech. As a side attraction, admire the amazing transformation of the University of Chicago main quad into a temporary outdoor auditorium able to hold 20,000 attendees.

Many people consider human evolution to be a done deal, something that happened in our distant, wild past. But as Nicholas Wade wrote last week in the New York Times, there is increasing scientific evidence that natural selection has continued to act upon humans, producing observable evolutionary changes as recently as 3,000 years ago. Studies have found that everything from high altitude tolerance in Tibet to dry earwax may have evolved in relatively recent human history, producing subtle but significant population differences in the frequency of certain rare gene variants.

One of the genetic approaches cited by Wade in his article is the work of Anna Di Rienzo, professor of human genetics at the University of Chicago. In a paper published earlier this year in the Proceedings of the National Academy of Sciences, a group from Di Rienzo’s laboratory led by graduate student Angela Hancock went looking for recently evolved human genes in an unusual way. Their results uncovered new ways humans evolved in the recent past, with consequences still felt in our modern age of obesity.

Many genetic studies take an intentionally “naive” approach to such a genetic hunt, comparing gene variants between regional populations with no preconceptions so as not to bias the data. But sometimes a little bias doesn’t hurt; in fact, it may help find differences that fall through the cracks of a broad, unbiased sweep. Hancock and colleagues hit upon the idea of filtering their comparisons by predictable selective pressures expected to drive evolution, such as ecology and diet.

“A lot of the studies done before have been done in a way that was sort of agnostic to the selective pressure,” Di Rienzo said. “We are using aspects of human environments to learn about natural selection and the way humans adapted specifically at genetic level. We use genetic as well as ecological data, and we think that this combination allows us to tap into a set of genetic adaptations that are not accessible by other studies.”

To do this, the team took a particular variable expected to drive evolution, such as polar ecoregion. Because modern humans first arose in the tropical temperatures of Africa, those populations who migrated to a colder environment would be expected to need dramatic genetic changes to survive. So the researchers (using data from the Human Genome Diversity Project, the International HapMap Project, and their own original sequencing) compared the genomes of polar populations against non-polar populations, to see if it revealed specific gene variant differences.

Indeed it did. Several genes were found to appear at different frequencies in the polar populations, and most were found to have the kind of function one would expect to be selected for in a cold environment. Genes that helped people regulate body temperature, for instance, were more likely to have changed in a polar population. Energy metabolism also appeared to have been selected for, with the genes for enzymes that degrade sugars showing differences. The results lined up nicely with a 2008 paper by Hancock and colleagues that used a different analysis method to detect a relationship between climate and genes associated with metabolic disorders.

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Six months ago, some of the world’s brightest evolutionary biologists and scholars gathered on the University of Chicago campus for a three-day birthday party celebrating Charlie Darwin’s 200th. At the time, the blog featured live-ish coverage of the event wherein I tried my best to capture the fascinating lectures and discussion on display at Rockefeller Chapel and Ida Noyes Hall. But if my words were insufficient, you can now watch a handful of videos from the conference, courtesy of the official website. The videos are not embeddable, but here’s a quick viewer’s guide.

Jerry Coyne (University of Chicago): “Speciation:  Problems and Prospects”

The author of Why Evolution is True discussed where he and Darwin disagree: the answer to the very title of Darwin’s seminal On the Origin of Species. Coyne explains the debate between sympatric and allopatric speciation, and how barriers - physical or otherwise - are usually the cause of new species formation.

Paul Sereno (University of Chicago): “Dinosaurs: Phylogenetic Reconstruction from Darwin to the Present”

Famed fossil hunter Sereno brought along the second-oldest bird skeleton ever found, but turned his focus from bones and digs to how morphologists - scientists who study the physical characteristics of specimens - can keep pace with the geneticists in constructing the Tree of Life.

David Jablonski (University of Chicago): “Paleontology and Evolutionary Biology: The Revitalized Partnership”

Speaking of paleontology, Jablonski pointed out how Darwin pointedly avoided using the fossil record in his classic writings because of its many holes and gaps in the mid-19th century. Today, fossil remains of species such as the bivalves that Jablonski studies provide scientists with a “trail of mayhem, destruction and heartbreak” that can be useful in reconstructing evolutionary history.

Neil Shubin (University of Chicago): “Great Transformations in Life: Insights from Genes & Fossils”

Shubin traveled to the unforgiving environment of the Canadian Arctic to make the landmark discovery of Tiktaalik, the earliest-known limbed tetrapod fossil. But the majority of his talk focused on the more comfortable setting of the laboratory, where genetic experiments on how limbs develop in sharks and skates offer clues to human evolution.

Robert J. Richards (University of Chicago): “Darwin’s Biology of Intelligent Design”

Co-organizer Richards represents the more historically and culturally-inclined upper half of the conference, presenting the provocative claim that Darwin believed natural selection to be a purposeful force rather than a blind machine of nature. ScienceLife founding father Jeremy Manier wrote about Richards’ lecture here.

Climate Scientists to Politicians: Enough Already

A pretty remarkable letter was published in the journal Science this week, signed by 250 members (including4 University of Chicago scientists) of the National Academy of Sciences and calling for “an end to McCarthy-like threats” surrounding climate change. The letter makes a stand for reason on both climate change specifically and science in general, arguing that the scientific process of constantly questioning and improving the knowledge of a particular subject should not be misinterpreted as flaws.

When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses a dangerous risk for our planet.

The letter comes on the heels of Oklahoma Sen. James Inhofe suggesting in March that U.S. and British scientists should be criminally investigated for their role in the “ClimateGate” hacked e-mails incident. Michael Mann, the Penn State climatologist who created the famous hockey stick graph showing the recent rise in global temperatures, was cleared by his university of any misconduct charges, but was targeted this week by Virginia Attorney General Ken Cuccinelli. Such efforts are political grandstanding at its most despicable, and seriously endanger the ability of scientists to conduct research in an open and unpolitical forum. Great coverage, as always, by Andrew Revkin at Dot Earth.

2010 BIO Coverage Roundup

To wrap up BIO week, I thought I’d cast a net for some of the other commentary from this week’s conference in Chicago. Bruce Japsen of the Chicago Tribune saw part of Al Gore’s speech and focused on how the global recession wounded the biotechnology industry. Tuesday’s keynote session with George W. Bush and Bill Clinton was controversially closed to the media, but Forbes ran a perspective on the event from a conference attendee. Industry magazine Fierce Biotech and the San Diego Biotechnology Network were also grinding out gavel-to-gavel coverage alongside our own.

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A radiograph of Darwinius masillae, aka "Ida"

It was the fossil infamously hyped as the scientific discovery “THAT WILL CHANGE EVERYTHING.” But one year after its controversial press conference debut, Darwinius masillae has come under increased scrutiny from a scientific community already skeptical about the 55-million-year-old primate fossil’s Hollywood roll-out. When scientists from Norway, Germany and Michigan published the original Darwinius paper (oh, and also released a book and a TV show), they argued that the tiny, lemur-like Ida was the earliest known primate ancestor of humans. But in October, a paper in the journal Nature used computer analysis of Darwinius’ physical features to place it about as far away from humans as possible on the primate evolutionary tree.

Last week, another blow was struck against the claim of Darwinius as an ancestor of humanity, this time in a direct reply to the original paper that was published in the Journal of Human Evolution. The JHE paper is a straightforward, business-like rebuttal that dissects the arguments used to place Darwinius in the lineage that eventually begat humans, employing additional anatomical evidence to reverse the original conclusions. But no punches were pulled by Callum Ross, one of four authors of the reply paper and a scientist already on record calling the original article “a travesty,” in our conversation about the controversy.

Ross emphasized that he does not question the scientific integrity of the authors who originally described Darwinius, even commending them for a “great” description of the specimen. But it’s their interpretation of that description, and their placement of Darwinius in the phylogenetic “tree of life,” that Ross has quarrel with - an analysis based on cherry-picking anatomical features.

“That aspect of it, the reconstructing evolutionary relationships part, is based on a 19th-century way of doing science,” said Ross, associate professor of organismal biology and anatomy at the University of Chicago. “You select the attributes of the organism that you think reflect the relationships, and that’s what you use.”

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Drosophila melanogaster (from Wikimedia Commons via Futurity)

Fruit Flies and Musical Language

Some interesting research on Futurity this week, covering a couple of my favorite scientific topics: fruit flies and music. The first, out of Caltech, used the humble little Drosophila melanogaster (only about 2.5mm in size) to study a very complex human behavior mystery: ADHD. While it might seem impossible to model the attention deficits of schoolchildren in a fly, Drosophila proves again and again that its relatively simple brain (with only 200,000 neurons) and its well-understood genetics make it the ideal lab animal - easy to store too!

In this study, researchers found that one thing flies do not like is being puffed with air, as they respond by flying chaotically around their chamber for several minutes after the puff. Some flies respond even more dramatically and quickly to the puffs, and these were found to have a mutation the receptor for the neurotransmitter dopamine - a frequent focus of the blog thanks to its role in addiction and learning. Dopamine is also thought to play a role in human ADHD - children with the disorder are given Ritalin, a stimulant drug that increases dopamine - so the hyperactive flies with deficient dopamine matches up nicely with the human data. In a separate study, the authors found that flies with the same dopamine mutation also have issues learning to pair an odor with a shock, suggesting that the learning disabilities of many ADHD kids may also be down to dopamine.

The second Futurity study to catch my eye this week came from Duke, and took on the challenging question of why humans like music. As a human that likes music, I was naturally intrigued. The Duke theory: we listen to music because it mimics speech. A paper by Kamraan Gill and Dale Purves asked why we only generally use five- and seven-note scales (Harry Partch excepted) to produce music when there are literally billions of scales available. Gill and Purves argue that this is because human speech itself can be organized into pentatonic or heptatonic scales, a trick they demonstrate in this video. The idea fits snugly into current theories of why music evolved in the first place - as an early language, or, as Steven Pinker calls it,  “auditory cheesecake”?

(Fun fact: Darwin’s theory on the origin of music was that “musical notes and rhythm were first acquired by the male or female progenitors of mankind for the sake of charming the opposite sex.” I think Mick Jagger would agree.)

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A sleeping zebra finch (courtesy of Margoliash lab)

One of the repeated themes of the Darwin/Chicago 2009 meeting two weeks ago was the history of the anti-evolution movement, a resistance that has actually changed form, even *cough* evolved, quite a bit since The Origin of the Species. At the opening night event in Rockefeller Chapel, science historian Ronald Numbers talked about differences between the anti-Darwinists led by William Jennings Bryan in the 1920’s (immortalized in the Scopes Monkey Trial and Inherit the Wind) and today’s intelligent design supporters and creationists. Surprisingly, Bryan and his followers were considerably less extreme than today’s anti-evolutionists, as Numbers explained that most who railed against Darwinism in the early 20th century were fine with the evolution of animals over billions of years, they merely could not abide that humans also evolved.

The evolution vs. creation debate has obviously become a lot more complicated since then, but Bryan’s primary objection has lingered - the core of most people’s opposition to evolution is the idea that humans must be somehow separate and different from the rest of the natural world. One “proof” of this uniqueness is the complexity of human language, a form of communication that, to the casual observer, appears in an entirely different league from the songs, gestures, or simple noises that animals use to share information. The assumption that the more complex forms of human language are unique is even held by some in the field of linguistics and psychology, including the legendary Noam Chomsky, who argued as much in a 2002 Science paper with cognitive psychologist (and Darwin/Chicago speaker) Marc Hauser.

That assumption is a handicap to the study of language, argue University of Chicago’s Daniel Margoliash and Howard Nusbaum in a recent issue of the journal Trends in Cognitive Science. The idea that human language is biologically unique, and thus the kind of “hopeful monster” geneticist Richard Goldschmidt coined to describe the sudden appearance of a new feature in evolutionary history, walls off language from the world of biology. Perceiving human language in its proper evolutionary context, and thus exposing it to the tools of comparative biology, will allow scientists to fully understand how language works and where it originated, Margoliash and Nusbaum conclude.

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Daniel Dennett chatting with Robert Richards at the Darwin/Chicago 2009 conference. Credit: Jerry Coyne

The philosopher Daniel Dennett looked slightly puzzled as Robert Richards finished his Oct. 30 talk at the Darwin/Chicago 2009 meeting, on the subject of “Darwin’s Biology of Intelligent Design.” Dennett and Richards have spent years writing about Darwin and the historical significance of his ideas about evolution. But Richards’ talk challenged a central theme of Dennett’s influential book, “Darwin’s Dangerous Idea” - that Darwin revolutionized modern thought by showing that a mindless, mechanical process can give rise to complexity and minds capable of understanding their origins. In fact, Richards argued that Darwin did not always envision evolution as mindless or mechanical. Richards cited out passage after passage in Darwin’s notebooks and early published writing, showing that he thought of humanity as “the great object for which the world was brought into its present state.” He didn’t talk about an intelligence guiding evolution, but he was comfortable - at least before the 1860s - with the idea of an intelligence behind natural laws.

In other words, Darwin once believed that we are the ones evolution was waiting for.

I walked up to Dennett after Richards’ talk and briefly asked what he thought. Dennett shrugged and shook his head. “I don’t believe it,” he said.

He’s not alone. The question is, why should anyone care? What does it matter if a 19th-Century naturalist thought a higher intelligence might have planned out evolution in some vague way? Lots of Darwin’s other notions got jettisoned along the way (blending inheritance, anyone?), so why should this one be different?

In part it may be because of the unusual - and possibly unhealthy - role that Darwin has assumed in debates about biology and human nature. He is an especially potent figure for creationists and atheists alike, because in many ways he made modern atheism possible. It muddles the picture if, as Richards said, Darwin’s theory “was formulated under the idea that an intelligent cause formulated the laws of nature.”

But it’s also clear that Darwin believed in that “intelligent cause” less and less as he got older. He’s still an important author of modern materialism, though perhaps a mushier one than we often imagine. Dennett admitted the possibility in his talk - “It would be wonderfully ironic, Bob, if the person we honor for having the best idea ever didn’t understand his own idea,” Dennett said. “But I don’t think that’s the case.”

4:15 p.m. - Of Mice and Mammoths

The last talk of the day (for me, as I had to leave before the final, final talk) made for a great reminder of how far the field of evolutionary biology, wrapped in a relatively simple story told engagingly by Hopi Hoekstra of Harvard. Hoekstra described her research quest as “the hunt for genes that make a difference,” and she uses a really nice model system - the oldfield mice of the southern United States. These mice typically are brown in color, but they have migrated in the recent (meaning thousands) of years to the gulf and atlantic coasts and taken up residence, like a retired couple, on the beach. But a brown mouse on a beach is a target, and their predators, which include birds and coyotes, find it all to easy to locate their brown fur on white sand and make a beachside snack out of them.

Cue natural selection - soon you have brown oldfield mice inland, and predominantly white oldfield mice that live on the beach. Hoekstra tested whether the fur color really does construe an evolutionary advantage with a simple experiment - make a bunch of clay mice colored brown or white, and leave them out on the beach. Sure enough, the brown clay mice quickly showed divots and bitemarks left by attacks from (presumably very frustrated) predators.

That would have been a fine experiment for the 1959 conference, but Hoekstra’s next step was pure 2009 - she took examples of brown and white mice back to the lab, bred them, and searched for the genes that determined fur color. Her laboratory narrowed the gene candidates down to three genes, and in one of them - a receptor called Mc1r - the substitution of a single amino acid flipped the switch from brown fur to white fur. Amazingly, when another group of scientists sequenced the genome of extinct mammoths in 2006, they found the same amino-acid substitution in the same gene, implying that mammoths, like the oldfield mice, came in different color varieties.

After so much high theory and methodological complexity, Hoekstra’s experiment sent all of us (or at least me) home with a warm feeling - not only was her experiments a beautiful example of evolutionary biology that would have been impossible in 1959, it was a great example of teachable science, the kind of story that a 3rd-grader could wrap their head around and begin to see the truth of evolution. The cloud hanging over Darwin/Chicago 2009 was the uneasy feeling that all this scientific progress was still losing out in the arena of public opinion, but Hoekstra’s work and charismatic speaking style (on the heels of similar ambassador figures Neil Shubin and Michael Shue) chased away some of the pessimism, and left me confident that the more examples we find of Darwin’s elegant theory at work in nature, the easier it will be to convince the world that it is true.

And with that, we’re finished. Happy Halloween to those of you who have followed me this far, and thanks very much for reading and perhaps linking to the posts. I’ll be back Monday with a digest post to help navigate the coverage of the last few days, and Jeremy Manier will be here Tuesday with his own thoughts on the conference.

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5:00 p.m. - Biomedicine and Bracketology

Here’s the final report from today’s session, join us again tomorrow for a full Halloween day of evolutionary science and philosophy! Also, continue to follow PZ Myers of Pharyngula and Skip Evans of Wisconsin Citizens for Science for their reports on the conference.

Both talks in the final session of the day focused on how the incredible advances in gathering genetic information over the last decade have done much to shake up the worlds of genetics and evolutionary biology. As we’ve written about previously, the 1959 conference helped solidify what’s known as the modern synthesis of evolution that incorporated the then-new information about DNA, genes and molecular mechanisms of inheritance, an arrangement that forever married the two fields. Well, could the participants in that conference have predicted that 50 years later we would have a reasonably complete genome for humans, not to mention 43 other vertebrate species? And did they know how much trouble it would cause?

Eric Lander, who was one of the leaders of the Human Genome Project, said he felt slightly out of place at a conference about Darwin, but the modern synthesis marriage sometimes makes strange bedfellows! Regardless, Lander’s talk was a great primer on how the dogma of genetics has been forever altered by what we learned from the HGP and the genomes of other animals: that we have far fewer genes than we thought (~20,000 vs. previous estimates of 100,000), that much of what is handed down between generations is “non-coding” DNA that doesn’t make proteins, that those “non-coding” sections may create important regulatory elements that help organisms develop. Lander, who described himself as a biomedical scientist, said much of what has been found since the explosion of genetic data has been bad news for medical geneticists - many disease-associated alleles have been found, but most have very marginal effects on the probability of a person developing that disease. But Lander said it was a glass half-full/half-empty situation:

“Those people who want to do personal genomics - take your DNA and tell you your risk of diabetes - they’re in trouble. This is not going to be the best way to do that,” Lander said. “But if I want to understand what diabetes is about…I start to get clues to the pathways that matter to diabetes.”

The final talk of the day covered how genetics has caused a similar reshuffling in the field of phylogeny - the science of organizing life into “trees” that show the evolution and relationships of species. Philip Ward, from UC-Davis, talked about the durability of the “Tree of Life” simile, which Darwin readily used in Origin of Species - the only figure in the book is an early phylogenic tree. Modern phylogeny produces beautifully complex trees that look like 10,000-team basketball tournaments run in reverse, with the winner being life’s common ancestor. But as biologists have turned to genetics to build these trees, they’ve found that they lead to completely different trees than the ones built from morphology, the physical characteristics of organisms.

One reason for this is a tricky effect called convergence - two species that are not closely related and live continents apart could form a resemblance because they evolved in similar environments. Ward studies a type of ant that is found in both Asia and America, and morphology would suggest that they are closely related species despite being so far apart geographically. However, genetic data showed the ants were more distantly related than previously could have been estimated from their looks, suggesting they evolved to look similar due to their similar environments, without a recent common ancestor.

But the Tree of Life remains a strong structural model, Ward said. So strong, in fact, that it has been adopted by creationists, who describe an “orchard of life” of animals that evolved after Noah’s flood. As with most mentions of creation “science” at the meeting, Ward’s slides about these theories drew mostly giggles from an audience decidedly on the side of Darwin, even as genetics reveals a world more complex than he ever could have imagined.

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