Wednesday, October 24, 2018

Flight: The Genius of Seeds
October 24, 2018, 3:52 AM
A lowly dandelion is stuck in the ground. It can’t move. It seems hopelessly chained to earth by its roots. But one day, it will give its young marvelous wings that will let it soar above the landscape, to enjoy a brief but wondrous journey, traveling possibly for miles till it gently descends to a paradise its ancestors could never imagine: a land of fertile soils and fountains. Your lawn.
You have to grudgingly admire those pesky weeds that thrive so easily against the garden plants you want that require so much sweat and coaxing. Now, you will admire them more to hear that the little parachute-bearing seeds fly using a technique scientists didn’t even know about till now. Nature says:
Every child knows that blowing on a dandelion clock will send its seeds floating off into the air. But physicists wanted to know more. How does an individual seed manage to maintain such stable flight?Researchers at the University of Edinburgh studied the fluid dynamics of air flow around the seed and discovered a completely new type of flight. It’s based on a previously unknown kind of vortex which may even be common in the plant and animal kingdoms, now that we know where to look. [Emphasis added.]
Jeremy Kahn, also writing in Nature, calls it an “‘impossible’ method never before seen in nature. A beautiful film clip describes how air flowing up through the bristles of the “pappus” as it is called creates a “separated vortex ring” above it that literally sucks the seed up into the air.
“Perhaps one day, even human technologies could be designed to fly as efficiently as the mighty dandelion seed,” the narrator says of this “completely new type of flight.”
The paper in Nature by Cummings et al. is titled, “A separated vortex ring underlies the flight of the dandelion.” The authors seem jazzed by what they found:
The porosity of the dandelion pappus appears to be tuned precisely to stabilize the vortex, while maximizing aerodynamic loading and minimizing material requirements. The discovery of the separated vortex ring provides evidence of the existence of a new class of fluid behaviour around fluid-immersed bodies that may underlie locomotion, weight reduction and particle retention in biological and manmade structures.
Heavenly Design
The editors of Nature took note of this study, appreciating the broader implications by saying in their Editorial, “The floating of a seed shows how appreciating the wonders of the Universe can begin with a new look at the everyday.”
The English poet and artist William Blake was no fan of the reductionism of Isaac Newton. True discovery, and therefore knowledge, Blake insisted in his poem ‘Auguries of Innocence’, was to be found in the everyday, where a world could be seen in a grain of sand and “heaven in a wild flower”.
The editors emphasize that the dandelion’s flight trick depends on finely-tuned parts:
All falling objects, from feathers to cannon balls, create turbulence in their wake. But it takes a rare combination of size, mass, shape and, crucially, porosity for the pappus to generate this vortex ring. Size is also particularly important, because from the point of view of something as small as a pappus, the air is appreciably viscous. At such a scale, a parachute consisting of a bunch of bristles is as effective as the aerofoil found in larger seeds that disperse from taller plants — such as the winged seeds of the maple. In the same way, the tiniest insects do not fly with solid wings, but swim through the air using ‘paddles’ made of bristles.
Perhaps most surprisingly, the trick depends on the blank spaces between the parts. What goes on there depends on the solid materials and how they are arranged.
The key lies not in the bristles of the pappus, but in the spaces between them. If projected on to a disc, the bristles together occupy just under 10% of the pappus’s area, and yet create four times the drag that would be generated by a solid disc of the same radius. The study shows that air currents entrained by each bristle interact with pockets of air held by its neighbours, creating maximum drag for minimum expenditure of mass. The pappus’s porosity — a measure of the proportion of air that it lets pass — determines the shape and nature of the low-pressure vortex.
Isn’t it wonderful what blind, unguided processes designed? Evolution is a genius. Its productions are simply heavenly:
It’s an example of how evolution can produce ingenious solutions to the most finicky problems, such as seed dispersal. There are many things unknown that are smaller than atoms, or larger than galaxies, or billions of years away in time. But there are secrets held by things that we take for granted — things on a human or near-human scale — that seem all the more precious for it. Heaven in a wild flower, even.
Other Ingenious Seed Dispersal Mechanisms
There are seeds that can float across oceans (coconut, mangrove). The filaments on wild oat seeds respond to moisture, turning into outboard motors that drive the seeds along the ground and into the soil. Storksbill seeds actually fold into a drill for driving the seeds into the ground. We all know, too, how Velcro was inspired by cocklebur seeds catching rides on the fur of cows.
Some seeds prefer traveling indoors in comfort on natural transportation services. One particular tropical forest tree in Thailand, an article on notes, seems to have a preference for elephants that eat the fruit and deposit the newly-fertilized seeds on the ground someplace else. Other seeds can fly as passengers in an airliner, hitching a ride through the “cabin” of a bird’s digestive tract, to disembark unharmed after landing miles away.
“Seed dispersal is an essential, yet overlooked process of plant demography,” says Utah State University ecologist Noelle Beckman in another article on that begins:
Though mostly rooted in the ground, plants have a number of innovative ways to disperse their seeds and get on with the business of propagation. They drop seeds or release them to the wind. Or they fling seeds with a dramatic mechanical detonation. Or they rely on seed transport by water or hitching a ride on a traveling animal (including humans).
Beckman calls seed dispersal “a central process in ecology and evolution,” but is it not more empirically valid to stop at the word ecology? What’s evolution got to do with it?
The scientists found dispersal ability is related to fast life histories with maximum dispersal distances positively related to high reproductive rates, a long window of reproduction and a low likelihood of escaping senescence or growing old.
“The faster the life history, the farther distances seeds are dispersed,”Beckman says. “This may allow the species to take advantage of environments that vary unpredictably.”
While this statement gives the appearance of a scientific explanation, appealing to a law-like pattern, there are problems. Surely there are many exceptions to the alleged rule. More important, the explanation says nothing about the origin of the exquisitely engineered mechanisms used by seeds to disperse. This is evident when you consider the details. How could a blind process, that feels only the immediate environmental pressure and is incapable of aiming at distant goals, accomplish these engineering marvels?
  • Carefully spaced filaments that generate a separated vortex ring
  • Chemical coats that can survive an animal’s digestive tract without trapping the seed in a box it cannot escape from
  • Propellers, such as those on a maple seed, of just the right length and curvature that can create lift in the breeze
  • Projectile mechanisms that can fling a seed tens of feet away from the plant at high speed
  • Cones that can insulate a seed with gases from a forest fire, then open up to drop the seeds after the fire has passed
  • Seed filaments that turn into motors and drills
Students might become more motivated to choose science as a career when teachers cultivate the awe and wonder in everyday things, instead of dowsing it with vacuous appeals to sheer dumb luck. If scientists are just now discovering new methods of flight in a dandelion seed, what other worlds are there in a grain of sand, and heavens in a wild flower?

Tuesday, October 16, 2018

The world’s simplest known animal is very poorly understood

World’s Simplest Animal Reveals Hidden Diversity
The first animal genus defined purely by genetic characters represents a new era for the sorting and naming of animals
·         By Charlie WoodQuanta Magazine on October 6, 2018

World's Simplest Animal Reveals Hidden Diversity

Two individuals from two different genera of the phylum Placozoa: Trichoplax adhaerens (left) and Hoilungia hongkongensis (right). The gross morphology and the internal structure are indistinguishable, and only genetics can tell them apart. Credit: Hans-Jürgen Osigus, ITZ Ecology and Evolution, Stiftung Tierärztliche Hochschule Hannover, Germany

The world’s simplest known animal is so poorly understood that it doesn’t even have a common name. Formally called Trichoplax adhaerens for the way it adheres to glassware, the amorphous blob isn’t much to look at. At just a few millimeters across, the creature resembles a squashed sandwich in which the top layer protects, the bottom layer crawls, and the slimy stuffing sticks it all together. With no organs and just a handful of cell types, the most interesting thing about T. adhaerens might just be how stunningly boring it is.
“I was fascinated when I first heard about this thing because it has no real defined body,” said Michael Eitel, an evolutionary biologist at the Ludwig Maximilian University in Germany. “There’s no mouth, there’s no back, no nerve cells, nothing.”
But after spending four years painstakingly reconstructing the blob’s genome, Eitel might know more about the organism than anyone else on the planet. In particular, he has looked closely enough at its genetic code to learn what visual inspections failed to reveal. The variety of creature that biologists have long called T. adhaerens is really at least two, and perhaps as many as a dozen, anatomically identical but genetically distinct “cryptic species” of animals. The discovery sets a precedent for taxonomy, the science of naming organisms, as the first time a new animal genus has been defined not by appearance, but by pure genetics.
The modern taxonomic system, little changed since Carl Linnaeus laid it out in the 1750s, attempts to chop the sprawling tree of life into seven tidy levels that grant every species a unique label. The two-part scientific name (such as Homo sapiens) represents the tail end of a branching path through this tree, starting from the thickest limbs, the kingdoms, and ending at the finest twigs, the genus (Homo) and then the species (sapiens). The path tells you everything there is to know about the organism’s relationship to other groups of creatures, at least in theory.
Ever since its discovery in the late 1800s, T. adhaerenshas been recognized as having a highly unusual body plan, and it has formally had the phylum of Placozoa (“flat animals”) to itself for almost half a century. Just one level more specific than kingdom, a phylum is a cavernous space to occupy alone: Our phylum, Chordata, overflows with more than 65,000 living species ranging from peacocks to whales to eels. Biologists have long suspected that Placozoa hid more diversity, and mitochondrial evidence strengthened that suspicion in 2004, when researchers found that short sequences from different individuals looked about as different as those of organisms from different families (one level more general than genus).
But that observation about the two Placozoa didn’t meet the accepted international standards for putting them in new taxonomic categories, which have historically been based on animals’ forms. “At the time we had just uncovered the genetic differences,” said Allen G. Collins, a co-author of the 2004 paper and a zoologist at the National Systematics Laboratory of the National Oceanic and Atmospheric Administration (NOAA). “Looking at the animals we had collected, it wasn’t discernible how they might differ morphologically.”
To finish what Collins started, Eitel and his colleagues decided to abandon the visual approach and search for defining characteristics in the placozoan genome itself.
They began by mapping out the phylum’s genetic territory with the same easy-to-sequence mitochondrial DNA Collins had used. By comparing data from this molecule, known as 16S, Eitel concluded that a particular variety of Placozoa from Hong Kong was the most distant relative of the standard strain, the genome of which had already been fully sequenced in 2008. If any group would qualify as a different species, this was the one.
He next needed to read, order and interpret the 80-odd million A, G, C and T nucleotide bases that make up the Hong Kong variant’s genome. Growing a few thousand placozoans, blending them to extract their nuclear DNA and converting the snippets of their genome into a digital format took a few weeks, but the hard work of shuffling those pieces into the right order and figuring out what each section does took four years of fiddling around with computer programs. When the team finally had a full genome ready for comparison, the payoff turned out to be worth the wait. “We expected to find differences, but when I first saw the results of our analyses, I was really overwhelmed,” Eitel said.
A quarter of the genes were in the wrong spot or written backward. Instructions for similar proteins were spelled nearly 30 percent differently on average, and in some cases as much as 80 percent. The Hong Kong variety was missing 4 percent of its distant cousin’s genes and had its own share of genes unique to itself. Overall, the Hong Kong placozoan genome was about as different from that of T. adhaerens as human DNA is from mouse DNA. “It was really striking,” Eitel said. “They look the same, and we look completely different from mice.”
So where do all those genetic changes manifest, if not in the animals’ flabby appearance?
“Even though the placozoan itself looks like a little ball of glue, it probably has cells that are doing some pretty sophisticated things,” said Holly Bik, a marine biologist at the University of California, Riverside, who studies tiny marine roundworms known as nematodes, which can also be cryptic. The Hong Kong Placozoa came from a brackish mangrove stream where large swings in temperature and salinity demand flexible body chemistry. “Physiologically, for organisms, that’s a pretty big thing to have to deal with. At the molecular level you need specific adaptations,” said Bik, who was not involved in the research.
By comparing the Placozoa variation with the average genetic differences between groups in other phyla, the German team concluded that the Hong Kong Placozoa qualified as not only a new species, but also a new genus. It might even have qualified as a new family or order in other areas of the animal tree, but to err on the conservative side, the team based their standard of genus variation on jellyfish, a genetically diverse phylum with relatively tidy divisions between levels.
All that remained was the naming. Taxonomic codes demand identifying characteristics, but don’t specify whether they should be visual or genetic, so the team picked out four genetic letters in the 16S mitochondrial genome that could uniquely differentiate the two lineages. Then, endorsed by peer review and PLOS Biology in late July, their work placed a new organism on our map of life.
The team gave their specimen the genus name Hoilungia, for a shapeshifting dragon king from Chinese mythology, and they named the species hongkongensis, for where it was collected. Similar genome-based classifications are common in the protist and bacterial worlds, and a relative handful of cryptic animal species have been named based on genetics. Namings (and renamings) that blend morphological characters with genetic ones, which recently re-classified a common houseplantSusanne Renner, a botanist at the Ludwig Maximilian University. “It’s just great.”
The researchers hope their work will make it easier for future genetic character–based naming, which is less subject to biases from attention-grabbing visual features like antlers and fins that may not accurately reflect evolutionary distance between groups. “Someone had to be the first one to fight for the right to define new general species based on genomics, and we luckily got it published,” Eitel said.
Renner says this work is the latest step in an ongoing shift toward genetic taxonomy. “It took a long time to take off and now it’s taking off,” she said. She points out that in contrast with the pages of text that can go into a formal description of a species, specifying an organism with just four letters as the German team has done lends itself to snappy efficiency. “Linnaeus would be happy to do it. He was envisioning very brief and sharp diagnoses.”
As precise as genetic classification can be however, it will likely complement traditional ways of telling animals apart, not replace them. Observing visual features doesn’t require years of a lab’s time. Even for other cryptic animals like nematodes, which can’t be raised in captivity, genetic techniques may find limited use. “For me, working with a single nematode worm, there’s never going to be enough DNA isolated from an individual to use some of these technologies,” Bik said.
But for cryptic animals that researchers can cultivate, genetic sequencing may be the perfect spotlight for illuminating the shaded parts of their evolutionary tree. Eitel said he learned a lot from the process of analyzing the H. hongkongensis genome and predicts that sequencing the next variant—a project already underway—will take months, not years. “There will probably be dozens of new species popping up in the future,” he said. “And more to come, because we’re constantly sampling.”
Reprinted with permission from Quanta Magazine, an editorially independent publication of the Simons Foundation whose mission is to enhance public understanding of science by covering research developments and trends in mathematics and the physical and life sciences.

[[My friend Dovid Moshe Yasnyi offers a very useful snapshot of the history of classification:

"The history of taxonomy. 
There are three periods. 

Era one: From Aristotle to Darwin
Names of living things reflected attributes, later focusing on form (morphology) and function (physiology). Linnaeus systematized it so that the names of different organisms contained information about the relationship between the organisms.

Era Two: From Darwin to Watson and Crick
Names based on evolutionary closeness.

Era Three: After Watson and Crick
Names based on genetic closeness which is understood to mean evolutionary closeness, but in practice involves a different approach."]]

Worm brain 302 neurons not understood

The Connectome Debate: Is Mapping the Mind of a Worm Worth It?
Scientists have mapped a tiny roundworm's entire nervous system. Did it teach them anything about its behavior?
·                     By Ferris Jabr on October 2, 2012

Credit: The OpenWorm Project, image generated by neuroConstruct
In the 1970s biologist Sydney Brenner and his colleagues began preserving tiny hermaphroditic roundworms known as Caenorhabditis elegans in agar and osmium fixative, slicing up their bodies like pepperoni and photographing their cells through a powerful electron microscope. The goal was to create a wiring diagram—a map of all 302 neurons in the C. elegans nervous system as well as all the 7,000 connections, or synapses, between those neurons. In 1986 the scientists published a near complete draft of the diagram. More than 20 years later, Dmitri Chklovskii of Janelia Farm Research Campus and his collaborators published an even more comprehensive version. Today, scientists call such diagrams "connectomes."

So far, C. elegans is the only organism that boasts a complete connectome. Researchers are also working on connectomes for the fruit fly nervous system and the mouse brain. In recent years some neuroscientists have proposed creating a connectome for the entire human brain—or at least big chunks of it. Perhaps the most famous proponent of connectomics is Sebastian Seung of the Massachusetts Institute of Technology, whose impressive credentials, TED talkpopular book, charisma and distinctive fashion sense (he is known to wear gold sneakers) have made him a veritable neuroscience rock star.

Other neuroscientists think that connectomics at such a large scale—the human brain contains around 86 billion neurons and 100 trillion synapses—is not the best use of limited resources. It would take far too long to produce such a massive map, they argue, and, even if we had one, we would not really know how to interpret it. To bolster their argument, some critics point out that the C. elegans connectome has not provided many insights into the worm's behavior. In a debate* with Seung at Columbia University earlier this year, Anthony Movshon of New York University said, "I think it's fair to say…that our understanding of the worm has not been materially enhanced by having that connectome available to us. We don't have a comprehensive model of how the worm's nervous system actually produces the behaviors. What we have is a sort of a bed on which we can build experiments—and many people have built many elegant experiments on that bed. But that connectome by itself has not explained anything."

Because a lone connectome is a snapshot of pathways through which information might flow in an incredibly dynamic organ, it cannot reveal how neurons behave in real time, nor does it account for the many mysterious ways that neurons regulate one another's behavior. Without such maps, however, scientists cannot thoroughly understand how the brain processes information at the level of the circuit. In combination with other tools, the C. elegans connectome has in fact taught scientists a lot about the worm's behavior; partial connectomes that researchers have established in the crustacean nervous system have been similarly helpful. Scientists are also learning how to make connectomes faster than beforeand to enhance the information they provide. Many researchers in the field summarize their philosophy like this: "A connectome is necessary, but not sufficient."

"Some people say we don't know anything about how C. elegans's brain works and I am like, 'Yes, we do!'" says Cornelia Bargmann of The Rockefeller University, who has studied the nematode for more than two decades and attended the Columbia debate. "A lot of what we know about C elegans's rapid behaviors we have learned through and with the connectome. Every time we do an experiment, we look at those wiring diagrams and use them as a starting point for generating hypotheses."

(An in-progress 3D reconstruction of the C. elegans connectome. Dots represent the cell bodies of neurons; long lines represent the neurons' axons and dendrites. Credit: The OpenWorm Project, image generated by neuroConstruct)

Early birds
As soon as Brenner and his colleagues at the University of Cambridge completed the 1986 draft of the C. elegans connectome, a few things became clear. First, scientists were able to label every one of the 302 neurons as either a sensory neuron (one that collects information from the environment, such as temperature or pressure); a motor neuron that controls muscles; or an interneuron, which connects the two. Scientists had already identified some neurons as motor or sensory by destroying them with lasers and observing what abilities the worm lost or retained. With the connectome, they could categorize all of C. elegans's neurons by referencing the number and types of connections between them. On average, sensory neurons make more presynaptic connections (sites where neurons spit out chemical messages) and fewer postsynaptic connections (where neurons receive chemical messages) because sensory neurons are mainly in the business of sending information to other cells. Motor neurons show the inverse trend. Each type of neuron constituted about one third of the C. elegans nervous system. The wiring diagram also allowed scientists to immediately identify how a neuron of interest was linked to other neurons. If a researcher zapped a neuron near the worm's head and discovered that the nematode no longer inched toward food, he could look up that neuron in the connectome and see exactly how it was connected to motor neurons.

In the 1980s, as a postdoctoral student in Brenner's lab, Martin Chalfie—now at Columbia University—used the C. elegans wiring diagram to explain one of the worm's behaviors: He identified the specific neural circuits responsible for the worm's tendency to wriggle backward when poked on the head and to squirm forward when touched on the tail. "The connectome was absolutely critical," Chalfie says. "Without it, we simply would not have known which cells were connected to which." By combining the wiring diagram with evidence from previous research, Chalfie predicted that a particular set of interneurons mediated forward movement and that another was involved in backward movement. Annihilating those neurons with lasers confirmed his predictions.

In the following 25 years researchers have continued to use the C. elegans connectome to study the worm's nervous system and behavior. In combination with genetic analysis and tools that eavesdrop on electrical activity within the worm's neurons, the connectome has helped researchers understand how C. elegans responds to temperaturechemicals and mechanical stimulation as well as how the worms mate and lay eggs. Scientists have also used the connectome to discover talents no one knew the nematode possessed: X. Z. Shawn Xu of the University of Michigan identified four neurons in the worm's body that respond to light—a surprising ability for a creature that lives between grains of soil in complete darkness. "Nearly every C. elegans neuroscience study (as long as it involves behavior) benefited from this connectome," Xu wrote in an e-mail message.

Although the C. elegans connectome has been a boon for scientists who study this nematode's behavior, the past two decades of research have also underscored the staggering intricacy of even a relatively small nervous system. "When you move onto behaviors that are more complex than a quick reflex, you're dealing with especially complicated pathways that are not immediately interpretable because they are not simple circuits—they are networks," explains Scott Emmons of Albert Einstein College of Medicine.
This past summer, in an attempt to confront some of that complexity, Emmons and his colleagues published a connectome of the male nematode's tail, which contains most of the 81 extra neurons that distinguish it from the hermaphrodite (giving the male a total of 383 neurons). It took Emmons and his team about three years to complete and publish the partial connectome: he used more or less the same techniques that Brenner relied on in the 1970s, albeit with faster computers, more powerful microscopes and digital cameras. The male C. elegansconnectome also features a crucial piece of information missing from the original draft of its counterpart: synaptic weights. The many connections between neurons are not equal in strength—the more two neurons communicate, the stronger their link becomes and the more likely one is to fire when the other fires. Neurons may also be genetically programmed to form stronger connections with certain partners as the nervous system develops.

Analyzing synaptic weights in the male nematode's connectome has already given Emmons some ideas about neural development. Some neuroscientists have proposed that genes tightly regulate the strongest connections between neurons in C. elegans, whereas weaker connections are more or less accidents—neurons hooking up with whomever they bump into. Emmons's preliminary analysis shows that homologous pairs of neurons on either side of the nematode's body form highly similar strong and weak connections, suggesting that even the weak connections are not entirely random.

Dynamic networks
Synaptic weights are just one of the many layers of information missing from typical connectomes. To understand how neural circuits work, one also needs to know whether the relevant neurons are excitatory—increasing the likelihood that linked cells fire—or inhibitory, muffling their partners instead. Further complicating things, neglected neurons shrivel in the developing brain and new neurons sprout to replace them; in the adult brain, neurons change the strength of their connections with one another daily—such flexibility is essential for learning and memory. Yet another level of complexity involves neuromodulators: certain kinds of neurotransmitters and other small molecules that linger in the fluid surrounding neurons, changing how neurons behave in ways we do not yet fully understand. A prediction about how information will flow through a particular circuit based on a wiring diagram and synaptic weights might be completely wrong if one does not know which neuromodulators are hanging around at any given time.

A good example of how a static connectome fails to capture the dynamics of living neural networks comes from research on the stomatogastric ganglion (STG), a pair of neural circuits in crustaceans—including crayfish, crabs, lobsters and shrimp—that generate rhythmic behavior in response to food. One subcircuit repeatedly constricts and dilates the pyloric region of the stomach, the foyer to the small intestines. Another subcircuit pulsates the gastric mill, a muscular pouch lined with chitinous teeth that help break down food. Mapping all the connections between the 30 neurons in the crustacean STG was an important first step toward understanding how the STG controlled the crustacean digestive system. But it was by no means sufficient. Eve Marder of Brandeis University and others have shown that the neurons in the stomatogastric ganglion do not always use the same unchanging set of connections to communicate with one another. In the presence of certain neuromodulators, a neuron that contributes to the pyloric subcircuit might switch teams, joining the gastric mill subcircuit instead by changing the tempo at which it fires.

Because any brain or nervous system is so much more complex than what a connectome by itself represents, Movshon is certainly not alone in thinking that researchers' limited resources are better devoted to other areas of neuroscience. "I'm all in favor of Seung and others," Bargmann says, "but I don't think we should have a Manhattan Project for the connectome with such a huge amount of resources. We are not quite good enough at reading them. It wasn't like the human genome project, where we knew how to sequence DNA and said, 'Yeah, let's go for it!' Scaling up connectomes is a different issue."

Oliver Hobert of Columbia, another longtime C. elegans researcher, agrees that connectomics only scratches the surface. "It's like a road map that tells you where cars can drive, but does not tell you when or where cars are actually driving," he says. "Still, connectomics of C. elegans has given us wonderful testable hypotheses in terms of how neural circuits work. What we have learned from C. elegans diagrams are not just specific worm behaviors—they are logical principles common to much of biology."

*Editor's Note: The author is a member of NeuWrite, a workshop of scientists and writers that organized the debate at Columbia.

Tuesday, October 9, 2018

 ‘Sokal Squared’: Is Huge Publishing Hoax ‘Hilarious and Delightful’ or an Ugly Example of Dishonesty and Bad Faith?

By Alexander C. Kafka October 03, 2018

Mike Nayna
James A. Lindsay, Helen Pluckrose, and Peter Boghossian, the academics who carried out a publishing hoax that targeted scholarly journals
Reactions to an elaborate academic-journal hoax, dubbed "Sokal Squared" by one observer, came fast and furious on Wednesday. Some scholars applauded the hoax for unmasking what they called academe’s leftist, victim-obsessed ideological slant and low publishing standards. Others said it had proved nothing beyond the bad faith and dishonesty of its authors.
Three scholars — Helen Pluckrose, a self-described "exile from the humanities" who studies medieval religious writings about women; James A. Lindsay, an author and mathematician; and Peter Boghossian, an assistant professor of philosophy at Portland State University — spent 10 months writing 20 hoax papers that illustrate and parody what they call "grievance studies," and submitted them to "the best journals in the relevant fields." Of the 20, seven papers were accepted, four were published online, and three were in process when the authors "had to take the project public prematurely and thus stop the study, before it could be properly concluded." A skeptical Wall Street Journal editorial writer, Jillian Kay Melchior, began raising questions about some of the papers over the summer.
Beyond the acceptances, the authors said, they also received four requests to peer-review other papers "as a result of our own exemplary scholarship." And one paper — about canine rape culture in dog parks in Portland, Ore. — "gained special recognition for excellence from its journal, Gender, Place, and Culture … as one of 12 leading pieces in feminist geography as a part of the journal’s 25th anniversary celebration."
Not all readers accepted the work as laudable scholarship. National Review took "Helen Wilson," the fictional author of the dog-park study, to task in June for her approach. "The whole reasoning behind Wilson’s study," wrote a staff writer, Katherine Timpf, "is the belief that researching rape culture and sexuality among dogs in parks is a brilliant way to understand more about rape culture and sexuality among humans. This is, of course, idiotic. Why? Because humans are not dogs."
Another published paper, "Going In Through the Back Door: Challenging Straight Male Homohysteria, Transhysteria, and Transphobia Through Receptive Penetrative Sex Toy Use," appeared in Sexuality and Culture. It recommends that men anally self-penetrate "to become less transphobic, more feminist, and more concerned about the horrors of rape culture."
The trolling trio wondered, they write, if a journal might even "publish a feminist rewrite of a chapter from Adolf Hitler’s Mein Kampf." Yup. "Our Struggle Is My Struggle: Solidarity Feminism as an Intersectional Reply to Neoliberal and Choice Feminism" was accepted by the feminist social-work journal Affilia.
Darts and Laurels
Some scholars applauded the hoax.
"Is there any idea so outlandish that it won’t be published in a Critical/PoMo/Identity/‘Theory’ journal?" tweeted the Harvard psychologist Steven Pinker.
"Three intrepid academics," wrote Yascha Mounk, an author and lecturer on government at Harvard, "just perpetrated a giant version of the Sokal Hoax, placing … fake papers in major academic journals. Call it Sokal Squared. The result is hilarious and delightful. It also showcases a serious problem with big parts of academia."
In the original Sokal Hoax, in 1996, a New York University physicist named Alan Sokal published a bogus paper that took aim at some of the same targets as his latter-day successors.
Others were less receptive than Mounk. "This is a genre," tweeted Kieran Healy, a sociologist at Duke, "and they’re in it for the lulz" — the laughs. "Best not to lose sight of that."
"Good work is hard to do," he wrote, "incentives to publish are perverse; there’s a lot of crap out there; if you hate an area enough, you can gin up a fake paper and get it published somewhere if you try. The question is, what do you hate? And why is that?"
Reviews of several of the papers "were partly conditional on claims to have done some sort of actual (very bad) fieldwork," Healy noted.
And that’s where the question of bad faith comes in.
"I am so utterly unimpressed," wrote Jacob T. Levy, a political theorist at McGill University, "by the fact that an enterprise that relies on a widespread presumption of not-fraud can be fooled some of the time by three people with Ph.D.s who spend 10 months deliberately trying to defraud it."
Karen Gregory, a lecturer in sociology at the University of Edinburgh, wrote that "the chain of thought and action that encourages you to spend 10 months ‘pulling a fast one’ on academic journals disqualifies you from a community of scholarship. It only proves you are a bad-faith actor."
Karl Steel, an associate professor of English at Brooklyn College and the Graduate Center of the City University of New York, called the trio’s work "simply not rigorous research" and described three objections to it. It is too narrow in disciplinary scope, he said. It focuses on exposing weaknesses in gender and ethnic studies, conspicuously ideological fields, when that effort would be better spent looking at more-substantive problems like the replication crisis in psychology, or unfounded scholarly claims in cold fusion or laissez-faire economics.
The trio could have reached out to colleagues in physics and other fields, but instead opted for "poor experimental design." And they targeted groups that are "likely to be laughed at anyway," showing not intellectual bravery but cowardice. "These three researchers have demonstrated that they’re not to be trusted," he said.
‘Deep Doubt’
Other online commenters said the hoax papers lack a control group of papers for comparative purposes.
Pluckrose, Lindsay, and Boghossian, reached by phone in Portland, said the papers that were rejected serve as a control of sorts. Better yet, they said, consider this meta-control thought experiment: Look at your journals and the articles they published, and see if you can distinguish them from the hoax articles. If the answer is often no, then there is your control.
Mounk, by phone, also said the control-group criticism is misguided. He called it a "confused attempt to import statistics into a question where it doesn’t apply." If the authors were claiming that their work proves that some publications are, say, 50 percent more susceptible to hoaxes than the average, or that 100 percent of articles published are nonsense because these seven articles were accepted, then you would obviously need controls. But the authors "do nothing of the sort. They demonstrate that it’s possible, with relatively little effort, to get bullshit published." It "sows deep doubt" about the nature of the academic enterprise in these disciplines.
Time will tell, the trio said, but they think the mega-hoax will effectively snuff out their academic futures. Pluckrose thinks she’ll have a hard time getting into a doctoral program, Lindsay predicted that he would become "an academic pariah," and Boghossian, who doesn’t have tenure, thinks he will be punished, and possibly fired. Still, this isn’t the first time that Lindsay and Boghossian have teamed up to mock trendy scholarship. Last year their spurious paper "The Conceptual Penis as a Social Construct" was published in the journal Cogent Social Sciences.
Meanwhile, Pluckrose and Boghossian are working on a book together, and Pluckrose is writing one on the 50-year development of grievance studies and the leftist academic culture of victimization.
If the three are exiled from academe, said Mounk, that will be unjust and a shame. Through "courage and quite a lot of work," they have shown that "clearly there’s a big corner of academia where the emperors wear no clothes." He called the hoax "a more serious contribution to our understanding of the world than many Ph.D. theses." The three of them, Mounk said, "should absolutely be celebrated."
Alexander C. Kafka is a senior editor and oversees Idea Lab. Follow him on Twitter @AlexanderKafka, or email him at