Some profoundly stupid questions about living with half a brain

You know what’s weird? It’s possible to be a happy, independent and intelligent person with only half a brain. It’s not always the case, but that it’s possible at all is still pretty dazzling.

I recently wrote an article for the Post-Gazette on the relative success of hemispherectomy for treating intractable childhood seizures. It involved some of the most satisfying reporting I’ve ever done, interviewing Suzann, a mother whose son had lost part of his brain in an accident. She was generous with her time, honest in conversation and let me interrupt her at all hours of the day with intrusive questions. Thankfully, she also loved telling her son’s story because his life had been so radically changed — for the better — by a hemispherectomy.

But there was one profoundly stupid question that I kept asking myself. Like a good reporter, I found a scientist and asked her to answer my stupid question:

“How can someone have half their brain removed and then wake up the same person?”

The scientist I asked was Marlene Behrmann, a cognitive neuroscientist at Carnegie Mellon who studies visual perception using fancy-pants brain imaging. Her lab has just started some studies on how visual processing adapts in hemispherectomy patients. Surprisingly little is known about the subject, despite the fact the surgery has become relatively routine in large pediatric epilepsy surgery units since the 1980s.

I figured the answer to my question would go something like: Our memories and consciousness don’t exist in a particular place in the brain, they exist in a network, like distributed computer systems or something. And like, processing happens in both hemispheres at once. And like, reasons and stuff. Or something. Did I mention I know nothing about neuroscience?

Marlene’s answer was not what I was expecting.

“I don’t know that they are the same person,” she said.

I thought about Evan, Suzann’s brain-injured son, who had woken up after his hemispherectomy with eyes so swollen he couldn’t open them. “I can’t see you Mama,” he had complained to Suzann. She was terrified that the half-field of vision that remained in his one functioning eye might have been disrupted by the surgery. She sounded joyful when she told the story of Evan’s third day after surgery. “Hi Mama!” he said, on waking up. “Can you see me Evan?” she had asked frantically. “I can see you Mama,” he replied.

Surely this Evan was the same person as before the surgery? He still had the same memories.

“It’s a really difficult question to answer,” Marlene had said and then apologized for her reluctance to speculate.

“What cognitive skills make a person a person? And when they change, what of those do you still need to have to be the same person? What if somebody has lost all of their memories? Does that mean they’re a different person?” she said. “I don’t know.”

I didn’t know either. I left the interview with even more stupid questions than I had before. How did I know Evan was the same person? What did I even mean by the same person? I suppose I was thinking of continuity of consciousness,  an unbroken sense of self. Presumably Evan felt like he was the same person when he woke up. But what did that feeling mean? Would I notice if I woke up tomorrow with different memories? Would I notice if I woke up with a different personality?

Then I remembered something I had read during my research. It was in an article about all the things scientists had learned from people whose brain hemispheres had been surgically disconnected from each other to prevent the spread of seizures. Both hemispheres remained intact and functioning, but the two halves could no longer talk to each other.

The isolation of each hemisphere had some spooky effects. For example, a patient who read a word presented in their right field of view might have been able to say the word aloud, but not if it were presented in their left field of view. That’s because the right visual field is processed by the left hemisphere, which is usually dominant in verbal processing. But the person might have been able to draw what was presented to their left visual field (right hemisphere).

Despite the independence of the two halves of their brain, the patients didn’t feel like two people in one:

patients never reported feeling anything less than whole. As Gazzaniga wrote many times: the hemispheres didn’t miss each other. Gazzaniga developed what he calls the interpreter theory to explain why people — including split-brain patients — have a unified sense of self and mental life3. It grew out of tasks in which he asked a split-brain person to explain in words, which uses the left hemisphere, an action that had been directed to and carried out only by the right one. “The left hemisphere made up a post hoc answer that fit the situation.” In one of Gazzaniga’s favourite examples, he flashed the word ‘smile’ to a patient’s right hemisphere and the word ‘face’ to the left hemisphere, and asked the patient to draw what he’d seen. “His right hand drew a smiling face,” Gazzaniga recalled. “’Why did you do that?’ I asked. He said, ‘What do you want, a sad face? Who wants a sad face around?’.” The left-brain interpreter, Gazzaniga says, is what everyone uses to seek explanations for events, triage the barrage of incoming information and construct narratives that help to make sense of the world.

This idea of a rationalizing, storytelling “interpreter” that helps maintain our sense of self makes me think that my original question — how Evan remained the same person after having so much of himself removed — is unanswerable. Evan will always be himself because the human experience of the world is jury rigged from whatever sensations are available and whatever stories our brains can construct.

Spiders make the front page

Spiders don’t usually get much good press. Whenever I told people I was writing a story for the Pittsburgh Post-Gazette on spider personalities, most people made a face like “ewww!!”

But spiders are some of the most interesting creatures you could imagine and — if you take the time to look at them — also beautiful.

Anyway, I tried to spread some of my enthusiasm by introducing Pittsburgh newspaper readers to behavioral ecologist and social spider personality expert extraordinaire  Jonathan Pruitt, who I wrote about here a couple of years ago. Now the story has ended up on the front page, complete with staged photo of Jonathan with his hands full of social spider webs, a la Spiderman. FYI, coating himself in spider webs is not something Jonathan does most days.

I also spent a fun day shadowing one of his visits to local schools, where students participate in spider research.

Sadly, one of my sidebars is missing from the online story, which included a description of how researchers use modified vibrators to simulate a prey item struggling in a web, to test communal foraging responses. Apparently it’s the most practical tool for the job 🙂

A Summer of Science News

I spent my summer getting to know DC, writing a crap ton of science stories and learning an absurd amount from the fabulous writers and editors at Science News. Rather than bombard you with random stories of variable quality, here are a couple of my faves from the summer:

Cabbage circadian clocks tick even after picking

In which I learn that cabbages can have jet lag.

Every six years, Earth spins slightly faster and then slower

I which I learn that the world is ringing like a bell and also discover that I love planetary geophysics.

On the Rebound

In which I learn that everything in modern history is tangled up in rubber.

Flagellum failure lets bacteria turn

In which I learn that ocean bacteria have a crazy-simple approach to steering.

Bacteria can cause pain on their own

In which I learn how bacteria get on your nerves.

Full moon may mean less sleep

In which I confirm that all the most memorable science starts at the bar.



The Natural & Logical Drains of Pittsburgh

On a rainy day in Pittsburgh, raw sewage spills out into the river. A marina employee hangs up an orange flag to warn boaters to avoid touching the water while a rowing team splashes past.

There are a lot of rainy days in Pittsburgh.

Typically, around 60 to 70 rainstorms per year cause a combination of sewage and stormwater to overflow at hundreds of points along Pittsburgh’s three rivers. These overflows disrupt the aquatic environment and contaminate the water with potentially disease-causing bacteria and viruses. Officials from the local sewage treatment authority say that fixing the problem will require the most expensive public works project the region has ever undertaken. Community activists say we could do it more economically by using “green” solutions. But whichever methods we choose, the Environmental Protection Agency (EPA) has made it clear: to continue to pollute our rivers is against federal law.

Pittsburgh is not the only city struggling with this problem. Joel Tarr, a professor of history at Carnegie Mellon University, says that large cities all over the Northeast inherited nineteenth century sewer designs that use the same pipes to carry both stormwater and household wastewater. These combined sewer systems were more economical to build than two separate systems and engineers of the time believed that running water purified itself. In 1912 the superintendent of the Pittsburgh Bureau of Construction even declared that “rivers are the natural and logical drains and are formed for the purpose of carrying the wastes to the sea.”

Four years before the superintendent made this statement, the City of Pittsburgh started filtering its water supply. In those four years, Pittsburgh’s typhoid rates — which had been the worst in the nation — dropped dramatically. In 1907, the year before filtration started, there were 4,283 typhoid cases in Pittsburgh. In 1912, there were only 188 cases. By treating the polluted water before people consumed it, Pittsburgh reduced its public health crisis, but that also meant it could continue discharging waste into the rivers. “Of course the downstream cities were not so happy about it,” Tarr says. Eventually, the Commonwealth of Pennsylvania enacted laws to regulate water quality in the rivers.

In 1959, after a protracted debate about the best way to satisfy these laws, the Allegheny County Sanitary Authority (Alcosan) finally opened what was then the largest sewage treatment plant in the nation. It was to treat sewage collected from more than 80 sewer systems, each owned and operated by a different municipality.

Until then, individual municipal sewer systems had discharged directly into the rivers at hundreds of outflow points. To divert these outflows into the treatment plant, Alcosan built an enormous collection system more than 100 feet under the river.

But the engineers were worried about Pittsburgh’s infamous wet weather. Every time it rains heavily, the volume of water in a combined system increases. Although Alcosan’s treatment plant could easily handle the amount of raw sewage entering on a dry day, it just did not have the capacity to treat all the water from a large storm. So they protected the system with hundreds of “escape valves.”

At each point where a municipal sewer reached the river, Alcosan built a shaft that directed the sewage down into the Alcosan system, and at each of these points where the two systems meet, they installed a regulator structure that could divert flow away from the collector system during storms. “Most of them are just big, flat plates,” says Arthur Tamilia, deputy executive director of Alcosan and its director of environmental compliance. “When a lot of water hits them, they tilt so that the majority of the water is directed into the river.” In the language of the EPA, this is a Combined Sewer Overflow (CSO) structure.

Tamilia says that the engineers who designed the CSOs assumed the dilution provided by stormwater would make the overflows less harmful and that the current would carry quickly away any pollutants.

Attitudes are different now. Every time sewage overflows into the rivers, the Allegheny County Health Authority issues an advisory that warns boaters and swimmers to “minimize direct contact” with the water, adding that anyone with a weakened immune system or open cuts is “especially vulnerable to infection from exposure to these contaminated waters.” Marinas and river access points hang out orange flags bearing “CSO” in black letters. On average, these flags fly for about half of the recreational boating season.

In addition to the overflow structures that were deliberately built into the combined sewer system, there are also unplanned overflows from the so-called sanitary sewers that serve the outer municipalities of Alcosan’s treatment area. Sanitary sewers are intended to carry only wastewater and are not connected to stormwater drains. However, stormwater frequently enters these systems anyway, both because aging pipes allow groundwater to leak into the system and because homeowners illegally connect their downspouts to the sanitary sewer system. This means that wet weather can cause overflows of concentrated sewage into nearby streams and eventually into the main rivers.

Sewer overflows of all types are now strictly regulated by the EPA. In 2008, Alcosan signed a legally binding agreement with the EPA that obliges it to eliminate sanitary sewer overflows and to limit combined sewer overflows to no more than 15% of the total wet weather volume of the combined sewer system.

Alcosan’s plan to meet this obligation is to expand their infrastructure. The biggest projects will be to increase the capacity of the treatment plant by around 60% and to build an enormous underground tunnel system to divert and store combined sewage overflows. They propose around 10 miles of 12-14 ft wide tunnels running underneath their existing collecting sewers, which would give the system an additional capacity of 62 million gallons of combined sewage. They estimate the cost at $2.8 billion dollars, which will be paid for by a doubling of homeowners’ sewage bills.

However, the plan still falls short of the EPA’s minimum requirements because 21% of the wet weather volume of the combined sewers would still reach the rivers. The requirement to eliminate sanitary overflows would also not be met, though the volume of sanitary overflows would be reduced by around 90%.

In their submission to the EPA, Alcosan argued that to satisfy their legal obligations by 2026 would require rate increases significantly above the EPA’s own affordability guideline of 2% of median household income. The EPA has yet to approve the modified plan, which was submitted in January, but many ratepayers still consider the plan too expensive.

“It’s the largest public works investment in the history of Allegheny County,” says Jennifer Kennedy, the campaign director for local advocacy group the Clean Rivers Campaign. “It’s going to cost more than Heinz Field, PNC Park, the Convention Center and the North Shore Connector combined.”

The problem, charges the Clean Rivers Campaign, is that Alcosan has focused exclusively on expensive “grey infrastructure” when it should have been pursuing the benefits of “green infrastructure.”

The Clean Rivers Campaign argues that the incorporation of green infrastructure into Alcosan’s Plan would not only be significantly cheaper than the current plan, it would relieve many other problems faced by the region, like flooding, poor air quality and urban blight.

While the goal of grey infrastructure projects is to increase the capacity of the sewer system, the goal of green infrastructure projects is to reduce the amount of rainwater entering sewers in the first place. One approach is to replace impermeable surfaces like concrete with porous paving designs that allow rainwater to soak into the soil and join the groundwater table.

Plants play a crucial role in many of these projects, since they absorb water and then release that water back into the atmosphere as vapor. For example, “green roofs” are partially covered with vegetation and “rain gardens” feature flood-resistant plants in a shallow depression that absorbs runoff. “Even a simple thing like a tree can soak up water and help it go into the air instead of going into our sewer system,” says Kennedy.

In addition to reducing the volume of water in the sewers, these strategies decrease the speed and intensity of runoff during storms, reducing flooding and erosion. Supporters claim the techniques improve air quality, reduce urban temperatures in the summers, provide habitat for wildlife, and even improve property values.

Above all, green infrastructure projects are small-scale and flexible. Matthew Jones, an engineer at a firm that specializes in green infrastructure projects, told the audience at a Clean Rivers Campaign event that one of the key benefits of the approach is that it can be rolled out incrementally and reach areas that might be inaccessible to very large construction projects.

However, this small scale also means that green approaches alone could probably not achieve the reduction in sewage overflows that is mandated by the EPA. What’s more, because the success of these projects is so heavily dependent on local conditions like soil type and weather, it’s difficult to estimate how effective they would be in Pittsburgh without an in-depth site evaluation.

Several non-profit organizations, including the Pittsburgh United coalition, are in the process of trying to quantify the potential of green infrastructure in Pittsburgh. But Tamilia says that the Alcosan plan had to be designed using existing evidence. “The information wasn’t available that would prove to the regulator’s satisfaction that it [green infrastructure] would make a significant difference.”

Kennedy says that the EPA actively encourages communities to embrace green infrastructure. She also says the activists’ dispute with Alcosan is about their failure to address any green approaches at all. “Instead of building giant tunnels first and then adding on green infrastructure later, we think it would be better to see how much water we can capture first, to see how big the tunnels should be” says Kennedy. “In Cincinnati, for instance, they’ve eliminated an entire tunnel system by being able to capture that water and keep it out of the system.”

Tamilia says Alcosan doesn’t have any objections to green infrastructure in principle, but they don’t have the legal power to implement it. The shared sewer authority can’t make urban planning decisions — like mandating green infrastructure standards for new developments — on behalf of its 83 constituent municipalities. “Every community still owns their own sewer system,” says Tamilia. “Right now we’re only able to control what we receive from those communities.”

Kennedy agrees that it’s a challenging issue, but says there are incentive strategies that Alcosan has the legal power to use.

But Alcosan is not the only organization under scrutiny. The municipalities are also being compelled to address the sewer overflow problem by the Allegheny County Health Department and the Pennsylvania Department of Environmental Protection. Although individual municipalities may be in a better position to implement green infrastructure strategies, their feasibility studies are not due until July of this year. This means Alcosan could not take the municipal plans into account in their stormwater plan that was due to the EPA in January. They built the plan around the assumption that municipalities would not reduce the amount of sewage they produce in the future.

When Alcosan released their stormwater plan for public comment last July, there was widespread community outcry about the cost and focus on grey approaches. In response, Alcosan requested an 18 month extension from the EPA to allow them to conduct its own feasibility study for green infrastructure.

Until the EPA reviews the stormwater plan, no one knows whether it will grant the extension. If there is an extension, it’s not clear whether Alcosan will judge green infrastructure approaches to be feasible or useful. Nor do we know whether Alcosan and its constituent municipalities will be able to work efficiently together or consolidate some of their infrastructure, as recommended by the Sewer Regionalization Review Panel, a committee of local stakeholders.

But one thing we do know is that grey infrastructure will be the backbone of Alcosan’s plan. “You will not be able to rely completely on green technology to cure these problems,” says Tamilia. “We’re looking at a combination of green and grey.” And since the proposed construction won’t be finished until at least 2026, Pittsburgh residents should continue to watch for orange flags flying along their rivers.

Picture of row crew in Pittsburgh

“Crew” by Flickr user Matthew Niemi

Where to learn more:

3 Rivers Wet Weather: 3RWW is a non-profit environmental organization that is helping Allegheny County municipalities work together to address sewer system problems. Their website has lots of educational information and resources.

And that concludes my little series of class assignments!

A Cocktail of Biology

DNA is not just found at crime scenes. It’s in every living thing – you, your cat, the bacteria on your hands and the grass under your feet. It’s in every meal you’ve ever eaten and, under the right circumstances, it’s even in your cocktail.

Strawberry picture

Supermarket strawberry. Hell yes I took this hazy photo with a $30 phone and a droplet of water.

The DNAquiri is a cocktail recipe that won Best in Show at the 2011 Science Hack Day San Francisco because it is also a protocol for extracting DNA from strawberries. The recipe calls for only three ingredients – frozen strawberries, pineapple juice and high-proof rum – but the final product is a complex cocktail of curiosities.

This post is another of my recycled school assignments, in which I was given the slightly daunting task of writing a story in the form of a list. I decided the best kind of list is a recipe, and the best kind of recipe is one that involves both science and cocktails. A deep bow and a tip of the hat to Margot at Hypatian Axis for drawing my attention to the quirky back story of the modern strawberry.

1) Strawberries

Strawberries are a convenient source of DNA because they are delicious and they are octoploid. Octoploid means that each cell in a strawberry contains eight copies of every gene. In contrast, human cells are diploid, with only two copies of each gene, one from mom and one from dad. In the same way, strawberry cells have four copies from mom and four copies from dad, and yes, strawberry plants do have parents. In fact, according to G.M. Darrow in The Strawberry: History, Breeding and Physiology,the mother and father of the cultivated strawberry were the stars of an unlikely transcontinental plant romance.

It all started in 1712, when some unusually plump strawberries caught the eye of a French spy in Chile. The spy was Amédée François Frézier, an engineer in the French Army Intelligence Corps who was spying on Spanish defenses in South America. He noticed that the strawberries cultivated by the locals were much larger than European strawberries and selected several specimens with excellent fruit to take back to France.

Although these plants survived an arduous 6-month voyage to Europe, they did not immediately live up to Frézier’s enthusiastic description. The king’s gardener could not get them to reliably produce oversized fruit “as big as a Walnut, and sometimes as a Hen’s Egg”. By choosing only fruiting plants, Frézier had inadvertently selected only females. At that time, nobody realized that strawberry species often have separate sexes, which is relatively unusual for plants. Male plants carry pollen, while female plants bear fruit, so those female strawberry immigrants were effectively infertile. This is where we meet dad.

Dad was the Virginia strawberry, a wild species still common in the Eastern US that was introduced into Europe in the 1600s. While botanical gardens initially struggled to produce Chilean strawberries, enterprising farmers succeeded by alternating rows with other strawberry varieties. These included some male plants with pollen that could fertilize the Chilean females. The Virginia strawberry gave the best results and the descendents of this pairing became the modern strawberry, which is strongly flavored like its Virginian ancestors, but large like the Chileans. Part of the reason the match worked genetically is that while the European strawberry varieties were mostly diploid (with two copies of each gene per cell), both the Virginia and Chilean strawberries were octoploid2.

This octoploid romance means that every cell of a supermarket strawberry is jam-packed with DNA, making it easier for us to extract enough DNA to see with the naked eye. But first, you need to get the DNA out of the cell.

When strawberries freeze, the water in the cells forms ice crystals that puncture the cell membranes. So if you put frozen strawberries in a Ziploc bag and then squash them, warm them to 50°C then chill them again, some of the DNA will spill out of the leaky cells. Force the pinkish mush through a strainer to get rid of the lumps and you’ll have a strawberry cell extract, otherwise known as juice.

2) Pineapples

The strawberry juice contains DNA, but it also contains all kinds of other stuff from inside the cells, including proteins. Proteins translate the genetic information in DNA into action; DNA sequences carry the instructions for making lots of different kinds of proteins, which in turn do many different jobs. But when all those strawberry proteins are released from the cell into the juice, some of those jobs interfere with the process of DNA extraction.

For example, some of the proteins wrap around the DNA strands, winding them into bundles that don’t extract well. Other proteins chop up the DNA. To counter the effects of all these proteins, you can add “protein-chopping” proteins called proteases. Proteases chop other proteins into bits and although they can be found in all cells, they are found in conveniently large quantities in pineapples. In fact, pineapples have such high concentrations they are used in industrial applications. They are even available in the supermarket, sold as a meat tenderizer that works by digesting the collagen protein that gives meat its structure.

Pineapple - up-close (macro)

Pineapple close-up. By Uri_Breitman (Flickr) [CC BY-NC 2.0]

This is also why pineapple has a bit of a bite to it — that burning sensation when you eat too much pineapple is from proteases damaging proteins on the surface of your tongue.

To digest away the protein in your strawberry mush, simply add some cold, unpasteurized pineapple juice and let the proteases do their work. Now your Ziploc bag contains strawberry DNA and strawberry proteins being chopped up by pineapple proteins. But the DNA is still invisible.

3) Rum

Your next step is to force the DNA to stick together into a clump that you can see. To do this you pour a layer of ice-cold, high-proof rum over the strawberry cell extract. “High proof” just means a high concentration of alcohol (ethanol), in this case 70%, which is about twice as high as normal rum.

In watery liquids, such as strawberry guts and pineapple juice, DNA is coated in a loosely bound layer of water molecules (called a “hydration shell”). This coating prevents the DNA, which is negatively charged, from binding the positively charged ions (like the sodium from table salt2) that are also floating around in solution. But ethanol disrupts the hydration shell and makes the DNA more attractive to positively charged ions. Under these conditions, the DNA will tightly bind positively charged ions that neutralize the overall charge of the DNA. Because the DNA molecules are now neutral, instead of repelling each other, they tend to stick to each other, forming much larger, visible blobs (see note 3 below for my original, quite wrong explanation).

Understandably, ethanol at a high enough concentration to cause DNA to stick together is highly toxic to cells (you could use high-proof rum as effective but expensive disinfectant). But the ethanol in your bottle of rum was originally made by cells — yeast cells.

Yeast are fungi, like mushrooms, but they are microscopic, consisting of only a single cell. They excrete ethanol during the process of extracting energy from fruit sugars. Grapes and other fruit are the natural habitat of yeast, at least during the summer. According to scientists at the University of Florence, yeast’s winter home is in the guts of wasps that feed on grapes. These wasps provide a warm and moist refuge from the elements while fruit is out of season and once the fruit ripens they provide transportation to the site of the annual sugar feast.

Yeast on grapes

Grapes. By Scharks [CC-BY-SA-2.0], via Wikimedia Commons

Preventing other microbes from joining in on the feast is part of the reason why yeast cells excrete ethanol. Yeast get their energy from sugar by converting it to ethanol and carbon dioxide, a process called fermentation. Fermentation generates much less energy than respiration, the method that humans use to metabolize sugar, but fermentation is much faster and has the added benefit of producing a toxic by-product, ethanol. When a wasp inoculates a grape with yeast cells, the yeast rapidly convert their surroundings into an acidic, alcoholic soup that is inhospitable to most other microbes.

Humans have taken advantage of yeast’s curious lifestyle to produce alcoholic drinks, but we have also used it to advance scientific knowledge. For example, studies of yeast fermentation overturned Louis Pasteur’s hypothesis that cells were powered by a mysterious vital force that fundamentally distinguished living from non-living things.

The basic unit of life is the cell, which can grow and divide to make more cells. Pasteur had found that some chemical reactions — like fermentation of sugar to alcohol — could only be catalyzed by live yeast. Vitalists like Pasteur argued that live cells possessed a “vital spark” that allowed them to become more than the sum of the biochemical reactions occurring inside their cell membranes.

As recounted by Christian Reinhardt in Nobel Laureates in Chemistry, 1901-1992, Pasteur’s strain of vitalism was dealt a death blow by Eduard Buchner, a German chemist who was trying to extract proteins from yeast cells without damaging the proteins in the process. He managed this in 1896 by grinding yeast with sand and then filtering out the slurry of broken cells to produce a non-living “yeast juice.” There were no yeast cells remaining in the juice, but it did contain many of the biochemicals, like proteins, that had once been inside the cells. To stop this mix from spoiling before it could be used in other experiments, Eduard, who had once worked in a cannery, tried the method that preserves fruit in jams — ­adding a high concentration of sugar. To his surprise, within 15 minutes of adding sugar to the yeast juice, it started to froth like a fermenting beer.

Rising bubbles from yeast fermentation

Bubbling yeast fermentation. By Jim Champion (Flickr: Rising bubbles) [CC-BY-SA-2.0], via Wikimedia Commons

Buchner was able to show that the proteins in the yeast juice could produce carbon dioxide and ethanol from sugar in a way that was identical to fermentation by live cells. Pasteur was wrong, and no vital force was necessary to explain the metabolic activities of the cell. Cells were really just the sum of their parts.

Buchner’s experiments were a key moment in the dawn of biochemistry, the field that uses non-living extracts of living things (like your strawberry juice) to understand the chemical reactions that allow cells to function. One of the most important discoveries of biochemistry has been that many of these chemical reactions are similar in all organisms, and that all living things share the same genetic code. So, once you see a white film form in a layer between the pink strawberry juice and the amber rum, take a cocktail stick, twirl it around in the film and remove a blob of DNA. This unassuming clump of slime is the hidden genetic material that helped make those delicious strawberries. Be sure to give your drink a good stir before you toast the shared heritage between yeast, pineapples, strawberries and yourself.

DNAquiri blob extraction

Blob of unknown identity. By me.

Sad taster’s note and party poopery: I’ve tried the DNAquiri recipe twice and each time have achieved a very respectable yield of white slime and an almost drinkable cocktail (it’s a bit strong for me). However, I’m going to guess that the slime is not actually DNA, but instead is pectin, a cell wall carbohydrate that gives fruit jams and jellies their gel-like consistency. I base this guess on a suggestion from the UK’s National Centre for Biotechnology Education and the fact that the slime isn’t as stringy as I’m used to for DNA. Please weigh in, all you fruit DNA experts! I want to know!

1More party poopery: Darrow’s story about the origin of the three strawberry flowers on the Fraser coat of arms is probably false. Darrow recounts an old myth that Frézier and the Scottish Fraser clan were descended from one Julius de Berry, who was knighted in 916 by the Emperor of France, King Charles the V. According to the legend, de Berry was knighted in reward for his miraculous ability to provide unseasonably ripe strawberries for a feast. He was given a new coat of arms and a new name, Fraise, which is French for strawberry.

2At this point, anyone who has ever done a DNA precipitation before will be all like “where’s the salt???!”  Typically, it is necessary to add salt to the mixture to provide enough positive ions to neutralize the DNA. The creators of the DNAquiri left the salt out so that the final cocktail was not profoundly disgusting, but I suspect that this favors the precipitation of polysaccharides (like pectin) more than nucleic acids. (note added May 25, 2013).

3 This is not the original version of the explanation I had. Embarrassingly, it originally read:

The interior of a cell is watery and DNA is a ”water-loving” or hydrophilic substance that dissolves readily. But just as oil and water don’t mix, hydrophilic substances don’t mix well with “water-hating” or hydrophobic substances, like ethanol. When immersed in ethanol, DNA molecules stick together into much larger, visible blobs.

Then @EricGumpricht called me out on my decision to call ethanol “water hating,” which was convenient for my word limit, but of course, not remotely true — cocktails wouldn’t be much fun if spirits weren’t miscible with water! I was trying to describe ethanol precipitation without turning this into a chemistry lesson and talking about dielectric constants and whatnot, but I failed miserably (as usual, I blame sleep deprivation and my unwillingness to proofread blog posts). I’ve experimented with an explanation that doesn’t mention polarity because otherwise I ended up with a pretty dull essay. If you have taken high school chemistry and are genuinely interested in how ethanol precipitation works, try these much better explanations:

Bitesize Bio: How ethanol precipitation of DNA and RNA works (requires registration)

Paul Zumbo: Ethanol precipitation (PDF)

(note added May 25, 2013).

ScienceSeeker Awards: The best of the best

The results of the  inaugural Science Seeker awards have been announced! Nominated by your excellent selves and judged by superstars  Fraser CainMaggie Koerth-Baker, and Maryn McKenna, the list of finalists and winners is a wonderful sampling of fine science blogging from the past year. Congratulations to all!

I got strangely nostalgic going through the list because it reminds me how fun it has been making my ScienceSeeker picks over the past year or so, even if I was a bit unreliable about blogging them!



Step 2 of my strategic plan: Post my favourite class assignments from the past year, which will start this week with manure and will eventually end with sewage. Enjoy.

We tend to think of nineteenth century cities like Pittsburgh as industrializing under the power of steam. But Joel Tarr argues that an older technology also drove the development of the great cities of the steam age.

In 1775 James Watt patented the steam engine, a machine that would become a symbol of the industrial revolution. Forty years later, Benjamin Latrobe opened a steamboat engine workshop on the banks of the Monongahela River in Pittsburgh. The power source that Latrobe used to build his engines? Two blind horses.

Horses like Latrobe’s were a central cog in the nineteenth century urban economy. They were hooked up to engines through circular sweeps, rotating platforms and treadmills, and harnessed to vehicles on wheels and tracks. City horses hauled steel, powered ferries, pressed bricks. They were the source of valuable manure and even more valuable carcasses. They were the catalysts for the paving of streets and the suburbanization of cities.

But, like the combustion engine, their great success as a technology also contributed to their eventual decline. Thanks to the work of Joel Tarr, a professor of history and policy at Carnegie Mellon University, and his colleague Clay McShane, a professor of history at Northeastern University, we are rediscovering how horses hauled cities like Pittsburgh into the modern age.

Horses at construction site

Horses at Cincinnati subway construction site, probably the 1920s. Image credit: University of Cincinnati Library.

Rediscovering the horse as an urban technology

Joel Tarr thought he was done with horse manure back in 1971. The Jersey City native had joined the faculty at Carnegie Mellon in 1967 with a background in urban political history and an interest in how the modern city had been shaped by transport technologies. During his research, he kept coming across historical complaints that he thought might be interesting to a general audience.

The article he submitted to the magazine American Heritage was a vivid account of the problems faced by a horse-driven city, including the staggering scale of manure logistics:

…as health officials in Rochester, New York, calculated in 1900, the fifteen thousand horses in that city produced enough manure in a year to make a pile 175 feet high covering an acre of ground and breeding sixteen billion flies, each one a potential spreader of germs.

“Urban Pollution— Many Long Years Ago”, American Heritage, 1971

Tarr noted that the eventual solution to these problems was the adoption of a new technology, one that harnessed machines rather than animals. “Apparently the editorial board got into a big fight about it because some of them thought that it was an apology for the automobile,” he recalls.

Controversial from the start, the article prompted several newspaper editorials and is still cited today in debates about pollution. But after creating a stir, Tarr moved on, reasoning that “someone else could worry about the horse manure.” And so he pursued his interests in the environmental and technological history of cities and left the subject of horses alone for more than twenty years.

But while the details of the manure problem lived on in the public imagination, Tarr knew that there was much more to say about the importance of horses in the history of our cities. In 1995, he refused to allow the manure article to be reprinted in an anthology and instead asked if he could write a new article on the topic with his friend McShane, who had recently published a history of cars in cities. From that first article, the project ballooned out into a decade of scholarship and co-authorship of their 2007 book on horses as an urban technology, The Horse in the City: Living Machines in the Nineteenth CenturyThe book is a detailed examination of the centrality of horses to cities, focusing on New York City, Boston, and Tarr’s adoptive home, Pittsburgh.

From steam power to horse power

Tarr and McShane emphasize that the horse was viewed as a “living machine,” valued primarily for its ability to provide power. As machines, horses were an integral part of the economy, even after the advent of the steam engine.

After refining the steam engine, James Watt invented a standard measure of mechanical work – 33,000 foot-pounds of work per minute, or 1 horsepower. This unit allowed customers to estimate how many horses an engine could replace and to gauge whether replacing their horses would be economic. In many cases, it wasn’t. For much of the nineteenth century, horses were the engine of choice for applications that required flexibility or mobility and for businesses that could not afford a large capital outlay.

But the one application in which horses were irreplaceable was ground transport within the city. Goods from the expanded railway and steamboat lines could only be distributed to their final destinations under the power of horses, which meant that horse-drawn transport grew more efficient in parallel with steam technology. Innovations in breeding produced larger and larger horses in the pursuit of (as one agricultural reformer put it) “the best machine for turning food into money.” These industrial-strength horses could pull even larger loads after the development of lighter vehicles made with modern materials.

One resident of Pittsburgh remembered the “pandemonium of noises” produced by horse transport in the 1860s:

Numerous wagons, hauling heavy pigs of iron and iron products, timber wheels with anywhere from six to fourteen horses from which huge and unwieldy vehicles hung castings of many tons’ weight, the clattering omnibus, the rattle of the mail wagons, drays […] and other conveyances common to traffic.

George Thornton Fleming,1904

This was the cacophony of Pittsburgh’s developing steel industry, the sound of a modern city propelled by coal and hooves.

Photo of 1897 traffic

Horse-drawn wagons and carriages, an electric trolley car, and pedestrians congest a cobblestone Philadelphia street in 1897. Image credit: National Archives and Records Administration, 30-N-36713.

Shaping the city

The structure of Pittsburgh’s neighborhoods today still reflects the age of horse-drawn vehicles. Public transport began with road vehicles called omnibuses, but gathered momentum with one of the most influential urban innovations of the nineteenth century, railed “horsecar” lines. These tracks, the precursors of the cable car and electric streetcar systems, provided a smooth ride that omnibuses could never achieve on cobbled pavements that were optimized for horseshoe traction. The benefits of the tracks were not just to the spines of riders, but to the speed the horses could travel, the number of riders they could haul, and the amount of profit their owners could make.

The first lines were laid in 1863 and by 1890 the average Pittsburgh resident took 192 horsecar trips per year. The tracks had grown along the lines of least resistance, following valleys and avoiding the worst of Pittsburgh’s steep hills. As the lines expanded, ridership increased at a rate much faster than population growth, reflecting Pittsburgh’s shift to the suburbs; Residents could now live further away from downtown and make a daily commute to work. Wards within an hour’s smooth ride of downtown were suddenly more desirable than when they were a longer, more expensive and more bone-jarring omnibus ride. The relatively flat Eastside saw the biggest growth – between 1870 and 1890 it grew from 5,350 dwellings to 17,604. Construction boomed in areas within a ten-minute walk of a horsecar line. Tarr and McShane write that “the greater speeds allowed Americans to fulfill the new dream of the middle class, a detached home with a yard on the outskirts of a city.” Meanwhile, downtown was losing residents to the new suburbs and slowly transforming into a true central business district.

Tarr and McShane point out that the horsecar alone did not cause these changes in Pittsburgh and other growing cities. Factors like economic expansion, population growth and a new appreciation for suburban life played an important role, but the horsecar was the technology that allowed these trends to play out, and it set the patterns that were extended in the twentieth century by the streetcar and the gas-fueled automobile.

Problems with the living machine

In 1872, American horses came down with a terrible case of the flu. Several Northeastern cities ground to a dramatic halt. The horse flu epidemic cut off city supplies, grounded fire departments, and isolated suburbs from their vital horsecar lines. When one commentator later warned that another epidemic would reduce New York City to “straits of distress,” he concluded that although “cities have been made by building around the horse there is no necessity for keeping him permanently as their centre.” As the century progressed, more and more objections were made to the city’s dependence on horses.

Like all technologies, horses had their downsides. They were living creatures, susceptible to disease, unreliability, and even personality. They required an enormous infrastructure of foul-smelling stables, with stockpiles of hay that posed a significant fire hazard. But above all, horses were prolific polluters. The average city horse unleashed 25-35 pounds of manure and two to three gallons of urine per day.

Horse manure started out as just one of the many hazards of urban life, but as the century progressed, the exploding city horse population became a source of public angst and newspaper editorials. To make matters worse, by the 1880s the bottom had fallen out of the manure market.

Fresh manure had long been a valued commodity, sold by stable owners and street sweepers to farmers on the urban periphery. But thanks partly to competition from new guano and rock phosphate fertilizers, the price of manure had fallen to less than a quarter of its worth. A New York Times editorial from 1881 conveys the confusion caused by a city decision to declare summer dumping grounds off-limits amidst the glut of manure: “Public health nuisance: No place for stable manure—What is to become of it?” By 1908, one journalist claimed that 20,000 New Yorkers died each year from “maladies that fly in the dust, created mainly by horse manure.” The biggest problem was that the accumulating piles were a favorite breeding ground for flies, a vector for life-threatening diseases like typhoid.

Part of the solution to the manure problem was technological. By 1902 most horsecar lines had transitioned to electric trolleys only a decade after they had been first introduced. But the manure problem itself was not necessarily responsible for the speed of this change. Tarr and McShane argue that in many cases, the new technology was rapidly embraced by horsecar companies because these companies did a tidy side business in land speculation. Horsecar lines had the reliable effect of pushing up property prices wherever they were laid, but by the late 1880s, horsecar lines had mostly expanded as far as they could within a one-hour commute of downdown. With the increased speed of electrified trolleys however, horsecar companies could expect to double that radius and reap the rewards in real estate. As a result, these companies became intimately involved in urban politics and in many cases bought themselves influence on city councils to ensure they received the necessary franchises. Within a decade, most of the lines had switched over to electric.

For a few more decades, horses were still favored for tasks like fighting fire, hauling waste, and making neighborhood deliveries. But by the end of World War II, even these jobs fell to the automobile. The horse manure problem was solved and the age of the car had begun.

The technological solution

Despite the initial optimism that cars were a clean and efficient alternative to the horse, the new technology has also become a victim of its own success. The burning of fossil fuels generates air pollution that can be as hazardous to human health as the diseases spread by flies, and it releases carbon dioxide that contributes to climate change. A century after the decline of the horse, we are again facing a chronic pollution problem.

Embedded among the engineers and policy faculty of Carnegie Mellon, Tarr has consistently pursued historical questions that provide perspective for contemporary policy debates, particularly the problems of urban waste. But ever since Tarr published that first article on the horse manure problem, commentators have repeatedly used the story as a parable about the wonders of technological fixes to environmental problems. For instance, Steven Levitt and Stephen Dubner used the story of the horse in their 2009 book SuperFreakonomics to justify the use of radical geoengineering solutions to climate change.

Tarr himself doesn’t believe technological change is always a panacea. “Why do we automatically assume that every new device will be better?” he asks. He has made urban technological change one of his specialties because he believes it is important that we understand the drivers of change. “History circles,” he explains.

This particular circle has come around quickly. In Tarr’s office there is a reproduction of a magazine photo hanging prominently amongst the accumulated books and papers; in it stands his father in a worker’s cap, cigarette between his lips, at work under the harsh light of the night shift at a shipyard. He had been one of those workers who built the urban landscape with the help of a living machine. “He had a horse,” Tarr says, “back when he was in the scrap business in New York. He had a horse called Shivers, and that’s just about all I know about it.”

Where to Find Out More

The Horse in the City: Living Machines in the 19th Century by Clay McShane and Joel Tarr Johns Hopkins University Press, 2007.

“The Centrality of the Horse in the Nineteenth-Century American City,” Clay McShane and Joel Tarr, In Raymond A. Mohl (ed.), The Making of Urban America Scholarly Resources, Inc., 1997.

“The Horse Era in Pittsburgh,” Joel Tarr, Western Pennsylvania History, Summer 2009, 28-41

Blobologist-approved reads: oops, is it May?

Apologies, my dear, neglected readers, for posting so infrequently, but things have been a little hectic in the House of Blob this semester. Sadly, this meant there was no time for blogging. On the positive side, I did at least spend that time writing about science, InDesigning up a storm, creating a hella professional social media strategy for a clinical research group and building a pretty respectable looking website for a local non-profit.

But now I’m left with a blobology backlog that I will address with the following strategic plan:

1) Present my ScienceSeeker picks from the past few months, even though they are now horrifically out-of-date

2) Post a couple of my favourite science writing class assignments

3) Mix myself a Dark ‘n’ Stormy

I might not follow this plan in the prescribed order.

My ScienceSeeker editor’s picks: The semester shell-shock edition

The Unresolved Mysteries of the Mold in Your House
Contains the answer to the question, “What do your dishwasher and fruit bat’s colon have in common?”
Rachel Adams at Your Wild Life (guest)

When #chemophobia isn’t irrational: listening to the public’s real worries.
Part of the on-going conversation about chemophobia, which is the blanket distrust that many people feel towards anything they consider “chemical.” But shouting at people that they don’t understand what that word means doesn’t help anyone, least of all chemists.
Janet D. Stemwedel at Doing Good Science

How genetic plunder transformed a microbe into a pink, salt-loving scavenger
A tale of genetic thievery on an epic scale.
Lucas Brouwers at Thoughtomics

How to protect lions?
Can we really protect lions by fencing them in or by hunting them?
Colin Beale at Safari Ecology

Ducks Meet the Culture Wars
A beautifully written defense of basic science and the point of studying duck penises.
Carl Zimmer at The Loom

The Narcissism of De-Extinction
If you follow me on Twitter you might have noticed that the TedX DeExtinction conference got me uncharacteristically irritated and even made me break out some ALL CAPS OUTRAGE. Thankfully, by the time I extricated myself from TweetDeck Hannah Waters was already ON IT, explaining much more thoughtfully and lucidly than I could why it was just ALL SO ANNOYING.
Hannah Waters at Culturing Science

Roller Derby Teammates Give Each Other Bacterial Hugs
Roller Derby teams are close and so are their skin microbes.
Kate Clancy at Context and Variation

The two ideas to fix the gender balance that do not make me cringe
Two recent (at least, they were recent when I made this pick) initiatives for addressing the fact there are not enough women in the most powerful positions in science.
Eva Amsen at Occam’s Typewriter (guest)

There Should Be Grandeur: Basic Science in the Shadow of the Sequester
On the risks posed to basic research by the sequester. Featuring the line: “paying for basic research is a bet a society makes on its future.”
Tom Levenson at Scientific American Guest Blog

Buzzsaw Jaw Helicoprion Was a Freaky Ratfish
So paleontologists finally solved the mystery of where to put the the spectacular buzzsaw jaws on their Helicoprion reconstructions.
Brian Switek at Laelaps

Carey Morewedge serves up an imaginary feast

Dear Blobologist,

I know I’ve been neglecting you recently. As a peace offering, here’s a class assignment I did a few weeks ago, based on an interview with a researcher from my university. I hope it will tide you over.


Cristy xx


Imagine your favorite food.

Chocolate, cheddar cheese, chicken tikka masala, whatever your weakness, picture it just out of reach, glistening enticingly.

Although this food isn’t real, your body might be responding as if it were. Perhaps your mouth is watering or maybe you’re feeling the pang of cravings. But Carey Morewedge, a psychologist at Carnegie Mellon University, says food fantasies can have an even stranger effect; he has shown that we can be satisfied by imaginary food.

When Morewedge and his collaborators, Young Eun Huh and Joachim Vosgerau, began their research into imaginary feasts, most psychologists believed that the more you thought about food, the more you craved it. The problem with this idea was that when you eat food in real life, you crave it less rather than more. Our first mouthful of a favorite dish makes us desire it more, but as we eat bite after bite, we start to lose interest. This loss of interest is called “habituation” and is part of every pleasurable experience, from food to sex to watching Gangnam Style.

So why doesn’t imagining food also make us lose interest? Morewedge and his group asked this question because when we imagine an experience, our bodies and minds often respond as if that imagined experience were real. They guessed that the reason previous studies had not observed habituation was because study participants didn’t take their imaginary experiences far enough.

“If I’m thinking about a Chipotle burrito, I’m thinking about the shape, what’s inside it, what it will taste like on the first bite, what it might smell like, or how warm it might be,” says Morewedge. “But I do not think about biting, chewing and swallowing the whole burrito.”

So the researchers asked people to think about biting, chewing and swallowing M&Ms. Each person in their study imagined performing 33 repetitive actions: either inserting 33 quarters into a laundry machine, inserting 30 quarters into the machine and then eating 3 M&Ms, or inserting 3 quarters into the machine and eating 30 M&Ms. Inserting quarters was chosen as a control for imagining an action similar to picking up candy.

After their mental exertions, the participants were allowed to eat as many M&Ms as they wanted during preparation for a fictitious “taste test.” Psychologists often include these kinds of deceptive scenarios to prevent people guessing what behavior is being measured, which can influence their response.

After each experiment, Morewedge’s team weighed the M&M bowl to see how much the participant had eaten. The results showed that people who had imagined eating 30 M&Ms ate almost half as many real M&Ms as those who imagined eating only three. In effect, they had satisfied their desire for M&Ms without actually eating any.

This only worked when people pictured eating the M&Ms. When they instead imagined moving the candy into a bowl, the people who moved more imaginary M&Ms ended up eating more real M&Ms, rather than fewer. That kind of imagery only whetted their appetites.

But was this really habituation? To test this, the researchers looked for one of the hallmarks of habituation, called sensory specificity or the “dessert stomach” effect.

“We’ve all heard of this phenomenon,” says Morewedge. “When you go to a restaurant, you finish your entree and you can’t even imagine eating another bite. And then someone rolls out a cart of cheese or cakes, and all of a sudden you have a renewed interest in food.”

Just like real habituation, the imaginary M&Ms did not affect participants’ desire for other types of food, in this case, cubes of cheddar cheese. It worked the other way as well: eating more imaginary cheddar cheese meant people tended to eat fewer real cheese cubes, but it had no effect on how many M&Ms they ate.

So does this mean you can think yourself thin? Probably not. The dessert stomach effect is one reason why Morewedge doesn’t think we’ll see their results become the next diet craze. Imaginary eating habituates you to the food you have imagined, but makes other foods seem even more appealing.

Instead of using the research to come up with a diet miracle, the group is trying to apply their results to other contexts, like cigarette smoking, to see if mental habituation might be a useful tool for modifying addictive behavior.

But even if we are never able to harness the power of that imaginary chicken tikka masala for practical use, Morewedge and his colleagues have made an important theoretical advance. The line between imagination and physical experience is blurrier that we used to believe — a pleasant idea to contemplate the next time you get a hankering for something just out of your reach.

m&ms on asphalt

Photo credit: Flickr user Zen. Shared under this Creative Commons license