The 2011 Pulitzer Prize in Explanatory Reporting honored the Milwaukee-Wisconsin Journal Sentinel’s coverage of a 4-year-old whose intestinal disorder was finally diagnosed after sequencing his exome. Once investigators assigned a gene to his symptoms, a bone marrow transplant saved his life. And a just-published study compared the exomes of 12 children with combinations of developmental delay, intellectual disability, and birth defects at the Duke University genetics clinic to reference exomes, revealing 7 mutations, 2 in genes not known to be associated with disease.

In the best-case scenario, mutations revealed by exome sequencing suggest a treatment, as it did for the 4-year-old. But that may be unusual. “We can’t treat most of the Mendelian diseases we know about, so we won’t be able in the near and medium term to treat most of the cases that are diagnosed by sequencing,“ says David Goldstein, PhD, director of the center for human genome variation at Duke and an author of the study. The new National Center for Advancing Translational Sciences may add to existing treatments and new drug discovery by providing access to compounds from three major pharmaceutical companies. One study’s reject could be another’s cure.

But for certain types of genetic disorders, exome sequencing won’t help. Understanding what, exactly, an exome is reveals why.

A little less than 2% of the 3.2 billion bases of a human genome encode protein. Most genes consist of sections that are transcribed (into RNA) and translated into protein — these are exons – and sections that are transcribed but are then snipped out before the protein forms – these are introns. The exome, including only exons, is to the genome what a Wikipedia entry about a book is to the actual book. It’s part of the story, albeit an important part.

Admission: Back in the Precambrian period when I was in high school, I read the CliffsNotes version of John Steinbeck’s “The Grapes of Wrath.” I read the actual book many years later, and what a difference! The meager plot summary I read in high school missed the nuances, the connections, the feel and the utter devastation of the final scene.

Analyzing an exome to understand a disease is, in some cases, like reading the CliffsNotes version of a classic book.

The 10 Exceptions

Understanding the limitations of exome sequencing is important because it’s already here. “Be one of the first to get your personal exome sequence,” proclaims 23andMe, about its pilot Exome80x project, offered direct-to-consumer, “for research and educational use only.”

The first CLIA-certified test, Clinical Diagnostic ExomeTM, became available from Ambry Genetics earlier this year. A news release announcing the diagnosis of three tough cases calls the technology “essentially a human genome project for an individual patient.” Said CEO Charles Dunlop, “Some of these families have been trying to figure out what was ailing their children for years, and we solved the riddle in weeks.”

But exome sequencing won’t help every family, and here’s my list of reasons why. The technology won’t detect:

1. Genes in all exons. A few exons, such as those buried in stretches of repeats out towards the chromosome tips, aren’t part of exome sequencing chips.

2. Mutations in the handful of genes that reside in mitochondria, rather than in the nucleus.

3. “Structural variants,” such as translocations and inversions, that move or flip DNA but don’t alter the base sequence (detectable other ways).

4. Triplet repeat disorders, such as Huntington’s disease and fragile X syndrome. Their mutations don’t change the DNA base sequence – they expand what’s already there.

5. Other copy number variants will remain beneath the radar, for they too don’t change the sequence, but can increase disease risk.

6. Genes in introns. A mutation that jettisons a base in an intron can have dire consequences: inserting intron sequences into the protein, or obliterating the careful stitching together of exons, dropping gene sections. For example, a mutation in the apoE4 gene, associated with Alzheimer’s disease risk, puts part of an intron into the protein.

7. “Uniparental disomy.” Two mutations from one parent, rather than one from each, appear the same in an exome screen: the kid has two mutations. But whether mutations come from only mom, only dad, or one from each has different consequences for risk to future siblings. In fact, a case of UPD reported in 1988 led to discovery of the cystic fibrosis gene.

8. Control sequences. Much of the human genome tells the exome what to do, like a gigantic instruction manual for a tiny but vital device. For example, mutations in microRNAs cause cancer by silencing various genes, but the DNA that encodes about half of the 1,000 or so microRNAs is intronic – and therefore not on exome chips.

9. Gene-gene (epistatic) interactions. One gene affecting the expression of another can explain why siblings with the same single-gene disease suffer to a different extent. For example, a child with severe spinal muscular atrophy, in which an abnormal protein shortens axons of motor neurons, may have a brother who also inherits SMA but has a milder case thanks to a variant of a second gene that extends axons. Computational tools will need to sort out networks of interacting genes revealed in exome sequencing.

10. Epigenetic changes. Environmental factors can place shielding methyl groups directly onto DNA, blocking expression of certain genes. Starvation during the “Dutch Hunger Winter” of 1945, for example, is associated with schizophrenia in those who were fetuses at the time, due to methylation of certain genes. Exome sequencing picks up DNA sequences – not gene expression.

3 Great Uses for Exome Sequencing

Exome sequencing is of great value in two obvious situations: (a) finding a mutation in a known gene behind an “atypical presentation,” such as Nicholas Volker, the saved Pulitzer boy; and (b), identifying mutations in novel genes, like 2 of the 7 children in the Duke University clinic.

Another application is subtle: exome sequencing reveals incomplete penetrance, a phenomenon in which a person gets lucky. He or she has mutations that should cause a particular trait or illness, but they don’t.

Exome sequencing of parent-child trios can reveal when an apparently healthy parent actually has the same mutation as the sick child, but for some reason escaped the genetic fate. A genetic counselor would use this information in predicting risk for siblings. If mom or dad contributes a mutation, the next kid faces a much higher risk than if the affected child has a new mutation. But there’s a bigger picture. Figuring out how the parent stays healthy can reveal new drug targets, and perhaps even lead to repurposing an existing treatment.

Happily, exome sequencing has a limited lifetime, because, like climbing a mountain or running a marathon, an end is in sight: knowing what all of our genes do.

With each new email comes a poignant story about a child whose world is silent. It is estimated that hearing loss affects 11% of school age children and even mild loss may adversely influence school performance, cognitive development and language acquisition. The most common type of hearing loss, sensorineural, is the result of injury to the hair cells of the inner ear’s Organ of Corti, most commonly due to infections, medication, noise and aging.

A digitalized image of a stem cell near hair follicles

Hair cells are mechano-transducers which convert sound energy received from the outer and middle ear structures into an electrical signal which is then transmitted by the cochlear nerve to the brain. If enough of a human’s 17,000 hair cells are damaged, then sufficient sound energy cannot be transmitted to the brain, and the result is hearing loss. While birds and reptiles replace damaged hair cells, mammals normally do not.

Although hearing aids and cochlear implants, the two main treatment modalities for sensorineural hearing loss (SNHL), have helped millions with impaired hearing around the globe, these devices do not restore or repair hearing. The idea of a cure has long been a dream for many parents of deaf children and the professionals who work with them. The sad reality, however, is that SNHL is currently considered irreversible. With the emergence of regenerative medicine and stem cell therapy, however, that dream may at last be within reach.

The Food and Drug Administration (FDA) has recently approved our groundbreaking trial to evaluate the safety of using a child’s own cord blood stem cells to regenerate damaged cells in the inner ear and potentially restore the child’s hearing. This trial builds on Dr. Baumgartner’s prior success treating traumatic brain injury (TBI) with stem cells, and encouraging pre-clinical data from Italy showing that cochlear damage in mice may be repaired by transplantation of human umbilical cord hematopoietic stem cells (HSC).

In the mouse study, researchers administered HSC intravenously to a mammalian mouse model in which permanent hearing loss had been induced by ototoxic medication, noise or both. Hair cell regeneration and repair of the Organ of Corti was only observed in mice that received HSC transplants. This experiment provided a proof of concept for our trial by suggesting that under certain conditions, mammals, like birds and reptiles, could replace their damaged hair cells.

Regenerative vs Immuno-modulatory Stem Cell Therapy

There is a general misconception that stem cells exert their effect solely by differentiating into functional cell types of the exact tissue that needs replacement. For most people (and researchers) this concept frames therapeutic strategies of stem cell therapy. In reality it is too simplistic and is only partially borne out by emerging evidence. There are two broad areas of stem cell research: regenerative and immunomodulatory.

Regenerative stem cell studies attempt to utilize pluripotent (embryonic, fetal, or induced pluripotent stem cells) to create an engineered cell line which can replace damaged or defective cells. Immunomodulatory stem cell studies attempt to adjust the immune response in a way that minimizes the damage associated with the initial injury, and then allows the individual’s native repair machinery to function optimally.

Dr. Fakhri in surgery

With even mild injury, the immune system is activated. Macrophages are a type of immune cell which participate in the post-injury immune response. With “classic” macrophage activation, the immune response is aggressively induced. Classically activated macrophages are described as having an “M1” phenotype. In the nervous system, the M1 immune response can increase the severity of an injury. Alternatively activated or “M2” macrophages, are associated with a less destructive pattern of immune system activation. This alternate/M2 response results in less immune mediated post-injury damage, as well as the possible disinhibition of native nervous system repair.

Following traumatic brain injury (TBI) children experience a loss of 12-15% of their brain tissue in the 12 months following their injury (Levin). In a study where we treated TBI children with their own bone marrow stem cells, there was minimal post injury brain volume loss in the year after TBI (Cox). In animal models of TBI, animals that experienced injury were found to have M1 macrophages throughout their injured brain tissue.

Animals treated with stem cells after TBI were found to have M2 macrophages in their brain parenchyma. Interestingly, if an animal’s spleen was removed before stem cell infusion, the benefit of the stem cell treatment was eliminated. Somehow stem cell infusion causes a change in the pattern of macrophage activation from M1 to M2, which results in a less aggressive immune response and less post-injury brain tissue death. This effect requires an intact spleen.

After a stroke, the severity of the immune response can be predicted by measuring the size of the patient’s spleen. If the spleen loses more than 30% of its volume, the immune response will be classically activated (M1) and the extent of injury will be larger. If, however, the spleen loses less than 30% of its volume, the immune response will be less extreme, and the injury will be milder. In experimental models of stroke and traumatic brain injury, stem cells migrate to the spleen, stabilizing its volume and apparently altering the type of immune cells released from the spleen.

In the Italian mouse study mentioned earlier, the intravenous administration of HSC led to regeneration of hair cells and repair of the Organ of Corti despite the fact that only a few human-derived stem cells actually migrated into the damaged cochlea. Surprisingly, the new hair cells were generated from mouse, not human cells (Revoltella). Somehow, the cord blood treatment allowed the existing, but normally suppressed, repair process to function. The most likely mechanism for this improved repair is immune modulation.

Where do the Stem Cells Go?

Researchers have tracked the migration of stem cells administered intravenously following an injury. At first the majority of the cells lodge within the lung, where they appear to interact with pulmonary macrophages altering the type of cell signaling molecules those macrophages release into the blood. Next the stem cells migrate to the organs of the reticuloendothelial system which includes the spleen. Surprisingly, less than 3% of infused stem cells migrate into brain tissue. So the immunomodulatory effect does not require the majority of infused stem cells to interact directly with injured brain tissue.

The Neuro-Immune Response

Recent research has revealed a dynamic interaction between the nervous and immune systems. Just as stress increases heart rate and blood pressure, it also promotes a more M1 immune response. In both cases the sympathetic nervous system causes the effect. Alternatively, meditation and relaxation decrease blood pressure and heart rate and promote a more M2 type of immune response. In this case the parasympathetic nervous system appears to cause the effect (Tracey). Immunomodulatory stem cell treatments almost certainly affect this nervous system-immune system interaction.

As our research proceeds, we hope to understand this process better in order to develop better treatments for hearing loss and other conditions. Just as antibiotics changed the treatment of infections, stem cells may revolutionize the future of nervous system repair.

The world of ocean pollution and litter prevention is filled with nice round numbers. Like those lists of how long various consumer goods take to go away once they escape into the environment…

Source: http://cmore.soest.hawaii.edu/cruises/super/biodegradation.htm

But recent finds on the beach have me asking: Are those numbers actually any good? Take aluminum.

An oft-repeated line says that aluminum takes 200 years to break down. Now I’ve found old pieces of aluminum — like this top to a steel can from the early pulltab era, most likely used on a Coke product c. 1971-72:

Found by author March 12, 2012, Bay View beach, Saco, Maine

This bit of aluminum, 40 years old, is on its way to disappearing. In something maybe not too far from the 200-year mark.

But you see, I’ve found other pulltab-era can tops that tell a very different story. This one, also about 40 years old, is still in remarkable shape:

Found by author April 10, 2012, Curtis Cove, Biddeford, Maine

On the flip side, this one, probably more like 30 years old, is more than half gone:

Found by author February 29, 2012, Bay View

And this very modern can is already turning into Swiss cheese after perhaps a year of exposure:

Found by author April 25, 2012, Bay View

It turns out, the breakdown of aluminum isn’t a set event, it’s a system. One in which all the pieces have to fall into place for it to corrode back to dust.

When iron rusts, the new compound — iron oxide, Fe2O3 — takes up more physical space than the old. That’s why rust blisters & bubbles out. Those blisters expose more fresh iron underneath, which then rusts, and on and on until it’s all gone.

But when aluminum oxidizes, the aluminum oxide doesn’t take up any more space. It maintains its tight bond with the underlying aluminum. It’s actually a brilliantly weathertight seal. An undisturbed piece of aluminum can exist for… well, indefinitely long.

Now if you take that aluminum outside its comfort zone pH of 4.5 to 8.5, its protective oxide film will fail and true corrosion can set in. But such pH levels are rare in the ocean.

So what happened to the aluminum I’ve found? Corrosion got a boost from something more mechanical: abrasion. Get currents to drag aluminum back and forth through sand and gravel. Over & over & over. Each scrape wears a little surface aluminum oxide away, revealing fresh aluminum, which then transforms into more aluminum oxide. Tide rolls in, scrape scrape. Tide rolls out, scrape scrape. Maybe something acidic settles on it briefly, dissolve dissolve. Do it just right, and you can erode away an entire can in a matter of months — not centuries.

Do it wrong, and you bury that aluminum under inert protective sediment.

Which brings me back to those photos. For the first year and a half at my beach, zero pulltab-era (30+ years old) can tops washed in. In the past six months six have washed in — four within one month!

Why now?

Well, in recent months a sand bar has appeared at my beach at low tide.

March 12, 2012, Bay View

Never seen it before, but it’s there now. All that sand has come from further offshore. Where it perhaps once covered, buried, and protected those old bits of aluminum — some for years, some for decades.

The study of how beached flotsam changes over time — and what that can say about larger environmental change like seafloor shifts — is interesting in its own right. But for the purpose at hand, it’s just a reminder: The world is not a static place. It’s ever-evolving. Things get moved, stuck, buried, freed, bashed. Each piece of debris has its own journey, and can tell a vastly different story.

Here’s one last photo.

Photo credit: Tim Wolter

Obviously, this isn’t aluminum. It’s a hewn log. This week a friend pulled it out of a ditch he was excavating at the Roman fort of Vindolanda, just south of Hadrian’s Wall in northern England. The ditch was in use around AD 200 and was sealed about AD 213, making this discarded chunk of wood ~1800 years old! It shouldn’t survive. But because of the soil conditions, it did.

If organics can do that, aluminum can do it that much more easily.

A blanket statement, like “Aluminum takes 200 years* to degrade,” denies the fact that the environment is a complicated thing. Worse, most often it just isn’t true (noted well on NOAA’s Marine Debris FAQ page).

One beer can lost today will be around in AD 4000. Another one will be gone by next year.

If the “facts” on aluminum are so far off, what does that say about the rest of these lists? 10 years for a polyethylene bag to completely go away? Where does that come from?

So a word of caution to environmental sites. Posting, as fact, nice round numbers that have no relation to reality (other than the metaphorical stopped clock being right twice a day) does a disservice. It misinforms — and it risks discrediting the site when a person sees different results with their own eyes. We should avoid the pitfall of pretending there is any scientific truth behind something that’s just, well, a nice round number.

—————

* This number gets hedged sometimes, from “80 to 200 years” in one direction, to “200 to 500 years” in the opposite. More evidence that there’s little if any science backing it up.

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Previously in this series:

Cigarette butts to the left, fishing rope to the right, plastic everywhere: what I found on the beach over a year.
Too Good to Be True: Sea Mammals, Plastic Pollution and a Modern Chimera
Tsunami Debris and North America: Is the Tail Wagging the Dog?

The Gravity of the Situation

Daria clung to the rope ladder, her knuckles white. Her arms and legs shook. Her eyelids were screwed shut, but tears still squeezed through.

This shouldn’t be this hard, she pleaded, but she knew no one was listening.

Her baby brother, Yuri, never had any trouble with the ladder. He loved swinging on it. He’d jump out of the tree house if Mom hadn’t forbidden it. So would his best friend, Timofy. They were having a blast up there now, laughing and shaking the ladder as hard as six-year-old arms could move it.

Daria knew she was barely three feet off the ground, but it made no difference. A chasm gaped below her feet, and the feeble swaying of the rope felt like an earthquake. She couldn’t let go. She couldn’t open her eyes. She could barely even breathe.

“Daria!”

The ladder shook harder. She gripped it tighter, her arms cramping.

“Daria, please!”

The words promised salvation, but to reach for them, she’d have to let go of the ladder. She couldn’t.“Come on, Daria. Everything’s okay. You’re perfectly safe. You’re here with me on Peregrine Station. Please wake up.”

Peregrine. With a gasp, Daria woke. She flipped over onto her back.

Eoin was propped up on one elbow next to her, frowning with concern. “You okay? That looked like one hell of a dream.”

“It’s an old one.” Daria blinked hard, clearing the last of the tears from her eyes. She wished she could shake the dream as easily. The feeling of motion, twenty years old, clung to her.

“Want to talk about it?”

“No.” The word shot out of her before she could make her tone match Eoin’s friendly one. She patted his arm in apology. “I’ll be fine in a minute.”

Eoin brushed a strand of hair out of her eyes. “Good.” He relaxed and lay back down, chuckling. “These bunks are pretty small even for two perfectly sound sleepers.”

“I’m sorry,” she said absently. She took a deep breath and concentrated on pushing her pulse back down. She hadn’t had that dream since college, but it seemed to be making up for lost time. She could still feel the ladder swaying. She sat up and turned to lean against the wall. Sound-dampening paint over smooth metal, it was chilly against her bare back, but it was solid.

Eoin sat up too. “Sure you’re okay?”

“I will be.” She smiled at the tall, black-haired Aussie, immensely glad she hadn’t been sleeping alone, more glad to wake up next to him. “Thanks.”

He sketched a half bow. “What are friends for?” The muscles in his bare chest rippled invitingly.

Daria had met Eoin when her company hired him for this mission. It had been lust at first sight, which had made her wary. It could make for a great assignment or the world’s longest yearlong trip, depending on his feelings and whether hers lasted once she got to know him.

Ten months in, everything was going beautifully. They even laughed at the same things. They hadn’t talked yet about what could happen when they were back on terra firma, but she thought this might be a good opportunity. She opened her mouth.

“Eoin–” The world wobbled. She grabbed his arm. “Did you feel that?”

“I feel fingernails.” He sounded a little too tolerant.

“Sorry.” She loosened her grip. “Just sit really still for a minute.”

She waited what seemed like forever, barely breathing and trying not to squeeze Eoin’s arm again.

He was less patient. “I’m sorry.” He shook his head. “I don’t–”

Daria felt a stronger heave. “Damn!”

Eoin’s eyes were wide “What was that?”

“The gravity unit’s destabilizing, I think.” She thought hard and quickly. “How secure is your lab?”

“Against gravity?” Eoin frowned. “I’m not sure. I thought your units were fail-safe?”

“It’ll cut out everything over a gee and a half, but you can do damage with a lot less.”

Eoin looked worried.

Daria wanted to reassure him, but she wasn’t sure there was time. “Okay, get your cute little butt over there and make it as stable as you can. Get anything fragile onto the floor. Spread out or brace anything that’s stacked. Be quick. Radio down to Malang and tell…” She glanced at the clock. “…Didi what’s happening. Then get someplace safe and stay there.” She patted his bunk. “This should be a good place to ride it out if you strap in.”

She stood up and started throwing on clothes. Eoin followed her lead. “Can you fix it?”

She shook her head. “Not the control module, which is what this feels like. It’s pretty rare for one to destabilize, but when they go, they’re very unpredictable. I’ve got backups.”

“Let me know when you’ve got it taken care of.” Shirtless and shoeless, he was gone after one quick kiss, running down the long gray hall toward his radiation lab.

“Be careful!” She headed the other direction, still buttoning her shirt. Daria’s lab, where she kept the modules, was near her cabin and the control room. It was a much longer trip from his. This place was far too big for the two of them. If everything went well, its final population would be much bigger. Then maybe there’d be some more color to the place.

She walked as quickly as she dared, bracing herself for another wobble in the gravity field. It came as she was putting a foot down. The floor seemed to drop away from under her, leaving her dangling over forever.

Then it was over, and Daria stumbled as her locked legs took her weight again. She staggered to the nearest wall and sagged, clinging to the recessed rungs on the wall for support. She fought for air. A small voice she hadn’t heard in years chittered in the back of her mind that she was going to die.

Daria forced herself to take a deep breath. Get a grip! She had a mess to fix.

She had invented the prototype for the gravity generator in college. Studying math at the Saint-Petersburg State Institute of Technology, she’d had access to all the science and engineering journals she could ever want. Lifelong acrophobia had kept her obsessively tracking the latest gravitational research, even though it was outside her field. In one article, she’d half-glimpsed a pattern in the data. She hadn’t been able to resist.

She’d pestered engineering students she knew with half-formed questions, bought bits and pieces at salvage, and learned to solder. She laughed at the resulting jumble and plugged in the power. The gravity surge bounced her tailbone painfully off the floor before the circuit blew.

She still didn’t understand all the details of how she’d accomplished it, but for a change, she was controlling gravity. The feeling was addictive. She changed her major to engineering and filed a very quiet patent application.

She decided against graduate school when no one would guarantee her a free hand to direct her own research. Instead, she shopped herself around to the multinationals until she found one that promised to fast-track her design. Contract negotiations went smoothly–once she convinced them that unless she could keep control of her project and oversee the dirtside testing, sh
e’d find another company.

There was very little culture shock involved in the move from St. Petersburg to Indonesia, mostly because Daria spent all her time in the lab. She and her team refined the unit until the power consumption made it practical for industrial use. Then she concentrated on making it space-worthy.

Once the generator was scheduled to be installed in an experimental orbiting station, Daria announced she was going with it. Acrophobia be damned. She wasn’t about to hand her baby over to someone else.

If the station had been a government project, her fears would have ruled her out immediately. As it was, she’d lied her way through psychological tests. She’d doped herself with sedatives and recited Pushkin from memory to keep her heart rate somewhere near normal for the medical tests. The doctors had still looked at her skeptically. But when she’d reminded the board about her contract and told them she could perfect the mechanism faster with first-hand data, they’d agreed she could go.

Daria had insisted on taking this job. Now she had to finish it, even though the serenity she’d faked for the tests was gone. Eoin was counting on her. The success of the mission, his experiments, even her control of her project, hinged on her doing this right.

She made herself loosen her grip. She shifted from rung to rung, not letting go of one until she was holding securely onto the next. It was progress, but it was slow.

Finally, resting her forehead against the cool metal wall, Daria knew it wasn’t working. She was no more than halfway to her lab and still further from the generator. The fluctuations in the field were coming more frequently, and they were starting to ripple, turning the corridor into a shifting hillside.

Each heave left her shaking, weaker and closer to panic. The babbling doom in her head was louder. She had to do something while she and the field were still experiencing stable periods. She waited where she was through three more cycles, trying to shut it all out. She looked for a calm inside of her she wasn’t sure existed.

She let go and ran, using the adrenaline from her fear to power her legs. The corridor flashed by unseen as she concentrated on her goal.

Daria could see the door to her lab when the world heaved again. The floor tilted away and she was falling downhill. She knew she should let herself go, tuck up and concentrate on landing, but her panic-laced body had its own ideas.

Her outstretched arms, braced against the fall, hit first. Her left wrist gave with a stab of pain. She would have screamed if her chin hadn’t landed next. Then she was too busy trying to stay conscious.

When her vision cleared, Daria pulled herself to her knees. Her left arm wouldn’t support her, so she limped along on three limbs. When gravity shifted, she clutched at the hard flooring and panted. She heard whimpering, but she didn’t have attention to spare to shut it off. She just kept dragging herself down the endless gray hall.

Then she was at her lab, then inside, in front of the cabinet where the extra modules were stored. They were up top, so she opened the door, a neutral gray like the rest of Peregrine, and hauled herself up the shelves. She’d just let go and pulled a module from its cradle when the world wobbled again.

It was weak compared to some she’d felt, but it was still too much. She dropped the module and grabbed again for a shelf. The module bounced hard off her bare right foot before hitting the floor. Pieces skittered into the corners of the lab, but Daria wasn’t in any condition to notice anything outside herself.

When everything stabilized, Daria gently moved the two remaining modules to the floor. Then she closed the cabinet door, leaned her back against it, and slid down beside them.

She indulged in a few tears, then found she couldn’t stop. She barely noticed the pain in her foot or wrist.

Daria knew what to do next. She needed to get back on her feet, grab a module and walk, without stopping or panicking, to the control room. She also knew it was impossible.

All her life, she’d watched people around her do things she couldn’t do–things she couldn’t think about without her heart racing and her knees buckling–and do them as easily as they breathed. So many rites of childhood had been closed to her because she couldn’t do something as simple as climb a tree or let go at the top of a slide.

One of her strongest childhood memories involved a family vacation in the forest. She didn’t know which forest, and she couldn’t remember what else they’d done on the trip. The part she remembered was sitting on the first landing of an old fire tower, unable to go any further up, unable to get back down alone.

There she’d sat, abandoned and terrified, while the rest of her family laughed and jumped around above her. Each time the tower swayed in the breeze, she’d been sure it would tumble. The shock of each footfall echoed in her thundering heartbeat.

Her father had grumbled about having to carry her back down. Her mother had told her she’d outgrow it. She hadn’t. Growing up had made no difference. All her work on controlling gravity hadn’t earned her a thing. She was just as useless as she’d been before she started.

The tears kept coming.

“Daria?”

She jerked her head up at the noise and bumped it lightly on the cabinet. She was swearing when the station’s communication system crackled again.

“Daria, can you hear me?” Eoin’s voice was tinny.

She scooted along the floor to her desk and pulled herself up. Another wobble dropped her into her chair. It rolled a little, and she grabbed the desk to steady it. When the surge passed, she hit Respond. “Are you okay? Didn’t I tell you to strap in?”

“I’m on my way there now. Just finished in the lab. There’s no major damage yet, but I’m not sure how secure everything is. Down is rather arbitrary just at the moment.” He sounded cheerful. “Is there anything I can do to help you?”

Daria considered handing the whole mess over to him. Unpredictable gravity didn’t seem to bother him and changing a control module wasn’t difficult, just plug and play. She could walk him thorough it over the com. He could handle it and she could….

What? Give up and huddle in the corner? Was she ready to be that useless? She sat up straight. “Thanks, Eoin, but I think the best thing you can do is be somewhere safe so I don’t have to worry about you.” She bit her lip, then took a deep breath. “I’ll call if I need help.”

“Yes, ma’am.” She could hear his grin. “You know where to find me.”

“I do. I will.” Then he was gone, and Daria slid back to the floor to crawl limpingly to the modules.

As she unbuttoned her shirt, she asked herself what she thought she was doing. She’d had a perfect opportunity to let someone else take care of everything, and she’d pushed it away. Eoin probably would have found the trip down the hallway fun, like those rollercoasters that everyone but her seemed to love.

At least he was safe. And within com reach if she needed him.

She tucked one module into each sleeve and twisted the shirt until they felt secure. Tying her shirt around her waist one-handed was exhausting. When she finished, she dragged herself over to the door.

She looked to her right down the corridor toward the equipment room. Crawling was tempting, and so was the panicky flight she’d used earlier. But she knew she wouldn’t get that far with just one good hand, nor could she afford to fall and break more modules.

She was going to have to do this on her own two feet, without any shortcuts. Leaning against the doorframe, she slowly stood up. Another heave made her wish desperately to be back on the floor. It was hard and tended to hit her unexpectedly, but the fluctuations in the field were less terrifying when she didn’t
have far to fall.

She tried looking toward her goal, but the long straight hallway stretching into the distance was too intimidating. Instead, she looked at her feet. She took one small step away from the door.

“Only five hundred or so left to go.” Even to herself, she sounded hysterically cheery. She concentrated on taking another step.

This pulled her hand off the doorframe, and she felt a moment of unthinking panic. She stepped back toward the wall, close enough that her hand could touch it, but far enough away, she hoped, that she wouldn’t smack into it if it were suddenly downhill.

The rungs weren’t far above her hand, but Daria avoided them carefully. If she grabbed onto one, it would take too much work to let go. She wanted all her energy for walking. She took another step.

She adopted a shuffling step that kept her feet close to the ground and her weight centered above them, like she was walking on ice. Still, when gravity dropped and the floor no longer pushed reassuringly on her soles, she reflexively slammed the foot in the air back down for support, sending her drifting. Normal gravity was restored before she got very high. She wanted to stop to recover, but she didn’t let herself. Another step.

She wasn’t as lucky with all the fluctuations in the field. One wave tilted the floor below her almost vertical, or so it felt, and she had to run to keep her feet under her. It was hard to stop running when everything stabilized. Without the throb from her wrist at each jog to remind her of the consequences…. She pulled herself back to a shuffle. Another step.

Each time Daria staggered away from the wall, she moved back to it before going on. Every time another heave brought the portentous babbling in her head to a crescendo, she was less sure of her ability to go on. Still she moved forward.

When the texture under her hand changed, she looked up. She was standing next to the viewing portal. She’d reached the center of the station. The equipment room was only another twenty feet away.

Relief flooded through her, leaving her wobbly. Daria sagged against the glass. It was cool, and she turned to rest her forehead against it.

Out the window, framed by the walls of the station, distorted by layers of glass, lay Earth.

Daria frowned at her old nemesis. Ever since she’d been old enough to understand how gravity worked, she’d resented the Earth, resented its ability to stop her life cold just by tugging on her. It had stolen so much. She thought about the decades of mindless terror, sweating palms and useless legs.

She’d dedicated her entire adult life to eliminating its power over her. As she looked at Earth, she realized for the first time what that meant. Somewhere along the way, in trying to escape from the planet’s grasp, she’d gone from letting it determine what she couldn’t do to letting it dictate what she did.

She still wanted to hate the planet. Yet from up here, her tormentor almost looked beautiful, blue and white and nearly small enough to hold. The feeble pull it exerted wasn’t even a factor in her current situation.

She thwacked her forehead gently against the glass. She’d left the Earth behind months ago. It wasn’t the problem now. She couldn’t blame the station’s fluctuating gravity either, since she’d had acrophobia all her life. The only constant in the situation was her–her fear.

She blinked. She’d spent all her efforts on the wrong piece of the puzzle. If she’d only carried her problems with her when she left Earth, all the time she’d worked to control gravity had been–

No. Daria laughed at herself. It hadn’t been wasted.

Despite the start of another upheaval in the gravity field, Daria smiled down on the planet far below her. She hadn’t escaped the thing she’d most wanted to leave behind her, but living in orbit around the planet, she could hardly claim her work hadn’t gotten her anywhere.

And after that kind of journey, how bad could twenty more feet of hallway be? Daria took a deep breath and pushed away from the window. Trailing her hand along the wall, she told herself, “One more step.”

***

“I take it everything’s fixed then?”

Daria lazily looked up from where she was slowly twisting the dial on the gravity generator back and forth. Eoin was leaning against the inside of the doorway. He looked a little green.

“Eoin!” Daria realized what she was doing and dropped her hand. Just as quickly, she reached for the knob again and dialed normal gravity.

He put a hand to his stomach. “Thank you, I think. Hopefully that will help everything stay down where it belongs.” He sighed. “You sure know how to make a man seasick.”

“I didn’t…I wasn’t….” Daria closed her mouth, then started over. “I’m sorry.”

Eoin waved that away. “I’ll be fine. I was a lot more worried about you, especially when you didn’t answer my call.”

“You called?” She looked at the com.

“Only about a dozen times. What’s the matter with–hey! You’re hurt.” He knelt beside her and touched her wrist.

She’d forgotten about it. She hissed in pain. It was about twice normal size and faintly purple.

“Yeah, that’s no good. You look a little shocky too. I should get you somewhere…”

Trying to figure out how to confess that her dazed condition wasn’t due to her wrist, Daria didn’t notice him reaching for the field generator. Eoin had it dialed half down and was turning back to her before she could protest.

She squawked as he swooped her up and stood. She buried her head in his shoulder and braced for the panic.

“Did that hurt? I figured it’d be best if I did it all at once.”

Daria frowned up at Eoin. “No. I…I’m fine.”

“Good.” He stepped out the door and headed back toward the cabins.

Daria took a deep breath. No fear. No chittering. She wasn’t comfortable, but…. She waited. The panic didn’t come.

Maybe it was exhausted. She certainly was. Or maybe Eoin’s arms were just a patently safe place to be. Either way, she’d take it. She’d earned it.

She snuggled closer. “So, Eoin, did I ever tell you I’m afraid of heights?”

======

Source

Image Source

We certainly did not invent this strategy of watching or listening in on others. Like most things, we’ve copied it from nature. Eavesdropping is ubiquitous across the animal kingdom. Whenever substantial time or resources are devoted to an activity there is usually a payoff to be found. This got me wondering, what is the payoff for eavesdropping?

Several advantages immediately come to mind. For example, perhaps you can increase your access to resources. One way to do this would be to avoid wasting time going after resources that someone else has already used up. This is frequently observed among competitors searching for similar resources. When one thinks of fierce competitors, two stingless bee species may not be the first thing that comes to mind.

Nevertheless, between two species of Trigona, the largest genus of stingless bees, Trigona hyalinata is able to increase its foraging efficiency (spend less energy/time looking for food) by avoiding visiting food sources that have been potentially depleted by the other species Trigona spinipes. Both species use pheremone (odor) trails to recruit others of their own species, but it appears that T. hyalinata detects and avoids the trails left by T. spinipes in order to not waste time on unprofitable resources.

Conversely, intercepting someone else’s signal could lead you to resources you might otherwise not know about, or would have to spend a considerable amount of time discovering on your own. Blatant thievery via eavesdropping is a common practice among animals, particularly among food-storing species.

Many rodents and birds store, or cache, their food. In general, if you have to store your food, it seems like a good idea to remember where you put it. Therefore we can predict that animals that put food in different locations will, at the very least, have superb spatial memory. Because of this, some animals also have the ability to find where others put their food, resulting in pilfering rates that can exceed 30%. This stealing is not limited to one’s own species, but often includes thievery between species that coexist in the same area.

The idea is obvious. Why not supplement your own stockpile and strike a blow to your competitor all in one fell swoop? Of course if you are the smaller of the two you might be able to hide your food in places that a larger competitor can’t get to and simultaneously steal their stash. For many rodents, it does seem as though the little guy does better in the robbing department. Pocket mice steal more from kangaroo rats than vice versa, yellow pine chipmunks find more of the larger golden-mantled ground squirrel’s cache sites, and the least chipmunk helps itself to more of the eastern chipmunks hidden food. The more interesting question, however, is how do these robbers find these caches?

In some cases, particularly rodents, it is frequently through smell. Unlike in the bee example, this would not really qualify as eavesdropping since the cacher is not deliberately leaving a scent for others to find. Instead it is tantamount to a kind of random search, except that there are some environmental cues giving you a hint. In most case then, you would be better off looking for food on your own rather than randomly searching around for where someone else hid their reserves. Unless, of course, you could somehow learn where they hid the food. In such situations, the would-be thief does eavesdrop by waiting and watching to see where the cacher plans to hide its food. This is widespread in the corvids, a group that includes ravens, pinyon jays, and the champion of cachers, the Clark’s nutcracker.

Ravens, known for their communication, problem solving abilities, and tool use, can add another specialty to their list: criminal mastermind. Since any reasonable individual would protect their stash, it would be advantageous to delay stealing someone else’s food so that you don’t have to engage in a direct confrontation (e.g., robbing the house when no one is home). Direct confrontation is costly unless you are dominant in some way, like the Somali warlords who sit and wait to intercept aid rations. A safer strategy for the majority of us is tactical deception.

While all corvids are known for their ridiculously fantastic spatial memory, ravens also watch where a competitor hides their food, wait a while, and then raid the cache after the individual doing the hiding leaves the area. Unlike other corvids that hide thousands of seeds over long periods of time (and also remember the location of where others hid their food), ravens hide valuable food on a more short-term basis. As a result, the one doing the watching tries to do so undetected, and the one doing the hiding tries to obfuscate the location of its treasure. As expected, countermeasures develop on both sides, much like the jamming and interception tactics developed by competing military operations. Overall, this ‘arms race’ for discovering information and preventing detection seen in ravens gives rise to one of the few examples of strategic or tactical deception in a nonprimate.

Certainly the value of a limiting resource like food lends itself to behavior such as eavesdropping, but what about other valuable resources? For a lot of animals out there, finding a mate involves a hard, long, drawn out battle. The fiddler crab has a lovely courtship approach. You have probably seen them along beaches or inter-tidal areas around salt marshes. The easiest way to recognize them is by the males, who have one large fiddle-shaped claw.

Sometimes these crab look like they are waving at you with their one big claw. Indeed the males are waving, not really at you, but at the females. This show-stopping waving action is designed to get the attention of, and impress, the female. Females are attracted to the rate at which a male is waving his claw, and faster is better. While it may get her attention, it also acts like a beacon to other males competing for her affections.

A recent study by Milner and colleagues found that male fiddler crabs eavesdrop on each other. If a male spots another male beginning to wave, he too starts waving. In addition, the eavesdropping male waves at a rate similar to the male who is in complete visual contact with the female. Thus, fiddler crab males use the signal of rivals to increase their chances of getting noticed by females. Similarly, male bush crickets will eavesdrop on a dueting pair and attempt to intercept the female, while the Broadley’s painted reed frog takes its cue, as in the case with fiddler crabs, from the calling of other males to determine when a female is around.

So far all of the examples have focused on avoiding depleted resources or gaining access to resources through clandestine means. In many more cases, and possibly more similar to what we, as humans do, eavesdropping is used to detect a potential threat. For example, in animal communication systems, alarm calls, once emitted, move into the ‘public domain’ creating an opportunity for others to intercept the call.

The challenge here is that to benefit from heterospecific alarm calls an eavesdropping species has to be able to interpret or decode the information sent out by the other species. In doing so, a species can garner several advantages, including 1) not having to spend their time watching for predators since they have a heterospecific sentinel system and 2) not having to produce their own alarm call, thereby revealing their location to the predator.

Of course for eavesdropping to evolve in a community, you need two species at risk from the same predator and one of the species must produce an alarm call. This form of threat eavesdropping has been documented in a wide range of species, including mammals, birds and lizards. It is especialy common in mixed-species groups of birds and social primates.

For instance, the superb fairy-wren likes to feed on the forest floor. This is a dangerous place to be. In some places superb fairy-wrens share the habitat with the noisy miner, a bird that forages in the canopy. Noisy miners are so named for their proclivity to be feisty and, well, noisy. They routinely attack, or mob, potential predators such as hawks. In addition to mobbing, they emit two different alarm calls, one when a raptor is in flight and one when the predator is perched or on the ground. Superb fairy-wrens have learned what the two alarm calls mean and by eavesdropping on noisy miners, they have a personal alarm system letting them know when its time to get out of dodge.

Aside from potential threats, eavesdropping might let you better discriminate between friend and foe, particularly if there is dishonesty afoot. In this way, being a ‘silent’ bystander can have a strong influence on your future willingness to cooperate. We can easily see how this is advantageous from a military perspective. Nations may appear to be allies, but eavesdropping can reveal divided loyalties. At a smaller scale, social eavesdropping can give individuals important information regarding their status or the willingness of others to share or be altruistic.

For example, little blue penguin males produce a ‘triumph’ display when they win a conflict against another male. When other males hear this call, not only are they less likely to instigate a fight with the winner, but they also have a stress reaction in response to all the fuss. This is similar to what was found in humans, where eavesdropping influenced the perceptions of dominance rank among men.

On the flip side, indirect evidence gained via eavesdropping can assist an individual in detecting cooperating versus cheating individuals. Sparrow males are aggressive with their neighbors until territories have been established. Once mating is underway it behooves both males to spare their energy and fight against strangers and not each other. Strategically this makes sense, but also sets up the potential for one male to not hold up his end of the bargain.

In other words, how can males determine if they should trust the truce reached? We have a saying that your ‘reputation’ precedes you and means everything, and it seems the same is true for sparrows. A given male will observe how his neighbor interacts with his neighbor’s neighbor. If he determines, through eavesdropping, that his neighbor is defecting from the peace treaty, he too will choose an aggressive strategy since he has observed, indirectly, that his neighbor is untrustworthy.

As with people, it has been reported that chimpanzees, client fish, and dogs may monitor interactions between two individuals to assess which individual is more altruistic and willing to cooperate. Though in the case of dogs, they can monitor the interaction between a pair of humans! Marshall-Pescini and colleagues examined whether, through social eavesdropping, dogs monitor, comprehend, and adjust their behavior when observing interactions between two people. Previous work had revealed that dogs console the loser in third-party interaction and also can tell if a person will make a good play partner based on watching that person interact with another dog. In this study dogs first observed a human begging for food from another human. The ‘selfish’ human gave no food to the ‘begging’ human, while the ‘generous’ human freely shared his/her food with the human asking for food.

The dogs were observed for their tendency to gaze at each of the players, and then tested to see if they preferentially approached the ‘selfish’ or ‘generous’ person in search of sausage. In the experimental group, dogs wasted no time with the ‘selfish human’. The dogs not only approached the generous food-sharer more frequently, but also interacted with them for significantly more time. Given that the humans were strangers, dogs used eavesdropping on a third-party interaction to gain valuable information about the likelihood that a particular person would share food with him or her. Not only do dogs have a better sense of smell than us, but also seem to be smarter about reading human behavior and intention than we sometimes are!

From the pheremone trails of stingless bees to the broadscale electronic surveillance undertaken by militaries around the world, it is clear that accessing information, particularly by indirect means via eavesdropping has adaptive benefits. The listener can avoid depleted resources, access additional resources, garner extra protection against predators, and determine their social status. In other social settings, both within and between species (e.g., humans-dog), where the interactions among indivduals are observed, assessing ones tendency to share, cooperate, or be fair may not only benefit the listener or observer, but could potentially discourage selfish behavior. On the other hand, countermeasures flourish in the presence of eavesdropping, so maybe all that listening just promotes more sophosticated deception.

Resources:

Akçay, C., Reed, V.A., Campbell, S.E., Templeton, C.N., Beecher, M.D. 2010. Indirect reciprocity: song sparrows distrust aggressive neighbours based on Eavesdropping. Animal Behaviour 80: 1041-1047. (doi:10.1016/j.anbehav.2010.09.009)

Bshary, R. & Grutter, A. S. 2006. Image scoring and cooperation in a cleaner fish mutualism. Nature, 441, 975-978.

Bugnyar, T. and Kotroschal, K. 2002. Observational learning and the raiding of food caches in ravens, Corvus corax: is it ‘tactical’ deception? Animal Behaviour 634:185-195. (doi:10.1006/anbe.2002.3056)

Dally, J. M., Clayton, N. S., & Emery, N. J. (2006). The behaviour and evolution of cache protection and pilferage. Animal Behaviour, 72, 13–23. (doi:10.1016/j.anbehav.2005.08.020)

Earley, R.L. 2010. Social eavesdropping and the evolution of conditional cooperation cheating strategies. Phil Trans R Soc B 365:2675-2686. (doi:10.1098/rstb.2010.0147)

Grodzinski, U. and Clayton, N.S. 2010. Problems faced by food-caching corvids and the evolution of cognitive solutions. Phil Trans R Soc B 365:977-987. (doi:10.1098/rstb.2009.0210)

Jones, B.C., DeBruine, L.M., Little, A.C., Watkins, C.D., Feinberg, D.R. 2011. ‘Eavesdropping’ and perceived male dominance rank in humans. Animal Behaviour 81:1203-1208. (doi:10.1016/j.anbehav.2011.03.003)

Leaver, L. A., L. Hopewell, C. Caldwell, and L. Mallarky. 2007. Audience effects on food caching in grey squirrels (Sciurus carolinensis): evidence for pilferage avoidance strategies. Animal Cognition 10:23–27.

Lichtenberg, E., Hrncir, M., Turatti, I.C., and Nieh, C. 2011. Olfactory eavesdropping between two competing stingless bee species. Behavioral Ecology and Sociobiology 65:763-774(doi:10.1007/s00265-010-1080-3)

Magrath, R.D. and Bennett, T.H. 2012. A micro-geography of fear: learning to eavesdrop on alarm calls of neighboring heterospecifics. Proc Royal Soc B 279:902-909. (doi:10.1098/rspb.2011.1362)

Marshall-Pescini, S. Passalacqua, C., Ferrario, A., Valsecchi, P., Prato-Previde, E. 2011. Social eavesdropping in the domestic dog. Animal Behaviour 81:1177-1183. (doi:10.1016/j.anbehav.2011.02.029)

Milner, R.N.C., Jennions. M.D., Backwell, P.R.Y. 2010. Eavesdropping in crabs: an agency for lady detection. Biology Letters 6:755-757. (doi:10.1098/rsbl.2010.0384)

Mouterde, S.C., Duganzich, D.M., Molles, L.E., Helps, S., Helps, F., Waas, J.R. 2010. Triumph displays inform eavesdropping little blue penguins of new dominance asymmetries. Animal Behaviour 83:605-611. (doi:10.1016/j.anbehav.2011.11.032)

Penner, J.L. and Davenport, L.D. 2011. A comparative study of cachin and pilfering behavior in two species, least chipmunks (Tamias minimus) and eastern chipmunks (Tamias striatus). Journal of Comparative Psychology, 125:375-384. (doi:10.1037/a0024562)

Subiaul, F., Vonk, J., Okamoto-Barth, S. & Barth, J. 2008. Do chimpanzees learn reputation by observation? Evidence from direct and indirect experience with generous and selfish strangers. Animal Cognition, 11, 611e623. Vander Wall, S. B., & Jenkins, S. H. (2003). Reciprocal pilferage and the evolution of food-hoarding behavior. Behavioral Ecology, 14, 656–667.

Images:

1. Raven by National Park Service at Wikimedia commons; 2. Fiddler crab by Ianaré Sévi at Wikimedia commons; 3. Superb fairy-wren by Cas Liber at Wikimedia commons.

So the faculty have to make this decision along the way to publish in an open access journal and give up perhaps some of the prestige that’s associated with one of the more established journals. So, sometimes what you’ll see is some of the junior faculty who are less inclined to publish in open access journals because they are focused on the career path and tenure track process.

The prestige problem has plagued open access from the start. Harvard’s Faculty Advisory Council addressed it directly in their memorandum, calling on faculty members to “move prestige to open access.” However, the memorandum offers no direction on how this is to be accomplished.

Meanwhile,  on the other side of the pond, the U.K. government has announced that researchers receiving public funding will be required to make their papers available via open access. (There is some helpful commentary on the Nature News blog.)

Watching these events unfold, I worry that the message is “if researchers and academia don’t figure it out, the government will just make it happen.” And the idea of taking more power out of the hands of the people who perform and write up the research seems like the wrong approach to me. Isn’t part of the current crisis in academic publishing that authors don’t have control over their content?

So how to put power back in their hands? By actually moving the prestige to open access. A big name endorsement of a journal article doesn’t have to come from publication in a big name journal. It can come from faculty at a big name university. It is possible that Harvard’s name might be big enough, and since their Faculty Advisory Council stuck their noses out with their memorandum, I am going to use Harvard as an example.

I propose that Harvard faculty members organize to volunteer their editorial services in identifying and recommending the best new open access articles in their field, after those articles have been published. Get the publications out there, decide if they’re important later. Yes, this is post publication peer review, which has been suggested before, but it involves the same peers as our current system of pre publication peer review.

I imagine, for example, a publication out of Harvard’s department of Organismic and Evolutionary Biology. I would name it something cute like Darwin’s List, but since we are talking about Harvard here, let’s pick a more dignified name, like The Harvard Evolutionary Biology List, or HEBL for short. The HEBL would consist of short reviews of important new open access articles by faculty members; reviews might be only a few sentences long, as the inclusion in the list itself would be the important thing.

Once such the HEBL publication was on its feet, it might even get submissions from  authors of published open access articles, seeking inclusion. One faculty member would serve as senior editor – an unenviable task involving herding the other faculty members into actually reviewing articles, I imagine, just as editors of journals have to do today. Junior faculty at Harvard and elsewhere could point to a mention of their open access publications in the HEBL in their resumes and expect the same prestige as if they had published the articles in big name journals.

Who’s going to actually read and review these articles? Well, the word on the street is that faculty members are withdrawing their volunteer (and paid) services as editors and peer reviewers of non-open access journals. Volunteering editorial and peer review services to a list like the HEBL would entail very similar work to what they had been doing for these journals.

How would the HEBL be published? Online only, I expect. There are existing software solutions that would work quite well.  Your institution’s IT department can almost certainly help you out.

Would inclusion in the HEBL be prestigious just because we say it is? I say, why not? The big name journals are prestigious just because we say they are, and because we make hiring and promotion decisions based on publication in them. My hope is that moving prestige to lists like the HEBL would be somewhat easier to do than according prestige to open access megajournals.

The big question, of course, is: who’s going to start such a project? I wish I could, but I’m not quite faculty at a big name school yet. Such a project does require someone to commit the time and energy to trying the experiment and creating the first list. But look, faculty members, this is something you can do about what has been described as a crisis in academic publishing. And you can do it right now, without waiting for someone on a hiring or promotions committee to suddenly decide that a publication in an open access journal is just as valuable as a publication in a big name journal.

By the way, I recognize that this is probably not a new idea, and probably not feasible in the exact form I describe for one reason or another. That’s okay. I’m mostly hoping to get the discussion going in a new direction, and to plant some seeds in someone’s mind.

In the end, my co-author and I did decide to submit to an open access journal. It’s too late for this paper, but I hope that by the time I write my next one, there will be veterinary publications to provide post-publication endorsement of my article’s value. By then, I may even be junior faculty.

Of Homeotic Mutations and The X-Files

Mutations in four genes give the fly in the lower right an extra pair of wings (Credit: FlyBase)

A homeotic mutation mixes up body parts, so that a fly grows a leg on its head, antennae on its mouth, or sports a double set of wings. Designation of body parts begins in the early embryo, when cells look alike but are already fated, thanks to gradients of “morphogen” proteins that program a particular region to elaborate particular structures. Mix up the messages, and a leg becomes an antenna – or, as in the AJHG article, a child develops two upper jaws, instead of an upper and a lower.

I once knew the homeotic mutants of Drosophila melanogaster intimately, as I archaically mapped their genes. Shortly after I left Thom Kaufman’s lab at Indiana University (where I penned a fruit fly romance novella, in addition to my thesis), post-doc Matt Scott and fellow grad student Amy Weiner were homing in on the homeobox, a 180-base-sequence that encodes a protein part that binds other proteins that turn on sets of other genes – crafting an embryo, section by section.

Soon, homeoboxes turned up in all manner of genomes, affecting the positions of petals, legs, and larval segments, the genes mysteriously arrayed on their chromosomes in the precise order in which they’re deployed in development. Homeotic mutants even starred in an episode of the The X-Files.

Homeotic mutations cause a few human diseases. In lymphomas, white blood cells detour onto the wrong lineage, and in DiGeorge syndrome, the missing thymus and parathyroids and abnormal ears, nose, mouth, and throat echo the abnormalities in Antennapedia, the legs-on-the-head fly in the photo. Extra and fused fingers and various bony alterations also stem from homeotic mutations.

Alas, no human homeotic seemed as compelling to me as a double-winged fly — until I saw photos of the tiny faces of the children with upper lower jaws.

Two Upper Jaws

3D CT scan of child with ACS. Lower jaw is small and malformed (left); same aged child with normal jaw (middle); lower jaw of child with ACS inverted over upper jaw of normal skull (right). (Credit: Image courtesy of Seattle Children’s).

Discovery of the homeotic mutations that turn a lower jaw (mandible) into an upper jaw (maxilla) began with an astute pediatrician. Michael L. Cunningham, MD, PhD, director of Seattle Children’s Craniofacial Center who also has training in anatomy and embryology, was examining the jaw of a little girl with what would become known as auriculocondylar syndrome or ACS.

The condition, originally described in 1978 and also called “Question Mark Ears” syndrome, can twist the ears into the shape of said punctuation marks, and disrupts development of the temporomandibular joint and mandible. The head and mouth are so small that children must undergo surgeries to be able to breathe and eat normally. ACS is a rare disease: fewer than 1 in 50,000 newborns have it.

Dr. Cunningham noted, in examining the girl in 1998, that the lower jawbone had unusual bony areas that fused with her cheekbones. “Seeing her mandible doing that gave us the idea that her lower jaw was patterned like an upper jaw. And the fact that her mother was also affected made me think that we had found a novel condition,” he said.

Over the years, when Dr. Cunningham’s team cared for the little girl, he noted fleshy tissue forming inside her mouth on both sides of her mandible that looked like halves of a duplicated soft palate with a uvula on each side – which is exactly what they were, just in the wrong place. “It was obvious that her lower jaw was patterned like a maxilla and zygoma (cheekbone),” he recalled.

Whole Exome Sequencing

Mutations in two genes endow the fruit fly in the bottom panel with legs on its head and mouth. (Credit: FlyBase)

The search to find a causative mutation began, as such searches often do, with an animal model – the Dlx5/Dlx6 mouse. Mutations in this Hox gene cause a small, malformed jaw in mice, “split-hand/foot malformation” in humans, and legs and antennae popping up where they don’t belong, or missing where they do belong, in flies.

But when Cunningham’s group and collaborators sequenced Dlx5/Dlx6 as well as a downstream gene called endothelin, in the patient and in a few others, the genes had no mutations. Something else was causing the oddly duplicated/deficient jaw of ACS.

The next step: whole exome sequencing, thanks to collaboration with Mark J. Rieder, PhD, from the department of genome sciences at the University of Washington and co-workers from France, Australia, San Francisco and Tucson. They compared the protein-encoding parts of the genomes in child-parent trios from five families, consulting a few additional pedigrees that other investigators provided.

The results were remarkable, in a few ways.

First, the researchers discovered “two distinct genetic causes of a single human malformation syndrome…in the same pathway….in one experiment,” said Cunningham, referring to genes called PLCB4 and GNAI3. Both affect the endothelin signaling pathway, but through different routes: PLCB4 mutations inactivate stimulation, whereas GNAI3 mutations boost an inhibitory signal. Clues came from zebrafish with similar jaws and a PLCB4 mutation. The GNAI3 mutation, however, had no known animal counterpart. (The researchers do not yet know exactly how the mutations cause ACS.)

The second unexpected result was that all of the mutations in both genes affect amino acids that are identical in all vertebrates, flies, and even fungus, indicating that the genes are essential to multicellular life.

Third, the mutations are not in Hox genes, but in their controls.

The Bigger Picture

Discovery of two genes behind ACS will surely help in diagnosis of this syndrome and related ones. But the implications are broader, in four ways.

#1 EVOLUTION When mutation derails development similarly in such different species as a human and a fly, descent from a common ancestor is a much more logical explanation than repeated identical genetic changes or being plopped down by a Creator.

#2 WHOLE EXOME SEQUENCING Obsolescence looms. “Exome sequencing is so powerful that the mutations will soon no longer be what we search for. Mutations will be easy to find, even boring. It’s the biology that will be tricky to figure out: protein function, regulation of expression, epigenetics, and developmental biology…..this is were we will be spending more and more of our time,” said Cunningham.

#3 MY CAREER CHOICE I realized, with the elegant work on the double-jaw in which a maxilla is seen from two perspectives, that the homeotic mutations are a metaphor for my career – using my knowledge of genetics to communicate research results, rather than investigating molecules and mechanisms.

#4 MODEL ORGANISMS Discovering the mutations behind ACS illuminates the value of research on model organisms. I’ll be writing news releases for the upcoming 2012 Model Organisms to Human Biology – Cancer Genetics Meeting in Washington, D.C. June 17-20. I hope to guest blog from the world of worms, zebrafish, frogs and mice – and of course, the noble fruit fly.

1. Software as a Service (SaaS) –providers install and operate applications for users to access over the internet, ranging from simple office processing to complex customer relationship management systems;
2. Platform as a Service (PaaS) – where providers offer use of a server with, for example, a database system already installed, onto which a user installs and runs their own applications;
3. Infrastructure as a Service (IaaS) – where providers offer access to what appears to be computer hardware, such as disk storage or servers.

Many of us use services, essentially IaaS, to store our files online with services such as Dropbox, Microsoft’s SkyDrive, Amazon’s Simple Storage Service (S3), Apple’s iCloud, and perhaps a relative late comer, launched last week, Google Drive.  Each has its own technical merits: some can be accessed from a greater range of devices; some provide support for editing document types using applications that are provided via your browser; and so on.

Whereas 40 years ago 1 Gigabyte of hard disk storage would have cost over £1.8m (assuming you could have produced it), today it costs pennies to produce. Storage has become a commodity and this allows businesses to offer services that promise to take away the routine housekeeping that goes with storing your data, for a price that makes it attractive. With Dropbox reportedly storing some 100 billion files by May 2011, and Amazon claiming that their Simple Storage Service (S3) contained some 905 billion “objects” at end of the first quarter of 2012, the last year appears to show a growing mass market adoption of cloud storage.

Not surprising then that competition in this market is increasing, prices are falling, and more ancillary services are being offered to help differentiate one provider from another.  However, concerns continue to surface, and the launch of a new service brings them back into the public consciousness.  These concerns are not necessarily only technical in nature, nor, surprisingly, are they about how secure the data is from external hackers, although this is clearly seen as a basic requirement of any such service.  The concerns revolve around more subtle issues such as who has what rights in the data you place in the keeping of an online storage provider, and who is liable if data is lost or misused.

When Google Drive launched last week, people’s attention was quickly drawn to the “terms of service”, which a user will be bound by if they upload their data.  I’m sure some users were surprised to see that Google retained the right to, for example, “…communicate, publish, publicly perform, publicly display and distribute…” your data.  Words such as these caused quite a reaction, with one article describing them as a “toxic brew”.  The terms do make clear that these rights were required for the operation and improvement of the Google Drive service but this is a remarkably broad definition I think it is also worth noting that other services have similar legal terms associated with their use, with others, who were earlier into the market, had to issue clarifications that they in no way were seeking to take ownership of the data stored with their services.  In the case of Google, there may have been added public concern as it came so soon after Google was obliged to explain the implications of its move to consolidate the privacy policies across all of its services, into a single policy.

What the negative reactions to these types of legal notices do show is that providers need to communicate the roles and responsibilities of everyone involved in the clearest possible terms, including those using the service.

If all you store in the cloud is files that you would openly publish on the web, or don’t mind losing, then you probably won’t care much about such terms and conditions.  However, if your data has intrinsic value or, potentially worse, would cause damage if it were revealed in some way, then you really need to conduct some checks before committing to a particular service provider.  Yes, read the terms and conditions for the service. Make sure you understand them, and, more importantly, that you’re happy with the roles and responsibilities of both you and the service provider. Likewise, the provider’s website should have answers to the questions you are likely to ask. If the language used is so complex or they give obscure answers that you can’t understand it, then move on: there are providers who do take the time to write terms of service in plain English.

In addition, and as part of informing your review of the terms of service, you need to think about items such as:

1. Viability of the company and/or service – some cloud storage companies have disappeared or have withdrawn a service at short notice.
2. Connectivity – does the provider support access from the devices you use?
3. Service availability – what commitments does the provider make for the availability of your data, and what can you do if your data is unavailable?
4. Protection – how does the provider protect against contamination, accidental deletion or copying, or hardware failures?
5. Deletion – does delete really mean delete, including from backups? Or is your data sensitive enough that you would want the storage media physically destroyed to prevent recovery?
6. Transparency – what else does the provider do with your data?  For example, do they “index” your data to allow for searching, and if so, who has access to this?

Opting for a well-known name is not necessarily the best choice if you also need to be careful about the geographical regions in which your data will be stored.  Very large providers often have data storage facilities spread around the world, and your data could be spread equally widely.  Although more for a business concern, in the UK if you hold certain types of personal data on others you will (or should) be registered with the Information Commissioner, and so should know that there are very particular rules under which you can transfer such data outside of the EU. There are Safe Harbor arrangements for transferring data between the UK and the US, but the rules are not trivial and some providers might not always be happy to oblige.  You might like to ask any provider who is located outside of your country if they can tell you where your data (or its backups) will physically reside.

You also have to be able to trust those that have access to the physical data storage on which your data resides.  Have a look to see if the provider says anything about how it controls such access or how the personnel are chosen.  If neither of these points is addressed, then look to see what responsibility, if any, the provider takes if your data were to be leaked.

The bottom line is that cloud storage providers are businesses and will seek to protect themselves first and foremost.  With prices being driven down by increased competition, businesses will attempt to put in place a contract (for that is what it is) that limits their liability to something that they consider proportionate to the value they earn from you as a user.  So, if you pay nothing you can largely expect the same level of liability and that might end up costing you rather more later. Take nothing for granted, and conduct a level of due diligence that is appropriate to the value and nature of data you are entrusting to your cloud storage provider.

Image source

Robojelly, shown here out of water. Photo courtesy of the University of Texas at Dallas News Center

The translucent bell-shaped figure pumps rhythmically upward through the water, the rise and fall of its body almost identical to that of the moon jelly, Aurelia aurita. The similarity is no coincidence. The figure in the tank is a prototype of an unmanned undersea vehicle designed to run on hydrogen-powered artificial muscles. The wild A. aurita, because of its relatively simple musculature and swimming movements, was the ideal model for Robojelly’s design.

The hydrogen-powered Robojelly was described in March in the journal Smart Materials and Structures by its creators, a team of scientists based at Virginia Tech and the University of Texas at Dallas. The vehicle’s design—nickel-titanium shape memory alloy wrapped in carbon nanotubes coated with a platinum catalyst, all tucked neatly under a silicone-based mesoglea—is truly unique in the world of robotics. In principle, Robojelly could swim indefinitely, its artificial muscles powered by heat produced from the reaction of platinum with the renewable resource of oxygen and hydrogen gas in water.

But Robojelly as a machine that mimics animal movement is one of dozens. Indeed, in recent years, increasing numbers of bioinspired robots have flapped, crawled, and climbed their way into the scientific literature, all striving toward autonomy. That is the objective, after all, for the field of bioinspired robotics—to develop autonomous machines with the ability to traverse complex terrain. The catch, however, is to do so not by relying on the high-level, computer-controlled artificial intelligence of traditional robotics, but rather by mimicking the basic sensory mechanisms, biomechanics, muscle properties, and nervous system functions of animals.

This novel approach seems logical enough. However, as Case Western Reserve University professor of engineering Roger Quinn explained, “It was widely considered that because animals use different materials, actuators, sensors, and control systems than were possible in robotics, animal designs did not make sense for robotics.”

Add to that the deceptive nature of seemingly simple structures like insect antennae and legs—Quinn and Case Western Reserve biologist Roy E. Ritzmann pointed out in a paper in 2003 that even the leg of the lowly cockroach has at least seven degrees of freedom—and attempting to capture biology effectively or efficiently in robotic systems begins to look like an exercise in self defeat, rather than creative science.

But robotics has reached a turning point. Engineers have begun to look to biology—and to neurobiology in particular—for solutions. As Quinn noted, “It has now become apparent to most in the robotics community that the principles found in animal design and control can be applied to improve robot designs.”

The Secret Sense

Antennae, compound eyes, electroreceptors, and other sensory systems, despite their morphological and functional diversity, share in common the basic feature of neurological control. The organization of these systems enables locomotion through reaction to the environment and integration of neural pathways. Thus, movement, whether in response to tactile, auditory, or visual cues, is linked to sensory feedback.

A plastic frog foot with silicone webbing, with simultaneous view of a living frog muscle (right) contracting to control the rotating motion of the robotic foot as it 'swims' forward. Muscle and robot are linked virtually via fast electronics that enable the muscle to transmit its force to the robot. Photo courtesy of Chris Richards and Christofer Clemente, Physiology Propulsion Lab, Rowland Institute, Harvard.

The different types of sensory systems can be viewed as discrete feedback loops that are orchestrated by the brain but not micromanaged in a centralized way. As a result, Quinn said, “Bioinspiration has led to control systems that are more distributed rather than being centralized, and therefore are more robust to unexpected disturbances.” Such disturbances, which include uneven terrain and obstacles that might be encountered while traversing unknown environments, have tripped up countless robots. Yet, the ability to navigate complex, unpredictable terrain is precisely what operations in military and civilian settings demand.

At the Case Western Reserve Center for Biologically Inspired Robotics Research, which Quinn directs, a variety of robots have been developed based on neurobiological principles. Among the center’s inventions are an autonomous cockroach-inspired legged robot that uses insect-like tactile antennae sensors to navigate over or around obstacles and a soft-bodied earthworm-inspired robot that moves using continuous wave peristalsis. Another of Quinn’s intriguing machines is a legged robot that hears, thanks to binaural ultrasonic sensors. The robot emits high-frequency sound waves and then measures the time delay between echo signals received in each of its “ears,” allowing it to avoid obstacles in much the same way bats and owls use sound detection for navigation.

In addition to harnessing sensory systems, biologists and engineers are working to incorporate muscle-like properties into robots. “The incorporation of flexible structures, which are very common in biology, will greatly advance robotics,” explained Christopher Richards, head of the Propulsion Physiology Lab at Harvard University. “One example is the pectoral fins of fish, which actively bend under the control of many muscles at the fin base. This mechanism allows exquisite control of propulsive forces to enhance thrust and reduce drag.”

Robotic Intuition

According to Richards, who is investigating the relationship between muscle dynamics (e.g., force) and hydrodynamics in swimming animals such as frogs and fish, “Robots are instruments to help us understand how animals solve certain physical problems. From this understanding, we might find novel principles that then can be applied to the engineering of autonomous robots to perform ‘useful’ tasks. Or we can incorporate these principles into improved bionic or prosthetic devices for medical uses.”

Concerning the latter, Richards cites among the most exciting advances in bioinspired research in recent years a powered ankle prosthesis that uses a biologically inspired system of motors and springs to mimic the behavior of muscles and tendons inside the leg. “In this device,” he said, “the engineers have ‘programmed’ the physiological behavior of muscle into the motor and the electronics that controls it. Not only is this an elegant approach for achieving realistic limb motion, [but] we can also use ‘muscle-mimicking’ devices to explore how the characteristics of muscle might influence locomotion.”

Another area in which bioinspired robotics has given back to biology concerns animal behavior. “An important aspect of biologically inspired robotics is the ability of such devices to help provide deeper insights into the mechanisms by which animals behave,” said Hillel Chiel, a biologist and neuroscientist at Case Western Reserve who for more than two decades has investigated the development of soft-bodied robots based on the marine slug Aplysia. “For example, a biologically inspired gripper device demonstrated that a single actuator, depending on the sequence in which it was activated, could cause opposite movements—it could move a grasper forward, or it could move it backwards.”

What Does This Action Signify?

Salamandra robotica, a salamander-inspired robot developed by researchers at the Biorobotics Laboratory, EPFL, in Switzerland. Photograph by A. Herzog, courtesy Biorobotics Laboratory, EPFL.

The applications of bioinspired robots are as diverse as the animals on which they are based. In broad terms, applications range from reconnaissance, surveillance, and search and rescue to supporting human exploration and operating in hazardous or unknown environments, such as those found inside volcanoes, underwater, in damaged nuclear facilities, or on other planets. Fish-like robots may be able to swim through water to detect oil, while snake-like robots may be able to maneuver through confining environments such as pipes to detect objects or chemicals.

“There is great interest currently in the insect nervous system, including the brain,” Quinn added.

Ritzmann has pioneered much of the neurobiological side of this work in his investigation of a region in the arthropod brain known as the central complex, which houses sensory neurons and appears to play a role in directing locomotion based on sensory inputs. Quinn explained that these studies could lead to the development of more robust robotic control systems and eventually to truly autonomous robots. Ultimately, the brain is essential for any level of autonomy. It integrates massive amounts of sensory information, makes rapid decisions about directing movement, and then sends commands to the local part of the nervous system to cause desired actions.

The Tea Party-backed candidate has a 10-point lead over U.S. Sen. Richard Lugar in a Hower/DePauw Indiana Battleground Poll heading into Tuesday’s Republican Primary. The poll conducted Monday and Tuesday of last week surveyed 700 likely voters to find Mourdock leading Lugar 48 to 38 percent with a 3.7 percent margin for error.

Mourdock, 60, faces a political icon on Tuesday whose longevity in office—spanning 40 years—is being called a liability in the current political climate.

If he makes it to November, Mourdock’s unusual background may be his biggest asset. At a time when Congress is tasked with developing energy policy for a changing climate, Mourdock is a scientist.

Mourdock, who holds a Master’s degree in geology from Ball State University, worked in the energy sector for more than 30 years. If elected he would join a small group of scientists in the 112th Congress—a group that contained around 30 scientists among the 535 senators and representatives in the 110th Congress.

“Those of us who are trained in the sciences look at problems differently,” says Mourdock. “We are more analytical and less ready to accept what appears to be the obvious answer.”

But is he prepared to balance the views of his conservative constituents with his own training in science when faced with issues of climate change, reproductive health and evolutionary science?

Incumbent Sen. Lugar, 80, is the longest serving U.S. Senator in Indiana’s history. Before being elected to the Senate in 1976, Lugar served on the Indianapolis Board of School Commissioners from 1964 to 1967. He was elected mayor of Indianapolis in 1967 and served two terms beginning in 1968.

Lugar studied politics, philosophy and economics as a Rhodes Scholar at Oxford University from which he holds Bachelor and Master’s degrees. During his Senate tenure, he has been influential in the dismantling of nuclear, chemical and biological weapons. He is perhaps best known in this regard for co-authoring the Nunn-Lugar Global Cooperative Threat Reduction Program.

Science in the Hoosier General Assembly

During the 2012 legislative session of the Indiana General Assembly, science came into the spotlight with the introduction of a bill that would have allowed Indiana schools to teach creationism alongside evolution in science classrooms.

The bill narrowly passed the Senate but was defeated in the House.

State Sen. John Broden, D-South Bend, voted against the bill.

“This is an issue that conservative groups have latched onto,” says Broden. “And it has some clout. Conservative Christian theology plays a very large role in who wins Republican primaries right now.”

Broden says that he’s never had a single constituent approach him about teaching alternative theories to evolution. No letters, phone calls or grocery market conversations.

But his conservative colleagues in the Senate have.

“A certain segment of [the Republican] base does view this as an important issue,” says Broden. “I don’t think they view the separation of church and state in the way that I might view it. I think that they might like to push the envelope, and it doesn’t bother them that there may be challenges.”

He says that scientists and people who respect the profession should be concerned.

“I sense that there’s a war on science. There seems to be a lack of respect for science and it’s growing,” says Broden. “I think scientists are under siege at the national level, and I think it’s growing at the state level.”

On the National Stage, Science in the Spotlight

Legislators at the national level are expected to weigh the evidence for and against complex science-related topics often without the rigorous training required to understand the scientific process.

For this reason Jamie Vernon, a Science and Technology Policy Fellow for the American Association for the Advancement of Science in Washington, D.C., is hesitant to proclaim a war on science underway.

“A lot of the time, policymakers don’t understand the complexity of science,” says Vernon. “They think that if you throw money at a scientific problem, you’re going to solve it.”

Through his fellowship, Vernon uses his science background to make policy recommendations that address energy challenges. He says it may be necessary to focus on the big picture and make sense of a particular science problem in a way that fits the agenda of a policymaker. This often includes highlighting the economic benefit of a particular science policy.

“People look at science differently. Facts are not what we used to think they were. They are not completely objective,” says Vernon. “To say that there’s a war on science implies that people are taking facts, ignoring those facts and purposefully, or disingenuously, making policy decisions in the face of science.”

Vernon concedes that while it appears that the Republican Party is sometimes misaligned with information that comes from the scientific community, he does not believe that it is a purposeful endeavor.

“I think they have a way of reasoning away what scientists say,” says Vernon. He says it is more likely that the credibility of science is under attack.

Mourdock agrees.

Restoring Faith in Science Through Active Legislative Participation

Mourdock says that his background in science will allow him to take an analytical approach to politics. He scoffs at the notion that conservatives are waging a war on science.

“I think that’s silly. Galileo was attacked. Darwin was attacked. I don’t know that this is a political attack so much as a societal attack,” says Mourdock. “If it’s political, it’s because so much in our lives, and I’m not just talking science here anymore, seems to require involvement of government.”

Mourdock says that topics like teaching creationism in schools should be debated at the local level, not the national level.

“Where I think there should be a debate on science, to really cut to the heart of it, is how we have government better support new technologies that only science can provide,” says Mourdock. “I became a geologist because the summer I graduated from high school, I saw people walking on the moon.”

That was 1969. Mourdock says the national feeling about science was different then.

“It was all about science. You couldn’t escape how the nation was involved in science,” says Mourdock. “That inspired a whole generation of people like myself.”

Mourdock says the national debate should be that if the government is going to be involved in science, how can it be involved in a way that “inspires people to love science, to study science, not knowing where it will take them, but just having that educational background?”

Mourdock does not expect a re-focusing of the national science debate to happen overnight.

“It takes real leadership from those of us who love science and understand its importance to society,” says Mourdock. “The reason it was happening [in the 1950’s and 1960’s] was because of the Cold War. The Soviet Union and the United States had this intense rivalry that spurred a space race.”

Fear that the Soviet Union could launch a nuclear attack as easily as it launched a space shuttle created a generation of science-savvy young adults. But that fervor soon faded.

“A renewal of that spirit is going to take some real sense of urgency that science can save us,” says Mourdock. “We have to look at science as what’s going to save our economy. How can we develop new technologies to make us better equipped to go forward in a very, very competitive world?”

Conservative Voice, Constituent Concerns

Mourdock self-identifies as a Christian, but he does not take a Creationist view on the origin of the Universe. He says it is important that political parties not be divided into a party for science and a party against science.

“I tell my Christian friends: when you look at the rock record, the fossil record, of course evolution occurred. It continues to occur,” says Mourdock. “It is important that we understand that others can disagree. I’m more concerned, frankly, when I see science misused by politicians.”

Specifically, Mourdock says the debate is not over on global climate change. He says that in science the debate never ends.

“That is the most anti-scientific stance that you can take,” says Mourdock. “It’s never over. One question leads to another, leads to another, leads to another.”

Mourdock says there will be a consensus of a majority on climate change, but his preference is that it be based on science that is questioned. (Read positions by AGU , GSA and AAAS.)

“Politicians are always going to do a horrible job of assessing science when there is no clear, obvious outcome,” says Mourdock, “because science is being used to drive a political outcome.”

The bottom line is funding, he says.

“One group will want one outcome because it may mean funding in this area,” says Mourdock, “and another group will want another outcome because it means there won’t be funding in that area. It’s not about what the science says. It’s about how the science is being used.”

But can we keep science from becoming politicized? Vernon says that the scientific process is one that we’ve trusted for hundreds of years and it’s paid off—aligning science with a political group may cause that trust to be eroded.

Mourdock is a proponent of increasing the presence of science in Congress.

“We need more people with a science background in physical sciences—physics, biology, geology, chemistry—in this public life,” says Mourdock.

He would like to become one of those people.

The Republican primary winner will face U.S. Rep. Joe Donnelly, D-Granger, in the November election.

In cartography, they teach that maps gain their power through the process of abstraction. Abstraction is the process through which a geographic reality is turned into a representation, the map. In the process of making a map, cartographers have to decide what information to include and what to exclude, and this process creates an abstraction of reality that has more power and more functionality then the entire reality itself.

Think about if you made a perfect map. To map everything in the state of Wisconsin, the map would have to be the size of the state of Wisconsin. Then it wouldn’t be very useful. So, instead, we distill down to the features that are relevant to the story that your map aims to tell. If you want to tell someone how to travel across Wisconsin, you include the major towns and roads that people will need to navigate.

However, the power of maps comes at a cost: when you distill the information, you introduce uncertainty. Maps, by definition, are not 100 percent accurate. Only reality is 100 percent accurate.

Cartographers call the process of deciding what to exclude from your map generalization. In Wisconsin, if you want to map state parks, you probably want to include lakes. If you are mapping dairy farms, you probably don’t need lakes. This process of meaningfully removing detail is critical because you know that if you try to include too much, you’ll crowd the map and no one will understand anything.

Science journalism is like that too. I’m writing my first long feature story, 2,500 words on a topic I’m passionate about – post-wildfire restoration in an ecosystem I love, the Mojave desert. I want to include everything, tell the full story, every interesting research experiment, every beautiful native shrub, every scorched mountain range, every scientist’s heartfelt description of why they love the landscape. But I’ve discovered that when I try, I lose the story, and then, I will lose the readers (that I hope to have). I need to make generalization decisions.

In journalism, we seem to have a continual debate about how best to navigate the fact that every story is subject to the lens of its writer. Bias is inherent in maps, just like in journalism, because of the conscious decisions made on how to design the story or the map, how to frame and present the information.

When you take spatial information from a round planet and try to present it on a flat paper or screen, you can’t preserve the geography perfectly. Size and shapes can become distorted, more so in maps with a larger view of the world. A map of Wisconsin is small enough to keep the distortion down. Many global maps, on the other hand, result in a huge Greenland and a small African continent, because of how the map was designed to focus on the European and US mid-northern latitudes.

Although every method of presenting geography requires some distortion, each method, called a projection, has explicit pros and cons. On every map, its designer will include a mention of how the map was projected, to inform the viewers how the geography has been distorted, and what has been preserved.

As a journalist, I’m envious of projections. It would be so handy to be able to tell readers, in a few simple words, here’s how I’ve framed this story for you, to quickly take implicit bias and make it explicit, and move on to the story.

But through my rose-colored glasses, I’m simplifying cartography. Designing maps requires so many more decisions than just projection, and the motivations of the cartographer can affect each step, just like journalism.

Maps make for powerful storytelling, when they are designed well. The constraints of telling a complete story in one image create an environment when every decision counts. But even though I have 2500 words to tell my story, I’ve realized that thinking like a cartographer, making careful design decisions, made it stronger.

The deep

A submersible climbs down the ladder

of the black water rung by rung

to where the crushing pressure

would end a human like a tin can

though glowing fishes swim by unbothered

their heads like meteors burning up.

At the floor, filamentous crabs

drag pale claws through the current

while mote-like animals sift downward

in a snow that falls for miles

and giant fronded worms stand in crowds

waiting for their arrival.

Next door to our apartment

is an old dog with threadbare skin

dying. Deaf and sightless,

she makes a keening at night

trying to recall the sound of her voice

or learn whether people still exist

but all she hears is a pressing quiet

that echoes with distant whales.

Although everything around is darkness

the animal gives off her own faint light.

She wants to find the bottom but

can’t quite travel deep enough.

~~~

Sulfur bubbles

Image Credit: NOAA

Previously in this series:

Tinea Speaks Up—a Fairy Tale by Cindy Doran (fairy tale, talking animals)
Animals Exposed to Virtual Reality Hold an Emergency Meeting by Ferris Jabr (fairy tale, talking animals, video)
The Making of a Mutant: A Fruit Fly Love Story by Ricki Lewis (fairy tale, talking animals)
Step One: A Medical School Pivot Point by Samyukta Mullangi (personal story)
A Noble Betrayal by Kirk Klocke (lablit)

He is a feral cat, sometimes known as a community cat. He probably lives in a small colony, and indeed there are several other individuals that I have seen around, although this is the only one who likes to sleep on my front step.

This orange cat seems to have a pretty good life, which is often true for cats living in colonies that are managed. This colony, as I’ve said, is at least getting fed regularly. However, his life is liable to be shorter than that of an owned cat, and in fact I have already taken two badly-injured community cats to the local veterinary hospital for euthanasia. (As the neighborhood veterinary student I find that one of my responsibilities is dealing with cats who have been hit by cars or attacked by other animals.)

He is also at risk of disease, such as feline leukemia or feline AIDS, because he has probably never been vaccinated. He is not the only one at risk; his colony may maintain a reservoir of these feline diseases which can then be transmitted into the population of owned cats who are allowed outside to interact with their feral cousins. Moreover, community cats are often sexually intact and certainly contribute to the overwhelming number of kittens that my community sees every spring and summer. And, of course, bird lovers complain of the depredations of community cats on the local wildlife.

Time was, people trapped community cats and euthanized them as a means of population control. This didn’t work as well as you might think, because when a colony of cats was depleted, new cats would move in to take their place. It turns out that maintaining a healthy colony keeps new cats out. In the last decade or so, volunteers and animal shelters have been implementing trap/neuter/return (TNR) programs. Cats are trapped and brought to veterinary clinics, where they are vaccinated and spayed or neutered.  They are returned to their colonies, which are managed by caretakers. In this way, colonies are kept small but healthy.

However, TNR programs are maintained at great expense. Veterinary surgeons are not cheap, and even with volunteer veterinarians, a surgical suite also has to be acquired. Cats have to be trapped on a specific day when a TNR clinic is scheduled, not an easy task itself, transported to the clinic and then transported back. The expense slows down the process, and it’s not clear that we can spay and neuter fast enough to keep up with the population.

A simple medical intervention would be much more efficient than surgery. The ideal chemical contraceptive would be inexpensive to make and easy to administer;  a single treatment would have a long term or even permanent effect; it would have a wide margin of safety for both cats and the environment (you wouldn’t want a dead cat to be full of some toxin that would endanger other animals); and it would have a rapid onset of action. Ideally, it would not just prevent litters, but would also reduce the nuisance behaviors associated with breeding, because cats having sex are extremely noisy. The contraceptive should be widely effective, although studies suggest that it only needs to affect 70-80% of female cats in order to achieve population reduction.

There are some possibilities already being studied. Both are vaccines – it’s an amusing idea to vaccinate against pregnancy, but of course vaccines do have a long term effect, so they’re logical choices for this situation. One vaccination target is the zona pellucida. This is the coating around the egg which allows in one, and only one, sperm; vaccinated animals produce antibodies which attack the ZP and therefore inactivate the egg. The nice thing about ZP vaccination is that is is highly species-specific – the ZP is, in fact, part of the mechanism that keeps species from being able to interbreed with each other. Unfortunately, the ZP vaccine which is currently available was not developed specifically against cat ZP, and does not work well in cats. A cat-specific ZP has also been tested but, surprisingly, is not highly effective either. Perhaps more research will sort the problem out, but for now this is not a viable alternative. Additionally, as you might guess from the mechanism, ZP vaccination doesn’t affect mating behaviors even when it works; it only affects conception. So cats will still yowl during sex after ZP vaccination.

A more promising alternative is vaccination against GnRH, the master hormone of the sex hormones. Through minion hormones, GnRH controls production of sperm and ovulation of eggs. Unlike the ZP vaccine, the GnRH vaccine reduces both pregnancy and mating behaviors. Its effectiveness is somewhat unpredictable, so some vaccinated animals keep right on getting pregnant. Its length of effectiveness is also somewhat variable, but can last up to several years in some studies. Although your housecat might live into its late teens, several years of birth control are probably sufficient in shorter-lived community cats.

A commerical GnRH vaccine, GonaCon, is approved in cervids and has been successfully used in white-tailed deer. It has been tested in cats in laboratory settings, but not in the field. The idea is enticing: volunteers could trap cats, then vaccinate them with GonaCon and the usual array of anti-disease vaccines right in the trap, then release them, never having had to bring them in to a veterinary clinic. Efficiency would be hugely increased. Hopefully initial trials would show that GonaCon is effective at population reduction in cats, something that hasn’t yet been proven.

Real life is never so simple, of course. I talked about contraceptive vaccination with a few vet techs at an animal shelter recently. They loved the idea, but pointed out that in our state, once you are providing any medical care for a cat, such as contraception, you have to make sure they are vaccinated for rabies, which legally requires the presence of a veterinarian. Once you have to bring in a vet, of course, the expense starts going up again. We batted around some ideas – maybe you could distribute an oral form of a vaccine in bait form, and get around the rabies vaccination requirement by dint of never actually touching the cat. In this case, the ZP vaccine might be better, as it is more species-specific and presumably could be eaten by other species without effect, but of course the ZP vaccine requires more work before it will be effective in cats.

So chemical contraceptives for community cats aren’t quite ready for prime time, but there are some promising candidates. My suspicion is that the biggest problem is simply willingness on the part of society to commit the resources necessary to develop a workable solution. Cat rescuers and animal shelters, both with notorious money problems, can’t possibly represent attractive markets to drug companies. Who will fund the necessary research and the advocacy for policy changes that are necessary? You can stay up to date with news as the story unfolds at the Alliance for Contraception in Cats and Dogs (http://www.acc-d.org). You can even donate to them. Community cats may be our responsibility, as domesticated animals gone feral, or they may not be, but either way they affect us and the animals we live with. Efficient and humane management of their populations benefits both them and us.

References:

* Julie K. Levy. Contraceptive Vaccines for the Humane Control of Community Cat Populations. American Journal of Reproductive Immunology, Special Issue: Special Issue on Contraceptive Vaccines, Volume 66, Issue 1, July 2011

* Julie K. Levy, JohnA. Friary, et al. Long-term fertility control in female cats with GonaCon(TM), a GnRH immunocontraceptive Original Research Article Theriogenology, Volume 76, Issue 8, November 2011, Pages 1517-1525.

* Alliance for Contraception in Cats and Dogs, http://www.acc-d.org

Nature Volume 485 Number 7396 pp5-142

The following is an editorial from Nature magazine, reposted here with permission. It was originally posted May 2 with the title, “Publishing risky research.”

This week sees the online publication of the paper ‘Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets’ by the Japanese–US team headed by Yoshihiro Kawaoka at the University of Wisconsin-Madison (M. Imai et al. Nature 10.1038/nature10831 (2012). See also pages 7 and 13, and H.-L. Yen and J. S. M. Peiris Nature http://dx.doi.org/10.1038/nature11192; 2012). Kawaoka’s paper was one of two submitted last August, reporting mammalian transmissibility of avian flu as a result of artificial genetic manipulation, the principal scientific interest of which arises from the small number of mutations found to be necessary. The other paper, by a team headed by Ron Fouchier at the Erasmus Medical Centre in Rotterdam, the Netherlands, is expected to appear soon in Science.

As has been much discussed in Nature, both papers were independently assessed by the US National Science Advisory Board for Biosecurity (NSABB) while being considered by the journals. The NSABB’s recommendation, communicated to the journals in November last year, was not to publish the essential methods and data. Although such a recommendation has no statutory force, it makes any researcher or publisher pause. There followed months of public debate and two two-day meetings involving flu experts and other stakeholders, one held by the World Health Organization (WHO) and the other by the NSABB. After the second, at the end of March, the NSABB essentially reversed its position, and Nature made its own decision to proceed.

Lessons learned
As the economist John Maynard Keynes reportedly said: “When the facts change, I change my mind.” But the essential scientific elements in the Kawaoka paper were unchanged between the first and second NSABB deliberations. It is now clear that the committee’s original deliberations were too limited, especially given the enormous implications for flu research of a recommendation against publication. Yet as a body that aims to anticipate and scrutinize the security risks of biological research, the NSABB is unique worldwide, and it is desirable to have such a forum. The discussion that followed the board’s first decision would not have been as valuable or as prompt had it concerned hypothetical cases. Yet there are justified concerns among the research community about the NSABB’s processes, and these processes should be reviewed.

Some lessons have emerged that point to actions and policies for the future. First, it was worth deliberating at length on the possibility of redacting the key findings of the paper instead of simply rejecting it. (Rejection has long been an option if Nature is advised by security experts that the risks of publication exceed the benefits.) There was also the option that the full paper might be distributed by some third party, to selected recipients only. Having now considered these matters in depth, the editors of this journal have decided that we will not consider either alternative for papers in Nature in the foreseeable future. A paper that omits key results or methods disables subsequent research and peer review. Furthermore, after much internal and external deliberation, we cannot imagine any mechanism or criterion by which to sensibly judge who should or should not be allowed to see the work. Nor do we believe that any restricted information distributed to university laboratories would stay confidential for long.

We are aware that the lack of an option for restricted publication has its own risks in a discipline in which results might be both beneficial to the public benefit and a threat to security. We will willingly explore ways out of this dilemma.

One major risk amid these discussions is that younger researchers might be discouraged from entering a field that is subject to security constraints. But the attitudes of biosecurity experts are more encouraging than is widely appreciated.

As far as Nature is aware, formal assessments by security agencies have led to recommendations that the Kawaoka paper be published. This includes an independent assessment that we commissioned from a non-US biological-defence agency, whose advice can be found at go.nature.com/wglsea. In subsequent discussions with biosecurity researchers, there has been a striking unanimity: where there is a benefit to public health or science, publish! It has been enlightening to see how scientists in this secretive arena see the open scientific enterprise as their best recourse in times of potential trouble.

The third most important lesson is about biosafety. Here there are real concerns: humans lack immunity to flu viruses with an H5 haemagglutinin protein, and an accidental release of a mammalian-transmissible H5 virus would have the potential to cause a pandemic were it to transmit between humans. A key component of the second round of NSABB deliberations was a clear presentation by Kawaoka of his team’s very rigorous security processes and set-up, including physical arrangements, training and due diligence exercised with personnel.

Such a reassuring picture is not globally applicable. The standards of these labs (fully described in the Kawaoka paper) were widely quoted as biosafety level (BSL) 3 enhanced. The WHO discussion considered such standards essential, and worried that to require the distinctly more demanding BSL-4 standard would shut down the research. However, ‘BSL-3 enhanced’ is not a formally established standard. What is more, not every country may have sufficient regulatory systems and robust laboratory cultures of safety. This is a key issue as the self-imposed moratorium on work by flu-transmissibility researchers continues.

The WHO will soon release guidelines about international standards for biosafety. The signs are that these will highlight key issues and aspects of good governance, but will not themselves provide a framework for strengthened implementation. The absence of such a framework is an urgent concern for all researchers working with dangerous organisms, and for all who fund and publish their work.

The wreckage and impact on business was acute in the wake of the gruesome violence. Yet there is a story of incredible resilience when examining the aftermath of the Sept. 11 attacks.

According to USC Price School of Public Policy professor and Center for Risk and Economic Analysis of Terrorism Events (CREATE) researcher Adam Rose, who has studied the economic ramifications of the attacks, many businesses situated near the World Trade Center site relocated to midtown Manhattan or Northern New Jersey.

“This adaptive behavior had the effect of reducing losses and saving 80 billion dollars,” explained Rose.

The economic harm was far less in the immediate aftermath than initial estimates predicted, according to a team of CREATE scientists at USC and affiliates at other institutions, whose study is funded by the Department of Homeland Security. The impact of the attacks in New York ranged from $40 billion to $120 billion for gross domestic product. Those numbers translate to roughly 0.5 percent to one percent of the GDP. Many of the behaviors exhibited by business owners, which included moving businesses or hastening clean up, helped to alleviate longer-term economic devastation.

However, while the immediate financial impact was lower than previously thought, longer-term economic and psychological impacts are undeniable, according to CREATE researchers. America has changed since the attacks on Sept. 11, 2001. Invasive security measures are now a norm, affecting everyone from train riders to air travelers to business owners. These changes haven’t merely imprinted themselves on the country’s collective psyche, but also impact economic development as Americans attempt to find a balance between security measures and commerce.

“You have different viewpoints about what the right level of security,” explained Stephen Hora, a decision analyst and a professor at the Viterbi School of Engineering and the Price School of Public Policy, who is leading the Urban Commerce and Security Study (UCASS). “The people that are primarily motivated to do business are concerned that too much security will negatively impact business. On the other hand you have people that are primarily motivated to keep us safe and secure.”

Using five different attack scenarios, which mirror al-Qaida attacks that have taken place from Madrid to Manhattan, the study examined the economic costs of a terror event and how to prevent them.

“The attack scenarios are representative of attacks that have happened elsewhere,” said Hora. “For instance one scenario is very much like the Mumbai-style attack [in 2008]—low technology, very deadly.”

Too much security can cause stagnation in business. Too little can also be damaging. This is clearly illustrated with the Port Authority of New York and New Jersey, which rents out property to businesses and maintains responsibility for security at the port—from which roughly 19,000 cargo containers flow into the U.S. daily.

“The inception of the Urban Commerce and Security Study project was born from a very high level meeting between the undersecretary at the Department of Homeland Security who is in charge of science and technology, and the executive director of the Port Authority for New York and New Jersey,” said Dave Newton, project coordinator for UCASS, which is funded by the Department of Homeland Security. “The Port Authority is an interesting stakeholder because of their security responsibilities and the fact they are one of the largest landlords in the greater New York area as far as real estate.”

Inspecting each container at the port would impede business but strong layers of security are important, as U.S. ports have already been used to illegally transport goods that have financed terrorism.

“When you have the counter measure in place you incur economic slowdown and the direct and indirect cost of the counter measure, but you reduce the probability of an attack and, perhaps, the consequences of the attack,” said Hora.

In recent years politicians have attempted to pass legislation mandating that more containers in U.S. ports undergo inspection. Due to high costs and difficulties in examining all containers, such measures have not been passed. Instead, the ports have worked to adopt a scientific model.

“Obviously there is a concern of what is coming into the United States and how it’s being examined,” said Bob Hamer, a retired FBI agent. Hamer’s last assignment was Operation Smoking Dragon, lasting from 2002 to 2005. Through sales of counterfeit Marlboro cigarettes and tax stamps, the FBI learned about many of the funding sources helping to finance terrorism through the transport of items via Southern California ports. “A lot of the profits from these counterfeit cigarettes were, particularly, going to support Hezbollah and Hamas,” said Hamer. “The whole thing began with counterfeit cigarettes. It eventually evolved into something much greater than that.” Operation Smoking Dragon also unveiled North Korea’s production of ‘supernotes’—counterfeit 100-dollar bills that were central to the plot of a Hollywood film, “Rush Hour 2,” but a serious real-life concern for those who seek to protect civilians.

The ongoing UCASS project examines the trade-off between security and commerce in the lower Manhattan area, and helps policymakers to identify optimal levels so that economic activity is not infringed upon. It’s a project that CREATE’s researchers also hope to adapt to Southern California.

“Security measures are most effective as systems with layers of security,” explained Samrat Chatterjee, a postdoctoral research associate with CREATE. “The effectiveness of security measures is not simply the aggregation or sum of the effectiveness of the different components within the security measures.”

In layman’s terms, security tactics cannot be evaluated in a simple manner by isolating just one measure and adding its effectiveness to another tactic’s effectiveness. For instance, a 50 percent reduction in risk cannot be added to another 50 percent reduction in risk to reach 100 percent. Instead that reduced risk would be another 25 percent.

“There is not going to be any such thing as 100 percent security,” explained CREATE director Hora. “We have to live with some risk, but we can reduce the costs of unnecessary security measures by calculating likelihood of attacks and effectiveness of security countermeasures..”

Besides surveys, CREATE researchers used computable general equilibrium (CGE) models, which are used widely in policy analysis, and elicitation and survey methods to measure reactions of policy-makers, and Manhattan residents, employees, businessmen and tourists. The researchers also developed a template for identifying all direct and indirect costs and benefits of the countermeasures, including spillover effects that reflect both positive and negative unintended side effects.

Lions and wolves also do not have the ability to find alternate protein sources, like we do. Yet it is not absolutely clear that these are better for us, or for the planet. Proponents of the paleo diet insist that legumes, including beans and nuts, are full of toxic lectins; paleo message boards and blogs are filled with former vegans claiming that they were at death’s door until they started eating meat again.

Soy can provide us with all of the essential amino acids, but some think that its high phytoestrogen content mitigates its nutritional value. Fish is a terrific source of protein, but our current appetite for it has brought the world’s fisheries to the brink of collapse and severely disturbed the oceans’ ecosystems. And of course dairy and eggs can provide protein – but the animals raised to provide us with dairy and eggs are not treated any better than those raised to provide us with meat.

Although I do not have a problem with the idea of eating meat, I do have a problem with torturing animals to make it cheaper for us to do it – so I pay more to buy meat from animals that have been “humanely and ethically” raised right up until the moment they are slaughtered so I can eat them. I buy from http://kolfoods.com/ and http://growandbehold.com/. I think of this as the truer cost of eating meat; industrially produced meat might cost fewer dollars when I am purchasing it, but I will pay for it in other ways – my health, my conscience, and the state of the environment.

Since the meat I buy is so very expensive, I definitely eat less of it than I otherwise might. Hopefully this ends up being better for my body, the animals I end up eating, and the planet, although it is certainly not better for my wallet. In eating this way I can practice curbing my primal carnivorous nature without completely denying it. But I know that this option is not available to everyone for financial reasons, and that is the crux of the problem we face.

With great power comes great responsibility, right? For better or worse, humans are the lords and stewards of this planet and the animals that inhabit it. While I do think it is within our rights to eat them, I do not think it is not within our rights to treat them cruelly just to save a few bucks.

Image: Robert Joppa, from KOL Foods

Lovelock envisioned the Earth as a living system, which he dubbed Gaia. Image Credit: NASA/NOAA/GSFC/Suomi NPP/VIIRS/Norman Kurin

Just because someone has had some brilliant ideas, it doesn’t mean every word he utters shines with truth. Let’s keep that in mind in the furor about James Lovelock, inventor of Gaia theory. Lovelock finally stepped back from his doomsday interpretation of climate change last week, but he’s still got a lot of the science wrong.

Lovelock is not a climate scientist, and he continues to misinterpret the climate science even in his retractions in an MSNBC article, as Joe Romm has pointed out for Climate Progress. What’s more, in his 2006 book The Revenge of Gaia, he basically invented a dire interpretation about how forests would respond to warmer temperatures with what he admitted were, in his words, “imaginary sketches.”

James Lovelock had claimed that both forests and people would not survive this century in the tropics. Here, Brook Kazmer hikes in tropical Puerto Rico. Photo by Melanie Lenart

This invention was unnecessary given that there’s plenty of evidence about how forests responded to past times when the planet suffered a hothouse existence. My 2010 book Life in the Hothouse – which delves into this evidence to re-examine how Gaia theory applies to the ongoing warming – was written in part to help counterbalance Lovelock’s overly active imagination as laid out in The Revenge of Gaia.

To address the climate issue first, clearly he was branching out into his own reality when he issued this claim in his book, repeated in a 2006 Independent column: “… before this century is over billions of us will die and the few breeding pairs of people that survive will be in the Arctic where the climate remains tolerable.” No other scientists supported that wild exaggeration.

And who knows where he got the idea that a continuous increase in carbon dioxide should lead to a continuous increase in temperature. It wasn’t from the climate models that he blames for the supposed error. No models project the atmosphere to behave so linearly – partly for the same reasons that Lovelock identified when he proposed Gaia theory. The Earth is too big, with moving parts that include life and ocean currents, to expect it to respond with such predictable precision.

Seeing the Earth as a complex living system is the crux of Gaia theory. As described in his seminal 1979 book, Gaia: A New Look at Life on Earth, Lovelock’s theory suggested that life on our planet helps keep global temperature within a survivable realm. In modern times, temperatures can range from the icy existence of penguin territory to the humid tropics where bugs thrive year-round. Life survives in every realm. In the distant past, the planet has passed though ice ages and hothouses. Life forged ahead, and here we are.

The atmosphere interacts with plants, such as in this fog-covered old-growth forest in Oregon. Photo by Melanie Lenart.

In his 1979 book, Lovelock provides some elegant insights into how life affects the atmosphere – the thin layer on the Earth’s surface where weather operates and sunshine penetrates to varying degrees. A chemist by training, Lovelock contributed vastly to the movement to see our planet as a living system in which animals, plants and bacteria play key roles in shaping the environment, including the atmosphere. It took decades before scientists really embraced his ideas, and still there aren’t many of us willing to call it Gaia theory rather than the more scientific-sounding phrase that evolved from it, Earth system science.

Like many people, I was inspired by his vision of a living, breathing planet. I admire Lovelock for coming up with this vision, and for having the courage to share it with a community of skeptics. Still, I allowed my respect for his creativity and courage to keep me from directly challenging his more outrageous suggestions as much as I should have.

Along with the comment that humans were heading toward extinction this century, there was another major flaw from The Revenge of Gaia that demanded an outraged response. On page 63, he featured three drawings that looked like very basic vegetation maps – one of a colder past, one of the present, and one of a warmer future. These are the drawings he rightly described as “imaginary sketches.” In his imagination, forests virtually covered the continents of the ice-age Earth, while only a few specks of forests remained near the poles in his rendition of a hothouse Earth.

In fact, the opposite situation is closer to the truth, based on evidence from fossils, sediments, peats and coals, and anything else that survived time’s passage. In the distant past, albeit in the absence of widespread human civilization, forests generally expanded during hothouse periods and shrank during ice ages. In addition to my book, recent articles in Scientific American and National Geographic have described abundant hothouse vegetation in places Lovelock pictured it absent.

Lovelock’s imagination has given the world many gifts. Another invention of his, the electron capture detector, helped point to the rise of chlorofluorocarbons. These are the CFCs that eat away at the ozone layer, the invisible stratospheric cloak that protects us from damaging ultraviolet rays. The depletion of the ozone layer was a disaster starting to happen. When measuring devices like his started backing up the scientific assessment by others that CFCs were accumulating in the atmosphere, we changed our habits as a global community.

Lovelock’s work at NASA on ways to detect life from a distance in the 1960s helped inspire his thinking of the Earth as a living system. Photo courtesy of NASA/GSFC.

A successful rescue of a planet with an altered atmosphere – it’s a tale that inspires many of us worried about climate change. Perhaps Lovelock, like many of us, had hoped for a repeat performance by calling attention to how the changing atmospheric was contributing to a dangerous condition – in this case, a warming and shifting climate.

Still, it’s one thing to invent a device to measure CFCs and other chemical compounds, or a theory proposing that the web of life on the planet affects the environment. These efforts are supported by facts. They’re akin to finding a pile of bones and fitting them together in a way that forms a plausible dinosaur skeleton.

It’s quite another thing to invent facts for imaginary sketches of how the Earth’s vegetation looked in the past, or to create single-handedly a climate change scenario in which humans dwindle off by century’s end. That amounts to building a dinosaur skeleton from wood and plaster, calling it a fossil, and then pointing to it as something alarming.

Lovelock deserves our respect for his visionary ideas, but not all of his thoughts are diamonds in the rough. Some are just rough sketches with no real basis in truth. It’s OK to toss around ideas like this with friends at a bar, but someone as influential as Lovelock should do his homework before sharing his thoughts with the world.

This memory is fresh in the minds of the crew and science party aboard this ship, many of whom experienced the events of March 11. The earthquake was larger than expected for this part of the coast, and the seismological community has been very active in the past 13 months revisiting everything we used to know about earthquake hazard. What’s more, the tsunami generated by this earthquake was bigger than expected – as you have seen in the photos and videos of waves topping the seawalls in towns along the Tohoku coast. For its size, this earthquake was alarmingly effective at creating a tsunami wave.

Why? What was so special about this earthquake? Clues started emerging in the days and weeks after March 11. Japan has the most detailed network of seismometers and GPS stations, all collecting data in real time, of any country in the world. The seismometers recorded the seismic waves generated by the earthquake, and the GPS stations tracked the motion of the Japanese islands toward the deep ocean trench. Data were collected from sensors on the ocean bottom that recorded the changes in water depth related to ground deformation, ships studied the bathymetry, which showed the horizontal displacement of the edge of the North American plate toward the west.

Within two months, the Japanese journal Earth, Planets, and Space collected the first scientific results and made them available for free to the public: you can download the papers here. These and other rapid reports started to paint a picture of a very unusual earthquake. First, the distance the fault slipped in less than 3 minutes seemed to have been greater than any earthquake ever observed (as much as 60 m) ². Second, whereas earthquakes usually show a pattern of larger slip distance at depth, decreasing toward the surface, the Tohoku earthquake actually increased to maximum slip near the surface, right to the ocean floor in the Japan Trench³. This bumped the sea floor straight up about 5 m — pushing the base of the water column in a sudden undercut ⁴. It was this great bump from below that created the tsunami wave.

So, what was so special about this fault on that particular day, which made it behave differently than faults do in typical very large earthquakes (if there are such things)? That’s what D/V Chikyu is here to find out. This expedition was rapidly assembled to capitalize on a rare opportunity, to access a fault that has slipped so much, while the fault is literally still hot from the friction. We know from studying faults on land, like the Chelungpu Fault in Taiwan or the Median Tectonic Line in Japan, that after an earthquake the fault zone rapidly changes. Cracks close up, groundwater flows through and cools things down, new minerals grow to repair the damage. So if we want to see the earthquake source when it’s hot and fresh, the only option is to drill into it, as soon as possible after the earthquake. The Tohoku earthquake, with its extreme slip at shallow levels, is offering us a window into the fault processes that usually only occur at greater depths. As our expedition co-chief Jim Mori recently told Nature, we have a rare “opportunity, maybe even a responsibility” to learn what we can from this event, and apply that to other areas where the risks are still unknown⁵.

Figure 1: Paleomagneticist Toshi Mishima from Osaka City College and legendary subduction geologist Casey Moore from UC Santa Cruz examine the LWD tools with Schlumberger engineer Michael Weng Feng.

We are here 6910 m above the sea floor at the Japan Trench, building drill pipe segments 40 meters at a time, as the drill bit descends almost 7 km below us. Built into the drill pipe are sensitive instruments that will reveal images of the world below the seafloor. Some data, the roughest picture, will be sent by the instruments up to the ship by acoustic signals running up through the down-flowing drilling mud. More detailed data, and higher resolution images, will be recovered from the instruments’ memory when they are back aboard ship. This will give us the first view of that rock which slid more than 50 m eastward on March 11, 2011. We’ll use the measurements of rock properties and maps of rock layers (and the damage) to try to precisely pinpoint the position of the fault. Then when we return to the seafloor with the coring bit to collect a long, thin, vertical sample of the fault zone, we will use these images and maps of properties to help us find the fault in the core, and extrapolate out of our 56 mm-wide window into the earth.

Logging-While-Drilling (LWD) and Measurement-While-Drilling (MWD)

On this expedition we are using two downhole measurement techniques: Logging-While-Drilling (LWD) and Measurement-While-Drilling (MWD). LWD tools measure properties of the rock in the wall of the borehole, while MWD tools collect information about the condition of the borehole. These data are sent back to the drillers in real time and used to maximize drilling efficiency and borehole stability.

Logging-While-Drilling allows us to get a picture of the subsurface strata before we drill to recover core samples, much in the way that a doctor might X-Ray before operating, and is a commonly used technique in the oil and gas industry. Without LWD, a hole might be drilled and the bit pulled out, then a string of similar tools on a “wireline” would be lowered into the hole to make measurements of the rock properties – assuming that the hole stayed open and stable! With LWD, the measurements are made just behind the bit while the hole is drilled.

The tools are built into pieces of pipe (Figure 1) and fitted between the bit and the drill string, so multiple measurements are taken simultaneously as the bit penetrates the sediment. Some tools carry their own batteries, while others use smallturbines to gain power from the flow of drill mud pumped from the ship above. These also use the flow of mud as a means of communication back to the drillers. By slight constrictions in the flow, they create an acoustic signal that travels up through the down-flowing mud to code for pressure, hole deviation, and temperature. A wire or cable would be problematic due to the rapidly rotating drill pipe. They collect a lot more data than can be sent in this way, which is stored in the instrument memory until they return to the boat.

Figure 2: Electrical resistivity images of a borehole drilled off the coast of southwest Japan on Expedition 314 in the Nankai Trough subduction zone.6

Figure 2 shows two electrical resistivity images of borehole walls taken in a similar subduction zone offshore southwest Japan⁶. The darker areas are conductive – often because there is more water there – and the bright yellow areas are resistive, solid rock. So the resistivity image allows logging scientists to pick out the details of the rock structure – beds of different types of sediment, or dark lines which are water-filled cracks. The great utility of LWD/MWD data is that they are a continuous, in situ dataset of the physical properties of the formations drilled downhole, and it enables drilling decisions to be made on the fly. In fragile, fractured and potentially unstable formations, this may be the only information which can be recovered. In our case, we will use these data to guide the core recovery. Physical properties will later be measured on pieces of core, in the ship’s laboratories, and in the home laboratories of the scientists on board, but these are small samples, and it’s impossible to completely avoid disturbance when coring. So the LWD information is a valuable field check on core observations, and offers a view of fractures in the wallrock which might be too widely spaced to be measured in drill core, but might be important for permeability around the fault. In the case that there are gaps in the core we recover (and there usually are a lot of gaps when drilling in damaged rock) we can compare our samples to the LWD logs to try to place them back in the right position.

Figure 3: Drilling crew tighten the logging tools into place in the drill string on the rig floor of Chikyu.

Logging While Drilling is one component of our research mission on Expedition 343, the Japan Trench Fast Drilling Project (JFAST).

For more information about JFAST and to track our progress with daily updates and tweets, see the Expedition website, in English or Japanese: http://www.jamstec.go.jp/chikyu/exp343/e/index.html.

¹ Jamstec Earth Discovery Web Magazine, The Tsunami and the CHIKYU, What Happened on 3/11: An Interview with Chikyu Captain Yuji Onda March 2012

² Lay, T., Yamzaki, Y., Ammon, C. J., Cheung, K. F. and Kanamori, H. (2011) The 2011 M₂ 9.0 off the Pacific coast of Tohoku Earthquake: Comparison of deep-water tsunami signals with finite- fault rupture model predictions. Earth Planets Space 63 797-801.

³ Fujiwara, T., Kodaira, S., No, T., Kaiho, Y., Takahashi, N. and Kaneda, Y. (2011) The 2011 Tohoku-Oki Earthquake: Displacement reaching the trench axis. Science 334 1240.

⁴ Ito, Y., Tsuji, T., Osada, Y., Kido, M., Inazu, D., Hayashi, Y., Tsushima, H., Hino, R. and Fujimoto, H. (2011) Frontal wedge deformation near the source region of the 2011 Tohoku-Oki earthquake. Geophysical Research Letters 38 L00G05.

⁵ Jones, N. (2011) Drilling ship to probe Japanese quake zone. Nature 479 16. October 31, 2011

⁶ Proceedings of the International Ocean Drilling Program Volume 314/315/316, Site summaries, Site C0001. Image provided by J. C. Moore.

Soon after he died, my mother presented me with a trove of my father’s magazines, saying, “He would have wanted you to have these.” I gasped as I thumbed through each dusty issue and recalled how my father had planted the seeds of a scientist’s curiosity in my young brain, seeds that would blossom years later when I returned to school to study for a Ph.D. in genetics.

I remembered some of the covers—the gull experiment picture on the cover of the October 1967 issue, the pre-Columbian medallion on the cover of the April 1966 issue and the salmon in a water tunnel on the cover of the August 1965 issue. I recalled how each magazine would sit proudly on our coffee table until the next month’s issue arrived.

As I examined my father’s collection, I saw on each cover–recorded in his handwriting–notes about the stories that most interested him. Each note elicited a memory or revealed something new about my father. “Holograms” he scrawled on the February 1980 cover. He and a buddy invented an aircraft trainer—the first that used holographic images he would tell me.

My father was trained in the Navy as an electronics technician. His first job after receiving his discharge papers was with AMF, the company that invented the electronic pin spotter. He mastered calculus, physics and optics on his own. Along the way he worked his way into the aerospace industry. Eventually he became a licensed engineer and by the end of his career his business card said “Senior Project Scientist”.

My father’s favorite section of Scientific American was “The Amateur Scientist”. “Seismomoter” [sic] he wrote on the cover of the September 1975 issue. Inside at page 183 was the design for a seismometer, which my father might have used to build the “earthquake detector” in the backyard of his Southern California home.

Notes about lasers appeared on the covers of a number of issues. In our living room for many years sat what he called his “laser”. I never saw a demonstration, but I have no doubt that it worked. When he died, my father had over a dozen patents in his name and the name of whatever company he worked for at the time each invention was conceived.

Some of the notes were cryptic: “Lemon meringue pie”, “Judo”, “Sailing”, “Hang gliding”. The pie was probably a reference to my father’s favorite desert, which my mother often baked. Were the other notes about dreams unfulfilled? I will never know now, but when I pick up one of the brittle magazines, I can imagine how excited he must have felt when a new, shiny issue of Scientific American arrived in the mail.

This is the third week of our Guest Blog weekend experiment, which we call #StorySatuday, in which we invite people to write something different – fiction, science fiction, personal stories, poetry, or comic strips. We hope you like it.

Prologue:

When Chloe received the hard copy of her degree certificate last summer, she opened the tube, unrolled it, and found a small white unmarked envelope. The next morning, she mailed her CV to a man at Building 18: To the attention of Dan Auckland, Ph.D.

Dear Dr. Auckland,

I recently learned of your work in nonmetal engineering, and would like to take a chance to introduce myself …

***

Danielle was waiting in line for coffee during intermission at the Schaubühne when she noticed a dull ache in her upper back. The 37-year-old mousy-blonde American expatriate worked long hours managing a boutique casting agency in Berlin; many of them she spent hunched in front of a screen with a phone receiver crunched between her ear and shoulder, one hand on the keyboard, and the other on a not-so-ergonomic mouse. The stress of being in charge had led her to gain a little weight over the past year, but she still saw herself as fairly fit, and the insane price of a pack of ‘reds had forced her down from a pack a day to just one or two, now and then. I should get a massage, she thought as she tapped an unused ticket that was meant to be for her date. Or maybe he could have given me a back rub, tonight. If he had showed up. His text right before the concert read: “Hey sry got stuck w/client dinner mtg ttys.”

Before the café clerk took her order, she drew a deep breath and held it for a few seconds, hoping the ache would go away. “Light roast, with room for milk,” she told him in German. He held up his thumb and two fingers and she put three Euros on the counter. The coffee wasn’t that great, so she poured it in a nearby drinking fountain and tossed the cup as soon as they flashed the lights.

The second half was better, and she was actually kind of glad to have an empty seat next to her. It had been a long week and it was more comfortable that way. She was enjoying the maestro’s strict interpretation of Lincolnshire Posy, but was having a more and more difficult time ignoring the pain creeping down her back and a cold tingling sensation in her finger tips and toes. By the downbeat of Lost Lady Found, she could feel herself turning ashen.

The room spun faster and faster with folk melody’s beat, and Danielle’s consciousness danced on a slice of darkness the color of the principal’s oboe.

Ashes, ashes, we all fall down

***

The northbound ICE was crowded, but after walking through three cars, Chloe and Dan found two open seats. Paar Nur, Bitte, a sign above the seats read. Below the words was a red heart.

“I suppose we’re together now,” Dan said with a slight sarcastic wink. “After you.”

His sense was humor was decent for a scientist – especially for an applied nonmetal materials engineer. In the course of many long, late nights in her advisor’s Building 66 lab, Chloe had heard about Dan – that he was fun to work with. Last year, when she was wrapping up a thesis on semiconducting nanowire arrays, she had no idea she’d end up in Dan’s group. But she was secretly happy she did. He had made her laugh almost every day since she joined his lab. She wasn’t sure if he was seeing anyone, but never asked and tried not to think of her new boss in that way. Outwardly he appeared clean cut, fit, dressed well (sometimes). But she had already seen his messy piles of papers and eccentric handwritten notes, and knew he danced that fine line between genius and insanity. At times, she wondered how some American men could be so disorganized, yet still somehow be productive. Her private British boarding school in Hong Kong had been a holdout for the classics. Rote memorization, penmanship, discipline, and more discipline. Her father, a trader of rare earth futures, would not have had it any other way. He had allowed her to quit ballet, but not math and science.

For that, she was glad. Chloe Chen at times had moments of doubt about whether the years she spent studying in the Barker stacks would pay off. Eventually she began to relate to a couple Asian friends on campus who were also raised in families where work and family were totally separate life silos. That helped.

There was something slightly thrilling to her about speeding through the German countryside from Frankfurt to Berlin, sitting next to an engineer who had taken her under his wing. As the excitement of Dan’s project assuaged some of her doubts about becoming a research engineer, she had a feeling her personal life and work were beginning to converge in a way that would be difficult to explain to her parents, and hard for them to accept. Which fellowships in China have you applied for so far, her dad asked her some weeks after she handed in her thesis. None.

“So, the non-stop ticket from Logan to Berlin was too much?” Chloe asked.

“They didn’t have any non-stop tickets,” he said. “Plus, this was like half the price, even with the train fare. You know, the prototype is going to eat up over half our grant, so we have to be careful this first year. I had to convince my administrator that this trip would be worth it.” He would suddenly get serious whenever she mentioned anything about money.

“Wasser?” A steward held out a tray of paper cups and an open plastic bottle of seltzer. Sure! They both took a cup. “Is this your first time traveling in Germany?” Dan asked, cracking another slightly devious grin. “Hope you have a taste for mineral water.”

It was Dan’s first time being a Principal Investigator. He had achieved a lot for someone in their mid-30’s, but it was his first time writing a National Institutes of Health RO-1 grant. It took nearly six months of going back and forth with the NIH’s Office of Rare Disease Research committees before he submitted a final proposal. That he had almost no background in applied medical research was mostly to blame for the hassle. Eventually the NIH saw the merit in his project and awarded his lab $150,000 a year for three budget years.

The end goal of his proposal was simple: to do something that would help make harvesting the rare element Xenon less expensive. Overwhelming evidence coming out of Europe pointed to the benefits for cardiac patients.

His engineering colleagues who had known him for several years were at times amused by his obsession with Xenon. Over pints of spring maibock on late Friday nights in Harvard Square, his freakish volume of knowledge about Xenon and all the industries it touches probably drove women away, but made for the kind of great theoretical pub banter you only hear in Boston.

He can remember really getting into it one night with a Boston University anesthesiology resident. “I’m telling you, it’s good stuff. Why aren’t we using it in the U.S.?” Dan asked. Because it’s too damn expensive.

The noblest of noble gasses, Xenon represents the scarcest gaseous slice of air we breathe. Its many uses and inert stability make it the fillet mignon of air. From 15,000-watt arc lamps that power Imax theaters to Star Trek-like “ion” engines that drive deep space probes, the stuff is very useful. Dan had been reading about it since grade school science class, when he asked his teacher how neon bulbs worked. Now he had a chance to play with it, but not as much as he would have liked – the resident that night was right. It is expensive and scarce. At 0.000009 percent of air, your entire bedroom contains about a marble size measure of Xenon.

Dan’s NIH grant project was inspired by renewed interest in Xenon for one of its most notable uses: surgical anesthesia. He never really had an interest in medicine, but as a scientist he found reading about the field of anesthesiology fascinating, because much of the research is based only on observable outcomes. A patient will never remember having their chest cracked open, but even the best anesthesiologists still don’t exactly know why. They sort of do, but they don’t. That sort of science can make an engineer cringe. Dan was the kind of man who needed to understand exactly how and why the Brooklyn Bridge never falls down.

He was staring out the window as a train zooming in the opposite direction shot by in a 2-second gray blur. “I’m really glad they’re going to let us watch a surgery,” Chloe said. “Not something I’d ever get to see.”

“Me too. Please remind me to ask the doctor if it was difficult to get Xenon on their hospital’s formulary. Since it’s a cardiac center I’m guessing not, but I’m just curious.” It had been a long time since his only surgery, a wisdom tooth extraction in high school. He remembered the experience was almost painless, but never really stopped to think more about it until Michael Jackson died. Propofol. Hey, I think I had that weird white stuff.

He turned to face Chloe, who was reading an Atavist story about hibernation on her e-book. “Have you ever had surgery?”

She looked up. “No, have you? Hope I don’t ever have to.”

“If you count wisdom teeth, then yes. Mine were deeply impacted so they had to use general anesthesia. I was just thinking about that the other day when I was reading some papers on PubMed about Xenon for our project. You know, a lot of patients don’t perceive time when they’re under. I definitely did. I woke up, felt like it had been 45 minutes, looked at the clock and I was off by only about a minute. Weird, huh?”

“Yeah, definitely,” she said. “Do you think they’ll let us talk to the patient before and after the surgery?”

He wasn’t sure, but he hoped so. If the project worked out as planned, having more anecdotal evidence on the benefits of medical Xenon might inspire the FDA to quit dragging their heels on approving clinical trials in the U.S. He didn’t know for sure, but he suspected that there were those in Washington whose personal interests were served by keeping new, more expensive treatments out of the U.S., even ones proven to be more economically effective in the long run. Maybe a Medicare thing. Maybe a FDA thing. Whatever. Accepting that government moves slowly would be part of the job, he figured mid-way through grad school. It took 15 years after the first proton beam therapy facility opened at Loma Linda University before the medical community expanded use of the technique. Distilling air was a problem on the orders of magnitude simpler than creating football field size facilities that accelerate cancer-zapping particles to a fraction of the speed of light. So he hoped his machine would make the elusive Xe atom more accessible.

Fortunately for him, someone at the NIH saw the potential value in finding a way to increase the supply of Xenon in the market. Historically, cardiothoracic surgeons in other countries have lauded Xenon anesthesia for its superior safety, seeming harmlessness, and even its potential to protect the heart and central nervous system during long procedures. And environmentalists praise it for not being a greenhouse gas. Though rare and difficult to capture, its medical use will never “endanger” it because it is not used up; it enters the cells and it leaves them with its 54 protons per atom still intact.  There are ways to make compounds out of Xenon, but they involve temperatures and pressures far more extreme than anything found in the human body.

They had only landed four hours ago, so fatigue of jet lag had not yet set in. He pulled a manila folder, a small aluminum metric ruler, and a mechanical pencil from his laptop bag. He had already submitted drawings of the prototype to a grad student in his lab who was more CAD-savvy than he, but he still liked to go through the pages and layers to look for possible problems before the expensive building process began. The machine shops at MIT were great at accepting last-minute changes, but he really hoped to nail it the first time.

“There I am,” Chloe touched the spot on the page he was looking at where her semi-conducting laser element was slated to go. The prototype had been on the drawing board for almost a year, and Dan was eager to see it in real life. The cylindrical device, about a meter in diameter and two meters tall would be as elegant as the Xenon atom itself.

It would essentially be a high-tech still. The bottom of the device would have a port for liquefied air. The liquid air would travel into a vacuum sealed helix made of three layers separated by only a millimeter of space. The first, the layer actually in contact with the liquid air, was to be made out of a highly conductive copper alloy. The 1-millimeter space between the primary tube and the insulation tube was the heart of Dan and Chloe’s experiment. The exterior of the copper tube would be covered in a lattice of nanowires made of a gold alloy blended to absorb a precise wavelength of light that would be shot into the thin space by a laser diode. The interior of the insulation tube would be plated with a polished reflective surface like the Cloudgate in Chicago’s Millennium Park. The ring of precise, powerful lasers would be a guided into the space by a computer adjusted semiconducting magnet – the design of which would be made easier because incoming liquefied air would make the ambient temperature at the base of the machine close to what the magnet would need to operate. An on-board loop of liquid nitrogen, also computer sensed and controlled, would make up the difference.

The integration of nanowires as microscopic heating elements and a wave guided laser diode would represent a leap forward in the 100-year-old craft of air distillation. Dan planned to optimize the machine completely for capturing Xenon. Nitrogen and oxygen would be sent outside as exhaust gas, and the other noble gasses in the order of their respective boiling points, Helium, Neon, Argon, Krypton, Xenon and Radon would be captured from the still at exact points along the machine’s helix where they would boil.

If Dan and Chloe could master the waveguide apparatus, they could achieve just the right temperatures along the distillation trail to capture the gasses in a pure enough form that they wouldn’t need lots of extra processing. Versions of the machine scaled up for industrial use could be located in cold climates for an extra measure of efficiency, much for the same reason several prominent glass factories make their home in Norway and Sweden.

Chloe went back to her e-book and Dan leaned against his seat back as far as he could. “I think I’m going to get some rest,” he said. He put his drawings in his briefcase and slid it beneath his seat. They woke up a couple hours later leaning against each other’s shoulders when the ICE came to a gentle stop at the Berlin Hauptbahnhof.

***

“What happened next?” Dr. Ekkehardt asked.

Danielle had been awake for a couple minutes, confused at first, but quickly figured it out. She could feel an IV needle in her left hand. She lifted her head slightly and looked down at her chest. The orchid silk blouse she had been wearing was gone, replaced by an ugly gray hospital gown. There was a desk and chair to the left of her bed. Light was shining through the window onto the alternating light-teal and off-white patterns on the wall. She could feel bed linens against her bare back.

“What…?”

“That’s okay, relax, everything is going to be okay. You collapsed at the Schaubühne Theater last night and they brought you here. You are at Deutsches Herzzentrum,” he said.

“Where’s my …”

“Right here,” Dr. Ekkehardt lifted her iPhone from the pocket of his white coat. He smiled. Patients always want to know if their phone is okay before anything else. “This is not to alarm you, everything will be okay. But you are probably going to need surgery.”

He explained to her what an esophageal echocardiogram was and told her that she would have to have one that morning. After he left the room, she just laid there for a few minutes, trying to piece together what happened. I was starting to feel sick. Started to get up to use the rest room toward the end of the concert.

The test confirmed what they suspected, based on the chest ultrasound they gave her when she arrived at the emergency room. She had an ascending aortic aneurism. The crucial pipeline that transports blood from her heart to her brain had expanded over the years partly as a result of a bicuspid aortic valve – two leaflets that open and close releasing fresh blood from the heart instead of the normal three. They suspected her longtime smoking habit led to high blood pressure, which caused her ascending aorta to expand and tear at an earlier age than it would have otherwise.

“So you’re saying I should quit smoking?” she asked Dr. Ekkehardt after he explained the result of her echo test.

“Let’s worry about that later,” he said. “I’m going to explain how the operation will work. This is an emergency, so we have to do it tonight.”

A cardiac physician’s assistant was by his side as he walked her through the steps of the operation on his iPad. The colorful images were beautiful, but inside she was having a difficult time accepting what was about to happen. She had no family in the country, no close friends in Berlin, and the guy who was supposed to see her the previous evening was not turning out to be reliable.

“I have a question for you,” the doctor said. “I know this has been a lot to think about very suddenly today, but we have a couple American researchers visiting Herzzentrum today, and with your permission, I’d like to introduce you to them. Their names are Dan and Chloe. Dan is your age and Chloe is 31. She just finished her Ph.D in engineering.”

Danielle had always associated the word “research” with “experiment, so she was at first taken aback by his question. What would they want with me? But she thought about it for a few moments, and without even knowing any details, she said, “Yes I’d love to meet them. What are they doing here? I have no family in Germany.”

He explained that Dan and Chloe were engineers looking for a cheaper way to produce the next-generation general anesthetic Xenon. They wanted to figure out how to make the substance more abundant and less expensive so the FDA in the U.S. would approve it and heart patients there could benefit from its milder side effects and faster recovery time.

“Is that what I’m getting? Not that I would have ever known the difference,” she asked. “I’m pretty nervous about all this happening at once. How long will I be here? How much is this gonna hurt?” As he continued to explain how his team would repair her dilated, slightly torn aorta, she thought it was some sort of relief that Americans her age wanted to see her. Even if they were just researchers who didn’t really care about her.

But they did. Dr. Ekkehardt’s pager vibrated and he leaned over to her bedside phone. “You know what,” he said. “This actually might be them.”

A nurse practitioner came in a few minutes later with a release form on a clipboard. Danielle had already decided she was okay with it, so she signed, allowing Dan and Chloe to come in and meet her. Meanwhile, another nurse at her side slipped the needle out of her hand and was rubbing iodine on her inner forearm with a Q-tip to place a new IV.

“They’re here.” Dr. Ekkehardt poked his head in the door and asked if it was okay for Dan and Chloe to visit her. She didn’t exactly know what to expect, but felt a sense of relief when she saw them. The attractive research pair were the only normally dressed people she had seen since awakening. “Hi! I bet you guys know what’s going on more than I do,” Danielle said.

“Not sure about that, but nice to meet you. My name is Dan and this is Chloe. I know you’ve been through a lot, but we’re wondering if you’d allow us to observe your surgery.”

Danielle paused for a moment and turned her head to the window. Outside she could see the tops of trees beginning to turn orange and red. Dan kept talking, not sure what to do in the situation, given that he was a scientist – not a doctor – who had never talked to a hospitalized patient before. She tuned out his awkward rambling on about interviewing anesthesiologists about the economics of their formulary. She turned her head back toward him and lightly touched his left shoulder with her right hand. “It’s okay,” she said. “I’m okay with it. I’m actually glad there is someone here besides all these doctors. I don’t have anyone else.”

Her candor caught Dan off guard. Chloe tried to say something supportive, but also felt awkward and just gave him and her a half nod and smile. “Well we really appreciate it,” Dan said. “I’m sorry you’re going through this, but this is really special for us – special for our project. They are so strict about this sort of thing in the U.S. It really can be over the top.”

With another light knock on the door, Dr. Ekkehardt came back in the room and told her they would need to start preparing her for surgery right away. Her torn, dilated aorta couldn’t wait any longer. With each passing hour the risk of a life threatening hemorrhage was increasing. She wasn’t having much pain, and that was typical of patients who have dilated aortas. “Well it was a pleasure meeting you, and if you don’t mind, we might come back to talk to you tonight after you get out of surgery,” Dan said.

The nurse put the bed rails up and started pushing her bed toward the door. “I’m craving a cig right about now,” they heard her mumble as she disappeared into the hallway.

The observation room of the newly renovated hybrid cardiac surgery suite was cramped. Room for two, and maybe three at best. Dan and Chloe sat on stools in front of a 4×6-foot window that gave them a view of the head of the operating table, which was about 12 feet away. It was cool in there, which didn’t bother Dan, but Chloe folded her arms, holding her clipboard tightly against her chest. “I didn’t actually start thinking about his much until now,” she whispered. “I’m not totally sure if I want to watch the, you know …”

“Yeah I know what you mean. I’ve come this far for this, though, I have to watch.”

Danielle remembered lying on the operating table and shivering as the nurses pushed equipment around and double checked her IV. Those O.R. nurses didn’t seem quite as friendly. Maybe they had a lot of unappreciative patients. One of them finally got a stack of warm blankets out of a heating cabinet and covered her feet, legs and waist. That felt better. Sounds of suction and a cold upward breeze reminded her of the dentist’s office.

“So they’re giving her Xenon?” Chloe asked.

“Yep, they prefer it for heart surgery here. We got lucky today to see our atom in action,” he said, ignoring her slight ‘Oh here he goes again’ eye roll.

“Are you ready?” Dr. Ekkehardt asked Danielle. She nodded and looked to her right, where a nurse anesthetist was touching colored boxes on a screen. “We’ll see you in about six hours.”

She almost immediately perceived a medication taste in her mouth that reminded her of the time she had to receive contrast material before an MRI on her knee. The line between consciousness and amnesia is thin, and she couldn’t remember exactly when it was. No one can, it seems.

Another nurse uncovered a tray that had several instruments, including one that reminded Dan of a diamond edged rotary cutter he had seen in his dad’s shop when he was a kid. They watched the nurses begin to paint Danielle’s chest with giant cotton swabs dipped in iodine. Chloe looked back at Dan. “Is this … really relevant to our project. I don’t think I can watch.”

Dan looked back into the suite. One nurse placed a face shield over Dr. Ekkehardt’s head as another picked up the cutting device and placed it in his purple glove laden hands and backed away from the table. He turned it on and the cutting wheel spun up to a blurry fast speed. The research pair faced each other in unison just before the spinning blade reached iodine stained peach fuzz atop her sternum.

“You know what,” Chloe said.

“Me neither. Let’s go. We can visit with her tonight,” Dan couldn’t watch either.  They flicked off the fluorescent light in the observation booth as they stepped out into the hallway. The rush of normal room temperature air felt hot at first compared to the operating suite.  Later that night as they were reading and catching up on the news in one of the hospital’s signature archway adorned atriums, they heard footsteps coming down the hallway. Chloe saw that it was Dr. Ekkehardt, so she grabbed the remote control on the coffee table and muted BBC America on the TV. He looked fatigued, understandably, as he had been on his feet in Danielle’s surgery for the last seven hours.

“Everything looks okay,” he said as he greeted them. “She has to lie very still tonight and probably won’t want to talk, so you should come back tomorrow.”

They spoke with him for a few minutes about he and his anesthesia partner’s use of Xenon so they had some notes, in case Danielle changed her mind about visiting with them after morning rounds. “The patients do seem to recover faster,” he said. “I can’t speak for docs in the U.S., but I can tell you if the price comes down and the stuff becomes less scarce, we’d use it for almost all of our patients. The German Health Ministry will be very happy. And we’d like to conduct more trials on patients in our cardiac ICU who we think might have better cognitive outcomes with Xenon than with Ketamine-induced comas.”

“Adjoining rooms?” asked the man at the front desk of their hotel. They looked at each other briefly, shrugged, and said yes. He handed them each a key card and a lukewarm chocolate chip cookie. “Wow, the cookie thing has spread to Europe. Look what America is doing to the world,” Chloe joked. After a long day and smelling like plane, train and hospital, she was more interested in a warm shower than a warm cookie.

Dan got to his room and changed into running shorts and a MIT “2008 One Pound Battery Competition” T-shirt. He was pleased that it was a non-smoking hotel. The smoke everywhere annoyed him last time he traveled to Europe. He sat on top of the bed and slipped the prototype file out of his briefcase. He had gone over it time and time again, and had a feeling he was missing something key. But he always felt that way, and that may have been why he had found success at such a young age. His thesis on non-rigid transformations applied to the tensile dynamics of an experimental earthquake-resistant foundation joint material raised eyebrows both in academia and industry.

He began to slip into that lost-in-thought mode, obsessing about details. The computer modeling of the evaporation points along the helix was … he heard a soft knock at the door, so he got up and peered through the peep hole into the hallway. No one was there. Another knock as he was walking past the softly humming mini fridge. It was the door to the adjoined room – Chloe.

“Hi, you’re still up,” he said. Chloe walked past him into his room, looked at the papers sprawled on his bed and asked what he was working on. “You know, same. Couldn’t sleep yet. Still feels like afternoon.” She skimmed the messy scene with her eyes and recognized a corner of one of the sheets that she had drawn.

“My laser is buried,” she said as she pointed at the page. This time it wasn’t the regular point, but the kind where a woman touches the thing she’s pointing at just hard enough that her index finger bends back slightly. Dan had been so buried in academia in his adult life that he was only just beginning to recognize signs of flirting. He had seen the bent-finger-point twice before, once when he was the tutor for an undergraduate physics lab, and another time late one night in the library.

She was wearing smooth blue yoga pants and a matching top. “Yeah I’ve been meaning to go over some of the numbers with you on that,” he said. “Do you mind?”

“No, not at all. I’m not tired at all.”

***

On the flight back to Boston, they discussed their interviews with Danielle’s doctor and anesthesiologist. “Do you think that was worth it?” Dan asked her.

“I don’t know, I mean they were obviously happy we’re doing some work on the economic part of this,” she said. “I think you were right. If our prototype works well this year, that, combined with the anecdotal evidence from these guys – we err I mean you should have a good case for a bigger grant to scale up the machine.”

The pair were stuck in the middle of the middle of row 41 on an A330. The flight attendant tried not to spill Sprite on the guy sitting next to them as she passed them their drinks and nuts. “I’m glad they brought back the nuts. Pretzels are cheap,” Dan said. “But anyways, yeah I hope you’re right. Haha you’ll still be in my lab. If I don’t fire you.”

She smiled and hit him lightly on the shoulder. “Hey do you have your laptop? Do you wanna split wifi for the flight?” she asked. He gave her his laptop. “Thanks! Hey what’s your password? They haven’t issued me a laptop yet.”

“Oh sure,” he said. Dan scribbled his password on a Post-It from his briefcase and stuck in next to the trackpad. The wifi service helped the seven-hour flight go by faster. Dan logged into MIT to check the status of his machine shop work order. “Pretty cool we can do this in flight. Hey it looks like they will be delivering the prototype in just a couple days.”

They got in to Boston mid Sunday morning. The maple and cherry trees had turned noticeably more orange in the 72 hours that they had been gone. Both of them felt like they had been out of town for a week. The weight of jet lag in both directions drove them home and begged them to sleep the day away. They woke early Monday morning with that unshakable malaise that is the guaranteed gift of jet lag.

It was an exciting day, for Dan, at least. Techs had arrived at Building 18 before he did. When he got there, six of them were wheeling the machine into the corner of the lab where it would live for the next two years. They had not yet affixed the sound dampening jacket around the cylinder, so he could see the shiny new helical backbone of the machine. He was on his hands and knees shining a pocket LED flashlight into the structure, admiring his work when Chloe got there. “Beautiful,” she said. “So that’s our $90,000 baby.”

In the days that followed, they continued to configure the machine, painstakingly attaching the temperature and pressure sensors that would allow their computers to compare the results of their virtual prototype with the actual machine in action. Chloe flushed liquid nitrogen through the semiconductor and calibrated her array of laser diodes while Dan wrote a poster that they would present at the upcoming AAAS meeting in Vancouver. University engineers had been working to connect the building’s shared supply of liquefied air to Dan’s lab.

The day finally came. They were ready to separate air and map the results. Dan, Chloe, and their two graduate students wrapped the cylinder it the heavy Velcro insulation jacket that the shop had created for it. They double checked all of the machine’s contact points, and everything appeared ready for them to begin flushing the helix with liquid air while slowing tuning the laser diode and ramping up the temperature of the nanowire lattice. Several screens on a nearby bench visualized the sensor data input in three dimensions, thanks to the computer savvy of one of the graduate students who had custom coded the control station.

“Do you want to do the honors,” Dan asked. She said no – that he should get to fire it up for the first time. He closed the Plexiglas door in front of the machine, pulled the safety lockout key, and an electromagnetic lock sealed the machine’s stall with a dull thump. He clipped the key to the edge of his right trouser pocket, clicked a dropdown box on one of the workstation’s screens, and selected “warmup flush.”

A faint whining of the air valve opening was lost in the dull rush of liquid filling the machine and a hiss followed, as high pressure gas shot into the lab’s special steel chimney that led to an exhaust port on the roof. Dots along the 3-D rendering of the helix on the screen changed colors to represent plummeting temperatures. The four of them stood with their arms crossed, staring at the screens and not saying a word at first. Chloe sat on a stool in front of another screen that was displaying temperature and pressure stats of the laser diode array. She clicked on a similar menu item that started the flow of liquid nitrogen into the magnet. Numbers in boxes along the side of the screen rapidly changed, and she took note of them every few minutes on a clipboard. The pencil she was using broke, so she went into her purse to find another one. She reached into the inner side pocket and felt the flap of an envelope. Her stomach dropped and she froze for  a second, then peered in Dan’s direction. She had read the contents over and over again and called the number on the bottom more than once. But it had been awhile since she thought about it.

Time had been flying so fast and so much had happened since summer. She had thought about shredding the envelope a couple times after her trip to Germany with Dan. But she just couldn’t bring herself to do it. There was a lot at stake and she didn’t know what was going to happen.

“Look,” Dan said. “Everything is going exactly as planned. Are you ready give it some heat, Cloh?”

The magnet had reached its target temperature. Chloe, with her grad student looking over her shoulder, applied power to the magnet and laser and started the program that would automatically tune the beam so the geometry of the helix would propel laser light to just the right spots. The next hour was the culmination of almost a year of work. They watched as the valves and sensors worked in concert, their software programs the director. The valve at the top of the machine slowly closed, elevating the pressure in the helix as the gold nanowires at the evaporation points created just the right environment for each of the noble gasses to separate and slip into the the gill-like funnels, where they were blown into tubes the diameter of automobile break lines. Sensors confirmed each of the key points were producing gasses. Precious Xenon was flowing at a rate that would allow the machine to pay for itself in the first year.

They were thrilled, especially Dan. The grad students watched the screens and listened to the steady muffled jet flow sound that was a work of aural beauty. “We have our first liter!” he exclaimed. “We’ve harvested our first $10 worth of Xenon.” He put an arm around Chloe and hugged her without thinking about it. She smiled up at him and made quick, furtive glance back at her purse sitting on an empty workbench. It sat there like her father and mother sat in the back of her mind, beckoning her to come home; to come back to her culture.

***

Dan couldn’t take Chloe to the AAAS in Vancouver. Funds were going to be tight in the lab for the remainder of the year. But he wished she could have come with him. The thrill of inventing something as part of a team for himself, for the university, and for the benefit of the health care industry had not yet worn off. There would certainly be bugs to work out, and there would certainly be infrastructure hurdles in scaling up the new distillation method. Creating liquefied air still took an enormous amount of energy. There were places in North Dakota and northern Minnesota where land was still cheap and the average temperature would make the process more viable from an industry standpoint.

By the time wheels touched down in Vancouver, Dan was tired – and slightly annoyed that he had to check and pay for his project tube as a piece of baggage. The stunning bayside vista and warm chocolate chip cookie upon check in made up for it.

Considering the thousands in attendance, he had hoped more people would come to the “Scales of Economy” breakout session, which was the only one where he appeared as a panelist. The few who were there, though, seemed to enjoy the brief Flip camera video he had cut together of the machine being delivered, tuned, and turned on for the first time. Initial data from the first couple weeks of distillation indicated that the design had the potential to reduce the cost of Xenon worldwide by at least 50 percent. That was yet uncertain and more research was an order.

That evening at the 5:30 p.m. reception, a man who identified himself as a pharmaceutical consultant approached Dan and asked him if he’d like to go out for dinner. “I know of a place that has true fresh caught wild salmon,” The Man said. “It’ll be on me, of course.”

The idea of a free dinner sounded great, regardless of what the guy wanted to talk about. A Towncar picked them up in front of the conference center. The place rivaled the best seafood restaurants in Boston. Two glasses of Argentinean sangiovese and a plate of sheep’s butter fennel risotto into the meal, The Man asked, “So, Dan. What are your plans after you finish this RO-1.” How did he know what kind of grant I was working on? Dan thought. Being approached by someone in industry was a first. At times he dreamed of what it would be like to earn an industry salary and be able to pay off his loans in a year.

“My client might be interested in an exclusive contract for the blue prints of your still,” The Man said. Dan looked across the round table at the The Man. He was wearing a conservative cut dark blue Italian wool suit coat and a neatly pressed light cream colored pinpoint oxford. He had taken off his maroon silk tie and unbuttoned his collar on the ride to the restaurant. “Well I really appreciate this,” Dan said, not exactly knowing what to say, as The Man was topping off his glass. “You know, I don’t really …”

“You know what,” The Man said. “I’m just going to give you my card. My car will take you to your hotel, and you can call me sometime after you get back to Boston.

The next morning, Dan woke up to two missed calls and a text message. It was from his administrator at Building 18.

CALL ME ASAP.

“Someone broke into your lab,” his administrator told him. “We need you to come in as soon as you get back tonight.” She went on to tell him more about what happened, and he sat on his bed and listened while staring blankly at the crumpled cookie envelope on the nightstand. Someone had taken the control workstation computer tower and removed several parts from the machine. “Whoever it was, the university police say they knew what they were doing,” she said. “Please call your team and have them meet us tomorrow morning at the lab.”

Dan was still shocked, taken aback, and confused. The news was so sudden and unexpected; he didn’t know how to process it. He thought back to the previous night’s wild caught salmon and got a sickening feeling. Who was that guy? I should have never accepted dinner. And what on Earth would anyone want my machine. It’s just not that exciting.

The flight to Boston was unpleasant, because there was nothing else to think about. His grad student assistants were shocked at the news, too, but they opted to stay for the final day of the conference. Before takeoff, he left a voicemail for Chloe and told her to call the administrator. He didn’t include any details, because he wanted to be the one to tell her in person that a piece of her work had been stolen, or was missing, at least.

As soon as the flight hit the ground, he turned on his phone and checked to see if she had left a message. There was a message, but it wasn’t her. “Come straight to campus when you land,” his administrator said. “We’ll talk when you get here. Say, have you ever let anyone use your network password?”

As he approached Building 18, he could see that all of the lights in his lab were on, and shadowy figures were moving about. Still in a state of raw fatigue and utter disbelief, he entered the lab, where two men in dark blue FBI windbreakers were knelt beside his machine with brushes and a jar of white power. Were they dusting for fingerprints?

“Dan, this is Agent Stephen Mankad,” his administrator said. “He’s here from the FBI.”

Agent Mankad shook Dan’s hand and asked him if he wanted a cup of coffee. “Let’s sit at one of your empty workbenches,” he said.

“How long have you known Ms. Chloe Chen?”

***

Epilogue

Eighty meters below a desolate, rocky landscape 32 kilometers northeast of Pyongyang, North Korea, technicians in white coats and hoods and steel-tipped boots wheeled a cylinder of liquid nitrogen into a concrete reinforced test chamber. The chamber’s 8-meter thick walls were designed to channel explosive energy up a chimney that led all the way to the surface. One tech with thick rubber gloves removed the lid while the other lowered a hook down into the foggy cauldron. He pulled up on the cable and withdrew a soup can size stainless steel cylinder. They put the cylinder on the floor, in the center of the test chamber and dropped a temperature sensor into the side of the small cylinder. At the bottom of the cylinder was a crystalline cube, about the size of a thimble. The cube sat atop a thin layer of cellulose dust.

Techs outside the test chamber monitored the temperature reading from a control panel. “How long before the Xenon trioxide reaches 25 degree?” their supervisor asked.

“We’re about to find out.”

A man from a nearby village was walking his family’s goat to the market on the outskirts of town, when he heard a dull thump somewhere off to the west. He looked up and saw a small plume rising. Against the deep orange sunset, the plume had a beautiful purple hue. He and his goat kept on walking. ♦

Viagra

Today’s news starkly juxtaposed this countries’ priorities.

First was news of the approval of yet another look-alike drug for erectile dysfunction, avanafil (Stendra).

Then “From First Cold To Grave: How Two-Month-Old Brady Died Of Pertussis.” Brady was too young to have been protected by receiving immunizations, but there are strategies for protecting newborns from pertussis, or whooping cough. One effective technique is called “cocooning.” In this strategy, the newborns are protected by instead vaccinating their family members before the baby is discharged from the hospital.

Estimates are that almost 75% of pertussis cases result from exposure to family members who are not known to be infected. (This was not reportedly the source in this case). In California, which has been experiencing an outbreak of pertussis, the mother is vaccinated during pregnancy, to provide the baby with protective antibodies that cross the placenta.  This is a safe, effective and relatively low-cost method of protecting newborns.

Hospitalization is required in 60-70% of infected infants less than one month old, and deaths occur in ~2%. The cost per dose of Tdap vaccine administered is estimated at $40; for the babies at Ben Taub, a large public hospital which employs the cocooning strategy, this totals about $800,000/year. While expensive, studies have shown cocooning or prenatal maternal immunization to be cost effective.

Pertussis

A major impediment to immunization for adults is the cost, as these adult vaccinations are not a routine part of maternal care payments, and are thus generally not covered by insurance. Unless a hospital provides the vaccination, as Ben Taub did, the cost is prohibitive for many families.

In contrast, the cost of drugs for erectile dysfunction is paid as a covered benefit by most insurers. These phosphodiesterase 5 (PDE5) inhibitor drugs (Viagra, Levitra, Cialis, and now Stendra) cost up to $9 to $11 per pill. By 2005, Medicaid alone spent $15 million annually on these drugs.

According to the University of Miami, US men “spend $1.7 billion dollars a year on products to improve their sexual function.” And although the laws changed with a ban on Medicare and Medicaid payment for “lifestyle” drugs in 2007, $3 million was paid for Viagra in 2007-8. The military continues to provide PDE5 drugs as a “core” benefit.

So, what should we, as a society, choose? Saving babies from pertussis or providing “lifestyle” drugs for aging men?

=============

Images: Viagra, by SElefant on Wikimedia Commons; boy coughing with Pertussis, by Jmh649 on Wikimedia Commons.

=============

Previously in this series:

Molecules to Medicine: Clinical Trials for Beginners
Molecules to Medicine: From Test-Tube to Medicine Chest
Lilly’s Shocker, or the Post-Marketing Blues
Molecules to Medicine: Pharma Trumps HIPAA?
Molecules to Medicine: Should pepper spray be put on (clinical) trial?
Molecules to Medicine: FDA at a Crossroads—a Tough Place to Be
Molecules to Medicine: Plan B: The Tradition of Politics at the FDA
Molecules to Medicine: “Conscience” Clauses versus Refusal: An Historical Perspective
Molecules to Medicine: When Religion Collides with Medical Care: Who Decides What Is Right for You?
A Taste of #TEDMED 2012: Appetizers
A taste of #TEDMED 2012: Main Course
Molecules to Medicine: Have You Thanked a Clinical Researcher Today?

Pauli Spin State Space

I was recently asked to comment for a BBC article whether quantum computing was “just around the corner”. Did I see quantum computers being here in 5 years? I don’t. But, being ever the optimist, I pointed out that the history of technology demonstrates that new technologies tend to emerge in combination with existing technologies. I felt that quantum effects would most probably be harnessed in computing in exactly this way. It’s only in retrospect that we tend to think of some area of technology as a “leap forward”. In reality, progress comprises a series of small steps; more evolution than revolution. And so I think it will be with quantum information technology.

It was only after we had done the BBC article that I realised that there is a good example of quantum information technology that is making its way from the lab branch into the world of everyday use: quantum cryptography. The term “quantum cryptography” means different things to different people, but here I’m referring specifically to Quantum Key Distribution (QKD). This is using quantum phenomena, combined with traditional cryptographic techniques, to solve a problem that has long plagued those attempting to send secret messages.

In so-called symmetric key cryptography, plaintext is encrypted using a known algorithm which uses a secret key. This secret key must be shared between the sender and the receiver, who are usually referred to as Alice and Bob (A and B). Claude Shannon, the father of modern Information Theory, proved that the most secure form of encryption is where the secret key is the same length as the message, and the secret key is used only once. This is known as the “one-time pad”.

What Alice and Bob are trying to do is prevent an eavesdropper (Eve) from intercepting and reading their secret message. Regardless of the algorithm in this scenario, the big issue is how the secret key is shared between Alice and Bob without Eve becoming privy to that key, and hence being able to decrypt their secret message. Despite the huge amount of work that has gone into producing ever more secure encryption algorithms, the weak link remains the transmission of the secret key.

In something like a military or diplomatic situation you can have secure couriers to take the secret key from Alice to Bob. Government organisations have whole departments and procedures for securely handling cryptographic key. Assuming you can trust the courier, and the process by which s/he carries the key, you can be reasonably sure that the key has not been compromised. However, as the world has become more interconnected, cryptography has been in demand from everyday users, for everything from securing emails to ensuring that credit card details remain confidential.

This problem was addressed by a number of researchers in the 1970’s, leading to the seminal paper in 1976 by Diffie and Hellman entitled “New Directions In Cryptography” and the work shortly afterwards by Rivest, Shamir and Adleman (famously known as RSA). This laid the foundation for public key encryption, also known as asymmetric encryption, which most people use today on the Internet, even if they don’t necessarily realise it.

In this, the key used in the encryption has both a private and a public element, and, by the use of appropriate protocols, encrypted messages can be passed between Alice and Bob with them having to pass only the public portion of the key. The reason this is possible is because there are some mathematical functions that are relatively easy to do, but extremely difficult to undo. The classic example is combining large prime numbers and subsequently trying to factor the resulting large number to determine the original prime numbers.

Linear polarization

However, there is always the danger that at some point someone will discover a hitherto unknown mathematical or computing technique that renders the mathematical problem upon which public key cryptography is based, easy to solve. (Of course, there is nothing to stop messages being intercepted now and being kept in case this becomes possible. There are some secrets that one might not want exposed even in 10, 20 or 30 years’ time.)

There is the added complication that public key encryption is a lot less efficient than symmetric encryption. Many implementations of what appear to be public key encryption actually use public key encryption for passing a secret key which is then used for the more efficient symmetric key encryption for the remainder of the communication.

So, the ideal solution would be to use symmetric key encryption, using a key that is the same length as the message being encrypted, and where the secret key can be exchanged such that Alice and Bob can guarantee for all time that the secret key has not been intercepted by Eve, or anyone else. That is the promise of Quantum Key Distribution.

In QKD, the secret key is transmitted using “qubits” instead of classic “bits” (0’s and 1’s). Qubits are simply a quantum level feature, such as the polarization of a photon (the particle that makes up light). For example, you might have vertically polarized light representing a 0 and horizontally polarized light representing a 1.

QKD relies upon the counterintuitive phenomenon of quantum indeterminacy. This says that a qubit can represent a 0 or a 1 or, crucially, both at the same time. If using vertically and horizontally polarized light (0 and 90 degrees), then, for a single photon, both states exist simultaneously right up the point where it is measured, when it takes on one value or the other.

In the case of polarization of light, you need to use a specific filter to determine which polarization was set by Alice. However, if you use a filter that is intended to measure a different orientation of polarized light then the measurement achieved is a random result. For example, if your filter measures whether the photon has diagonal polarization (45 and 135 degrees), then any photon polarized using vertical/horizontal orientation will be randomly measured as having as 45 of 135 degrees rather than 0 or 90 degrees. The reverse is also true.

The clever part of QKD is the protocols that have been developed to make use of the fact that measuring the photon causes it to take on a definite state, and one which is dependent upon how you measure it.

Probably the most familiar protocol used in QKD is known as BB84 which was published in 1984 by the eponymous Bennett and Brassard. In BB84 Alice transmits the secret using two sets of possible states. Let’s assume they are the two sets of polarized light described above. When Bob receives the photons he does not know which set of polarizations were used so randomly chooses a filter with which to make his measurement. If the filter selected was incorrect set he will obtain a random result. If Bob chooses his filter at random, this will happen 50% of the time.

Now Bob tells Alice he has received the key and she tells him, potentially using a public channel, which set of polarizations she was using for which photon. From this they can tell which photons Bob will have measured correctly and hence which to discard. From those they retain they construct a secret key.

If Eve has intercepted the photons and retransmitted them to Bob, s/he will have the same problem in having to choose a filter at random. Hence, s/he will introduce errors in the same way that Bob has, but because Eve and Bob have chosen at random, Bob will find that he has more errors than he would expect. By comparing how many errors are in the photons that Alice and Bob would like to use for their secret key, they can determine if it has been intercepted, and if necessary reject it and start again.

Being sure that their secret key is known only to the two of them, Alice and Bob can use traditional symmetric key algorithms to encrypt the message that they want to pass. In the example of using light down a fibre optic cable this can all be done so quickly that the secret keys can, if implemented correctly, be as long as the messages that are being encrypted. Hence, Alice and Bob can have truly secure communications.

Of course, real world engineering means its not quite that simple and errors are also introduced by the transmission medium (eg the fibre optic cable) and other pieces of the equipment being used. This is allowed for when setting the level of errors to be tolerated before discarding a key as having been compromised. Since BB84 was published there have been other protocols developed, including employing different phenomena such as quantum entanglement.

And yes, QKD is still open to all sorts of attack, particularly the so-called side channel attacks where it’s not the encryption that is attacked but some other weak link, usually the people. Plus, unless Alice and Bob do use keys that are the same length as the message there is always the possibility that someone will find a weakness in the algorithm or be able to use the increasingly powerful cryptanalysis techniques on the encrypted messages.

But QKD, if implemented rigorously, holds the promise of fast, provably secure communications. It is for this reason that in the last ten years it has left the lab bench, and equipment has become commercially available to deploy QKD. There are limitations: currently the fibre optic based implementations typically can transmit for between 100 and 200km and the data rates are not as high as the modern networks might expect. But, with more companies entering the market, and with some cities such as Geneva and Tokyo choosing to implement QKD networks, this journey from theory to commercial product does suggest that quantum phenomena will indeed be in everyday use in our computing infrastructure within the foreseeable future.

Images: Pauli Spin State Space by CSTAR on Wikimedia Commons; Linear polarization schematic from Wikimedia Commons.

To find out, Brenner and his team exposed the students to legal scenarios. In one, a plaintiff named Mr. Thompson visits a drug store for a routine union visit. The store manager informs him that according to the union contract with the drug store, plaintiffs cannot speak with the union employees on the floor. After a brief deliberation, the manager calls the police and Mr. Thompson is handcuffed for trespassing. Later the charges were dropped, but Mr. Thompson is suing the store for false arrest.

All participants got this background information. Then, they heard from one of the two sides’ lawyers; the lawyer for the union organizer framed the arrest as an attempt to intimidate, while the lawyer for the store argued that the conversation that took place in the store was disruptive. Another group of participants – essentially a mock jury – heard both sides.

The key part of the experiment was that the participants were fully aware of the setup; they knew that they were only hearing one side or the entire story. But this didn’t stop the subjects who heard one-sided evidence from being more confident and biased with their judgments than those who saw both sides. That is, even when people had all the underlying facts, they jumped to conclusions after hearing only one side of the story.

The good news is that Brenner, Koehler and Tversky found that simply prompting participants to consider the other side’s story reduced their bias – instructions to consider the missing information was a manipulation in a later study – but it certainly did not eliminate it. Their study shows us that people are not only willing to jump to conclusions after hearing only one side’s story, but that even when they have additional information at their disposal that would suggest a different conclusion, they are still surprisingly likely to do so. The scientists conclude on a somewhat pessimistic note: “People do not compensate sufficiently for missing information even when it is painfully obvious that the information available to them is incomplete.”

In Brenner’s study, participants were dealing with a limited universe of information – the facts of the case and of the two sides’ arguments. But in reality – especially in the Internet era – people have access to a limitless amount of information that they could consider. As a result, we rely on rules of thumb, or heuristics, to take in information and make decisions. These mental shortcuts are necessary because they lessen the cognitive load and help us organize the world – we would be overwhelmed if we were truly rational.

This is one of the reasons we humans love narratives; they summarize the important information in a form that’s familiar and easy to digest. It’s much easier to understand events in the world as instances of good versus evil, or any one of the seven story types. As Daniel Kahneman explains, “[we] build the best possible story form the information available… and if it is a good story, [we] believe it.” The implication here is that it’s how good the story is, not necessarily its accuracy, that’s important.

But narratives are also irrational because they sacrifice the whole story for one side of a story that conforms to one’s worldview. Relying on them often leads to inaccuracies and stereotypes. This is what the participants in Brenner’s study highlight; people who take in narratives are often blinded to the whole story – rarely do we ask: “What more would I need to know before I can have a more informed and complete opinion?”

The last several years have seen many popular psychology books that touch on this line of research. There’s Ori and Rom Brafman’s Sway, Dan Ariely’s Predictably Irrational and, naturally, Daniel Kahneman’s Thinking, Fast and Slow. If you could sum up the popular literature on cognitive biases and our so-called irrationalities it would go something like this: we only require a small amount of information, often times a single factoid, to confidently form conclusions and generate new narratives to take on new, seemingly objective, but almost entirely subjective and inaccurate, worldviews.

The shortcomings of our rationality have been thoroughly exposed to the lay audience. But there’s a peculiar inconsistency about this trend. People seem to absorb these books uncritically, ironically falling prey to some of the very biases they should be on the lookout for: incomplete information and seductive stories. That is, when people learn about how we irrationally jump to conclusions they form new opinions about how the brain works from the little information they recently acquired. They jump to conclusions about how the brain jumps to conclusions and fit their newfound knowledge into a larger story that romantically and naively describes personal enlightenment.

Tyler Cowen made a similar point in a TED lecture a few months ago. He explained it this way:

There’s the Nudge book, the Sway book, the Blink book… [they are] all about the ways in which we screw up. And there are so many ways, but what I find interesting is that none of these books identify what, to me, is the single, central, most important way we screw up, and that is, we tell ourselves too many stories, or we are too easily seduced by stories. And why don’t these books tell us that? It’s because the books themselves are all about stories. The more of these books you read, you’re learning about some of your biases, but you’re making some of your other biases essentially worse. So the books themselves are part of your cognitive bias.

The crux of the problem, as Cowen points out, is that it’s nearly impossible to understand irrationalities without taking advantage of them. And, paradoxically, we rely on stories to understand why they can be harmful.

To be sure, there’s an important difference between the bias that comes from hearing one side of an argument and (most) narratives. A corrective like “consider the other side” is unlikely to work for narratives because it’s not always clear what the opposite would even be. So it’s useful to avoid jumping to conclusions not only by questioning narratives (after all, just about everything is plausibly a narrative, so avoiding them can be pretty overwhelming), but by exposing yourself to multiple narratives and trying to integrate them as well as you can.

In the beginning of the recently released book The Righteous Mind, social psychologist Jonathan Haidt explains how some books (his included) make a case for how one certain thing (in Haidt’s case, morality) is the key to understanding everything. Haidt’s point is that you shouldn’t read his book and jump to overarching conclusions about human nature. Instead, he encourages readers to always think about integrating other points of view (e.g., morality is the most important thing to consider) with other perspectives. I think this is a good strategy for overcoming a narrow-minded view of human cognition.

It’s natural for us to reduce the complexity of our rationality into convenient bite-sized ideas. As the trader turned epistemologist Nassim Taleb says: “We humans, facing limits of knowledge, and things we do not observe, the unseen and the unknown, resolve the tension by squeezing life and the world into crisp commoditized ideas.” But readers of popular psychology books on rationality must recognize that there’s a lot they don’t know, and they must be beware of how seductive stories are. The popular literature on cognitive biases is enlightening, but let’s be irrational about irrationality; exposure to X is not knowledge and control of X. Reading about cognitive biases, after all, does not free anybody from their nasty epistemological pitfalls.

Moving forward, my suggestion is to remember the lesson from Brenner, Koehler and Tversky: they reduced conclusion jumping by getting people to consider the other information at their disposal. So let’s remember that the next book on rationality isn’t a tell-all – it’s merely another piece to the puzzle. This same approach could also help correct the problem of being too swayed by narratives – there are anyways multiple sides of a story.

Ultimately, we need to remember what philosophers get right. Listen and read carefully; logically analyze arguments; try to avoid jumping to conclusions; don’t rely on stories too much. The Greek playwright Euripides was right: Question everything, learn something, answer nothing.

====

The author personally thanks Dave Nussbaum for his helpful editorial comments and criticisms. Dave is a social psychologist who teaches at the University of Chicago. Follow him on Twitter and check out his homepage.

Image: by Wyglif on Wikimedia Commons.

If you have had a beer lately, especially if it was in a can and cost less than two dollars, it was probably a lager. Lager has become almost synonymous with “beer,” yet the story of lager is among the most enigmatic of all the stories of the foods and drinks we ferment. It is just one of the mysteries I have been thinking about lately, the other involves a monkey.

The first mystery—As we moved around the world from where yeast was first relied upon for the production of alcohol, we took particular strains of yeast with us, accidentally, on our fruits, grains and vessels. We did not know we were carrying them and yet we depended on them for our golden drinks and rising foods. These strains evolved so as to be able to better take advantage of the conditions and foods we provided in different regions. In the light of evolution, many of the specific histories of many drinks make sense¹. Then there is lager, beer.

The very first beer would have been distinct from modern beers, but relied on yeasts similar to those found in ales and wines, not lagers. Eventually, Germanic and Celtic tribes took it north and west in the first century AD. Some tribes pillaged gold. Leave it to the Germans and Celts to pillage beer and, although they did not know it, yeast. Historically, most beer was made when conditions were relatively warm. The yeast found in most foods and drinks, Saccharomyces cerevisae, likes to live at temperatures between 15° and 24° C². But while warm brewing conditions are good for beer-making yeasts, they are also good for other less beneficial species of yeasts and bacteria. Many vats of beer were lost to bad yeasts, bacteria, and chance—acts of microbes.

Beginning in the 1400s, Bavarians appear to have taken some of the chance out of the equation through a bit of ecological subterfuge. They carried their fermenting beer to caves in the Bavarian mountains, where beer could be brewed at cooler temperatures and then aged for several weeks. The same caves that once gave shelter to Neanderthals came to protect the yeasts dividing on the bottom of vessels, slowly, in the cold, yeasts producing lagers.

With time, brewing what we now call lagers in cold conditions became the definition of good Bavarian brewing. In 1516 the Bavarian government, troubled by the preponderance of bad beer, instituted the Beer Purity Law, which specified that beer could not be brewed in the summer (and must be brewed only using barley, hops and water). They all but enforced the production of beer under cool conditions.

Storing beer under cool conditions during fermentation is part of what makes a lager a lager rather than an ale, but why do cooler conditions produce a different beer? The magic is in the yeast. When yeast biologists began to consider the story of lagers, they hypothesized that fermentation in caves and other cold realms had favored varieties of S. cerevisae, humanity’s yeast, with greater tolerance to the cold (which in turn produced different flavors, etc…)⁴.

The yeasts used in lager beers are indeed more tolerant of cold than those involved in making nearly all other yeast-dependent foods and drinks. But lager yeast is not just a strain of S. cerevisae, it is an entirely different species. Breads, sake, wine, warm weather beer, even palm, they all rely on one species, Saccharomyces cerevisae. Not lager.

A new species is discovered in (and making) lager beer—Early genetic studies revealed lager yeast (now called Saccharomyces pastorianus) to be a hybrid between “humanity’s yeast,” Saccharomyces cerevisae, and another species. Lager yeast has two versions of most genes, one like those found in S. cerevisae and one from another species. But what is the other species?

One would be forgiven for imagining such a yeast species would come from Bavaria. The new kink in the narrative is the revelation that the yeast that came together in love and peace with humanity’s yeast to hybridize and produce lager yeast is not from Bavaria or even from Europe, or even for that matter from the Middle East, Africa or Asia. It comes from Patagonia, where it was, until recently, an unnamed species^{3, 4}.

The yeast in lager beer is a hybrid of humanity’s yeast and a newly named species of yeast from cold forests at the bottom of the Earth, now called Saccharomyces eubayanus. This hybridization happened twice. In the first instance, the hybridization gave rise to the yeast now used in Saaz type beers, now produced in the Czech Republic and in Carlsberg breweries in Denmark. In the other, the hybridization gave rise to the Frohberg-type yeast now usually used in the Netherlands and in the other (non-Carlsberg) Danish breweries. Twice, humanities yeast and S. eubayanus came together in the dark of a vat and lager appeared.

The problem with this new Lager beer story, the first mystery, is timing. Lager beer was apparently first brewed in the 1400s. How do you get a yeast from Patagonia into a brewing vat in Bavaria before European ships had gone to Patagonia and back?

The second mystery—The second mystery that has preoccupied me lately is the case of the marsupial monkey. In the same forests in which one of the two ancestors of lager yeast lives, also lives the monito del monte. Monte in Spanish is the untamed woods. A monito is a little mono, a little monkey. But the monito is not a monkey, it is a possum-like marsupial with opposable thumbs and so, where there were no monkeys, it seemed close enough to be called the little monkey, a monito.

The monito of the woods is a very interesting marsupial. Like other marsupials it has a pouch, but in a variety of ways it seems more like the marsupials of Australia than it does like those of the Americas. Even knowing it is a marsupial and not a monkey, in other words, leaves one with questions. Because it seems quite different than all of the other marsupials in South America, the first is where it came from.

Recently, two separate evolutionary studies have found the monito to be most closely related to Australian marsupials (in one case the wild and crazy marsupial mole). How could the monito, a tree-dwelling mammal the size of a large rat, have made it to Patagonia⁵?

Occam’s whimsical resolution?–So now we have the two mysteries, how a yeast species got from Patagonia to Bavaria and how marsupial got from Australia to Patagonia. Ironically, these stories are connected, at least superficially, and maybe ecologically. The monito consumes fruit on which yeast is likely to grow, perhaps the same yeast that helped to produce lager beer. Assuming that these fruits are sometimes a little fermented, these monitos may have been the first to sample some hint of the taste of what lager beer might become.

Unfortunately, drunk monitos, however adorable, do not explain anything.

Let’s come back to the question of how the monito got to Patagonia, and how a Patagonian yeast got to Bavaria. For the yeast, one possibility is it was actually floating around many places but was outcompeted each time it landed by other yeasts and only in the moment when brewers in Bavaria started putting out their vats in caves did it find a source of food of which it could easily take advantage.

This is more plausible than it seems. Many single-celled species seem to have the ability to ride around the world in the wind and clouds and, in doing so, to be nearly everywhere at least some of the time, even if they do not find success everywhere.

Alternatively, the Patagonian yeast might have been brought back from Patagonia by early explorers, perhaps even in their old beer containers which would have been common on the ships. The problem is the first explorers to Patagonia arrived hundreds of years after the first lagers appear to have been brewed, though maybe those very first lagers were different than the modern ones.

The most plausible explanation for the monito’s modern distribution appears to include a mix of geology and magic. When Antarctica and Australia were still connected, before they broke along their geologic seams and went very different ways, a lineage of marsupials diversified. Most members of the lineage stayed in Australia, but one or more made their way to South America and diversified a little more, with one species, the monito, surviving until today in Patagonia. It all makes sense, I guess. But how did it make its way to the new world? Via some as yet unknown bridge? Floating?

All of these ideas are reasonable starting points for more study of each of these independent mysteries. But conversations with my friend Pajaro Morales offered another possibility. Pajaro studies the monitos, lives in Patagonia, has an office down the hall from the authors of the Patagonian yeast paper, and is a font of ideas. Talking with him led to a single explanation for both mysteries.  Maybe the monitos can fly and, when they do, they carry the yeast with them. I wish we could say we were under the influence of lager when we came up with this idea, but alas we were under the influence of nothing more than Occam’s razor.

William Occam—who was exiled to Bavaria, though before the advent of lager—argued that the solution requiring the fewest assumptions tends to be the right one. In fields where general principles hold strong sway Occam’s argument—often called his razor—is both sharp and reasonable. The elegant explanation often wins in population ecology or physiology.

But biogeography—the field charged with telling the stories of the distributions of creatures like yeast and monitos—is a historical science. Occam’s razor, in confronting the strange histories of the monito and the lager, would unite them. It favors the flying monito hypothesis which assumes monitos can and do secretly fly, but nothing else.

This time then, Occam is almost certainly wrong. The beauty of biogeography, like the beauty of history itself rests not in the general stories, but instead in the specific narratives of individual species as they move around the Earth encountering and resolving (or failing to resolve) problems. So, when, in a few weeks, Pajaro and I meet up for the first time in quite a few years in Scotland to enjoy some of the consequences of yeast’s specific history, we will have to come up with some new ideas ⁶. Though it seems equally fun to keep our eyes on the sky, on the off chance that monitos covered in yeast really know how to fly.

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1-Sicard, D., Legras, J.-L. (2011). Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex. C. R. Biologies 334 (2011) 229–236. This is a great article. The evolutionary tree in this article could spawn a dozen other essays. Note, for example, that lab strains of yeast seem to be most closely related to palm wine strains.

2-This is why you put yeast into warm water when making bread. Bread yeasts are the descendents of wine yeasts in most of the world, though just which wine your bread’s yeast descends from depends on where you live^.

3-Libkind, D. et al. (2011). Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. PNAS 108: 14539–14544

4-The word for this yeast’s product, lager, in turn, comes from the German for storehouse, the process of making the beer embedded in its name.

5-Palma, R. E., Spotorno, A. E. (2009). Molecular Systematics of Marsupials Based on the rRNA 12S Mitochondrial Gene: The Phylogeny of Didelphimorphia and of the Living Fossil Microbiotheriid Dromiciops gliroides Thomas. Molecular Phylogenetics and Evolution. 13: 525-535.

6-Though Scotland it should be said is a land not of lagers but of ales, which are brewed using a lineage of humanity’s yeast, not lager yeast.

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Images: Safety razor by Hustvedt at Wikimedia Commons; The Brewer, designed and engraved in the Sixteenth Century by J Amman by Mikhail Ryazanov at Wikimedia Commons; Monito del Monte by WolfmanSF at Wikimedia Commons; William of Ockham, from stained glass window at a church in Surrey by Moscarlop at Wikimedia Commons.

Back then, computers were people; they compiled actuarial tables and did engineering calculations. As the Allies prepared for World War II they faced a critical shortage of human computers for military calculations. When men left for war the shortage got worse, so the U.S. mechanized the problem by building the Harvard Mark 1, an electromechanical monster 50 feet long. It could do calculations in seconds that took people hours.

The British also needed mathematicians to crack the German Navy’s Enigma code. Turing worked in the British top-secret Government Code and Cipher School at Bletchley Park. There code-breaking became an industrial process; 12,000 people worked three shifts 24/7. Although the Polish had cracked Enigma before the war, the Nazis had made the Enigma machines more complicated; there were approximately 10¹¹⁴ possible permutations. Turing designed an electromechanical machine, called the Bombe, that searched through the permutations, and by the end of the war the British were able to read all daily German Naval Enigma traffic. It has been reported that Eisenhower said the contribution of Turing and others at Bletchley shortened the war by as much as two years, saving millions of lives.

As the 1950s progressed business was quick to see the benefits of computers and business computing became a new industry. These computers were all Universal Turing Machines—that’s the point, you could program them to do anything.

“There will positively be no internal alteration [of the computer] to be made even if we wish suddenly to switch from calculating the energy levels of the neon atom to the enumeration of groups of order 720. It may appear somewhat puzzling that this can be done. How can one expect a machine to do all this multitudinous variety of things? The answer is that we should consider the machine to be doing something quite simple, namely carrying out orders given to it in a standard form which it is able to understand.” – Alan Turing

By the 1970s a generation was born who grew up with “electronic brains” but they wanted their own personal computers. The problem was they had to build them. In 1975 some hobbyists formed the Homebrew Computer Club; they were excited by the potential the new silicon chips had to let them build their own computers.

An Apple I computer in a homemade wooden case

One Homebrew member was a college dropout called Steve Wozniak who built a simple computer around the 8080 microprocessor, which he hooked up to a keyboard and television. His friend Steve Jobs called it the Apple I and found a Silicon Valley shop that wanted to buy 100 of them for $500 each. Apple had its first sale and Silicon Valley’s start-up culture was born. Another college drop-out, Bill Gates, realized that PCs needed software and that people were willing to pay for it—his Microsoft would sell the programs.

Turing’s legacy is not complete. In 1950 he published a paper called “Computing machinery and intelligence.” He had an idea that computers would become so powerful that they would think. He envisaged a time when artificial intelligence (AI) would be a reality. But, how would you know if a machine was intelligent? He devised the Turing Test: A judge sitting at a computer terminal types questions to two entities, one a person and the other a computer. The judge decides which entity is human and which the computer. If the judge is wrong the computer has passed the Turing Test and is intelligent.

Although Turing’s vision of AI has not yet been achieved, aspects of AI are increasingly entering our daily lives. Car satellite navigation systems and Google search algorithms use AI. Apple’s Siri on the iPhone can understand your voice and intelligently respond. Car manufacturers are developing cars that drive themselves; some U.S. states are drafting legislation that would allow autonomous vehicles on the roads. Turing’s vision of AI will soon be a reality.

In 1952 Turing was prosecuted for gross indecency, as being gay was then a crime in Britain. He was sentenced to chemical castration. It’s believed that this caused depression, and in 1954 Turing committed suicide by eating an apple poisoned with cyanide. Outside of academia Turing remained virtually unknown because his World War II work was top-secret. Slowly word spread about Turing’s genius, his invention of the computer and artificial intelligence, and after a petition campaign in 2009, the British Prime Minister Gordon Brown issued a public apology that concluded:

“…on behalf of the British government, and all those who live freely thanks to Alan’s work, I am very proud to say: we’re sorry. You deserved so much better.”

June 23, 2012 is the centenary of Alan Turing’s birth. I’m happy to say that finally Turing is getting the recognition he deserves, not just for his vital work in the war, but also for inventing the computer—the Universal Machine—that has transformed the modern world and will profoundly influence our future.

Image of Apple I computer via Wikimedia Commons