Discover 11.2018
Discover 11.2018
Discover 11.2018
70
Discover
SCIENCE FOR THE CURIOUS
®
NOVEMBER 2018
LIFE IN THE
QUANTUM
REALM
How the Smallest
Particles Make the
Biggest Impact P.30
PLUS
Driverless Cars on
Every Road? Dream On P. 48 BONUS
ONLINE
When the First Farmers CONTENT
CODE p.3
Changed History P. 38
Contents
NOVEMBER 2018
Website access code: DSD1811
Enter this code at: www.DiscoverMagazine.com/code
to gain access to exclusive subscriber content.
30 Your
Daily Dose
of Quantum
The effects of quantum
mechanics aren’t just
relegated to crazy
experiments — they’re also
part of our everyday lives.
BY TIM FOLGER
38 he Farmer
and the
Forager
Along a European river
8,000 years ago, two very
different groups met for
the irst time. Humanity
would never be the same.
BY MARK BARNA
48 Baby,
Can You Drive
My Car?
Plans to bring autonomous
vehicles to the public are
in the fast lane, but it may
be time for a rest stop.
BY HANNAH FRY
54 All in
the Fold
When it comes to proteins
— life’s building blocks
— the key is how they’re
folded. One biochemist is
studying the how and why
of proteins’ crucial crimps
IBREAKSTOCK/SHUTTERSTOCK
6 EDITOR’S NOTE
Perceiving Reality
Motorcycle riding, heightened
awareness and the quantum world.
7 INBOX
Readers weigh in on eating insects
and the psychology of personality.
9 THE CRUX
The art of microscopic
photography; a look back
at preparing astronauts for
a crazy-long journey; the
financial cost of breast cancer;
the secret to developing math
and reading skills; and more.
doctors can’t explain. BY TONY DAJER Though individually tiny and LIFE IN THE
disposable, a fleet of probes could QUANTUM
play a big role in space exploration.
26 MIND OVER MATTER BY STEVE NADIS
REALM
How the Smallest
Particles Make the
Knock on Wood Biggest Impact P.30
of Nobels, helped
64 ORIGIN detect lost cities
STORY and chronicled ON THE COVER
Know Your the drift of Why We’re Superstitious p.26
Enemy the moon. World’s Tiniest Satellites Ready for Launch p.70
BY ERIKA K.
Research on deadly CARLSON
Life in the Quantum Realm: How the Smallest
ancient pathogens Particles Make the Biggest Impact p.30
4 DISCOVERMAGAZINE.COM
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Discover
SCIENCE FOR THE CURIOUS
Editor's Note ®
Perceiving Reality
GEMMA TARLACH Senior Editor
BILL ANDREWS Senior Associate Editor
ELISA R. NECKAR Production Editor
MARK BARNA Associate Editor
LACY SCHLEY Associate Editor
DAVE LEE Copy Editor
I’m still a relative newbie to AMBER JORGENSON Editorial Assistant
motorcycling. It took about a Contributing Editors
TIM FOLGER, JONATHON KEATS, LINDA MARSA,
year of being on the back of my KENNETH MILLER, STEVE NADIS, ADAM PIORE,
husband’s BMW before I was COREY S. POWELL, JULIE REHMEYER, STEVE VOLK,
PAMELA WEINTRAUB, JEFF WHEELWRIGHT,
itching to be on my own bike. DARLENE CAVALIER (SPECIAL PROJECTS)
So, when I swing a leg over my ART
Suzuki V-Strom, I’m hyper-tuned ERNIE MASTROIANNI Photo Editor
ALISON MACKEY Associate Art Director
to everything — the smell of the
dry autumn air, the sound of the DISCOVERMAGAZINE.COM
ERIC BETZ Digital Editor
wind sliding around my helmet NATHANIEL SCHARPING Assistant Editor
and the feel of the bike as it picks Bloggers
ERIK KLEMETTI, NEUROSKEPTIC, SCISTARTER,
up speed in second gear. And AMY SHIRA TEITEL, TOM YULSMAN
I’m constantly assessing risk and Contributors
BRIDGET ALEX, RONI DENGLER, KOREY HAYNES
tweaking my behavior.
When you’re new to riding, ADVERTISING
STEVE MENI Advertising Sales Manager
your perception of reality is in 888 558 1544
smeni@discovermagazine.com
overdrive. Maybe it’s like when
Rummel Media Connections
we’re little kids, our senses KRISTI RUMMEL Consulting and Media Sales
lighting up as we explore a new 608 435 6220
kristi@rummelmedia.com
space. As adults, our reality is so
MELANIE DECARLI Marketing Architect
established, we take it for granted. BOB RATTNER Research
We expect things in our everyday world to behave in a certain DARYL PAGEL Advertising Services
way: coffee is our kick-starter, the garden’s roses offer up their KALMBACH MEDIA
DAN HICKEY Chief Executive Officer
perfume each year and that bench will support us as we sit. CHRISTINE METCALF Senior Vice President, Finance
While our perception of reality underlies our behavior as we STEPHEN C. GEORGE Vice President, Content
NICOLE MCGUIRE Vice President, Consumer Marketing
move through the world, in the super-small realm of quantum BRIAN J. SCHMIDT Vice President, Operations
mechanics, it’s the opposite. The behavior of these teeny-tiny SARAH A. HORNER Vice President, Human Resources
particles lies at the bedrock of our perception. And their DAVID T. SHERMAN Senior Director, Advertising Sales
and Events
behavior can be pretty weird. An electron, for example, can SCOTT REDMOND Advertising Sales Director
exist as a particle and a wave at the same time. A photon can be LIZ RUNYON Circulation Director
MICHAEL SOLIDAY Art and Production Manager
in two places at once — and just maybe our eyes can see both. CATHY DANIELS New Business Manager
In this issue’s cover story, Contributing Editor Tim Folger KATHY STEELE Retention Manager
KIM REDMOND Single Copy Specialist
takes us through the wacky world of the quantum, and how it’s
SCIENCE GROUP
embedded into our lives, without us even realizing it. TIM PAULSON General Manager
Those unseen mechanics will be rolling around at the back of BECKY LANG Executive Editor
my brain on the two-wheeled commute to work. DAN BISHOP Design Director
SUBSCRIPTIONS
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CONNECT WITH US editorial@discovermagazine.com
WILLIAM ZUBACK/DISCOVER
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6 DISCOVERMAGAZINE.COM
Inbox
ADDRESS LETTERS TO: — how it’s generated by our molten two-tier society.
DISCOVER core, the magnetic ield’s composition
21027 Crossroads Circle, P.O. Box 1612
Waukesha, WI 53187-1612 and its numerous beneits, of course.
EMAIL: editorial@DiscoverMagazine.com Steve Brooks Feedback is edited for space and clarity.
Seattle November 2018 DISCOVER 7
GLASS GALAXY
A plain crystal ball at a Santiago flea market recently caught the eye of astronomer Juan Carlos Muñoz-Mateos, who studies galaxy formation
from the Paranal Observatory in Chile. He works with the world’s most advanced telescopes, and he saw the common glass sphere’s potential
as a different kind of astrophotography lens. A few nights later, he placed it on a handrail outside the observatory, focused his camera on
the ball and made this 30-second-exposure photo, trapping the Milky Way in a cosmic marble against its own backdrop. ERNIE MASTROIANNI;
PHOTOGRAPH BY JUAN CARLOS MUÑOZMATEOS
10 DISCOVERMAGAZINE.COM
BIG IDEA more using cellular networks.
Facebook wasn’t the only tech
agency to crash and burn. Back in
countries found just 19 boast affordable so many other companies developing access technologies,” says Nathan
internet, deined as 2 percent or less autonomous Wi-Fi hotspots. Kundtz, CEO of Kymeta, whose
of average monthly income for one Facebook closed their lab, and flat-panel satellite antennas came on
gigabyte of mobile data. Across Africa, they’ve partnered with Airbus on their the market last year. “Ultimately, I
the 2015 average cost was more than drones. Now, they’re testing plane- expect that the expansion of internet
17.5 percent of monthly income. mounted lasers like Aquila’s. They’re access into developing countries will
That’s prompted interest from tech also working on OpenCellular, an open- continue, and that it will be a force
companies. It can seem altruistic, but source, low-powered base station that for positive economic and social
these endeavors are also driven by the Facebook hopes will connect billions development.” TROY FARAH
12 DISCOVERMAGAZINE.COM
Q When you started in 1978, what was the
state of microscopy?
CAN WE GO TO MARS insights into how we’ll deal. 2001 article — and colleagues published
without going crazy? In May Participants endure months in a study in 2014 reporting two Mars-500
2001, Discover’s cover story cramped confines in analog crew members accounted for 85 percent
asked exactly that, exploring missions at NASA’s facilities of the mission’s reported conflicts.
unanswered questions about in Houston, as well as remote Clearly, selecting voyagers with the
the psychological perils of places like Antarctica, the right psychological profile is critical to
humans crammed together floor of the Atlantic Ocean mission success. Though we still don’t
and flung through space. and atop a Hawaiian volcano. know what that profile looks like, it’s
At the time, scientists The European Space Agency’s becoming easier to see what won’t
didn’t have much data to CAVES program, started in 2011, work. “Having six Type A personalities
predict how people would handle the sends participants into unmapped Italian on a long, boring voyage may not be
six-month journey. Researchers realized caverns to test and train their cooperative the best combination,” says psychologist
interpersonal skills and camaraderie exploration skills. Then there’s the final Gary Strangman, who works with the
would be critical to success. run of Mars-500, another international Translational Research Institute for Space
We’re still not sure how things would Martian analog, where six men from four Health, a collaboration between NASA
go. But growing interest in the mental countries simulated an entire mission to and a consortium led by the Baylor
risks of space travel — which NASA lists as the Red Planet over 17 months, from 2010 College of Medicine in Houston.
one of the biggest threats to astronauts to 2011, in a tiny Moscow facility — the Jack Stuster, a cultural anthropologist
— has spawned a wave of new research closest we’ve gotten to the real thing. who has studied journals kept by both
and technology. Those projects suggest space agencies astronauts and earthbound explorers,
Experts are developing stress- are taking the psychology of astronauts says behavioral issues are a surmountable
management systems, including virtual more seriously than it did in 2001, says challenge. Enthusiasm for putting the
reality programs and robotic companions, David Dinges, a professor of psychiatry at first footprints on Mars, he thinks, will
to help interplanetary travelers cope on the University of Pennsylvania Perelman inspire resilience: “Humans will endure
their trip. And projects that simulate long- School of Medicine. Good thing, too, almost anything to be among the first.”
term space travel are giving researchers since Dinges — who was featured in our STEPHEN ORNES
Missions like
this one on
the Mauna Loa
ROSS LOCKWOOD
volcano in Hawaii
help astronauts
train for Mars-
like conditions.
14 DISCOVERMAGAZINE.COM
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16 DISCOVERMAGAZINE.COM
Notable Moments in
Who’s Using What? Tech Media History
Percentage of Americans
who say they use social media 35% 24%
(2018)
Instagram Twitter
68% WhatsApp
becomes widely available with
the emergence of affordable
personal computers and
Pinterest web browsers like Netscape.
24%
27%
Facebook
LinkedIn
Snapchat
FROM TOP: ZUMA PRESS INC./ALAMY STOCK; TED THAI/THE LIFE PICTURE COLLECTION/GETTY IMAGES; DAVID PAUL MORRIS/BLOOMBERG VIA GETTY IMAGES; CARL BERKELEY VIA FLICKR
Percentage of U.S. Adults Who Use Multiple Times a Day (2018) 1999: Apple offers Wi-Fi
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Facebook 51% laptops, the first tech company
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Twitter 26% wide trend.
Instagram 38%
Snapchat 49%
18 DISCOVERMAGAZINE.COM
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BOTTOM LEFT: DMITRY GUZHANIN/SHUTTERSTOCK. RIGHT COLUMN FROM TOP: ZHANG ZONGDA; NASA/CXC/M.WEISS; TATYANA VYC/SHUTTERSTOCK. OPPOSITE: ALBERTO HORNERO/SWANSEA UNIVERSITY
DOLLARS A Snack Fit for a Star
14% AND
CENTS
17% In a first, astronomers may have witnessed a star eating
a planet — well, sort of. The star in question, RW
SPENT
$
LOST Aur A, is about 450 light-years away, but it’s been on
more than more than
10 percent of
experts’ radars for decades because it has a history of
10 percent of
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because of on out-of-pocket shine. Recently it’s been dimming a lot more than usual.
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Aur A, resulting in dust and gas
WHICH DOCTORS DISCUSS FINANCIAL BURDENS WITH PATIENTS? that obscured the star. Seeing
Medical oncologists* 50.9% this event and continuing to
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Radiation oncologists 43.2% help scientists learn more
Surgeons 15.6% about how planetary bodies
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*Use chemotherapy as well as hormonal, biological and targeted therapies their survival.
20 DISCOVERMAGAZINE.COM
Olive Protection
Europe’s olive trees are suffering. The culprit — Xylella fastidiosa, a devastating bacterium that’s common in the Americas
— can infect up to 350 different plant species. The pathogen made its way across the pond only recently. Farmers in Europe
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symptoms: withered branches and scorched leaves. The system, which uses a combination of thermal and electromagnetic
imaging, can flag infected trees with over 80 percent accuracy. This thermal image shows the severity of symptoms of an
orchard in southern Italy from blue (least severe) to red (most severe).
people experience a spinning sensation might have an irregular heartbeat, as having a repeat migraine attack. In
when they move their head. Another her neurologist thought. The condition an odd twist of neurology, and to the
possibility was a hyperthyroid condition, is known to bring about dizziness, diagnostic confusion of doctors, people
but that usually causes a fast heartbeat. lightheadedness and shortness of can have migraines without headaches.
I dismissed both in part because breath. But Alana’s electrocardiogram, Even odder, the same person can
Alana was experiencing pain which checks the electrical activity of have a different series of symptoms
throughout her body, something not the heart, revealed no issues. at different times.
usually associated with vertigo or Sometimes when I’m stumped about The trigger of the attack can also
22 DISCOVERMAGAZINE.COM
“he race to space was a thrilling time.”
JIM LOVELL, APOLLO 8 & 13
Relive the historic lunar landings and the events that led up to
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• A comprehensive tale of the space race by Astronomy Editor David J. Eicher.
• New stories from the astronauts and cosmonauts whose shared perspective
turned competing explorers into fast friends.
• 150 stereo photos of the Apollo missions and space race, the largest collection
ever published — many never before seen in stereo.
• Special 3-D viewer and introduction to stereoscopic photography by Brian May.
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P33941
change. For a while it might be a certain Moreover, not all headaches come
smell. Then it shifts to, say, being in a with an aura.
stressful situation.
Eventually we igured out that Peggy CALM AFTER THE STORM
had an abdominal migraine, which is Migraine treatments are tailored
accompanied by nausea, vomiting, belly to the speciic phases of the attack.
pain and, in her case, that distinctive At the irst sign of a migraine aura
sulfur taste. Despite multiple medical or a throbbing headache, a person
work-ups and even hospitalizations, can be prescribed serotonin-like
it had gone undiagnosed since she was drugs of the so-called triptan class,
8 years old. taken by injection or pill. Introduced
25 years ago to great fanfare, the
ANOTHER KIND OF ACHE drugs work for many patients, but
“Have you ever had migraines?” I not all. They are most effective
asked Alana as she lay on the stretcher, Vestibular migraines occur when electrical early in an attack. Other early
waves propagate through the brain’s
arms clutching her chest. cerebellum, shown in red. phase mainstays include naproxen,
“Yes,” she said. “As a teenager, the caffeine and aspirin.
headaches were so bad, I’d have to take “How do you feel?” By the time patients get to the
loads of Advil and lie in a dark room emergency room, their migraines
for hours.” I asked. She rewarded are usually peaking. In those cases,
My hunch was that Alana was in the our go-to intravenous drugs include
middle of a vestibular migraine, a vari-
me with her irst smile anti-inflammatories like Toradol and
ant where the brain’s electrical waves since her arrival. anti-dopamine agents like Reglan,
propagate through the cerebellum, the which we gave Alana.
brain’s balance center. A vestibular “It’s gone,” she said. Thirty minutes later, I peeked into
migraine is often not accompanied by her room. She was curled up sleeping. I
a headache, and its symptoms mirror according to this theory. The result is shooed out two of her visiting friends,
those of peripheral vertigo. “migraine aura,” the non-headache left the room and closed the door.
Vestibular migraines strike 1 in barrage of symptoms that has been I checked on her two hours later.
100 people. The singer Janet Jackson described in medical literature for She looked clear-eyed and refreshed.
is among them; her attacks have been centuries. Wavy lights are the classic “How do you feel?” I asked.
so intense that in 2008 she had to cut manifestation, but there are many other She rewarded me with her irst smile
short a concert tour. aura symptoms. since her arrival. “It’s gone,” she said.
Doctors have plenty of theories on The list includes pain in the arms and Alana’s neurologist placed her
migraine causes. The latest is called legs, and sensitivity to light, noise and on migraine preventatives — daily
cortical spreading depression, which smells. Also possible are stomach pain magnesium supplements and vitamin
refers to a spontaneous electrical wave and nausea, as Peggy had experienced, B2. She was given sumatriptan, now
that travels through the brain’s cortex. and chest tightness and vertigo, Alana’s one of the more widely used migraine
Migraines, this theory holds, start primary symptoms. In addition, medicines, to take at the irst sign
when the spreading electrical wave migraine auras can cause temporary, of trouble.
activates the trigeminal ganglion, partial or full blindness, as well as Months later, I asked her neurologist
a cluster of neurons that sit close to muscle weakness. how Alana was doing. She hadn’t had
the brainstem. This sets off a chemical One recent patient at the emergency any migraine episodes, he said.
cascade that releases inflammatory department was unable to speak. The storm had blown offshore, but
proteins along the meninges, the multi- We’d almost treated her for a stroke, Alana would still need to guard against
layered outer envelope of the brain but something didn’t it. After the incoming waves. D
SCOTT CAMAZINE/SCIENCE SOURCE
that is crammed with pain-producing attack passed, she said her migraines
sensory nerves. This produces the often appear as strokes. Tony Dajer is director of the emergency
jackhammer headache. Migraine auras and pounding department at New York-Presbyterian/Lower
But that’s not the end of it. The headaches are inconstant partners. Manhattan Hospital. The cases described in
electrical and chemical ripples can An attack might precede or accompany Vital Signs are real, but names and certain
stimulate neurons throughout the brain, a headache. Or it might go solo. details have been changed.
24 DISCOVERMAGAZINE.COM
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superstitious behaviors,
and how to give them up.
BY GALADRIEL WATSON
13th. Superstitions like these abound. — most children tried to ind a natural crazy, but I’m going to do this.’ We have
In 2015, a poll by 60 Minutes and Vanity explanation. But 5- and 6-year-olds [these beliefs] because they’re the output
Fair found that 60 percent of respon- also often credited miracles or luck. of pretty basic cognitive processes.”
dents admitted to knocking on wood. These supernatural explanations started We have two ways of thinking, she
26 DISCOVERMAGAZINE.COM
Back by Popular Demand!
Discover
SCIENCE FOR THE CURIOUS
16th Annual M AG A Z I N E
explains. One is intuitive: fast, eficient recite its attached poem. But if she had
and quick to jump to conclusions. company in the car, “I might look like a
This can provide a seeming rationale fool, so I’m not going to do it,” she says.
for those crazy beliefs. Did my roof Woolley explains that, once a
collapse? No. Therefore, my knocking superstition is established, we do a
on wood must have been effective — cost-beneit analysis that can make
I’ll do it again next time. it seem like not performing the ritual
Then we have a slower, more deliber- poses a risk. Skipping it can even give
ate way of thinking. It may jump in some people anxiety. So if no one is
to point out my faulty reasoning and around to think the superstitious ritual
recognize that my knocking has nothing is crazy — and add a cost to performing
to do with whether or not the roof to (eventually) sleep. “These beliefs and it — we are more likely to complete
caves in. But, Risen says, “detecting behaviors actually do end up regulating it out of a “better safe than sorry”
an error in your intuitive belief doesn’t your emotions,” says Risen. “When mindset, indicating we must believe in it
necessarily lead you to correcting it. you knock on wood, you may worry at least a little bit.
It seems that some intuitions are just about this less.” I also wonder if parenthood has
very dificult to shake.” And it never hurts to hedge your bets anything to do with the strength of my
People also like to feel a sense of — usually. Woolley provides her own beliefs. I don’t only knock on wood to
KELLIE JAEGER/DISCOVER
control. I may not have been shoveling example of owning a “parking angel” save my roof, but to save my children.
on the roof, but at least I was doing that once hung from her rearview mir- Is my son at a party? Please bring him
something. And it may have given me ror. If she were alone and desperate for home safe. Is my daughter on a road
enough peace of mind to allow me parking, she might rub the angel and trip? Please keep the roads clear.
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COVER STORY
30 DISCOVERMAGAZINE.COM
Your Daily Dose of
QUANTUM
How the science of the super small
lets you smell, see, touch and more.
BY TIM FOLGER ILLUSTRATIONS BY JAY SMITH
34 DISCOVERMAGAZINE.COM
Some 93 million miles separate the sun and Earth,
and it takes photons just over eight minutes to cover
that distance. But the bulk of their journey occurs
inside the sun, where a typical photon spends
a million years trying to escape.
by a vibrational theory of smell irst proposed impulses that create the perceptions of different
by chemist Malcolm Dyson in 1938. After smells in the brain.
Turin irst caught scent of Dyson’s idea in the Tucked away in our noses, then, might be a
1990s, he started looking for molecules that sophisticated electronic detector. How could our
would allow him to test the theory. He hit upon noses have evolved to take advantage of such
sulfur compounds, which have a unique odor quantum strangeness? “I think we underestimate
and a characteristic molecular vibration. Turin the technology, so to speak, of life by a couple of
then needed to identify a completely unrelated orders of magnitude,” says Turin. “Four billion
compound — one with a different molecular shape years of R&D with unlimited funding is a long
than sulfur but possessing the same vibrational time. And I don’t think this is the most amazing
frequency — to see if it would smell anything thing that life does.”
like sulfur. Eventually, he found one, a molecule
containing boron. And sure enough, it reeked of SIGHT UNSEEN
sulfur. “That’s when the penny dropped,” he says. OK, so you’re quafing your coffee, nearly
“I thought, ‘This cannot be a coincidence.’ ” awake. Your eyelids are gearing up for daytime
Since that odoriferous eureka moment, Turin has mode, blinking, letting in a bit of the light that’s
been gathering experimental evidence to support streaming through the window. As you sip your
the idea, collaborating with Horsield to work out brew, ponder this: The particles of light warming
the theoretical details. Five years ago, when Turin your face and entering your eyes originated a
and colleagues designed an experiment in which million years ago in the center of the sun, around
some of the hydrogen molecules in a musk-scented the time our not-quite-human ancestors started
fragrance were replaced with deuterium — a to use ire. The sun wouldn’t even be sending out
variety of hydrogen containing an extra neutron — those particles, named photons, if not for the
they found that people could smell the difference. same phenomenon that might underlie our sense
Since hydrogen and deuterium have identical of smell — quantum tunneling.
shapes but different vibrational frequencies, Some 93 million miles separate the sun and
the results again suggested that our noses could Earth, and it takes photons just over eight
indeed detect vibrations. Similar experiments with minutes to cover that distance. But the bulk of
fruit flies complemented those results. their journey occurs inside the sun, where a
Turin’s idea remains contentious — typical photon spends a million years trying to
his experimental data have divided the escape. Matter is so tightly packed at the center of
interdisciplinary community of olfactory our star — the hydrogen there is about 13 times
researchers. But if he is right, and we do smell denser than lead — that photons can travel only
vibrations in addition to shapes, how do our noses an ininitesimal fraction of a second before being
manage the feat? Turin speculates that a quantum absorbed by a hydrogen ion, which then spits the
effect called tunneling might be involved. photon out for another soon-to-be-interrupted
In quantum mechanics, electrons and all other journey, ad ininitum. After about a billion trillion
particles possess a dual nature; each is both such interactions, a photon inally emerges from
a particle and a wave. This sometimes allows the surface of the sun, having zigged and zagged
electrons to spread out and travel, or tunnel, randomly for a thousand millennia.
through materials in ways that would be forbidden But the photons never would have been born,
to particles under the rules of classical physics. and the sun wouldn’t shine, were it not for quantum
The molecular vibrations of a scent molecule tunneling. The sun and all other stars generate
might provide the right jump down in energy that light by nuclear fusion, smashing hydrogen ions
electrons need to tunnel from one part of an odor together to form helium, a process that releases
receptor to another. The tunneling rate would energy. Every second, the sun converts about
change with different molecules, triggering nerve 4 million tons of matter into energy. But hydrogen
36 DISCOVERMAGAZINE.COM
In Hoffman’s view, evolution has shaped our
brains to operate in much the same way, as a
graphical interface that doesn’t reproduce the
world with any sort of idelity. Evolution doesn’t
favor the development of accurate perceptions; it
rewards ones that enhance survival. Or as Hoffman
puts it, “Fitness beats truth.”
Hoffman and his graduate students have run
hundreds of thousands of computer models in
recent years to test his ideas. In the simulations,
artiicial life-forms compete for limited resources.
And in every case, the organisms programmed to
emphasize itness outcompete the various ones
primed for accurate perceptions. For example,
if one organism is tuned to accurately perceive,
say, the total amount of water present in an
environment, it will lose out to an organism that’s
tuned to perceive something simpler: the optimal
amount of water needed to stay alive.
So while one organism might construct a
more accurate representation of reality, that
representation doesn’t enhance its survivability.
Hoffman’s studies have led him to a remarkable
conclusion: “To the extent that we’re tuned to
itness, we will not be tuned to reality. You can’t
More than do both.”
His ideas align with what some physicists
99.9999999999 believe to be a central message of quantum theory:
percent of an atom Reality is not completely objective — we cannot
consists of empty separate ourselves from the world we observe.
Hoffman fully embraces that view. “Space is just
space, with nearly all a data structure,” he says, “and physical objects
its stuff concentrated are themselves also data structures that we create
on the fly. When I look at that hill over there, I
in the nucleus. When create that data structure. Then I look away and
you exert pressure I’ve trashed that data structure because I don’t
need it anymore.”
against a cup with your As Hoffman’s work shows, we haven’t yet come
hand, the seeming to grips with the full meaning of quantum theory
and what it says about the nature of reality. Planck
solidity comes from himself struggled for most of his life to understand
the resistance of the theory he helped launch, and always believed
in an objective universe that exists independently
electrons in the cup. of us. He once wrote about why he decided to go
into physics against the advice of his mentor: “The
outside world is something independent from man,
something absolute, and the quest for the laws
which apply to this absolute appeared to me as the
Hoffman likens the picture our brain constructs most sublime scientiic pursuit in life.” Maybe it
of the world to the graphical interface on a will take another century, and another revolution,
computer screen. All the colorful icons on the to prove whether he was right, or as mistaken as
screen — the trash can, the mouse pointer, the Professor von Jolly. D
ile folders — bear no resemblance at all to what’s
really going on inside the computer. They’re Tim Folger is a contributing editor to Discover and series
abstractions, simpliications that allow us to editor of The Best American Science and Nature Writing,
interact with complex electronics. an annual anthology. He lives in New Mexico.
40 DISCOVERMAGAZINE.COM
ROMANIA Dam
IRON
GATES I
r
ive
eR
ub
Lepenski Vir
n
Da
SERBIA
ARCHAEOLOGICAL SITES
Dam
Open-air sites IRON
Danu Cave/rock shelter GATES II
b e Ri
ver
TURKEY
(Ancient Anatolia)
Spre
ad of agriculture
Source: "Radiocarbon and Stable Isotope Evidence of Dietary Change from the Mesolithic
to the Middle Ages in the Iron Gates: New Results From Lepenski Vir," Radiocarbon, 2004
▲ Neolithic
farmers migrating
that those earlier farmers interacted FISHERMEN FORAGERS out of Anatolia
with local hunter-gatherers. Home to scores of prehistoric brought their way
of life to a corner
Before the ifth millennium B.C., settlement sites, this nearly 100-mile of southeastern
or 7,000 years ago, farmers and for- stretch of river is known as the Europe. The
region, rich in
agers rarely crossed paths; examina- Iron Gates region, named after two archaeological
tion of burial remains shows genetic dams built decades ago. Just as the sites, is now
separation, says Burger. “They Danube is a resource for modern known as the Iron
Gates, named
probably saw each other from a dis- populations, it sustained the hunter- after Cold War-era
tance occasionally and just stared gatherer bands that lived there more dams erected
along the Danube
at each other, thinking, ‘Oh, those than 8,000 years in the past. River there.
strange people.’ ” While many forager groups in
Whether farmers or foragers, other parts of the world moved with
groups were small and scattered, the seasons, hunting game and gath-
dwarfed by the limitless European ering plants, Iron Gates bands stuck
landscape. In addition, they sought close to the river valley. Excavations
different environments, says Stephen Shennan, an of their encampments reveal large amounts of ish
archaeologist at the University College London bones; dietary clues preserved in the foragers’
and author of the book The First Farmers of bones showed heavy ish consumption.
Europe. Foragers opted for forests and mountains Their favorite catch was apparently sturgeon,
full of game, or rivers and coasts teeming with some specimens longer than a man, as they swam
ish. Farmers chose flatland with fertile soil in upriver in spring from the Black Sea to breed
ALISON MACKEY/DISCOVER
44 DISCOVERMAGAZINE.COM
generations, ancient DNA shows, the two groups buried there: Nearly 200 human remains have
were having sex and raising families. “For people been recovered, some beneath buildings.
to marry into another population, there must be From about 9,500 years ago, when only hunter-
a high economic attraction underlying this pro- gatherers lived in the area, to about 7,500 years
cess,” says Burger. “Otherwise, you wouldn’t do ago, when Iron Gates was the sole domain of
it. It’s not like you fall in love and it’s a romantic farmers, Lepenski Vir was variously a ishing
story. You are attracted because you think you camp, a social destination, a settlement, a burial
can have a better life.” site and perhaps a spiritual center. It might have
been all or a combination during some periods.
A CULTURAL POTPOURRI The river site offers a wealth of evidence for cul-
Among the Iron Gates settlements is Lepenski tural exchange during the transition.
ZARKO DJOKIC/SHUTTERSTOCK
Vir, named after the whirlpool at its doorstep. Consider how the bodies were buried. In south-
(Vir means “whirlpool” in Serbian.) Perhaps only eastern Europe, hunter-gatherers buried their
a few dozen people occupied it at any one time, dead on their backs with hands usually placed on
according to the paper in Archaeological and the stomach and legs straight. Anatolian farmers
Anthropological Sciences. But many people were buried their dead on their sides in a curled position.
46 DISCOVERMAGAZINE.COM
▲ From left:
Limestone
lead author and an archaeologist at the University appears to have been the region’s irst multicul- beads found in
of Edinburgh. tural nexus. “That might have contributed to the an Iron Gates
grave, statues
Rather than feasting on, say, a plate of catish creativity we see at the site, and what makes the that may depict
in the years before his death, Burial 7/I might site so important,” says Bori . fishlike gods, a
reconstructed
have spooned up calorie-rich porridge, a mix of Within hundreds of years of irst contact house at the
cereals and goat’s milk. Here was the Neolithic in Iron Gates, complex agricultural societies Lepenski
transition embodied in one person. sprang up in southeastern Europe, along with Vir site and
CLOCKWISE FROM LEFT: DUSAN BORIC; ALBUM/ALAMY STOCK PHOTO; PAVLEMARJANOVIC/SHUTTERSTOCK; BORIC; ALBUM/ALAMY STOCK PHOTO
perforated
Despite the dietary turn, the ways of his other advances, such as intricate metalwork. shell beads all
ancestors didn’t completely escape him: The man Meanwhile, agriculture was also spreading provide clues
to how farmers
was laid to rest on his back, body straight, palms outside southeastern Europe. By the middle and foragers
on his belly. of the sixth millennium B.C., some 400 years interacted
8,000 years
The conclusions in the Radiocarbon study are after Burial 7/I, farming was in central Europe ago.
controversial. Originally excavated in the 1960s, and on the Iberian Peninsula, according
Burial 7/I’s remains have been moved to differ- to a paper published in Nature in February.
ent storage locations and sometimes mishandled, By the end of that millennium, agriculture
says Roksandic, who examined the skeleton had reached Eastern Europe, which included
in the late 1990s and is the paper’s co-author. farming settlements in the Ukraine of hundreds
Contamination is possible, she acknowledges. of people.
But Bonsall says bone collagen is relatively resis- The swiftness of the agricultural revolution
tant to postmortem alteration. He hopes that makes the interaction at Iron Gates all the more
future analysis of the skeleton’s DNA and teeth interesting. An ancient subsistence strategy
will answer questions raised by colleagues. was starting to vanish. A cultural watershed,
By the time the man died, about 8,000 years perhaps the most signiicant in human history,
ago, hunter-gatherer culture was in its twilight was underway. Change was happening on an
at Iron Gates. “It takes not more than 300 years, unprecedented level. But from the viewpoint of
and the whole area is full of farmers,” says Burger. an individual living through it, the transition
“The hunter-gatherers have been replaced.” was pretty casual — manifesting, on occasion,
as foragers and farmers talking shop above the
FARMER BOOM thrum of a river. D
Before the foragers were fully absorbed into the
farming communities, however, Lepenski Vir Mark Barna is an associate editor at Discover.
48 DISCOVERMAGAZINE.COM
he sun was barely above the horizon on March 13, a hill — at which point the tires started spinning and, without
2004, but the Slash X saloon bar, in the middle a human to help, carried on spinning until they caught ire. It
of the Mojave Desert, was already thronging was over by late morning. A DARPA organizer climbed into a
with people. helicopter and flew over to the inish line to inform the waiting
The bar is on the outskirts of Barstow, a journalists that none of the cars would be getting that far.
California town between Los Angeles and Las The race had been oily, dusty, noisy and destructive —
Vegas. It’s a place popular with cowboys and off- and had ended without a winner. All those teams of people
roaders, but on that spring day it had drawn the had worked for a year on a creation that had lasted, at best,
attention of another kind of crowd. A makeshift stadium that a few minutes.
had been built was packed with engineers, excited spectators But the competition was anything but a disaster. The rivalry
and foolhardy petrol heads who all shared a similar dream: had led to an explosion of new ideas, and by the next DARPA
to be the irst people on Earth to witness a driverless car win Grand Challenge in 2005, the technology was vastly improved.
a race. An astonishing ive driverless cars completed the race without
The race had been organized by the U.S. Defense Advanced any human intervention.
Research Projects Agency, or DARPA (nicknamed the Now, more than a decade later, it’s widely accepted that
Pentagon’s “mad science” division). The agency had been the future of transportation is driverless. In late 2017,
interested in unmanned vehicles for a while, and with good rea- Philip Hammond, the British Chancellor of the Exchequer,
son: Roadside bombs and targeted attacks on military vehicles announced the government’s intention to have fully driver-
were a major cause of death on the battleield. Earlier that less cars — without a safety attendant on board — on British
year, DARPA had announced its intention to make one-third roads by 2021. Daimler, a Germany-based auto manufacturer,
of U.S. ground military forces vehicles autonomous by 2015. has promised driverless cars by 2020, and Ford by 2021.
Up to that point, progress had been slow and expensive. Other manufacturers have made similar forecasts for their
DARPA had spent around half a billion dollars over two driverless vehicles.
decades funding research at universities and companies in the On the surface, building a driverless car sounds as if it should
hope of achieving its ambition. But then came an ingenious be relatively easy. Most humans manage to master the requisite
idea: Why not create a competition? The agency would invite skills to drive. Plus, there are only two possible outputs: speed
anyone in the country to design their own driverless car and and direction. It’s a question of how much gas to apply and
race them against each other on a long-distance track, with how much to turn the wheel. How hard can it be?
a prize of $1 million for the winner. It would be a quick and But, as the irst DARPA Grand Challenge demonstrated,
cheap way to give DARPA a head start in pursuing its goal. building an autonomous vehicle is a lot trickier than it looks.
On the morning of the 132-mile race, a ramshackle lineup of Things quickly get complicated when you’re trying to get
cars gathered at Slash X, along with a few thousand spectators. an algorithm to control a great big hunk of metal traveling
Things didn’t quite go as planned. One car flipped upside down at 60 mph.
in the starting area and had to be withdrawn. A self-driving
motorbike barely cleared the start line before it rolled onto its BEYOND THE RULES OF THE ROAD
side and was declared out of the race. One car hit a concrete Imagine you’ve got two vehicles approaching each other at
wall 50 yards in. Another got tangled in a barbwire fence. speed, traveling in different directions down a gently curved
The scene around the saloon bar began to look like a robot county highway.
graveyard. A human driver will be perfectly comfortable in that scenario,
The top-scoring vehicle, an entry by Carnegie Mellon knowing the other car will stick to its own lane and pass safely
University, managed an impressive 7 miles before misjudging a few feet to the side. “But for the longest time, it does look
50 DISCOVERMAGAZINE.COM
like you’re going to hit each other,” explains Paul Unfortunately, the answer to that
Newman, professor of robotics at the University question is probably not anytime soon.
of Oxford and founder of Oxbotica, a company That driverless dream we’re all waiting for
that builds driverless cars. might be a lot further away than we think.
How do you teach a driverless car not to panic That’s because there’s another layer of
in that situation? You don’t want the vehicle to dificulty to contend with when trying to
drive off the side of the road trying to avoid a build that sci-i fantasy of a go-anywhere,
collision that was never going to happen, says do-anything, steering-wheel-free driverless
Newman. But, equally, you don’t want it to be car, and it’s one that goes well beyond the
complacent if you really do ind yourself on technical challenge.
the verge of a head-on crash. Remember, too,
these cars are only ever making educated guesses THE PEOPLE FACTOR
about what to do. A fully autonomous car will also have to
How do you get it to guess right every deal with the tricky problem of people.
single time? That, says Newman, “is a hard, “People are mischievous,” says Jack Stilgoe,
hard problem.” a sociologist at the University College
It’s a problem that puzzled experts for a long London who studies the social impact of
time, but it does have a solution. The trick is to technology. “They’re active agents, not
build in a model for how other — sane — driv- just passive parts of the scenery.”
ers will behave. Unfortunately, the same can’t be Imagine a world where truly, perfectly
said of other nuanced driving scenarios. autonomous vehicles exist. The No. 1 rule
“What’s hard is all the problems with driving that have noth- in their onboard algorithms will be to avoid collisions wherever
ing to do with driving,” says Newman. possible. And that changes the dynamics of the road. If you
For instance, how do you teach a self-driving algorithm to stand in front of a driverless car, it has to stop. If you pull out
understand that you need to be extra cautious upon hearing in front of one at a junction, it has to behave submissively.
the tunes of an ice cream truck, or when passing a group of “People who’ve been relatively powerless on roads up till
kids playing with a ball on the sidewalk? now, like cyclists, may start cycling very slowly in front of
Even harder, how do you teach a car that it should some- self-driving cars knowing that there is never going to be any
times break the rules of the road? What if an ambulance with aggression,” says Stilgoe.
its lights on is trying to get past on a narrow street and you Getting around this problem might mean bringing in
need to drive up on the sidewalk to let it through? Or if an oil stricter rules to deal with people who abuse their position as
tanker has jackknifed across a country lane and you need to cyclists or pedestrians. It’s been done before, of course: Think
get out of there by any means possible? of jaywalking. Or it could mean forcing everything else off the
“None of these are in the [U.K.] Highway Code,” Newman roads, as happened with the introduction of the automobile.
points out. And yet a truly autonomous car needs to know That’s why you don’t see bicycles, horses, carts, carriages or
how to deal with all of these scenarios if it’s to exist without pedestrians on an expressway.
ever having any human intervention. Even in emergencies. If we want fully autonomous cars, we’ll almost certainly
That’s not to say these are insurmountable problems. have to do something similar again and limit the number of
“I don’t believe there’s any level of intelligence that we won’t aggressive drivers, ice cream trucks, kids playing in the road,
be able to get a machine to do,” says Newman. “The only roadwork signs, dificult pedestrians, emergency vehicles,
question is when.” cyclists, mobility scooters and everything else that makes the
52 DISCOVERMAGAZINE.COM
Other autonomous car programs are inding the same Researchers found that, after an alarm sounded for passen-
issues. Although Uber’s driverless cars require human gers to regain control, it took them about 40 seconds to do it.
intervention every 13 miles, getting drivers to pay attention Ironically, the better self-driving technology gets, the worse
remains a struggle. In March, an Uber self-driving vehicle these problems become. A sloppy autopilot that sets off an
fatally struck a pedestrian in Tempe, Arizona. Video foot- alarm every 15 minutes will keep a driver continually engaged
age from inside the car showed that the “human monitor” and in regular practice. It’s the smooth and sophisticated auto-
sitting behind the wheel was looking away from the road in matic systems that are almost always reliable that you’ve got to
the moments before the collision. watch out for.
“The worst case is a car that will need driver intervention
A PLAN FOR THE INEVITABLE once every 200,000 miles,” Gill Pratt, head of Toyota’s research
Though this is a serious problem, there is an alternative. The institute, told technology magazine IEEE Spectrum in 2017.
car companies could accept that humans will be humans, Pratt says someone who buys a new car every 100,000 miles
acknowledge that our minds will wander. After all, being might never need to take over control from the car. “But every
able to read a book while driving is part of the appeal of self- once in a while, maybe once for every two cars that I own, there
driving cars. would be that one time where it suddenly goes ‘beep beep beep,
Some manufacturers have already started to build their cars now it’s your turn!’ ” Pratt told the magazine. “And the person,
to accommodate our inattention. Audi’s Trafic Jam Pilot is typically having not seen this for years and years, would . . . not
one example. It can completely take over when you’re in slow- be prepared when that happened.”
moving highway trafic, leaving you to sit back and enjoy the
ride. Just be prepared to step in if something goes wrong. But ADJUSTING EXPECTATIONS
there’s a reason why Audi has limited its system to slow-moving As is the case with much of the driverless technology that is so
trafic on limited-access roads. The risks of catastrophe are keenly discussed, we’ll have to wait and see how this turns out.
lower in motorway congestion. But one thing is for sure: As time goes on, autonomous driving
And that’s an important distinction. Because as soon as a will have a few lessons to teach us that apply well beyond the
human stops monitoring the road, you’re left with the worst world of motoring — not just about the messiness of handing
possible combination of circumstances when an emergency over control, but about being realistic in our expectations of
happens. A driver who’s not paying attention will have very what algorithms can do.
little time to assess their surroundings and decide what to do. If this is going to work, we’ll have to adjust our way of
Imagine sitting in a self-driving car, hearing an alarm and thinking. We’re going to need to throw away the idea that
looking up from your book to see a truck ahead shedding its cars should work perfectly every time, and accept that, while
load onto your path. In an instant, you’ll have to process all mechanical failure might be a rare event, algorithmic failure
the information around you: the motorbike in the left lane, almost certainly won’t be.
the van braking hard ahead, the car in the blind spot on your So, knowing that errors are inevitable, knowing that if we
right. You’d be most unfamiliar with the road at precisely the proceed we have no choice but to embrace uncertainty, the
moment you need to know it best. conundrums within the world of driverless cars will force us
Add in the lack of practice, and you’ll be as poorly equipped to decide how good something needs to be before we’re willing
as you could be to deal with the situations demanding the to let it loose on our streets. That’s an important question, and
highest level of skill. it applies elsewhere. How good is good enough? Once you’ve
A 2016 study simulated people as passengers, reading a built a flawed algorithm that can calculate something, should
book or playing on their cell phones, in a self-driving car. you let it? D
THE
David Baker
changed
the study
of proteins
influenza, others are betting on David Baker. look like child’s play. When the denaturant unfolded
After revolutionizing the study of proteins — Aninsen’s ribonuclease, there were myriad ways it
molecules that perform crucial tasks in every cell of could refold, resulting in structures as different as an
every natural organism — Baker is now engineering origami crane and a paper airplane. Much as the folds
them from scratch to improve on nature. In late 2017, determine whether a piece of paper can fly across a
the Open Philanthropy Project gave his University of room, only one fold pattern would result in functioning
Washington Institute for Protein Design more than ribonuclease. So the puzzle was this: How do proteins
$10 million to develop the Death Star and support “know” how to refold properly?
Rosetta, the software platform he conceived in the “Aninsen showed that the information for both
1990s to discover how proteins are assembled. Rosetta structure and activity resided in the sequence of amino
has allowed Baker’s lab not only to advance basic acids,” says University of California, Los Angeles,
science and pioneer new kinds of vaccines, but also to biochemist David Eisenberg, who has been researching
create drugs for genetic disorders, biosensors to detect protein folding since the 1960s. “There was a hope that
56 DISCOVERMAGAZINE.COM
it would be possible to use sequence information to get
three-dimensional structural information. Well, that
proved much more dificult than anticipated.”
“We’ve figured out
Baker was interested enough in protein folding and a way to put these
other unsolved mysteries of biology to switch majors
and apply to grad school. “I’d never worked in a lab building blocks
before,” he recalls. He had only a vague notion of what
biologists did on a daily basis, but he also sensed that
together at the
the big questions in science, unlike philosophy, could right angles to form
actually be answered.
Grad school plunged Baker into the tediousness these very complex
and frustrations of benchwork, while also nurturing
some of the qualities that would later distinguish
nanostructures.”
him. He pursued his Ph.D. under Randy Schekman,
who was studying how molecules move within cells,
at the University of California, Berkeley. To aid microscope, Baker concentrated on preserving cell
in this research, students were assigned the task of structure. If the cell were a wristwatch, his approach
dismantling living cells to observe their internal would be equivalent to focusing on the relationship
molecular trafic. Nearly half a dozen of them, between gears, rather than trying to keep it ticking,
frustrated by the assignment’s dificulty, had given while taking it apart.
up by the time Baker got the job. “He was completely obsessed,” recalls Deshaies,
Baker decided to follow his instincts even though who was his labmate at the time (and one of the
it meant going against Schekman’s instructions. students who’d surrendered). Nobody could stop
Instead of attempting to keep the processes within Baker, or dissuade him. He worked for months until
a cell still functioning as he dissected it under his he proved his approach was correct: Cell structure
INSTITUTE FOR PROTEIN DESIGN
Protein molecules play critical roles in every aspect of life. The way each protein folds determines its function, and the ways to fold
are virtually limitless, as shown in this small selection of proteins visualized through the software platform Rosetta, born in Baker’s lab.
ROSETTA MILESTONE
Every summer for more than a decade, scores
of protein-folding experts convene at a resort in
Washington’s Cascade Mountains for four days of
hiking and shop talk. The only subject on the agenda:
how to advance the software platform known as 1 DNA
Rosetta. They call it Rosettacon. Stored in the nucleus of the cell and
made up of four chemical building
Rosetta has been the single most important tool blocks — A, C, T and G, for short.
in the quest to understand how proteins fold, and to DNA contains an organism’s
design new proteins based on that knowledge. It is the blueprints, or instructions, for life.
link between Aninsen’s ribonuclease experiment and
Baker’s Death Star vaccine. 2 mRNA
Because a cell’s protein-making
When Baker arrived at the University of Washington factory cannot directly interpret
in 1993, researchers knew that a protein’s function was the instructions encrypted in DNA,
determined by its structure, which was determined by an enzyme converts the directives
the sequence of its amino acids. Just 20 different amino into a message know as mRNA.
acids were known to provide all the raw ingredients.
(Their particular order — speciied by DNA — 3 RIBOSOME
ILLUSTRATION ABOVE: NATIONAL SCIENCE FOUNDATION. ILLUSTRATIONS BELOW: JAY SMITH
58 DISCOVERMAGAZINE.COM
3
Protein Structures
Made of long chains of amino acids, each protein folds into elaborate, precise structures that determine how they function.
While the folding patterns are unique and complicated, they can be thought of in four different levels of complexity:
Phe Gln
Gly Ile
Thr Arg
Gln
Ser Arg Arg
Arg Gly
Thr
Gly Gly Met Thr
Arg Gly Arg
Cell
PRIMARY PROTEIN TERTIARY PROTEIN QUATERNARY PROTEIN
STRUCTURE SECONDARY PROTEIN STRUCTURE STRUCTURE
Sequence of a chain STRUCTURE Three-dimensional folding Protein consisting of more
of amino acids. The amino acids fold into patterns of protein. than one amino acid chain.
repeating patterns in the
shape of pleated sheets
or an alpha helix.
their amino acids must align in equilibrium. The trouble protein-folding prediction from a parlor game into
is that the equilibrium state is just one of hundreds of legitimate science.
thousands of options — or millions, if the amino acid In addition to incorporating fresh insights from
sequence is long. That’s far too many possibilities to the bench, team members — using a janky collection
test one at a time. Nature must have another way of of computers made of spare parts — found a way to
operating, given that folding is almost instantaneous. run rough simulations tens of thousands of times to
Baker’s initial approach was to study what nature determine which fold combinations were most likely.
was doing. He broke apart proteins to see how They successfully predicted structures for 12 out of
individual pieces behaved, and he found that each the 20 proteins. The predictions were the best yet, but
fragment was fluctuating among many possible still approximations of actual proteins. In essence, the
structures. “And then folding would occur when they picture was correct, but blurry.
all happened to be in the right geometry at the same Improvements followed rapidly, with increased
time,” he says. Baker designed Rosetta to simulate computing power contributing to higher-resolution
this dance for any amino acid sequence. models, as well as improved ability to predict the folding
Baker wasn’t alone in trying to predict how proteins of longer amino acid chains. One major leap was the
fold. In 1994, the protein research community organized 2005 launch of Rosetta@Home, a screensaver that
a biennial competition called CASP (Critical Assessment runs Rosetta on hundreds of thousands of networked
of Protein Structure Prediction). Competitors were given personal computers whenever they’re not being used by
the amino acid sequences of proteins and challenged to their owners.
anticipate how they would fold. Yet the most signiicant source of progress has been
The irst two contests were a flop. Structures that RosettaCommons, the community that has formed
competitors number-crunched looked nothing like around Rosetta. Originating in Baker’s laboratory and
folded proteins, let alone the speciic proteins they were growing with the ever-increasing number of University
BRIAN DALBALCON/UW MEDICINE
meant to predict. Then everything changed in 1998. of Washington graduates — as well as their students and
colleagues — it is Baker’s communal brain writ large.
FUNCTION FOLLOWS FORM Dozens of labs continue to reine the software,
That summer, Baker’s team received 20 sequences from adding insights from genetics and methods from
CASP, a considerable number of proteins to model. machine learning. New ideas and applications are
But Baker was optimistic: Rosetta would transform constantly emerging.
60 DISCOVERMAGAZINE.COM
The communal brain has answered Aninsen’s big
question — a protein’s speciic amino acid alignment
creates its unique folding structure — and is now
“Proteins that just
posing even bigger ones. evolved by pure,
“I think the protein-folding problem is effectively
solved,” Baker says. “We can’t necessarily predict blind chance can do
every protein structure accurately, but we understand
the principles.
all these amazing
“There are so many things that proteins do in things. What happens
nature: light harvesting, energy storage, motion,
computation,” he adds. “Proteins that just evolved by if you actually
pure, blind chance can do all these amazing things.
What happens if you actually design proteins
design proteins
intelligently?” intelligently?”
DE NOVO DESIGN
Matthew Bick is trying to coax a
protein into giving up its sugar thousands of designs, each
habit for a full-blown fentanyl representing a modiication
addiction. His computer screen of the amino acid sequence
shows a colorful image of predicted to envelop fentanyl
ribbons and swirls representing instead of sugar molecules. An
the protein’s molecular structure. algorithm then selected the best
A sort of Technicolor Tinkertoy several hundred options, which
floats near the center, representing Bick evaluated by eye, eventually
the opioid. “You see how it has really Matthew Bick
choosing 62 promising candidates.
good packing?” he asks me, tracing the The protein on Bick’s screen was one
ribbons with his inger. “The protein kind of his favorites.
of envelops the whole fentanyl molecule like a “After this, we do the arduous work of
hot dog bun.” testing designs in the lab,” Bick says.
A postdoctoral fellow in Baker’s With another image, he reveals
lab, Bick engineers protein his results. All 62 contenders have
biosensors using Rosetta. The been grown in yeast cells infused
project originated with the U.S. with synthetic genes that spur
Department of Defense. “Back the yeasts’ own amino acids to
in 2002, Chechen rebels took a produce the foreign proteins. The
bunch of people hostage, and transgenic yeast cells have been
Protein (in green)
there was a standoff with the enveloping
exposed to fentanyl molecules
Russian government,” he says. fentanyl molecule tagged with a fluorescing
The Russians released a gas, chemical. By measuring the
widely believed to contain a fentanyl fluorescence — essentially shining
derivative, that killed more than a ultraviolet light on the yeast cells to
hundred people. Since then, the Defense see how many glow with fentanyl — Bick
Department has been interested in simple can determine which candidates bind to the
ways to detect fentanyl in the environment in case it’s opioid with the greatest strength and consistency.
TOP: CONRADO TAPADO/UW MEDICINE. BOTTOM: BICK ET AL. ELIFE 2017
used for chemical warfare in the future. Baker’s lab has already leveraged this research to
Proteins are ideal molecular sensors. In the natural make a practical environmental sensor. Modiied to
world, they’ve evolved to bind to speciic molecules glow when fentanyl binds to the receptor site, Bick’s
like a lock and key. The body uses this system to customized protein can now be grown in a common
identify substances in its environment. Scent is one plant called thale cress. This transgenic weed can cover
example; speciic volatiles from nutrients and toxins it terrain where chemical weapons might get deployed,
into dedicated proteins lining the nose, the irst step and then glow if the dangerous substances are present,
in alerting the brain to their presence. With protein providing an early warning system for soldiers and
design, the lock can be engineered to order. health workers.
For the fentanyl project, Bick instructed Rosetta to The concept can also be applied to other biohazards.
modify a protein with a natural afinity for the sugar For instance, Bick is now developing a sensor for
xylotetraose. The software generated hundreds of aflatoxin, a residue of fungus that grows on grain,
causing liver cancer when consumed by humans. He acid sequence. And he can use any amino acids at all
wants the sensor to be expressed in the grain itself, — thousands of options, some already synthesized and
letting people know when their food is unsafe. others waiting to be designed — not only the 20 that
But he’s going about things differently this time are standard in nature for building proteins.
around. Instead of modifying an existing protein, he’s Without the freedom of de novo protein design,
starting from scratch. “That way, we can control a lot Baker’s Death Star would never have gotten off the
of things better than in natural proteins,” he explains. ground. His group is now also designing artiicial
His de novo protein can be much simpler, and have viruses. Like natural viruses, these protein shells
more predictable behavior, because it doesn’t carry can inject genetic material into cells. But instead of
many million years of evolutionary baggage. infecting you with a pathogen, their imported DNA
For Baker, de novo design represents the summit would patch dangerous inherited mutations. Other
of his quarter-century quest. The latest advances in projects aim to take on diseases ranging from malaria
Rosetta allow him to work backward from a desired to Alzheimer’s.
function to an appropriate structure to a suitable amino In Baker’s presence, protein design no longer seems
so extraordinary. Coming out of a brainstorming
session — his third or fourth of the day — he pulls me
aside and makes the case that his calling is essentially
“The current world the destiny of our species.
“All the proteins in the world today are the product
is quite a bit different of natural selection,” he tells me. “But the current
world is quite a bit different than the world in which
than the world in we evolved. We live much longer, so we have a
which we evolved. We whole new class of diseases. We put all these nasty
chemicals into the environment. We have new needs
live much longer, so for capturing energy.
“Novel proteins could solve a lot of the problems
we have a whole new
BRIAN DALBALCON/UW MEDICINE
62 DISCOVERMAGAZINE.COM
BACK BY POPUL A R DEMAND
Revised and updated with the latest discoveries, this special issue from
P32959
DiscoverMagazine.com/trips-tours M AG A Z I N E
Origin
Story
Know
Your
Enemy
A surge of research into
ancient killers may help us
outsmart them in the future.
BY GEMMA TARLACH
CLOCKWISE FROM BOTTOM LEFT: NICOLE NICKLISCH; ALEXEY A. KOVALEV; PHANIE/SCIENCE SOURCE; BEN KRAUSE-KYORA ET AL./ELIFE 2018;7:E36666
But indings about the origins and genome of the hepatitis B virus online journal eLife, a separate team
evolution of other scourges, including (HBV) in Nature in May. The roughly reported additional HBV genomes
leprosy, hepatitis B and syphilis, have 4,500-year-old sample was one of a up to 7,000 years old, including now-
been elusive or contradictory. dozen ancient HBV genomes found as extinct strains previously unknown
Now, two key advances — a surge the researchers sifted through one of to science.
in ancient DNA samples and powerful the largest databases of ancient human
computer programs to process the DNA ever assembled. NEEDLES IN A HAYSTACK
data — are allowing scientists to study Mühlemann, a co-lead author Hunting ancient pathogens is a recent
disease-causing bacteria and viruses of the paper, says advances offshoot of paleogenetics, which focuses
like never before. are being made not just in on the extraction and sequencing of
“There were very few ancient how far back researchers ancient DNA (aDNA) from animals,
human virus samples can ind ancient including humans, and plants. The
even six months ago,” pathogens, but primary challenges of working with
says Terry Jones, a in how many aDNA from these macroorganisms are
computational biologist they’re inding: degradation — genetic material breaks
at the University of “Where before down over time — and contamination.
Cambridge. “In terms we saw maybe Paleogeneticists interested in
of being ‘ancient,’ 300 one genome sequencing human aDNA, for example,
years was considered sequenced, now will extract a sample from human
old, and that was only remains, ilter out both modern
two or three samples. A partial skull from and non-human genetic material
a 7,000-year-old site
Now we’re inding in Karsdorf, Germany, — generally the result of microbial
viruses up to 7,000 years old. provided DNA from contamination — and look at what’s
the hepatitis B virus,
… We’ve gone from zero to the oldest sample left. The ancient pathogen hunters,
this almost out of the blue.” ever obtained. on the other hand, will take that same
64 DISCOVERMAGAZINE.COM
Two key developments allowed the current
flood of research into ancient pathogens:
powerful new data-crunching software and
many more ancient genomes available for
study, such as from these 4,500-year-old
skeletons in Mongolia (left) and a partial
jaw from Germany (right), both of which
contained the hepatitis B virus (above).
sample and try to identify every single Researchers estimate WRITTEN IN BONE
fragment of genetic code. Bacteria, however, can be easier to ind.
That’s where things get chaotic. that there may be up Some bacterial diseases, such as leprosy
Researchers estimate that there and syphilis, can leave distinctive marks
may be up to a trillion species of
to a trillion species of on victims’ bones. Mycobacterium
bacteria and closely related archaea, bacteria and closely leprae, which causes leprosy, damages
compared with about 8 million peripheral nerves, reducing sensation.
species combined of plants, animals, related archaea, Over time, this leads to increased risk
fungi and algae. To complicate of injuries and infections that cause
matters, bacteria in particular
compared with about localized cell death. Bones, especially
are notorious for horizontal gene 8 million species of the extremities, appear to dissolve.
transfer: picking up bits of DNA Syphilis, one of a handful of diseases
from other organisms and integrating combined of plants, caused by the bacterium Treponema
it into their own. Then there are pallidum, leads to inflammation of the
viruses, some of which carry their
animals, fungi and algae. connective tissues surrounding bones
genetic code in DNA, and others in and can cause bone lesions.
RNA, complicating identiication. from organisms across a broad In June, University of Zurich
“We don’t choose what to study. We spectrum of biodiversity. paleogeneticist Verena Schuenemann
look at the data and see what comes Limits remain, however. Viruses and colleagues published three
out,” says Jones. “It may be genetic in particular are wily targets. Blood- T. pallidum genomes after sampling
material from the host, or a parasite, borne HBV, for example, lingers in an human remains with bone lesions. The
or bacteria, or another virus, or DNA individual, including their bones, for genetic material may not seem ancient
from the food they ate the day before years. But many other viruses cause — the individuals were buried in a
they died, or even from something acute infections, fatal or otherwise, 17th-century Mexico City cemetery
they came into contact with.” without leaving a trace of their — but they are the oldest T. pallidum
Powerful new software tools can presence behind. genomes known, and the irst to
sort through all the ancient genetic “The number of viruses you can be sequenced from archaeological
fragments in a sample and match expect to ind in ancient human DNA material, a feat researchers in an
them to millions of sequences samples is not very large,” Jones says. earlier study considered “not possible.”
understand the evolution of M. leprae that M. leprae may have originated years ago in Norway. What’s surprising
concluded that the pathogen most in Western Eurasia, perhaps is that the particular variety found
likely arose in the Middle East or Europe itself. is rare today in Europe and North
Eastern Africa, with only a few strains America; it’s much more common
making it to Europe. But the newly THE BIG PICTURE in Asia and Africa. A bacterium of
published ancient genomes reveal Ideas about the origins of syphilis are the same type was also identiied
almost all of the major strains of the also up for revision. It’s often been in 16th-century victims in Mexico,
bacterium were present in Europe. called a New World disease, thought according to a January study in
“The evolutionary history of to have spread globally only after Nature Ecology & Evolution.
M. leprae is much more complex widespread European contact with Combined, the data allowed
than previously thought to be,” says Native Americans. But there’s some researchers to dig deep into
66 DISCOVERMAGAZINE.COM
Origin
Story
1 cm
Different subspecies of Treponema pallidum (left) cause syphilis and other treponemal
diseases. Researchers long thought it impossible to find the bacterium in archaeological
remains due to DNA degradation. In June, however, a team identified and sequenced
T. pallidum genomes from bones (above) interred at a centuries-old Mexican cemetery.
S. enterica’s past, something that just started to open the window to see
was previously impossible to do
While the what the truth is, but we’re nowhere
because only modern genomes of the chronological cutof near the bottom of it.”
pathogen were available for study. The new research is not just about
Their conclusions: The bacterium was point for inding hindsight. Nearly a million people
once much more widespread globally die each year from complications
and thousands of years older than
genetic material from of hepatitis B infection, and leprosy
thought — and may have jumped to ancient pathogens is still infects more than 200,000 people
humans through contact with early annually. Syphilis is considered a
domesticated pigs. still unknown, each re-emerging global public health
Similar recent studies on lesser- new genome found threat, with about 6 million new cases
known pathogens are redeining each year.
our shared histories. Jones and ofers hints about an “Working on ancient pathogens
Mühlemann collaborated with has implications for modern-day
colleagues on a study published in even deeper past. pathogens: Understanding the
July in PNAS that used aDNA to evolution of a bacterium, its past
change our understanding of human While the chronological cutoff spread and diversity leads to a
parvovirus B19 (B19V). The virus point for inding genetic material from better knowledge of how this
LEFT: SCIENCE SOURCE. RIGHT: JV SCHUENEMANN ET AL./PLOS NEGLECTED TROPICAL DISEASES, JUNE 21, 2018
causes a common, mild childhood ancient pathogens is still unknown, bacterium changed over time and
disease but can have more serious each new genome found offers hints adapted to environmental changes,”
consequences in adults. Previous about an even deeper past. Schuenemann says.
research based on modern strains The three ancient HBV genomes And thanks to gene transfer and
suggested B19V arose in the early presented in the eLife study earlier other quirks of evolution, bacteria and
1900s, but the PNAS study found it this year, for example, are more viruses are especially wily at adapting.
in human remains that were up to closely related to strains that still “Fossilized animals that are extinct
6,900 years old. infect non-human primates in Africa are not coming back, but in the case
Just how far back will ancient than they are to modern strains. That of viruses, they can come back,” says
pathogen hunters ind their quarry? could bolster a theory that the virus Jones. “Parts of them can come back.
“The general assumption for the may have found its irst human hosts You’ll never see, for example, an
survival of aDNA is 1 million years,” on that continent. Jones believes it’s elephant with a mammoth head, but
says Schuenemann, who adds that some even possible that HBV was present in that can happen with viruses. When
microbes are more likely than others to species ancestral to our own. we study the past, we know what may
be preserved. “I actually have hope to “What’s the chance of it not happen in the future. It gives us a way
ind very old M. leprae DNA; it has a infecting an earlier species?” he asks. to anticipate future changes.” D
very thick additional cell wall layer that “The virus has been around for
seems to also protect its DNA.” hundreds of millions of years. We’ve Gemma Tarlach is senior editor at Discover.
68 DISCOVERMAGAZINE.COM
Out
here
“Don’t worry,” says Manchester, a — roughly the size and weight of a graduate studies at Cornell University,
Stanford University professor of standard sugar packet. following up on earlier work by
70 DISCOVERMAGAZINE.COM
he next big challenge — so named because Manchester
inanced the mission through a
is to get Sprites crowdfunded KickStarter campaign.
But the Sprites’ release had to
flying freely in space, wait more than two weeks because
where they can talk of a NASA request to keep the area
clear for a Russian Soyuz launch.
with each other and After that delay, KickSat-1 failed to
discharge its Sprites because of an
with Earth-based electrical problem likely caused by
command posts. exposure to radiation. As a result, the
whole spacecraft burned up during
atmospheric re-entry without having
released the Sprites.
A LOOMING LAUNCH
Hopes now rest on KickSat-2, another
shoebox-sized craft set to launch in
November from NASA’s Wallops
Flight Facility in Virginia. It took
Manchester more than four years
to try again because of dificulties
securing a Federal Communications
Commission (FCC) license, required to
communicate with ground facilities in
the United States. The FCC was also
concerned about orbital debris and the
ability to detect the minute spacecraft,
which can be dificult to track.
“That has posed a problem for
the entire small-satellite research
Zac Manchester holds the original 2014
community,” says Manchester. He
KickSat, full of Sprites. A new version, managed to skirt this issue by handing
KickSat-2, should launch in November. over responsibility for the mission to
NASA Ames Research Center, for
The shoebox-sized KickSat releases numerous
tiny Sprite satellites in this illustration. The
Manchester’s Sprites went on to fly whom he had previously worked.
cheap, abundant and self-contained Sprites on the hulls of the Latvian-German Once KickSat-2 enters its prescribed
could represent the next step in space tech. Venta 1 satellite and the Italian- orbit, Manchester and his team can issue
German Max Valier satellite, which commands from the ground to release
his adviser Mason Peck and fellow launched into low-Earth orbit in June its roughly 100 Sprites from a spinning
graduate student Justin Atchison. By 2017. The Sprites are still attached container, so that they’ll naturally spread
early 2011, he had already produced to their host satellites today, having out in space. “They’ll fly for a few days
some preliminary versions of the Sprite. demonstrated they can harness solar to a couple of weeks, at most, before
When a last-minute spot opened up on energy and successfully communicate they burn up, which makes for a short-
a space shuttle flight that year, he and with ground stations. lived experiment,” he says.
Peck managed to get their experiment The next big challenge is to get The mission’s primary goal is to
to the ISS. Astronauts mounted three Sprites flying freely in space, where establish communications among the
of the devices to the outside of the they can talk with each other and with minute satellites through an approach
CORNELL UNIVERSITY
space station during a space walk. Earth-based command posts. The irst called mesh networking, which involves
Three years later, all were still working, attempt came in April 2014, with the passing messages to nearby satellites so
proving the electronics could withstand launch of around 120 Sprites aboard a that information eventually propagates
the harsh space environment. shoebox-sized satellite called KickSat-1 to all the Sprites. Although it’s a
Although KickSat-2 is meant to be radio range. These observations cannot probe in 1990 as it started leaving the
a technology demonstration project, be done from the ground, Burkhart solar system.
Manchester is eager to start doing explains, because Earth’s ionosphere “I’m hopeful that in a few
actual science, too. The swarms of interferes with those frequencies. Such decades, we’ll get a picture like
low-cost, disposable flying objects radio waves also have huge wavelengths, this,” Manchester says, “not looking
could perform tasks that no single in the tens and hundreds of meters, so back at Earth, but looking toward a
spacecraft can do on its own. observations could require a telescope new Earth.” D
He’s already teamed up with Harvard a few kilometers across, Manchester
University astronomer Blakesley estimates. If researchers can overcome Steve Nadis, a contributing editor to Discover
Burkhart, devising a plan to deploy a a few minor bugs, an array made up and Astronomy, plays handball and volleyball in
separate swarm of small satellites to of Sprites could perform the job of a Cambridge, Massachusetts, where he also lives.
72 DISCOVERMAGAZINE.COM
TOTAL SOLAR ECLIPSE: Ancient Paths to the Present
Journey from Peru’s Sacred Valley of the Incas to the ancient mountaintop city of
Machu Picchu — and enjoy an unforgettable view of the July 2 total solar eclipse!
Join us for a once-in-a-lifetime South American odyssey with a dramatic focal point: a total solar eclipse.
Our itinerary weaves together two dimensions of this fascinating continent: spectacular landscapes with
unmatched views in remote areas of Chile and Peru; and a legacy of engineering, architecture, art, and
philosophy that includes a tradition of astronomical observation dating back two millennia.
P32424
Discover
SCIENCE FOR THE CURIOUS
DiscoverMagazine.com/trips-tours/2019-chile-northbound M AG A Z I N E
20 Things You Didn’t Know About …
1 Chances are, you can thank a laser for helping bounce back, and determines how far away an object
you get through the day. The technology lets us do is, like bats using echolocation to ind dinner. 12 It’s
everything from scan groceries at the checkout to not batty to think lidar will be part of driverless
remove regretted tattoos. 2 The word laser, coined car technology. Engineers are experimenting with
in 1957, is an acronym for “light ampliication it to monitor the vehicle’s surroundings and judge
by stimulated emission of radiation.” Since that when to brake. 13 Archaeologists use aircraft-based
-er ending makes a laser seem like a doer of . . . lidar to map a different kind of surrounding: sites
something, it soon spawned the verb “to lase.” hidden beneath dense forest canopies. 14 In 2016,
3 Unlike the sun or a flashlight, which shines in a researchers using lidar described vast ancient cities
broad range of colors combined to produce white in Cambodia’s rainforests. The extensive urban
light, lasers lase by producing a concentrated beam network reached its zenith in the 12th century and
of a single wavelength, or color. 4 In 2016, scientists may have been the largest empire on Earth at the
created a new type of microlaser, smaller than a time. 15 Astronomers, meanwhile, use lasers to
red blood cell, which could lead to innovations in measure real-time turbulence in Earth’s atmosphere.
COUNTERCLOCKWISE FROM TOP RIGHT: ZEPHYRMEDIA/SHUTTERSTOCK; LAWRENCE LIVERMORE NATIONAL LABORATORY; GIPHOTOSTOCK/SCIENCE SOURCE; MARK WALTERS VIA SKETCHFAB/CC 4.0; NASA
medical imaging. 5 That same year, the world’s most With this information, they can adjust telescope
powerful laser, China’s Superintense Ultrafast mirrors to account for atmospheric blurring and
Laser Facility (SULF), ired a single pulse make sharper images, a technique called adaptive
equivalent to 5.3 petawatts — 5.3 quadrillion optics. 16 If an aircraft flew into one of these laser
watts! 6 SULF isn’t the world’s largest beams, the crew could be disoriented. Facilities that
laser, however. That would be California’s use adaptive optics employ spotters whose sole job is
National Ignition Facility (NIF), about the to watch the night skies for planes straying too close,
size of three football ields. The megalaser ready to flip an emergency shut-off switch. 17 The
can deliver the same amount of energy precision afforded by adaptive optics has resulted in
released by a couple pounds of TNT to a target images of exoplanets in other star systems and even
the size of a pea. 7 Ultimately, researchers want to two supermassive black holes colliding hundreds
use NIF’s energy to trigger a nuclear fusion reaction, of millions of light-years away. 18 The laser-based
squishing the nuclei of hydrogen atoms together to Strategic Defense Initiative, proposed in 1983 and
make helium and producing energy the same way nicknamed “Star Wars,” soon fell into a metaphori-
stars do. 8 Speaking of stars, give a big gold one cal black hole, but laser weapons aren’t all iction.
to the true inventor of lasers, whomever that may The Department of Defense is developing systems
be. Three scientists shared the 1964 Nobel Prize for that can take down drones and even small planes
work leading to the irst lasers, but grad student and boats. 19 Star Wars the movie featured a giant
Gordon Gould designed one before the laureates planet-destroying laser, but when scientists shoot
Counterclockwise — one of whom was also his adviser. 9 Gould sued lasers at our moon, it’s for peaceful purposes. The
from top right:
Laser tattoo
and inally received patent rights in 1977. A ifth beams ire at mirror arrays placed on the lunar land-
removal; workers scientist actually built the irst working laser, in 1960. scape by astronauts from several Apollo missions.
at the world’s 10 Since then, lasers have landed a lot of Nobels, 20 Aiming lasers at these moon mirrors measures
largest laser facility,
in California; including in 2017. That award went to team leaders the precise distance to our satellite sidekick, and has
a beam reflected at the Laser Interferometer Gravitational-wave revealed that the moon is slowly moving away from
off a mirror; a map
of hidden buildings Observatory (LIGO), who were irst to measure us. Hey, Moon, was it something we said? D
found through long-predicted ripples in space-time. 11 Lasers play
lidar; mirrors
placed on the moon a starring role in another measuring method: light Erika K. Carlson grew up in Livermore, the home of
decades ago to detection and ranging. A lidar system shoots out a NIF. She writes this in fond memory of physics professor
measure distance
using Earth-based
laser pulse, calculates how long it takes the pulse to Alfred Kwok, who had an infectious enthusiasm for lasers.
lasers.
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