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The Key Question
Seed’s Tear-outable tool for living in the 21st century in Climate Science:

Cribsheet #2 How much will the earth’s

CLImAtE chAnge
temperature rise as humans
double the amount of carbon
dioxide in the atmosphere
through use of fossil fuels?

The Greenhouse effect 7 clouds


1 SOLar radiation As the earth warms, more water evaporates,
Radiation from the sun enters the atmosphere. creating more clouds. Since clouds are white and
Some of it is reflected back into space, reflective, they bounce a lot of sunlight into
but a good portion is absorbed by the space, which would have warmed the
atmosphere and the earth’s surface. earth. This is negative feedback. At the
same time, clouds are made up of
2 Infrared radiation concentrated greenhouse gas, and
The surface, in turn, heats up can also provide positive feedback.
and emits infrared radiation. Clouds will play an important role
in climate change, but no one
3 Greenhouse gas is sure yet whether they will
Greenhouse gas molecules ultimately end up warming
absorb radiaton from the or cooling the earth.
sun and earth, heat up,
and emit infrared radiation. 6 Sea ice
Some infrared radiation is
Ice is reflective. When sun-
directed back toward the
light is reflected into space,
earth, contributing to the
it doesn’t contribute to the
warming of the surface.
greenhouse effect. So the ice
caps help to limit warming.
Feedback As things heat up, the ice

4 What are melts, revealing the darker


FEEDBACK LOOPS? ocean beneath, which
Feedback loops are self-perpetuating cycles absorbs more radiation and
that enhance or dampen the greenhouse effect. warms, melting more sea ice.
The ones illustrated here are just a few examples of This cycle is a positve
the many feedback loops at work on the climate. Without feedback loop.
feedback, humans could double the amount of CO2 in the
atmosphere (which we’re in the process of doing) and the earth’s 5 Water vapor
average temperature would rise by about 1.2ºC. That’s enough to cause Water vapor is a greenhouse gas, and helps to
noticeable changes in climate, but probably not catastrophic ones. With warm the earth. At higher temperatures, more
feedback the problem is more complicated. It boils down to climate water evaporates, putting more water vapor into
sensitivity: Will negative and positive feedbacks cancel each other out, the air, which heats the earth even more. This
or will they cause a catastrophic rise in temperature? is another important positive feedback loop.

Global Temperature and co2 CLIMATE treaty map


.8 380
Each point on the temperature line represents
.6 an average taken over five years. The global
temperature average taken for 1935-1940, for 360
instance, is just under 0.1ºC above the baseline.
.4
340
˚C
.2 ppm
Global temperature average
0 320
(1950–1980)
-.2
300
-.4

-.6 280
Year 1900 1920 1940 1960 1980 2000

Global Temperature Change (5-year mean) Kyoto Treaty Members Members of both
Atmospheric CO2 Concentrations Asia-Pacific Partnership for Clean No action
Development and Climate Members
ILLUSTRATION: SILO

The issue: What is the best way to deal with these changes? soundbite
The earth’s average temperature is likely to rise by 2º to 6º C as a result of a projected doubling of the amount of CO2 in the atmosphere from preindustrial More carbon dioxide was added
levels, to 560 parts per million by mid-century. The effects could be severe. Sea levels could rise by as much as 6 meters as the icecaps melt; deserts may become to the atmosphere in the past 200
larger, storms more severe, heat waves more common, and snow could turn to rain, reducing our ability to collect water for drinking and irrigation. The Kyoto years than between the last Ice
Protocol, effective this year, is an agreement by member nations to limit their carbon emissions. The alternative supported by the U.S. and Australia, the Age and the Industrial Revolution.
Asia-Pacific Partnership, seeks to incentivize the creation and deployment of green technologies, but doesn't limit carbon emissions and sets no target dates.
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The Key Question
Seed’s Tear-outable tool for living in the 21st century in nuclear engineering:
Cribsheet #5
How can reactors be designed
to work at maximum efficiency,
to be safe and self-regulating,
and to minimize nuclear waste?

Nuclear Fission 2 steam generation


Nuclear fission occurs when a neutron strikes the nucleus of This superheated water is pumped through a pipe that runs,
an atom and splits it apart. Most of the nucleus of the like a heating element, through a second chamber called
original atom goes to form new, smaller atoms. In the steam generator. The steam generator is partially filled
steam generator
addition, several neutrons may split off from with clean water, which is boiled by the
the original atom during fission. But the heated pipe running from the reactor
mass of all these neutrons and fission generator vessel. The steam generator is also
turbine
Graph Data: IAEA

products does not add up to the mass kept at high pressure (though it’s
of the original atom. That’s because 2 lower than that of the reactor vessel).
when the atom splits, some of its mass 3

is converted directly into energy.


1

Nuclear reactors and warheads can 3 electricity


Map Data: The Nuclear Energy Institute / The International Atomic Energy Agency (IAEA)

employ the uranium isotope U-235. generation


4
When the U-235 atom splits, it frees Superheated steam forces its way out of
two or three neutrons, which then the steam generator. It cranks a
fly off and split other U-235 turbine, which produces
atoms in close proximity, pump
electricity. As the water in the
starting a chain reaction. steam generator boils, it also
control rods condenser siphons heat away from the water
in the pipe flowing to the reactor
cooling tower
vessel. This helps to cool the reactor. In
BASIC PRINCIPLE
Heat flows from one part of the power another type of nuclear plant, called a
plant to the next. As one part warms up, boiling water reactor, the steam powering the
heat flows out of the previous one,
allowing it to cool, so safe operating
turbine comes directly from the reactor vessel.
temperatures are maintained.
In warheads, the chain reaction multiplies exponentially,
giving off a huge amount of energy at once in a nuclear
explosion. In nuclear reactors, a chain reaction must be
4 steam condensation
controlled to create a safe, harvestable source of energy. After the steam cranks the turbine, it is condensed back
into a liquid as it runs over a pipe filled with cold water
flowing from the cooling tower. It is then recycled into the
Consultants: Per Peterson and Daniel Kammen, Professors, Nuclear Engeneering at UC Berkeley

steam generator. The water from the cooling tower heats


1 the nuclear reaction reactor
up during this process and some of it is released as steam.
In the reactor vessel, cylindrical uranium pellets are stacked It is then replaced from a nearby body of water.
into long fuel rods. It is within bundles of these rods that reactor vessel
the chain reaction occurs. Together they are called the
reactor. To keep the reaction under control:
• Low concentrations of U-235 are used in the reactor, so Much of the energy released by the chain reaction is self regulation
not every neutron will strike a nucleus. manifested as heat. The fuel rods are placed inside a Modern reactors are designed to be safe and self-regulating.
• Retractable control rods, made of a material that absorbs pressurized chamber full of water. Because this reactor In the same way that an airplane is designed to level out
neutrons, can be lowered into the reactor to siphon off vessel is kept at high pressure, the water will reach naturally after being jostled, reactors are engineered to
neutrons that would otherwise multiply the chain reaction. temperatures much greater than 100º C. maintain safe levels of chain reaction under any circumstances.

world energy consumption by source power needs supplied by nuclear plants


450
6.34%
Nuclear This graph shows the steady increase in global 2.22%
400
Hydro energy consumption since 1970. Combustible 6.75%
350 Biomass liquid and solid fuels, like gasoline and coal,
Gases remain our dominant sources of energy.
23.04%
300 Solids
Liquids
250

200 26.08%
23.9 MEGATONNES OF OIL)
Writer: Joshua Braun

150 Percent
by country
(EQUIVALENT TO
1018 JOULES

100 1-20
35.09% 20-40
50
40-60
Year 60-80
0
1970 1975 1980 1985 1990 1995 2000 2004
Illustrator: Cybu Richli - www.cybu.ch

The issue: Why are some people concerned about nuclear power? soundbite
Uranium used in reactors has been enriched to create a higher concentration of U-235 than occurs in nature. Countries with the technology to enrich uranium Nuclear reactors are an important
for power can expand their capabilities to create highly enriched uranium for weapons. Some reactors use plutonium, another weapons material, or create it as carbon-free source of power. We
a waste product. Due to proliferation concerns, the International Atomic Energy Agency keeps close tabs on how and where nuclear materials are used. Even are likely to see a surge in their
regular nuclear waste—the radioactive and heavy metals that are the products of fission—is dangerous, making it a concern everywhere nuclear power is used. construction in the next few years.
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1

4 1

ILLUSTRATION NOTE
The sample biome includes a river, an ocean, a volcano,
and a glacier. Geometric shapes such as spheres, cones, and
icosahedrons indicate different species, and deceased
1
organisms are darkened.
2

4
5 1
H
He H
C
O
Si He
Fe

C
He
C
Ne
He

H
H

4 C
2
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light
CriBsheet #13 What is light and where
does it come from?
How can light be used
to investigate the world
around us?

Magnetic field
Light is energy that travels as a wave through space. Most of the light we encounter in everyday life is produced by nuclear fusion in stars or the
energetic excitation of electrons in atoms. A wave of light actually has two components: an electric field, and a magnetic field. Consequently
light is also called electromagnetic radiation. Electricity and magnetism are interdependent: One can produce the other. Similar to how passing
a magnet over a coil of copper wire briefly generates electricity, or how a constant electric current can magnetize iron, a light wave‘s oscillating
electric and magnetic fields reinforce each other and propagate through empty space at nearly 300,000 kilometers per second. This value is
Electric field
known as the speed of light, and appears to be the universe‘s ultimate speed limit—nothing travels through space faster.

Wavelength
1
2

Lower energy / Longer wavelength Higher energy / Shorter wavelength

All forms of light—radio waves, microwaves, infrared, visible, ultraviolet, x-rays,


and gamma rays— are identical except for their wavelength. Light‘s wavelength 3
determines its energy; the shorter wavelengths have higher energy. Light from most
natural sources contains multiple wavelengths. White light contains all visible wave-
lengths. Refracting it through a prism separates them into a continuous spectrum .
LIGHT aND MaTTER
Each kind of atom in a substance
absorbs characteristic wavelengths
Interference
pattern
Ejected of light; all other wavelengths
electron
are reflected back or transmitted
Low intensity, through. Different mixtures of
high energy
light
atoms reflect different wave-
Metal plate
lengths, creating the diversity of
colors we perceive in the world
around us.

Because light can originate from the


excitation of electrons in atoms, and
each element of the periodic table
has a unique atomic configuration
of electrons, the elemental
composition of any substance can
be discovered through observing
the spectrum it produces when its
High intensity,
electrons are energized. For
low energy instance, burning a sample of
light hydrogen gas creates light. Running
Light source
that light through a prism produces
a distinct emission spectrum 2 .
Conversely, light passing through
WaVE-PaRTICLE DUaLITY But when light of different wavelengths shines on a metal surface, a cool cloud of hydrogen gas and
Light usually behaves like a continuous wave, but it can also act as if it is the existence of individual photons becomes clear. If an electron in the then a prism produces a unique
composed of discrete particles of energy called photons. metal absorbs more than a threshold amount of energy, it breaks free absorption spectrum 3 . By
and zips away. Since shorter wavelengths contain more energy, a very studying spectra like these, we can
Light‘s wave-like nature can be revealed when light diffracts through two slits bright but long-wavelength light will have no effect on the metal, measure the chemical composition
and shines onto another surface. Light passing through the slits acts as two while a very dim but short-wavelength light will release electrons. of practically anything on Earth,
waves that disrupt and interfere with each other. Where the waves‘ peaks The energy of ejected electrons increases not with greater amounts of as well as the atmospheres of other
and troughs overlap, they combine to produce a characteristic interference light, but with more energetic wavelengths. This means each electron planets, the Sun, and even the
pattern of light and dark bands. ejection depends on the energy of an individual photon. distant stars.

The Electromagnetic Spectrum Redshift/ Blueshift


Radio waves Microwaves Infrared Ultraviolet X-rays Gamma rays
Visible
Reference: Universe, Robert Dinwiddie et al., DK Publishing Inc., 2005
Writer: Lee Billings

Wavelength

10km 1km 100m 10m 1m 10cm 1cm 1mm 100µm 10µm 1µm 100nm 10nm 1nm 100pm 10pm 1pm 100fm 10fm 1fm

In theory, light‘s shortest possible wavelength is trillions of times smaller than the diameter of a proton, and light may have Like the sound of a passing siren that rises and then falls in pitch as it approaches and recedes, light waves from a source
no upper limit on its wavelength. In practice, we can detect light with wavelengths ranging from thousands of kilometers moving in relation to an observer exhibit similar shifts. As a light source approaches an observer its light is compressed
down to less than the size of an atomic nucleus. The electromagnetic spectrum is the continuum of wavelengths between to shorter wavelengths — this is a blueshift. As a light source recedes, its light is stretched— this is a redshift. The
these extremes. Our eyes can only see light between 400 and 700 nanometers in wavelength— a miniscule portion of the redshifts and blueshifts for most slow-moving, earthbound objects are too small to be easily noticed. But on astronomical
Illustrator: Cybu Richli — www.cybu.ch

entire electromagnetic spectrum. scales, we can measure the motions of planets, stars, and galaxies using this effect.

THE ISSUE: Harnessing Light SOUNDBITE


Many of the past century‘s major scientific and technological advances came from studying the physics of light, and this trend is certain to extend Light is electromagnetic radiation
well into the future. Our understanding of light has allowed us to study the universe on the smallest and largest of scales. It has given us applications that moves through space at 300,000
like radio, television, radar, medical x-rays, microwave ovens, and wireless computer networking, to name but a few. Now, emerging technologies kilometers per second and acts
like quantum computing, efficient solar power, and light-based spacecraft propulsion are poised to further transform science and our society. as both a wave and a particle.
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exoplanets
CriBsheet #14 Do planets form around
other stars? How can
we detect and study
them? Are there other
planets like Earth?
Illustrator: Southsouthwest — www.southsouthwest.com.au Writer: Lee Billings Consultant: Greg Laughlin, Professor of Astronomy and Astrophysics, University of California, Santa Cruz. Habitable Zone: Derived from an image created by Gabriel Rodriguez Alberich, viewable at http://en.wikipedia.org/wiki/Image:Habitable_zone-en.svg.

In 1543, Polish astronomer Nicolaus Copernicus published On the But perhaps the Copernican principle is wrong. Compared to other terrestrial
Revolutions of the Heavenly Spheres, showing that the Earth, far from planets in our solar system, the Earth seems special. It alone has oceans of microlensing
being the privileged center of the universe, is just another planet orbiting water, plate tectonics, and a large moon. As far as we know, it alone hosts Gravitational microlensing is a
the Sun. Since then, the discovery that our Sun is a typical star among the life. Since the first detections of planets orbiting other stars in the mid-1990s, newer technique to find exoplanets
billions in the Milky Way, which in turn is but one of the billions of we've discovered hundreds of exoplanets, but none resembles the Earth. that uses effects predicted by
galaxies we observe in all directions, has strengthened the notion that Could we and our world be unique? In the near future, this question will be Einstein's theory of general
our place in the universe is merely ordinary. This assumption of our answered by one of three detection methods: stellar radial velocity, relativity. Just as a magnifying glass
cosmic mediocrity is called the Copernican principle. planetary transits, and gravitational microlensing. can enlarge an image, a star's
gravitational field can bend
space and magnify light in a
process called microlensing. When
radial velocity a distant bright star aligns with a
A planet orbiting a star causes the dimmer lensing star that is closer to
star to “wobble” back and forth. Earth, the distant star’s light
Absorption Spectrum The radial velocity method detects brightens A . If planets orbiting the
this wobble by examining the color lensing star are perfectly aligned,
1 2
of starlight: As the star moves they too will magnify the distant
toward an observer, its light star's light, allowing astronomers to
becomes bluer ; as it moves away, estimate their mass and orbital
its light becomes redder 2 . By distance B . Microlensing works
analyzing these color shifts over best for planets orbiting their stars
time, the presence of planets, along at Earth-Sun distances or greater.
This Habitable Zone image is used and released under the terms of the GFDL (http://en.wikipedia.org/wiki/GNU_Free_Documentation_License). Lowest Exoplanet Masses: Jean Schneider's Extrasolar Planets Encyclopedia, http://exoplanet.eu/

with their masses and orbits, can Since each chance alignment only
be inferred. So far most exoplanets occurs once, microlensing can't be
have been found using radial used to closely study individual
velocity measurements. planetary systems, but rather
provides a statistical sample of
exoplanet populations.
Time

Brightness
Lightcurve

3
Time A B

Lightcurve
Brightness

Background
Star

planetary transits Lensed


Image
The transit method finds planets by looking at the total amount of light from a star over time.
If a planet passes in front of its star as viewed from Earth, the star's light slightly dims during Planet
the planet's transit 3 . Measuring how much the starlight diminishes reveals the planet’s diameter.
Many exoplanets can be studied with both radial velocity and transits. The combined data can Lensing
Star
allow astronomers to estimate not only a planet's size, mass, and orbit, but also its density,
temperature, and atmospheric composition. Telescope
Both radial velocity and transit methods overwhelmingly favor detecting Jupiter-mass planets that
orbit their stars at a fraction of the distance between Mercury and our Sun.
1 2 3 4

refining the search haBitaBle zones


1
HD 16141 b
Habitable Zone
2
Planetary Mass (1= Jupiter)

Jupiter
51 Peg b Saturn
Mass of star relative

55 Cnc e Uranus
0.1
HD 75289 b Neptune
Gl 581 c
to Sun

HD 49674 b 1
Earth
0.01 Mars
Earth
OGLE-05-390L b Venus
Mercury
0.5
0 0.1 1 10 40 Radius of orbit relative
0.001
Not to scale to Earth’s
1995 2000 2005 2010 2015
The vast majority of detected exoplanets have been gas giants like Jupiter and Saturn that closely orbit their stars. But as Life as we know it requires liquid water. If a planet orbits its star too closely, any water evaporates into steam; too far away,
observational data accumulate and new search projects come online, scientists have begun discerning the telltale signatures and water freezes into ice. The sweet spot between these extremes is the "habitable zone" (HZ). A star's mass determines
of smaller, terrestrial exoplanets several times the Earth's mass. This graph plots the diminishing size of the smallest known its HZ; the more massive a star is, the brighter it shines, pushing the HZ further out. Astronomers now believe the first
exoplanets: In little more than a decade, the record has dropped over an order of magnitude. Extrapolating from this trend, Earth-mass exoplanet within an HZ will be found around a red dwarf, the smallest, dimmest, most numerous type of star in
astronomers should begin detecting Earth-mass exoplanets around 2011 or 2012, though this may happen much sooner. our galaxy: Planets in a red dwarf's HZ orbit so closely that they should be detectable with radial velocity or transit searches.

THE ISSUE: discovering haBitaBle worlds SOUNDBITE


Astronomers using radial velocity, transit, or microlensing searches are racing to discover the first Earthlike exoplanet. New telescopes, improved We have found nearly 300 exoplanets
data analysis, and the realization that red dwarf stars are excellent planet-hunting targets imply that the first Earth-mass exoplanet in a “habitable using radial velocity, transits, and
zone” will be found in the next few years. If that planet transits its star, we may be able to analyze its atmosphere. If its atmosphere contains water, microlensing, and are likely to find an
oxygen, carbon dioxide, and methane, we’ll have found more than a habitable world—we’ll have discovered the first credible signature of alien life. Earth-mass exoplanet in the near future.
the Key Questions of
Seed’s Tear-outable tool for living in the 21st century Quantum computing:
CriBsheet #15 What is a quantum

QUANTUM COMPUTING
computer, and how does
it differ from modern
computers? How can we
use quantum computing?
Intel cofounder Gordon Moore famously observed nearly half a century Miniaturization may ultimately lead to quantum computers, which use
quantum computing 101
ago that the number of transistors economically crammed into a single quantum effects to perform calculations. Quantum computers could, in
computer chip was doubling every two years. This trend toward miniatur- principle, solve certain problems exponentially faster than the best known 0
ization is seen throughout the history of modern computing. Today ele- “classical” methods with far-reaching consequences for cryptography and
ments of microchips are only tens of nanometers in size, and if miniaturiza- the simulation of quantum physics. Simple quantum computers have al-
tion continues, microchip components will eventually reach atomic scales, ready been built, but most experts believe robust and powerful systems
where their properties will be dictated by quantum mechanics. remain many years away.

Hundreds or thousands of qubits would be needed


to factor very large numbers. For convenience, here we’ve
The encryption vital for modern secure communications as- illustrated only four.
sumes that factoring large numbers in a reasonable amount
of time is beyond the capabilities of today’s commercial
FINDING aN aNSWER
computers. In 1994 computer scientist Peter Shor devised an The ability of quantum objects to simultaneously hold
algorithm allowing a quantum computer to quickly factor multiple, seemingly conflicting values is at the heart of
large numbers. Thus, a powerful quantum computer could
break the world’s dominant encryption schemes, resulting quantum computing. This state is called a quantum
in the need for new security methods. For perspective, to- superposition (at right). Superpositions occur
day’s quantum computers are scarcely powerful enough to
factor a number like 15. At right, a schematic illustration
all the time at the quantum level. In fact, any
outlining how Shor’s algorithm works: Place the isolated quantum object like an atom or a 1
qubits in a superposition photon is in a superposition. But as soon
over all of their
as the object interacts with some- Both classical and quantum computers
possible configurations
interference patterns in preparation thing else, such as another atom perform calculations by manipulating
The latent possibilities within a for initiating a or photon, the superposition is information. Classical computers
quantum interference represent information as binary digits,
superposition can actually interfere pattern. liable to collapse. The collapse
with each other, constructively of a superposition is called or bits, which can have values of
reinforcing or destructively decoherence. Decoher- either 0 or 1. Quantum computers
canceling each other to ence is essentially an act represent information as quantum
form the final definite of measurement, where bits, or qubits. Many different
state. The programmer all possible states in the physical objects can be used as qubits,
of a quantum computer superposition collapse such as atoms, photons, or electrons.
must choreograph the into the one ultimately Paradoxically, a qubit can represent
calculation in such a way observed. If the quantum 0 and 1, as well as other possible
Choreograph
that computational paths quantum computer’s qubits suffer too values, at the same time, in what is
leading to a “wrong” answer
interference to allow
much decoherence before the called a quantum superposition.
paths to correct
will destructively interfere with calculation is completed, the in- This allows a qubit to simultaneously
Illustrator: Thomas Porostocky — www.porostocky.com Writer: Lee Billings Consultant: Scott Aaronson, Assistant Professor of Electrical Engineering and Computer Science,

answers to reinforce
each other, canceling each each other.
formation will be irretrievably use many more informational
other out and leaving lost and the probability of states for computation and is
only the “right” producing a correct responsible for quantum computing’s
answers to be answer becomes advantages over classical computing.
observed. essentially zero. In the illustration above, an atomic
spin represents a qubit. An “up”
spin corresponds to 0; a “down”spin
equates to 1. A quantum superposition
encompasses 0, 1 and all possible
values in between.
Perform a measurement, collapsing the qubits’ superposition. By repeating these steps and combining the results, we can reliably obtain the factors of a very large number.

What ProBlems Can a Quantum Computer Solve?

NP
Computational time

Factoring
a very
large
Easily solved BQP number
by quantum
computers
Testing if 2n
a number is
prime n2
Easily solved P
by classical n
computers
0 1 2 3 4 5 6 7 8 9
Problem size (bits)

Computer scientists classify a problem’s difficulty by the number of computational steps an algorithm requires to solve it. such as 2n. Every P problem is also an NP problem, but computer scientists believe that not all NP problems are P problems.
Problems that a classical computer can quickly solve are called P (polynomial time) problems. In P problems, as the problem BQP (bounded-error, quantum polynomial time) problems are the class of problems that quantum computers can effi-
size n increases, the number of steps to solve it grows polynomially, for instance by n2. Determining whether a number is ciently solve. Factoring the product of two large prime numbers is an example of a problem that is both an NP and a BQP
prime is an example of a P problem. NP (nondeterministic polynomial time) problems consist of all problems for which the problem. Though no one knows for certain, it appears that BQP does not include most NP problems. This means that for
Massachusetts Institute of Technology

answers are easy to check, even though finding those answers may take an exponential number of computational steps, most NP problems, quantum computers may offer no significant advantages over classical computers.

THE ISSUE: can we Build a sophisticated quantum computer?


A company called D-Wave Systems has exhibited what it controversially calls the world’s first commercial quantum computer, but most experts Quantum computers could theoreti-
treat these claims with considerable skepticism. Some of the best minds in physics today are struggling to build simple quantum computers, and cally revolutionize our ability to solve
computer scientists are still seeking their ideal applications. It seems that even if practical, powerful quantum computing existed today, we prob- certain kinds of computational prob-
ably wouldn’t know how to best use it. Ironically, if building sophisticated quantum computers turns out to be impossible in principle, this may lems, but first we must discover how
be the biggest breakthrough of all, as it would imply that our fundamental understanding of the quantum world is incorrect. best to build and use them.
the Key Question of
Seed’s Tear-outable tool for living in the 21st century SYNTHETIC BIOLOGY:
CriBsheet #16 Can we learn to

SynThetic biology
program DNA and living
organisms as well as or
better than we currently
program computers?
Life, even at its most minuscule, can elicit incredible change on a planetary After biologists learned to decode genes, they soon learned to redirect
Biotechnology Basics
scale. Consider the oxygen you’re breathing. Its presence in Earth’s the power of life by manipulating DNA. Scientists have developed
atmosphere is a biochemical accident, a waste product of photosynthesizing numerous techniques to read and modify DNA; those techniques form the Genetic information is encoded by
organisms. Together, organisms cycle essential nutrients like carbon and basis of genetic engineering, but many are inefficient. Synthetic biology is four nucleotides, or bases, that are
nitrogen around the planet; even on its own, an organism can fabricate an effort to develop better tools and technologies for engineering biological part of DNA’s molecular structure.
useful materials, and each—thanks to its cellular machinery—is capable of systems, with the overarching goal of creating new biological functions To obtain this information, scientists
processing the information found in its genetic code. and enhancing those that already exist. read these bases in a process
called DNA sequencing 1. Once a
constructing dna 1 Sequence data ...GATTACAGATTA... sequence is known, it can be isolated
DNA sequencing allows researchers by restriction enzymes, proteins
Raw materials (bases)
to read genetic material, converting that sever DNA strands at specific
information encoded within DNA sequences 2. A genetic engineer
molecules into sequence data. DNA can insert such snippets of DNA into
synthesis allows biologists to write other DNA strands 3. Snippets of
genetic material from scratch, using DNA can also be amplified (copied
Synthetic
sequence data to assemble DNA DNA many times) by the polymerase chain
molecules 1. Researchers are working reaction (PCR), making them easier
to improve the power of DNA synthesis to work with 4. Polymerases are
technology, but the bigger challenge is to molecules that travel along a strand
invent new languages and grammars of DNA to perform various tasks.
that enable the writing of many new 2 Researchers also use PCR to selectively
genetic “programs,” each coding for mutate small portions of genes.
RNA polymerase
useful behaviors, such as the production These methods enable researchers to
Extracellular
of fuels, foods, or medicines. signaling molecule manually edit DNA, which can then
be incorporated into living organisms
via several techniques collectively
genetic programs called DNA transformation.
To make programming DNA easier,
synthetic biologists are creating banks of
standardized DNA sequences, or parts,
that each perform a specific function. For
1
Illustrator: Thomas Porostocky — www.porostocky.com Writers: Lee Billings and Drew Endy Consultant: Drew Endy, Assistant Professor of Biological Engineering, Massachusetts Institute of Technology

example, the BioBricks Foundation, an


open-source initiative from MIT, Harvard, BioBrick receiver
and the University of California, San ...GATTACAG...
Francisco, is doing this by developing
BioBrick parts, functional sequences 3 4
of DNA with uniform prefix and suffix
2
sequences. This structural standard
allows BioBrick sequences to link together
and act as interchangeable parts.
+ =
3

An efficient genetic machine also requires a communications standard. molecules flow down a DNA strand. The strength of the PoPS current
For example, one type of BioBrick part acts as a receiver for extracellular controls how strongly a “plugged in” BioBrick part will respond.n A BioBrick
nd.
signals (conveyed via a modified sugar molecule, 3OC6HSL ) and produces sequence recently developed by college students produces bubbles bbles of
an intracellular signal that other BioBrick parts can respond to. BioBrick protein, called vesicles , inside a cell. Plugging the bubble BioBrick
B
Brick part
parts communicate using RNA polymerase ; the more sugar fed to into the PoPS current from a BioBrick receiver creates a new e genetic
ew
a receiver, the more polymerase it will emit each second 2. There is a program 3 that can alter the number of vesicles created within n a cell; 4
direct analogy to electricity: Just as an ampere is the unit that describes more sugar means more PoPS, which in turn produces more vesiclesv and a
how many electrons flow past any given point on a wire each second, more buoyant cell 4. This is but one example of a genetic programg
gram made
polymerase per second, or PoPS, describes the rate at which polymerase possible by standardized synthetic biological parts.

Cost of Commercial Gene Synthesis Cumulative size of BioBrick


i
ioBrick dataBase
20 2000
($ per base pair) # of Standard Parts
18 1800
16 1600 2000
14 1400
12 1200
$4-8
10 1000
$10-16
8 $2 $1-1.50 800 200 400
$2-4 1100
6 600 12 60
$1-2 $0.75-1.25 100
4 400
2 200
0 0
2002 2003 2004 2005 2006 2007 2008 2002 2003 2004 2005 2006 2007 2008

As costs plummet, the largest barrier against more individuals taking advantage of DNA synthesis is the inherent complex- Since BioBrick parts are open source and in the public
ublic domain, anyone can use or modify existing BioBrick sequences free
ity of biological systems. Just as software developers used to painstakingly program in binary machine language but now of charge and also submit new ones to online databases.
atabases. This openness has driven significant growth in the number of
rely on software compilers and sophisticated programming languages, synthetic biologists today await powerful comput- BioBrick parts, as well as the creation of academic
i contests like the annual international Genetically Engineered Machine
ic
er-aided abstraction tools that simplify biology’s complexity into easier formats. Many need to be developed. (iGEM) competition. As more BioBrick sequences accumulate, the collective power of synthetic biology increases.

THE ISSUE: the democratization of Biotechnology


If synthetic biologists continue crafting tools that simplify genetic engineering, it will become much easier for anyone, regardlesss of training, Powerful new tools and technologies
to construct novel biological systems. Synthetic biology techniques are “dual use”: The same methods that could lead to a cancer-fi fighting bac- will ultimately give individuals the
terium might also make deadly biological weapons; the same methods that promote ecologically unsound crop monocultures could uld also cause ability to design and modify custom
beneficial flowerings of engineered biological diversity. Ultimately, governments, large corporations, and international regulatory
o bodies by
ory genomes and construct artificial liv-
themselves may not be able to control whether synthetic biology is wisely used—that choice will also be up to each of us. ing organisms from scratch.
THE KEY QUESTIONS
Seed’s Tear-outable tool for living in the 21st century OF BIOFUELS:
CriBsheet #18 Are biofuels a viable

biofuels
replacement for fossil
fuels? How are they made,
and can their production
be improved?

RISING ENERGY COSTS and con- pretreatment and


cerns over climate change from extraction
emissions of CO2 have renewed After harvest, neither corn nor cellulose
GROWTH &
interest in moving beyond fossil HARVEST GLUCOSE is immediately convertible to ethanol,
fuels. This is especially true where ENZYME (AMYLASE) which is a direct product of the sugar
transportation is concerned, as that’s extracted and fermented. Several
it accounts for 70 percent of STARCH different processes can extract sugar
oil burned in the United States. from corn and cellulose, but each
Biofuels—fuels made from requires pretreatment of the source
living things—are one potential material to make extraction easier. For
Illustrator: Bryan Christie — www.bryanchristiedesign.com Writer: Lee Billings Graph data: Annual Energy Outlook 2008, US Department of Energy, Energy Information Administration. / A Farrell et al. (2006) “Ethanol Can Contribute to Energy and Environmental Goals.” Science 311:506-508

replacement. Biofuels come in corn, the kernels are milled to produce


many forms, such as wood, ma- cornstarch 1, a mixture of two large
nure, and animal and vegetable 1
molecules comprising chains of the sug-
oils. Unlike fossil fuels, biofuels ar glucose; an enzyme called amylase
are renewable and potentially then breaks down the mixture into glu-
carbon-neutral: Burning a plant 3 cose 2. Getting glucose from cellulose-
releases no more carbon than it rich plant material is more difficult. The
PRETREATMENT &
absorbed while growing. In the EXTRACTION material is pretreated with acids, steam,
US today’s predominant biofuel is CELLULOSE or ammonia to free the cellulose from
2
ethanol. Typically produced from plant-cell walls 3. Like starch, cellulose
corn, American ethanol works is made of chains of glucose molecules,
as an alternative to gasoline in but its molecules have far more bonds
most cars and trucks. But corn- 4 between them. And so, cellulose
based ethanol may cause more requires multiple enzymes to break up
problems than it solves. 6 into glucose 4. Lignin, another com-
FERMENTATION
ponent of plants, must be separated
YEAST from the glucose-rich mixture before
out of frying pan, 5 GLUCOSE
fermentation 5. Consequently, cellulosic
into fire ethanol production currently lags far
Using the same crop as a source behind ethanol production from corn,
for both food and energy sugarcane, and other food crops.
increases demand for it, which ENZYMES
can cause rapid increases in food GLUCOSE DISTILLATION
prices. When using corn, only fermentation and
the kernels are used and energy 7 distillation
stored in other parts of the plant Once the sugar is extracted from the
goes to waste. Fortunately, reliance on fossil fuels cornstarch or cellulose, it is mixed with
a more complex process can decreases the ratio of yeast or other microbes 6. The microbes
create ethanol from cellulose, energy provided by the ferment the sugar into alcohol, releasing
the main component of plant ethanol versus the energy carbon dioxide as a byproduct and leav-
stems and leaves; this process is spent in growing its source ing behind an unfermented mass called
less disruptive to the food supply crop. While corn is easier stillage, which can be recovered and
and uses material that would than cellulose to convert into used as a feed supplement for livestock.
otherwise be wasted. ethanol, it requires more resources When fermentation is complete, the
Though in theory ethanol to grow than many other cellulose making ethanol mixture is distilled and treated with
can be carbon-neutral, in sources. In general, using agricultural crops for biofuel Producing ethanol from either corn or cellulose chemicals to remove water, resulting
practice growing and harvesting poses problems of environmental degradation and re- requires four basic steps: growth and harvest, in fuel-grade ethanol that can then be
corn or cellulose uses substantial source depletion similar to those that occur in other forms pretreatment and extraction of sugars, fermen- blended with gasoline and transported
amounts of fossil fuels. This of industrial agriculture. tation, and distillation. to pumping stations for distribution 7.

Biofuel Content of U.S. Gasoline Supply fossil fuels for Biofuels

150

MEGAJOULES OF FOSSIL
ENERGY NEEDED TO PRODUCE
BILLION GALLONS

100 EACH MEGAJOULE OF FUEL

0.10 Cellulosic Ethanol

50 0.774 Ethanol Today


Biofuel content

Fossil Fuel content


1.19 Gasoline
2006 2015 2030

As US biofuel production ramps up, more ethanol will be mixed with the gasoline supply. Even Today both ethanol and gasoline production rely on energy from fossil fuels. Producing ethanol
by 2030, however, fossil fuels are projected to remain the primary constituents of gasoline. from cellulose rather than crops like corn will almost certainly require much less fossil-fuel energy.

THE ISSUE: THE NEXT GENERATION OF BIOFUELS


The first generation of modern biofuels was made from food crops like corn because processing these plants is relatively easy, but their energy Though promising as alternative energy
yields are low and their negative effects are many. “Second generation” biofuels like cellulosic ethanol are made from inedible materials like sources, biofuels can have social, envi-
agricultural waste and wood chips, but their production has yet to be perfected, and the amount of energy they could deliver is unlikely to fulfill ronmental, and energy costs rivaling
the entirety of our growing energy needs. Viable biofuels await us in the third generation or beyond, when highly energy-efficient production those of fossil fuels. Future generations
of fuel from algae or genetically modified microorganisms could become a reality. of biofuels may solve these problems.

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