125 Qs we don't know

Scientists Researching What We Don't Know

CLINTON PARKS
UNITED STATES
1 JULY 2005

Though it is often--and justifiably--maligned, it is ignorance--and recognizing where it exists--that drives scientists to do groundbreaking science. For early career scientists, ignorance--and knowing what areas we are ignorant of--also provides compelling professional opportunities.

That is why we have chosen to supplement Science magazine's 125th Anniversary Issue: 125 Questions: What We Don't Know, which examines the gaps in scientific knowledge with profiles of a few of the young researchers who are trying to fill those gaps.

Philip Goulder, a researcher at Oxford University, studies the influence of an individual?s genetics on HIV infection. His work could help explain why some individuals with a specific tissue type (HLA) can mount an effective immune control of HIV. If successful, Goulder's work may lead to the production of an HIV vaccine, which would deliver the same protection. Licia Verde, a cosmologist at the University of Pennsylvania, examines the varied composition of the universe, including dark energy and dark matter, as well as how the universe formed and how it continues to evolve. Eva Barroso, a genetics researcher at the Spanish National Center for Cancer Research (CNIO), attempts to determine whether disease susceptibility and treatment outcome are written in our DNA by producing an effective analysis of gene susceptibility for specific diseases. Harmit Singh Malik, a researcher at the Fred Hutchinson Cancer Research Center, is finding rapidly evolving genes in a place known for its evolutionarily stability--centromeres--with possible implications for how, where, and when genes are expressed.

 

http://www.sciencemag.org/cgi/content/summary/309/5731/75

 

The Top 25
Essays by our news staff on 25 big questions facing science over the next quarter-century.

>	What Is the Universe Made Of?
>	What is the Biological Basis of Consciousness?
>	Why Do Humans Have So Few Genes?
>	To What Extent Are Genetic Variation and Personal Health Linked?
>	Can the Laws of Physics Be Unified?
>	How Much Can Human Life Span Be Extended?
>	What Controls Organ Regeneration?
>	How Can a Skin Cell Become a Nerve Cell?
>	How Does a Single Somatic Cell Become a Whole Plant?
>	How Does Earth's Interior Work?
>	Are We Alone in the Universe?
>	How and Where Did Life on Earth Arise?
>	What Determines Species Diversity?
>	What Genetic Changes Made Us Uniquely Human?
>	How Are Memories Stored and Retrieved?
>	How Did Cooperative Behavior Evolve?
>	How Will Big Pictures Emerge from a Sea of Biological Data?
>	How Far Can We Push Chemical Self-Assembly?
>	What Are the Limits of Conventional Computing?
>	Can We Selectively Shut Off Immune Responses?
>	Do Deeper Principles Underlie Quantum Uncertainty and Nonlocality?
>	Is an Effective HIV Vaccine Feasible?
>	How Hot Will the Greenhouse World Be?
>	What Can Replace Cheap Oil -- and When?
>	Will Malthus Continue to Be Wrong?

 

So Much More to Know …

From the nature of the cosmos to the nature of societies, the following 100 questions span the sciences. Some are pieces of questions discussed above; others are big questions in their own right. Some will drive scientific inquiry for the next century; others may soon be answered. Many will undoubtedly spawn new questions.

Is ours the only universe?
A number of quantum theorists and cosmologists are trying to figure out whether our universe is part of a bigger "multiverse." But others suspect that this hard-to-test idea may be a question for philosophers.

What drove cosmic inflation?
In the first moments after the big bang, the universe blew up at an incredible rate. But what did the blowing? Measurements of the cosmic microwave background and other astrophysical observations are narrowing the possibilities.

When and how did the first stars and galaxies form?
The broad brush strokes are visible, but the fine details aren't. Data from satellites and ground-based telescopes may soon help pinpoint, among other particulars, when the first generation of stars burned off the hydrogen "fog" that filled the universe.

Where do ultrahigh-energy cosmic rays come from?
Above a certain energy, cosmic rays don't travel very far before being destroyed. So why are cosmic-ray hunters spotting such rays with no obvious source within our galaxy?

What powers quasars?
The mightiest energy fountains in the universe probably get their power from matter plunging into whirling supermassive black holes. But the details of what drives their jets remain anybody's guess.

What is the nature of black holes?
Relativistic mass crammed into a quantum-sized object? It's a recipe for disaster--and scientists are still trying to figure out the ingredients.

Why is there more matter than antimatter?
To a particle physicist, matter and antimatter are almost the same. Some subtle difference must explain why matter is common and antimatter rare.

Does the proton decay?
In a theory of everything, quarks (which make up protons) should somehow be convertible to leptons (such as electrons)--so catching a proton decaying into something else might reveal new laws of particle physics.

What is the nature of gravity?
It clashes with quantum theory. It doesn't fit in the Standard Model. Nobody has spotted the particle that is responsible for it. Newton's apple contain ned a whole can of worms.

Why is time different from other dimensions?
It took millennia for scientists to realize that time is a dimension, like the three spatial dimensions, and that time and space are inextricably linked. The equations make sense, but they don't satisfy those who ask why we perceive a "now" or why time seems to flow the way it does.

Are there smaller building blocks than quarks?
Atoms were "uncuttable." Then scientists discovered protons, neutrons, and other subatomic particles--which were, in turn, shown to be made up of quarks and gluons. Is there something more fundamental still?

Are neutrinos their own antiparticles?
Nobody knows this basic fact about neutrinos, although a number of underground experiments are under way. Answering this question may be a crucial step to understanding the origin of matter in the universe.

Is there a unified theory explaining all correlated electron systems?
High-temperature superconductors and materials with giant and colossal magnetoresistance are all governed by the collective rather than individual behavior of electrons. There is currently no common framework for understanding them.

What is the most powerful laser researchers can build?
Theorists say an intense enough laser field would rip photons into electron-positron pairs, dousing the beam. But no one knows whether it's possible to reach that point.

Can researchers make a perfect optical lens?
They've done it with microwaves but never with visible light.

Is it possible to create magnetic semiconductors that work at room temperature?
Such devices have been demonstrated at low temperatures but not yet in a range warm enough for spintronics applications.

What is the pairing mechanism behind high-temperature superconductivity?
Electrons in superconductors surf together in pairs. After 2 decades of intense study, no one knows what holds them together in the complex, high-temperature materials.

Can we develop a general theory of the dynamics of turbulent flows and the motion of granular materials?
So far, such "nonequilibrium systems" defy the tool kit of statistical mechanics, and the failure leaves a gaping hole in physics.

Are there stable high-atomic-number elements?
A superheavy element with 184 neutrons and 114 protons should be relatively stable, if physicists can create it.

Is superfluidity possible in a solid? If so, how?
Despite hints in solid helium, nobody is sure whether a crystalline material can flow without resistance. If new types of experiments show that such outlandish behavior is possible, theorists would have to explain how.

What is the structure of water?
Researchers continue to tussle over how many bonds each H₂O molecule makes with its nearest neighbors.

What is the nature of the glassy state?
Molecules in a glass are arranged much like those in liquids but are more tightly packed. Where and why does liquid end and glass begin?

Are there limits to rational chemical synthesis?
The larger synthetic molecules get, the harder it is to control their shapes and make enough copies of them to be useful. Chemists will need new tools to keep their creations growing.

What is the ultimate efficiency of photovoltaic cells?
Conventional solar cells top out at converting 32% of the energy in sunlight to electricity. Can researchers break through the barrier?

Will fusion always be the energy source of the future?
It's been 35 years away for about 50 years, and unless the international community gets its act together, it'll be 35 years away for many decades to come.

What drives the solar magnetic cycle?
Scientists believe differing rates of rotation from place to place on the sun underlie its 22-year sunspot cycle. They just can't make it work in their simulations. Either a detail is askew, or it's back to the drawing board.

How do planets form?
How bits of dust and ice and gobs of gas came together to form the planets without the sun devouring them all is still unclear. Planetary systems around other stars should provide clues.

What causes ice ages?
Something about the way the planet tilts, wobbles, and careens around the sun presumably brings on ice ages every 100,000 years or so, but reams of climate records haven't explained exactly how.

What causes reversals in Earth's magnetic field?
Computer models and laboratory experiments are generating new data on how Earth's magnetic poles might flip-flop. The trick will be matching simulations to enough aspects of the magnetic field beyond the inaccessible core to build a convincing case.

Are there earthquake precursors that can lead to useful predictions?
Prospects for finding signs of an imminent quake have been waning since the 1970s. Understanding faults will progress, but routine prediction would require an as-yet-unimagined breakthrough.

Is there--or was there--life elsewhere in the solar system?
The search for life--past or present--on other planetary bodies now drives NASA's planetary exploration program, which focuses on Mars, where water abounded when life might have first arisen.

What is the origin of homochirality in nature?
Most biomolecules can be synthesized in mirror-image shapes. Yet in organisms, amino acids are always left-handed, and sugars are always right-handed. The origins of this preference remain a mystery.

Can we predict how proteins will fold?
Out of a near infinitude of possible ways to fold, a protein picks one in just tens of microseconds. The same task takes 30 years of computer time.

How many proteins are there in humans?
It has been hard enough counting genes. Proteins can be spliced in different ways and decorated with numerous functional groups, all of which makes counting their numbers impossible for now.

How do proteins find their partners?
Protein-protein interactions are at the heart of life. To understand how partners come together in precise orientations in seconds, researchers need to know more about the cell's biochemistry and structural organization.

How many forms of cell death are there?
In the 1970s, apoptosis was finally recognized as distinct from necrosis. Some biologists now argue that the cell death story is even more complicated. Identifying new ways cells die could lead to better treatments for cancer and degenerative diseases.

What keeps intracellular traffic running smoothly?
Membranes inside cells transport key nutrients around, and through, various cell compartments without sticking to each other or losing their way. Insights into how membranes stay on track could help conquer diseases, such as cystic fibrosis.

What enables cellular components to copy themselves independent of DNA?
Centrosomes, which help pull apart paired chromosomes, and other organelles replicate on their own time, without DNA's guidance. This independence still defies explanation.

What roles do different forms of RNA play in genome function?
RNA is turning out to play a dizzying assortment of roles, from potentially passing genetic information to offspring to muting gene expression. Scientists are scrambling to decipher this versatile molecule.

What role do telomeres and centromeres play in genome function?
These chromosome features will remain mysteries until new technologies can sequence them.

Why are some genomes really big and others quite compact?
The puffer fish genome is 400 million bases; one lungfish's is 133 billion bases long. Repetitive and duplicated DNA don't explain why this and other size differences exist.

What is all that "junk" doing in our genomes?
DNA between genes is proving important for genome function and the evolution of new species. Comparative sequencing, microarray studies, and lab work are helping genomicists find a multitude of genetic gems amid the junk.

How much will new technologies lower the cost of sequencing?
New tools and conceptual breakthroughs are driving the cost of DNA sequencing down by orders of magnitude. The reductions are enabling research from personalized medicine to evolutionary biology to thrive.

How do organs and whole organisms know when to stop growing?
A person's right and left legs almost always end up the same length, and the hearts of mice and elephants each fit the proper rib cage. How genes set limits on cell size and number continues to mystify.

How can genome changes other than mutations be inherited?
Researchers are finding ever more examples of this process, called epigenetics, but they can't explain what causes and preserves the changes.

How is asymmetry determined in the embryo?
Whirling cilia help an embryo tell its left from its right, but scientists are still looking for the first factors that give a relatively uniform ball of cells a head, tail, front, and back.

How do limbs, fins, and faces develop and evolve?
The genes that determine the length of a nose or the breadth of a wing are subject to natural and sexual selection. Understanding how selection works could lead to new ideas about the mechanics of evolution with respect to development.

What triggers puberty?
Nutrition--including that received in utero--seems to help set this mysterious biological clock, but no one knows exactly what forces childhood to end.

Are stem cells at the heart of all cancers?
The most aggressive cancer cells look a lot like stem cells. If cancers are caused by stem cells gone awry, studies of a cell's "stemness" may lead to tools that could catch tumors sooner and destroy them more effectively.

Is cancer susceptible to immune control?
Although our immune responses can suppress tumor growth, tumor cells can combat those responses with counter-measures. This defense can stymie researchers hoping to develop immune therapies against cancer.

Can cancers be controlled rather than cured?
Drugs that cut off a tumor's fuel supplies--say, by stopping blood-vessel growth--can safely check or even reverse tumor growth. But how long the drugs remain effective is still unknown.

Is inflammation a major factor in all chronic diseases?
It's a driver of arthritis, but cancer and heart disease? More and more, the answer seems to be yes, and the question remains why and how.

How do prion diseases work?
Even if one accepts that prions are just misfolded proteins, many mysteries remain. How can they go from the gut to the brain, and how do they kill cells once there, for example.

How much do vertebrates depend on the innate immune system to fight infection?
This system predates the vertebrate adaptive immune response. Its relative importance is unclear, but immunologists are working to find out.

Does immunologic memory require chronic exposure to antigens?
Yes, say a few prominent thinkers, but experiments with mice now challenge the theory. Putting the debate to rest would require proving that something is not there, so the question likely will not go away.

Why doesn't a pregnant woman reject her fetus?
Recent evidence suggests that the mother's immune system doesn't "realize" that the fetus is foreign even though it gets half its genes from the father. Yet just as Nobelist Peter Medawar said when he first raised this question in 1952, "the verdict has yet to be returned."

What synchronizes an organism's circadian clocks?
Circadian clock genes have popped up in all types of creatures and in many parts of the body. Now the challenge is figuring out how all the gears fit together and what keeps the clocks set to the same time.

How do migrating organisms find their way?
Birds, butterflies, and whales make annual journeys of thousands of kilometers. They rely on cues such as stars and magnetic fields, but the details remain unclear.

Why do we sleep?
A sound slumber may refresh muscles and organs or keep animals safe from dangers lurking in the dark. But the real secret of sleep probably resides in the brain, which is anything but still while we're snoring away.

Why do we dream?
Freud thought dreaming provides an outlet for our unconscious desires. Now, neuroscientists suspect that brain activity during REM sleep--when dreams occur--is crucial for learning. Is the experience of dreaming just a side effect?

Why are there critical periods for language learning?
Monitoring brain activity in young children--including infants--may shed light on why children pick up languages with ease while adults often struggle to learn train station basics in a foreign tongue.

Do pheromones influence human behavior?
Many animals use airborne chemicals to communicate, particularly when mating. Controversial studies have hinted that humans too use pheromones. Identifying them will be key to assessing their sway on our social lives.

How do general anesthetics work?
Scientists are chipping away at the drugs' effects on individual neurons, but understanding how they render us unconscious will be a tougher nut to crack.

What causes schizophrenia?
Researchers are trying to track down genes involved in this disorder. Clues may also come from research on traits schizophrenics share with normal people.

What causes autism?
Many genes probably contribute to this baffling disorder, as well as unknown environmental factors. A biomarker for early diagnosis would help improve existing therapy, but a cure is a distant hope.

To what extent can we stave off Alzheimer's?
A 5- to 10-year delay in this late-onset disease would improve old age for millions. Researchers are determining whether treatments with hormones or antioxidants, or mental and physical exercise, will help.

What is the biological basis of addiction?
Addiction involves the disruption of the brain's reward circuitry. But personality traits such as impulsivity and sensation-seeking also play a part in this complex behavior.

Is morality hardwired into the brain?
That question has long puzzled philosophers; now some neuroscientists think brain imaging will reveal circuits involved in reasoning.

What are the limits of learning by machines?
Computers can already beat the world's best chess players, and they have a wealth of information on the Web to draw on. But abstract reasoning is still beyond any machine.

How much of personality is genetic?
Aspects of personality are influenced by genes; environment modifies the genetic effects. The relative contributions remain under debate.

What is the biological root of sexual orientation?
Much of the "environmental" contribution to homosexuality may occur before birth in the form of prenatal hormones, so answering this question will require more than just the hunt for "gay genes."

Will there ever be a tree of life that systematists can agree on?
Despite better morphological, molecular, and statistical methods, researchers' trees don't agree. Expect greater, but not complete, consensus.

How many species are there on Earth?
Count all the stars in the sky? Impossible. Count all the species on Earth? Ditto. But the biodiversity crisis demands that we try.

What is a species?
A "simple" concept that's been muddied by evolutionary data; a clear definition may be a long time in coming.

Why does lateral transfer occur in so many species and how?
Once considered rare, gene swapping, particularly among microbes, is proving quite common. But why and how genes are so mobile--and the effect on fitness--remains to be determined.

Who was LUCA (the last universal common ancestor)?
Ideas about the origin of the 1.5-billion-year-old "mother" of all complex organisms abound. The continued discovery of primitive microbes, along with comparative genomics, should help resolve life's deep past.

How did flowers evolve?
Darwin called this question an "abominable mystery." Flowers arose in the cycads and conifers, but the details of their evolution remain obscure.

How do plants make cell walls?
Cellulose and pectin walls surround cells, keeping water in and supporting tall trees. The biochemistry holds the secrets to turning its biomass into fuel.

How is plant growth controlled?
Redwoods grow to be hundreds of meters tall, Arctic willows barely 10 centimeters. Understanding the difference could lead to higher-yielding crops.

Why aren't all plants immune to all diseases?
Plants can mount a general immune response, but they also maintain molecular snipers that take out specific pathogens. Plant pathologists are asking why different species, even closely related ones, have different sets of defenders. The answer could result in hardier crops.

What is the basis of variation in stress tolerance in plants?
We need crops that better withstand drought, cold, and other stresses. But there are so many genes involved, in complex interactions, that no one has yet figured out which ones work how.

What caused mass extinctions?
A huge impact did in the dinosaurs, but the search for other catastrophic triggers of extinction has had no luck so far. If more subtle or stealthy culprits are to blame, they will take considerably longer to find.

Can we prevent extinction?
Finding cost-effective and politically feasible ways to save many endangered species requires creative thinking.

Why were some dinosaurs so large?
Dinosaurs reached almost unimaginable sizes, some in less than 20 years. But how did the long-necked sauropods, for instance, eat enough to pack on up to 100 tons without denuding their world?

How will ecosystems respond to global warming?
To anticipate the effects of the intensifying greenhouse, climate modelers will have to focus on regional changes and ecologists on the right combination of environmental changes.

How many kinds of humans coexisted in the recent past, and how did they relate?
The new dwarf human species fossil from Indonesia suggests that at least four kinds of humans thrived in the past 100,000 years. Better dates and additional material will help confirm or revise this picture.

What gave rise to modern human behavior?
Did Homo sapiens acquire abstract thought, language, and art gradually or in a cultural "big bang," which in Europe occurred about 40,000 years ago? Data from Africa, where our species arose, may hold the key to the answer.

What are the roots of human culture?
No animal comes close to having humans' ability to build on previous discoveries and pass the improvements on. What determines those differences could help us understand how human culture evolved.

What are the evolutionary roots of language and music?
Neuroscientists exploring how we speak and make music are just beginning to find clues as to how these prized abilities arose.

What are human races, and how did they develop?
Anthropologists have long argued that race lacks biological reality. But our genetic makeup does vary with geographic origin and as such raises political and ethical as well as scientific questions.

Why do some countries grow and others stagnate?
From Norway to Nigeria, living standards across countries vary enormously, and they're not becoming more equal.

What impact do large government deficits have on a country's interest rates and economic growth rate?
The United States could provide a test case.

Are political and economic freedom closely tied?
China may provide one answer.

Why has poverty increased and life expectancy declined in sub-Saharan Africa?
Almost all efforts to reduce poverty in sub-Saharan Africa have failed. Figuring out what will work is crucial to alleviating massive human suffering.

The following six mathematics questions are drawn from a list of seven outstanding problems selected by the Clay Mathematics Institute. (The seventh problem is discussed on p. 96.) For more details, go to www.claymath.org/millennium.

Is there a simple test for determining whether an elliptic curve has an infinite number of rational solutions?
Equations of the form y² = x³ ax b are powerful mathematical tools. The Birch and Swinnerton-Dyer conjecture tells how to determine how many solutions they have in the realm of rational numbers--information that could solve a host of problems, if the conjecture is true.

Can a Hodge cycle be written as a sum of algebraic cycles?
Two useful mathematical structures arose independently in geometry and in abstract algebra. The Hodge conjecture posits a surprising link between them, but the bridge remains to be built.

Will mathematicians unleash the power of the Navier-Stokes equations?
First written down in the 1840s, the equations hold the keys to understanding both smooth and turbulent flow. To harness them, though, theorists must find out exactly when they work and under what conditions they break down.

Does Poincaré's test identify spheres in four-dimensional space?
You can tie a string around a doughnut, but it will slide right off a sphere. The mathematical principle behind that observation can reliably spot every spherelike object in 3D space. Henri Poincaré conjectured that it should also work in the next dimension up, but no one has proved it yet.

Do mathematically interesting zero-value solutions of the Riemann zeta function all have the form a bi?
Don't sweat the details. Since the mid-19th century, the "Riemann hypothesis" has been the monster catfish in mathematicians' pond. If true, it will give them a wealth of information about the distribution of prime numbers and other long-standing mysteries.

Does the Standard Model of particle physics rest on solid mathematical foundations?
For almost 50 years, the model has rested on "quantum Yang-Mills theory," which links the behavior of particles to structures found in geometry. The theory is breathtakingly elegant and useful--but no one has proved that it's sound.