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Science

The best in science news, commentary, and research
The reproducibility problem in science is a familiar issue, not only within the scientific community, but with the general public as well. Recent developments in social psychology (such as fraudulent research by D. Stapel) and cell biology (the Amgen Inc. and Bayer AG reports on how rarely they could reproduce published results) have become widely known. Nearly every field is affected, from clinical trials and neuroimaging, to economics and computer science. Obvious solutions include more research on statistical and behavioral fixes for irreproducibility, activism for policy changes, and demanding more pre-registration and data sharing from grantees. Two Perspectives in this issue (pp. 1420 and 1422) describe how journals and academic institutions can foster a culture of reproducibility. Transparency is central to improving reproducibility, but it is expensive and time-consuming. What can be done to alleviate those obstacles? Author: Stuart Buck

In science news around the world, DNA sequencing shows that the 8500-year-old Kennewick Man was Native American, experts with the International Whaling Commission again conclude that Japan's lethal research whaling program isn't scientifically justified, astronomers decide to restart construction of the Thirty Meter Telescope on Hawaii's Mauna Kea, a clinical trial of a promising Ebola drug in Sierra Leone is halted early after it fails to show a benefit to patients, and more. Also, the invasive, predatory New Guinea flatworm is found on the U.S. mainland for the first time. And vulture populations in Africa have plummeted over the past 3 decades, due primarily to farmers poisoning carcasses to target lions or hyenas.

More than 16,000 people have survived the Ebola outbreak in West Africa, the biggest in history. While the virus is still spreading in parts of Guinea and Sierra Leone, some scientists are turning their attention to these survivors. Many of them report symptoms ranging from hearing loss and eye problems to fatigue and erectile dysfunction. In a joint effort, the Liberian ministry of health and the U.S. National Institute of Allergy and Infectious Diseases are investigating how many people are suffering from this "post-Ebola syndrome" and what might cause it. A similar study is going on in Guinea. Investigators also hope to find out whether there is a chance that some survivors might still transmit the virus to others. Ebola virus has been found in the semen of one survivor and the eye of another months after it had been cleared from the blood. Author: Kai Kupferschmidt

Although researchers have scrutinized genes as if they were Hollywood celebrities, the stretches of regulatory DNA called enhancers have largely stayed in the background, their workings a mystery. A recent genetics meeting signaled a change: In talk after talk, researchers described where and how these quiet fixers exert their influence. One group showed how enhancers maintain the right level of sensitivity to other signals, so that they switch on genes only at the right times and places. Others explored how cells package genes and their enhancers so that they can work together properly, and how DNA forms loops that bring enhancers right to the target gene. The advances even point to strategies for exploiting these regulatory elements to treat disease, by switching off disease genes and turning up the activity of healthy ones. Author: Elizabeth Pennisi

Soaring traffic on global fiber optic networks could reduce the Internet to gridlock within a couple of years. But new work reported this week in Science could push that "capacity crunch" back several years. Researchers at the University of California, San Diego, targeted fluctuations in the wavelength of the lasers that generate data-carrying light pulses. Those tiny changes create "noise" that builds up with distance, limiting the range of optical signals. Because the noise is random, it's usually impossible to filter out. But the scientists discovered an optical trick that converts it into a form that's easier to separate from the main signal. As a result, they say, light pulses can either carry twice as much data or travel twice as far before needing to be amplified. Author: Robert F. Service

The Comprehensive Nuclear-Test-Ban Treaty (CTBT) has spawned a globe-girdling network of 300 detector stations that sniff out radionuclides, listen for low-frequency sounds, and record tremors—all to discern whether countries are carrying out clandestine nuclear weapons tests. And the treaty has not yet even come into force; the United States remains a prominent holdout. But the CTBT's $1 billion International Monitoring System is 90% complete and has scored notable successes. Among them: sizing up North Korea's nuclear tests, plotting the spread of radionuclides from the Fukushima nuclear accident, and tracking the spectacular Chelyabinsk meteorite as it broke up over Siberia in 2013. This global stethoscope is amassing a treasure trove of data. Initially, the CTBT Organization (CTBTO), based in Vienna, didn't share, but after the 2004 Indian Ocean tsunami—when the monitoring system could have given an early warning—things have loosened up. Now, timely data are sent to tsunami warning centers in 13 countries, as well as to civil aviation authorities and nuclear regulators. This glasnost is due in large part to Lassina Zerbo, director of CTBTO's International Data Centre from 2004 to 2013 and, since then, the organization's executive secretary. Zerbo spoke with Science for this Q&A on the eve of the 5th CTBT Science and Technology Conference. Author: Daniel Clery

In the fall of 2013, emails arrived in the inboxes of dozens of scientists informing that their work had been chosen for scrutiny by a project aiming to replicate 50 high-impact cancer biology papers. The Reproducibility Project: Cancer Biology, an ambitious, open-science effort to test whether key findings in top journals can be reproduced by independent labs, has stirred concerns in the community. Almost every scientist targeted by the project who spoke with Science agrees that studies in cancer biology, as in many other fields, too often turn out to be irreproducible. But few feel comfortable with this particular effort, which plans to announce its findings in coming months. Leaders of the project say it will ultimately benefit the field by gauging the extent of the reproducibility problem in cancer biology. Author: Jocelyn Kaiser

On 14 July, NASA's New Horizons spacecraft will swoop past Pluto, the gatekeeper to a region of thousands of icy bodies known as the Kuiper belt. Alan Stern is the principal investigator for the $700 million mission—the largest and most expensive ever controlled by a non-NASA employee. Equal parts taskmaster, entrepreneur, and showman, Stern has been working for 25 years to get a spacecraft to Pluto—10 years to muster political and scientific will, 5 years to build a spacecraft, and nearly 10 years to make the trip. Like the instrument-studded spacecraft—delivered on time and on budget —Stern is packed with purpose. Author: Eric Hand

Even while getting a NASA spacecraft to Pluto, Alan Stern has found time to set up two companies on the side. One, called Golden Spike, plans to sell billion-dollar trips to the moon to other nations. Another, called Uwingu, promotes gimmicky campaigns—such as selling unofficial naming rights to martian craters—in order to raise money for space research. Author: Eric Hand

Week after week, news outlets carry word of new scientific discoveries, but the media sometimes give suspect science equal play with substantive discoveries. Careful qualifications about what is known are lost in categorical headlines. Rare instances of misconduct or instances of irreproducibility are translated into concerns that science is broken. The October 2013 Economist headline proclaimed “Trouble at the lab: Scientists like to think of science as self-correcting. To an alarming degree, it is not” (1). Yet, that article is also rich with instances of science both policing itself, which is how the problems came to The Economist's attention in the first place, and addressing discovered lapses and irreproducibility concerns. In light of such issues and efforts, the U.S. National Academy of Sciences (NAS) and the Annenberg Retreat at Sunnylands convened our group to examine ways to remove some of the current disincentives to high standards of integrity in science. Authors: Bruce Alberts, Ralph J. Cicerone, Stephen E. Fienberg, Alexander Kamb, Marcia McNutt, Robert M. Nerem, Randy Schekman, Richard Shiffrin, Victoria Stodden, Subra Suresh, Maria T. Zuber, Barbara Kline Pope, Kathleen Hall Jamieson

Transparency, openness, and reproducibility are readily recognized as vital features of science (1, 2). When asked, most scientists embrace these features as disciplinary norms and values (3). Therefore, one might expect that these valued features would be routine in daily practice. Yet, a growing body of evidence suggests that this is not the case (4–6). Authors: B. A. Nosek, G. Alter, G. C. Banks, D. Borsboom, S. D. Bowman, S. J. Breckler, S. Buck, C. D. Chambers, G. Chin, G. Christensen, M. Contestabile, A. Dafoe, E. Eich, J. Freese, R. Glennerster, D. Goroff, D. P. Green, B. Hesse, M. Humphreys, J. Ishiyama, D. Karlan, A. Kraut, A. Lupia, P. Mabry, T. A. Madon, N. Malhotra, E. Mayo-Wilson, M. McNutt, E. Miguel, E. Levy Paluck, U. Simonsohn, C. Soderberg, B. A. Spellman, J. Turitto, G. VandenBos, S. Vazire, E. J. Wagenmakers, R. Wilson, T. Yarkoni

In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions (1). Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species (2). Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels (3). However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities (see the image). Author: James K. Fredrickson

Commensal bacteria underlie, in part, our nutritional status, immune function, and psychological well-being. The trillions of beneficial microbes within our intestinal tract convert dietary nutrients, inhibit pathogen colonization, regulate immune processes, and produce neural signals (1, 2). Advances in our understanding of the importance of microbes have motivated the commercial development of products intended to boost “good” commensals and confer health benefits. Probiotic dietary supplements contain live beneficial microbes hoped to subsequently colonize the gut. Prebiotic nutrients are thought to enhance good gastrointestinal microflora by preferentially nourishing beneficial microbes. Even “psychobiotics” are being explored to ameliorate symptoms of psychiatric illness. These live organisms influence the brain through metabolites and neuroactive compounds in rodent models and preliminary human studies (3). How to most effectively be the landscape architects of our microbial community, however, often remains unclear. An opportunity to gain insights into how natural selection has shaped the coevolution of hosts and microbes can be found in mammalian mother-infant dyads, as our microbiota are ecologically engineered by mothers and breastmilk. Such insights can be leveraged to improve clinical management and nutritional technologies, enhancing human health not just in infancy, but across the life course (4, 5). Authors: Katie Hinde, Zachery T. Lewis

Under high pressure, electrons can be squeezed out of the covalent bond that holds the hydrogen molecule together. Under these conditions, condensed hydrogen can become metallic, but the pressures required can be obtained only through the gravitational field of gas giant planets, or fleetingly in shock waves. On page 1455 of this issue, Knudson et al. (1) report experiments using the Z machine at Sandia National Laboratories that uses an aluminum plate propelled by giant capacitors to generate concentrated shock waves in a tiny sample (2). They observe metallic liquid hydrogen at pressures around 300 GPa and temperatures between 1000 and 2000 K created for a tenth of a microsecond. By shock wave standards, that is remarkably cold and slow. Author: Graeme J. Ackland

Marine organisms play a key role in the global sulfur cycle by producing dimethyl sulfide (DMS), a volatile compound that is emitted into the atmosphere. On page 1466 of this issue, Alcolombri et al. (1) report how the abundant marine phytoplankton Emiliania huxleyi (see the image) produces DMS from dimethylsulfoniopropionate (DMSP). Using a series of classical biochemical approaches, augmented by genomic and proteomic analyses, the authors isolated the enzyme and corresponding gene (termed Alma1) that cleaves DMSP into acrylate and DMS. They also found a functional Alma1-like enzyme in a dinoflagellate, a very different type of abundant single-cell marine plankton, emphasizing the widespread importance of this newly discovered DMSP lyase. Author: Andrew W. B. Johnston

Ocean waves form between air and water, and both winds and currents decay exponentially with distance from the water surface. Similar evanescent surface waves may occur whenever two substances with differing physical properties meet—but some are special cases because they must exist for topological reasons. Such mandated surface modes occur in the low-energy quasi-particle spectrum of p-wave superconductors and superfluids and constitute the defining feature of the electronic properties of topological insulators. On page 1448 of this issue, Bliokh et al. (1) suggest that we add evanescent solutions of Maxwell's equations to this list of special cases, and in particular, the coupled oscillations of the electromagnetic field and the near-surface electrons in a metal that are known as surface plasmon-polaritons. Author: Michael Stone

The introduction of an extra gene into a genome—transgenesis—is frequently used as an experimental approach to study gene function but also has applications in biotechnology and gene therapy efforts. In mammalian cells, transgenes are often integrated in a random manner leading to variable levels of expression, with differences as great as three orders of magnitude depending on the integration site (1). The complications of unpredictable levels of transgene expression are well recognized, but the mechanisms leading to variable expression are poorly understood. On page 1481 of this issue, Tchasovnikarova et al. (2) determine that a protein complex silences extra genes that are inserted into heterochromatin, regions of compacted DNA. This represents a new aspect of gene regulation that depends on chromatin context. Authors: Thijn R. Brummelkamp, Bas van Steensel

"If anything in the world is alive, is not radium alive?" asked the physician and journalist C. W. Saleeby in 1906. Writing at the height of a radium craze that swept across Europe and America in the early 20th century, Saleeby was one of many observers who connected radium and radioactivity to the mysteries of life. These couplings—and the curious, marvelous, and mostly forgotten scientific investigations that emanated from them—are the subject of the historian Luis A. Campos's fascinating history of radium and its uses in biological experimentation. Reviewer Helen Anne Curry praises the book's capable use of radium to reveal long-lost secrets of science and history alike. Author: Helen Anne Curry

Anyone teaching a course at a university is likely to have a notion of what face-to-face teaching should look like through his or her experience as a student, as a teacher, and through depictions in media. Yet as Claire Howell Major points out in her book, Teaching Online, most of us do not have similar notions for online courses because we have little to no experience with them. She aims to provide the guidance needed to envision and implement online teaching. Reviewer Erin Dolan finds that much of the book's guidance is also highly relevant for face-to-face teaching, and encourages disciplinary faculty to engage with the book's evidence-based strategies. Author: Erin Dolan

A listing of books received at Science during the week ending 19 June 2015.

Author: David W. Martin

Authors: Elena Bekerman, Shirit Einav

Authors: Jinqi Zhan, Qiang Weng

Tedersoo et al. (Research Article, 28 November 2014, p. 1078) present a compelling study regarding patterns of biodiversity of fungi, carried out at a scale unprecedented to date for fungal biogeographical studies. The study demonstrates strong global biogeographic patterns in richness and community composition of soil fungi. What concerns us with the study is what we do not see. Unfortunately, this study underestimates the fungal diversity of one key group of soil fungi due to reliance on a single primer with known flaws. Authors: Christopher W. Schadt, Anna Rosling

Rugani et al. (Reports, 30 January 3015, p. 534) tested 3-day-old domestic chicks using an innovative experimental setup and demonstrate the presence of the mental number line. We raise concerns regarding this conclusion by highlighting the possible loopholes in the experimental design and the data analysis procedures. We further suggest auxiliary experiments that can substantiate the authors’ claim. Authors: Madhur Mangalam, Shraddha Madhav Karve

Rugani et al. (Reports, 30 January 2015, p. 534) presented evidence that domestic chicks employ a “mental number line.” I argue that the hypothesis testing used to support this claim unjustifiably assumes that domestic chicks are unbiased when choosing between identical stimuli presented to their left and right. Author: Christopher Harshaw

Mangalam and Karve raise concerns on whether our results demonstrate a mental number line, suggesting auxiliary experiments. Further data analyses show that their methodological concerns are not founded. Harshaw suggests that a side bias could have affected our results. We show that this concern is also unfounded. Authors: Rosa Rugani, Giorgio Vallortigara, Konstantinos Priftis, Lucia Regolin


Author: Sacha Vignieri

Author: Marc S. Lavine

Author: Zakya H. Kafafi

Author: Paula A. Kiberstis

Author: Peter Stern

Author: Angela Colmone

Author: Guy Riddihough

Author: Nicholas S. Wigginton

Author: H. Jesse Smith

Author: Ian S. Osborne

Author: Beverly A. Purnell

Author: Beverly A. Purnell

Author: Ian S. Osborne

Author: Brent Grocholski

Author: Nicholas S. Wigginton

Author: Stella M. Hurtley

Author: Guy Riddihough

Author: Julia Fahrenkamp-Uppenbrink

Author: Lisa Chong

Author: John F. Foley

Author: Laura M. Zahn

Author: Valda Vinson