Author’s Corner: Open data, open review and open dialogue in making social sciences plausible

Guest post by Quan-Hoang Vuong of Centre for Interdisciplinary Social Research, Western University Hanoi, Vietnam

A growing awareness of the lack of reproducibility has undermined society’s trust and esteem in social sciences. In some cases, well-known results have been fabricated or the underlying data have turned out to have weak technical foundations.

Dr Quan Hoang Vuong

{credit}Quan Hoang Vuong{/credit}

Many researchers have investigated the plausibility of findings in the social sciences and humanities. A typical example is the mysterious Critical Minimum Positivity Ratio 2.9013 by Fredrickson and Losada (2005), which claimed to show that there exists such a positivity ratio and that “an individual’s degree of flourishing could be predicted by that person’s ratio of positive to negative emotions over time”. This ratio had once been a well-known, highly influential and greatly admired psychological “constant” until it was shown by Brown, Sokal and Friedman (2013) to be an unfounded, arbitrary and meaningless number.

To address the plausibility problem, I suggest that a combination of open data, open peer-review and open community dialogue, could serve as a feasible option for the social sciences.

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Author’s Corner: Revisiting the personalities of wild chimpanzees

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Alexander Weiss

Guest post by Alexander Weiss of the University of Edinburgh, United Kingdom

Early on in her behavioural observations of the chimpanzees at what is now known as Gombe National Park, Jane Goodall was struck by their personalities, which were as distinct as our own1. However, upon sharing her observations with a ‘respected ethologist’, she was told that, yes, animals differed in their behaviour, but that this was best ‘swept under the carpet’ (pp 11-12)2. Continue reading

Author’s corner: Providing incentives and ensuring quality in citizen science

Guest post by Steffen Fritz, Linda See & Ian McCallum of the International Institute for Applied Systems Analysis, Laxenburg, Austria

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{credit}Steffen Fritz, Linda See & Ian McCallum{/credit}

Citizen science, the collection or analysis of research data by the general public, has existed in one form or another for centuries, with contributions ranging from plant and animal observations to weather phenonmena1. In the field of land cover and land use, however, its application is relatively new2. Previously this was a task left largely to governments, research institutes and global bodies. With the recent availability of high resolution satellite imagery, this has changed, opening up new possibilities for citizen participation3. In our recent article in Nature Research’s Scientific Data4, we have made available a global dataset of crowdsourced land cover and land use reference data, containing the results of our first four citizen-science campaigns. Continue reading

Author’s corner: A testbed for reproducible and standardized human MRI connectomics

Guest post by Xi-Nian Zuo, Project Coordinator and Co-Founder of Consortium for Reliability and Reproducibility (CoRR), Professor of Psychology and Director of the Magnetic Resonance Imaging Research Center in the Institute of Psychology at Chinese Academy of Sciences, China.

XI-NIAN ZUO

{credit}Xi-Nian Zuo{/credit}

About a decade ago (2006), as a PhD student graduating from the School of Mathematics at Beijing Normal University, I stepped into the field of neuroimaging of the human brain by way of a short job interview offered by Dr. Yu-Feng Zang, my postdoc mentor in China. The most important thing that I learned and developed during my post doc training was how to question a study, an indication likely of my somewhat different background (mathematics versus brain sciences). Probability and statistics became my major tools in bridging new learning experiences with my existing knowledge, pushing me to further pursue research training offered by Dr. Michael Peter Milham at New York University. Ongoing work in his laboratory really interested me, particularly test-retest reliability of resting-state functional connectivity1, the first study of test-retest reliability in the nascent field of functional connectivity. However, an obvious limitation existed to that study, and a series of test-retest reliability studies I carried out subsequently2; the small sample size. This directly motivated me to seek and build up a truly big data set for test-retest reliability in connectomics. Continue reading

Author’s corner: Sharing proteomics data to build community-based resources

Ruedi Aebersold & George Rosenberger photo

{credit}Ruedi Aebersold & George Rosenberger{/credit}

Guest post by Ruedi Aebersold, Professor of Systems Biology with a joint appointment at ETH Zurich and the University of Zurich, & George Rosenberger, PhD student in the Aebersold group at the Institute of Molecular Systems Biology, ETH Zurich.

Mass spectrometry-based proteomics is a data-intense research discipline that primarily aims at identifying and quantifying the proteins that constitute the proteome1. This is achieved by generating large numbers (104 to 106) of fragment ion spectra that represent peptides generated by proteolysis of the respective proteome. Mass spectrometers can operate in different data acquisition modes, referred to as data-dependent acquisition (DDA), targeted acquisition exemplified by selected reaction monitoring (SRM) or data-independent acquisition (DIA)2 exemplified by SWATH-MS3,4. Specific software tools then generate from these raw data processed mass spectra – from which sets of identified peptides, proteins and their abundance are inferred and annotated with metadata. Both, the generation and the processing of such raw data sets are resource and time intensive.  Further, if unique, irreplaceable samples are being analyzed, as is often the case with clinical cohorts the data cannot be re-generated. Therefore, the proteomics community has started to embrace data sharing by the means of different specialized public repositories, for example GPMDB5, PRIDE6, PeptideAtlas7 or ProteomicsDB8. For the last few years, the ProteomeXchange9 consortium has provided centralized deposition of raw data and their meta-annotation. Continue reading

Author’s Corner: Advancing the sharing and standardization of metabolomics data

Mark Viant photo

{credit}Mark Viant{/credit}

Guest post by Mark Viant, Professor of Metabolomics in the School of Biosciences at the University of Birmingham, UK, and Director of both the national NERC Biomolecular Analysis Facility – Metabolomics and the Phenome Centre Birmingham

In 2014, my research team published the first Scientific Data Data Descriptor for metabolomics measurements, Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control. This article described in great detail the many steps that are critical for ensuring the production of high quality (direct infusion) mass spectrometry (DIMS) data. It was our intention that this publication would help to establish the benchmark for DIMS metabolomics, derived using best-practice workflows and rigorous quality assessment. The data was also made freely available in the MetaboLights public database for metabolomics data (dataset MTBLS79).1

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Author’s Corner: Is fame fair?

Guest post by Amy Yu and César A. Hidalgo, MIT Media Lab, Cambridge, Massachusetts, USA

Is fame superficial? Or can it be a signal of accomplishment?

In a world where many media outlets seem dominated by characters of inexplicable fame (such as the Kardashians), asking ourselves if our social reward systems are misfiring is both a fair question and a relevant one. The relevance of this question stems from the fact that humans are social learners – we are a species whose success depends on the ability of individuals to learn from others. But choosing whom to learn from, in a world populated by more people than we can meet, is not easy. To facilitate those choices, humans have evolved cognitive biases that nudge us to learn from those who demonstrate skill, accomplishments, and also, fame or prestige[1]. Continue reading

Author’s Corner: Mapping Crimean-Congo haemorrhagic fever

tracking the human Crimean-Congo haemorrhagic fever virus

By Jane P. Messina, Senior Postdoctoral Epidemiologist, Department of Zoology, University of Oxford, United Kingdom.

Crimean-Congo hemorrhagic fever (CCHF) is one of the most widely distributed tick-borne diseases in the world, ranging from southern Russia and the Black Sea region to the southern tip of Africa. It is caused by a virus which is transmitted to humans by ticks, and is considered as “emerging” across the globe, with countries such as Albania, Turkey, and Georgia reporting new infections in humans in recent decades. Human CCHF infection has also been recently reported after long periods of absence in some locations, for example in south-western Russia and Central Africa. The main genus of ticks that transmit CCHF to humans (Hyalomma ticks) are adapted to warmer and dry or semiarid environments, and are found in many parts of Africa, Asia, and Europe. In addition to humans these ticks feed on wild and domesticated animals, which can also become infected with CCHF virus but which do not show any disease symptoms. However, infection of these animals leads to further CCHF transmission to humans, as new ticks feed upon these animals and become infected. Continue reading

Author’s Corner: Are lakes warming?

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by John Lenters, PhD, Scientist, LimnoTech, Ann Arbor, Michigan, USA

It is now widely recognized that global and regional climate change has important implications for terrestrial and aquatic ecosystems. Recently published studies, for example, have revealed significant warming of lakes and reservoirs throughout the world. This has been evident not only in studies of individual lakes at specific sites (i.e., from “in situ” datasets), but especially in broader, satellite-based studies of lake surface temperature trends. Remarkably, these previous studies have also found that the observed rate of lake warming is sometimes greater than that of ambient air temperature. These rapid, unprecedented changes in lake temperature have profound implications for lake mixing, hydrology, productivity, and biotic communities. Continue reading

Author’s Corner: Digitizing odor

by Joel D. Mainland PhD, Louise Slade Assistant Member at the Monell Chemical Senses Center, Philadelphia

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Why is it that we all know that red, green, and blue are primary colors, but nobody knows a set of primary odors? Why is it that every smartphone user can now pull out their phone, take a picture, send it to a friend halfway across the world nearly instantaneously, archive it nearly indefinitely, and look at it repeatedly with no degradation using only a device connected to a power source, but none of this is currently possible in olfaction?
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