Wednesday, October 30, 2013

You can’t read just one: Reproducibility and multiple sources By Bonnie Swoger

There are lots of ways to mess with the heads of undergraduate students. Giving them a research assignment and failing to specify a minimum number of references needed is just one example.
“Include as many sources as you need to make your point and illustrate your thesis.”
For students, finding one scholarly article on their topic often seems to be enough. Researchers did an experiment, got some results, and answered the research question the student started with. All done, all set, time for dinner.
But science doesn’t work that way. One experiment may suggest something interesting, but it doesn’t prove anything. In fact, it is quite easy to point to many examples of intriguing scientific studies that were either proved false or that couldn’t be reproduced later on. Scientific ideas that are true should be reproducible: other researchers should be able to repeat the experiments and get similar results or use other methods to arrive at the same conclusions. You can’t say that you discovered something new if someone else can’t reproduce your result.

This fundamental scientific idea, reproducibility, may be in crisis. A recent article by Vasilevsky et al. in the journal PeerJ suggested that many scientific journal articles don’t provide the information that other scientists would need in order to replicate their results. Key information about chemicals, reactants or model organisms is often missing, despite journal requirements to include such information (Vasilevsky et al., 2013). And a recent item in The Economist suggests that this might not matter that much. The emphasis placed on new research (by funding agencies and tenure and promotion committees) means that few scientists even attempt to replicate the work of others (“Unreliable research: Trouble at the lab,” 2013).

All of this means trouble from the very beginning of a research project, before an experiment is even designed, when scientists start to do background research on their topics. In the same way that experimental scientists can’t rely on the results of just one experiment to prove something, relying on just one information source for knowledge is a sure way to end up with unreliable information. Journalists look for corroborating sources, wikipedia flags articles that need a wider variety of citations, and scholars need to find multiple scholarly articles to support their ideas.

Some innovative people, companies and publishers are trying to sort this mess out. A collaboration between PLOS ONE, Mendeley, Figshare and the Science Exchange will be attempting to replicate the results of selected projects as a part of the Reproducibility Initiative. The Reproducibility Project is a crowdsourced effort to evaluate the reproducibility of experimental results in psychology. And the Reproducible Science project aims to make the results of computational experiments reproducible by ensuring the sharing of code and data and by making that information available to reviewers who can test the results described in a manuscript they are reviewing.
Unfortunately, these innovative programs are just a drop in the bucket of modern science. Funding agencies, publishers and tenure and promotion committees still value original work more highly than verification work. Scientists who concentrated on replicating the work of others would risk their careers.
As a result it is important for students and scholars to be aware of the challenges facing the reproducibility of science. We teach students in introductory science classes that reproducibility is one of the hallmarks of science. As they learn more about their disciplines, they need to be aware of the practical challenges involved in reproducing the work of others, and the importance of finding multiple sources about a topic needs to be emphasized.

As a librarian, part of my job is to help students find additional sources related to their research topics, even if there isn’t a published reproduction of an original source. This isn’t about which database to use or whether to put quotes around a phrase. It is about getting them to think critically about their topics. For example, while there might not be a second study that repeated the experiment of the first, students can look for:
  • Studies that examined the same topic in a different way
  • Studies that used the same methodology on a different species, geographic area, etc.
  • Background studies on individual aspects of their research question, including the statistical analyses used
  • Studies that cite the original study (even if no one has tried to reproduce the results, other scholars might express doubts about their conclusions when they cite the original).
The issues surrounding reproducibility in science won’t be solved overnight, and it will take a concerted effort from scientists at all levels of the modern scientific enterprise to steer this very big ship. In the meantime, students and scholars can make special efforts to ensure that they are using the highest quality information available as the basis of their original studies.

Works Cited:
Unreliable research: Trouble at the lab.” (2013, October 19). The Economist, 409(8858), 26-30.
Vasilevsky, N. a, Brush, M. H., Paddock, H., Ponting, L., Tripathy, S. J., Larocca, G. M., & Haendel, M. A. (2013). On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ, 1, e148. doi:10.7717/peerj.148.

Sunday, October 27, 2013

Ten Steps You Can Take Right Now Against Internet Surveillance

by Danny O'Brien - Electronic Frontier Foundation

One of the trends we've seen is how, as the word of the NSA's spying has spread, more and more ordinary people want to know how (or if) they can defend themselves from surveillance online. But where to start?
The bad news is: if you're being personally targeted by a powerful intelligence agency like the NSA, it's very, very difficult to defend yourself. The good news, if you can call it that, is that much of what the NSA is doing is mass surveillance on everybody. With a few small steps, you can make that kind of surveillance a lot more difficult and expensive, both against you individually, and more generally against everyone.
Here's ten steps you can take to make your own devices secure. This isn't a complete list, and it won't make you completely safe from spying. But every step you take will make you a little bit safer than average. And it will make your attackers, whether they're the NSA or a local criminal, have to work that much harder.
  1. Use end-to-end encryption. We know the NSA has been working to undermineencryption, but experts like Bruce Schneier who have seen the NSA documents feel thatencryption is still "your friend". And your best friends remain open source systems that don't share your secret key with others, are open to examination by security experts, and encrypt data all the way from one end of a conversation to the other: from your device to the person you're chatting with. The easiest tool that achieves this end-to-end encryption is off-the-record (OTR) messaging, which gives instant messaging clients end-to-end encryption capabilities (and you can use it over existing services, such as Google Hangout and Facebook chat). Install it on your own computers, and get your friends to install it too. When you've done that, look into PGP–it's tricky to use, but used well it'll stop your email from being an open book to snoopers.
  2. Encrypt as much communications as you can. Even if you can't do end-to-end, you can still encrypt a lot of your Internet traffic. If you use EFF's HTTPS Everywhere browser addon for Chrome or Firefox, you can maximise the amount of web data you protect by forcing websites to encrypt webpages whenever possible. Use a virtual private network (VPN) when you're on a network you don't trust, like a cybercafe.
  3. Encrypt your hard drive. The latest version of Windows, Macs, iOS and Android all have ways to encrypt your local storage. Turn it on. Without it, anyone with a few minutes physical access to your computer, tablet or smartphone can copy its contents, even if they don't have your password.
  4. Strong passwords, kept safe. Passwords these days have to be ridiculously long to be safe against crackers. That includes the password to email accounts, and passwords to unlock devices, and passwords to web services. If it's bad to re-use passwords, and bad to use short passwords, how can you remember them all? Use a password manager. Even write down your passwords and keeping them in your wallet is safer than re-using the same short memorable password — at least you'll know when your wallet is stolen. You can create a memorable strong master password using a random word system like that described at
  5. Use Tor. "Tor Stinks", this slide leaked from GCHQ says. That shows much the intelligence services are worried about it. Tor is an the open source program that protects your anonymity online by shuffling your data through a global network of volunteer servers. If you install and use Tor, you can hide your origins from corporate and mass surveillance. You'll also be showing that Tor is used by everyone, not just the "terrorists" that GCHQ claims.
  6. Turn on two-factor (or two-step) authentication. Google and Gmail has it; Twitter has it; Dropbox has it. Two factor authentication, where you type a password and a regularly changed confirmation number, helps protect you from attacks on web and cloud services. When available, turn it on for the services you use. If it's not available, tell the company you want it.
  7. Don't click on attachments. The easiest ways to get intrusive malware onto your computer is through your email, or through compromised websites. Browsers are getting better at protecting you from the worst of the web, but files sent by email or downloaded from the Net can still take complete control of your computer. Get your friends to send you information in text; when they send you a file, double-check it's really from them.
  8. Keep software updated, and use anti-virus software. The NSA may be attempting to compromise Internet companies (and we're still waiting to see whether anti-virus companies deliberately ignore government malware), but on the balance, it's still better to have the companies trying to fix your software than have attackers be able to exploit old bugs.
  9. Keep extra secret information extra secure. Think about the data you have, and take extra steps to encrypt and conceal your most private data. You can use TrueCrypt to separately encrypt a USB flash drive. You might even want to keep your most private data on a cheap netbook, kept offline and only used for the purposes of reading or editing documents.
  10. Be an ally. If you understand and care enough to have read this far, we need your help. To really challenge the surveillance state, you need to teach others what you've learned, and explain to them why it's important. Install OTR, Tor and other software for worried colleagues, and teach your friends how to use them. Explain to them the impact of the NSA revelations. Ask them to sign up to Stop Watching Us and other campaigns against bulk spying. Run a Tor node, or hold a cryptoparty. They need to stop watching us; and we need to start making it much harder for them to get away with it.