Domain: peerj.com
Stories and comments across the archive that link to peerj.com.
Stories · 14
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Giant Predatory Worms Are Invading France (qz.com)
An anonymous reader quotes a report from Quartz: In a Peer J study published on May 22, "Giant worms chez moi!" zoologist Jean-Lou Justine of the Museum National d'Histoire Naturelle in Paris, entomologist colleagues, and Pierre Gros, outline a discovery that "highlights an unexpected blind spot of scientists and authorities facing an invasion by conspicuous large invasive animals." About 100 citizen scientists ultimately contributed to the assessment of this alien invasion, identifying five giant predatory worm species in France that grow up to 10 inches long. The study relied on contributors' worm sightings, reported "mainly by email, sometimes by telephone." Researchers requested photographs and details about locality. In 2013, the Washington Post reports, "a group of terrorized kindergartners claimed they saw a mass of writhing snakes in their play field." These were giant flatworms! The study concludes that the alien creatures appear to reproduce asexually. They prey on other, smaller earthworms, stunning them with toxins. "The planarian also produces secretions from its headplate and body that adhere it to the prey, despite often sudden violent movements of the latter during this stage of capture," researcher note. In other words, the hammerheads produce a substance that allows them to stick to victims while killing them. The study points out that invasive alien flatworms have been spotted in New Zealand, Papua New Guinea, Brazil, and Australia. But the five species of hammerhead flatworms invading France are giants, growing up to 27 centimeters. -
Subscription Journals Are Doomed Because of Sci-Hub's Big Cache of Pirated Papers, Suggests Data Analyst (sciencemag.org)
An anonymous reader quotes a report from Science Magazine: There is no doubt that Sci-Hub, the infamous -- and, according to a U.S. court, illegal -- online repository of pirated research papers, is enormously popular. But just how enormous is its repository? That is the question biodata scientist Daniel Himmelstein at the University of Pennsylvania and colleagues recently set out to answer, after an assist from Sci-Hub. Their findings, published in a preprint on the PeerJ journal site on July 20, indicate that Sci-Hub can instantly provide access to more than two-thirds of all scholarly articles, an amount that Himmelstein says is "even higher" than he anticipated. For research papers protected by a paywall, the study found Sci-Hub's reach is greater still, with instant access to 85% of all papers published in subscription journals. For some major publishers, such as Elsevier, more than 97% of their catalog of journal articles is being stored on Sci-Hub's servers -- meaning they can be accessed there for free. In a chat with ScienceInsider, Himmelstein concludes that the results of his study could mark "the beginning of the end" for paywalled research. -
Scientists Create AI Program That Can Predict Human Rights Trials With 79 Percent Accuracy (theverge.com)
An anonymous reader quotes a report from The Verge: Computer scientists have created an AI program capable of predicting the outcome of human rights trials. The program was trained on data from nearly 600 cases brought before the European Court of Human Rights (ECHR), and was able to predict the court's final judgement with 79 percent accuracy. Its creators say it could be useful in identifying common patterns in court cases, but stress that they do not believe AI will be able to replace human judgement. As described in a study published in the journal PeerJ Computer Science, the AI program worked by analyzing descriptions of court cases submitted to the ECHR. These descriptions included summaries of legal arguments, a brief case history, and an outline of the relevant legislation. The cases were grouped into three main violations of human rights law, including the prohibition on torture and degrading treatment; the right to a fair trial; and the right to "respect for private and family life." (Used in a wide range of cases including illegal searches and surveillance.) The AI program then looked for patterns in this data, correlating the courts' final judgements with, for example, the type of evidence submitted, and the exact part of the European Convention on Human Rights the case was alleged to violate. Aletras says a number of patterns emerged. For example, cases concerning detention conditions (eg access to food, legal support, etc.) were more likely to end in a positive judgement that an individual's human rights had been violated; while cases involving sentencing issues (i.e., how long someone had been imprisoned) were more likely to end in acquittal. The researchers also found that the judgements of the court were more dependent on the facts of the case itself (that is to say, its history and its particulars) than the legal arguments (i.e., how exactly the Convention on Human Rights had or had not been violated). -
Women Get Pull Requests Accepted More (Except When You Know They're Women) (peerj.com)
An anonymous reader writes: In the largest study of gender bias [in programming] to date, researchers found that women tend to have their pull requests accepted at a higher rate than men, across a variety of programming languages. This, despite the finding that their pull requests are larger and less likely to serve an immediate project need. At the same time, when the gender of the women is identifiable (as opposed to hidden), their pull requests are accepted less often than men's. -
Study: People Emit a "Germ Cloud" of Bacteria As Unique As a Fingerprint
An anonymous reader writes: According to a new study, we are all surrounded by a personal "germ cloud" as unique as a fingerprint. Lead author of the study Dr James Meadow says: "We expected that we would be able to detect the human microbiome in the air around a person, but we were surprised to find that we could identify most of the occupants just by sampling their microbial cloud. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud." The findings were published today in the journal PeerJ. -
Empirical Study On How C Devs Use Goto In Practice Says "Not Harmful"
Edsger Dijkstra famously opined in 1968 on the danger of Goto statements. New submitter Mei Nagappan writes with a mellower view, nearly 50 years later: By qualitatively and quantitatively analyzing a statistically valid random sample from almost 2 million C files and 11K+ projects, we find that developers limit themselves to using goto appropriately in most cases, and not in an unrestricted manner like Dijkstra feared, thus suggesting that goto does not appear to be harmful in practice. (Here's the preprint linked from above abstract.) -
Empirical Study On How C Devs Use Goto In Practice Says "Not Harmful"
Edsger Dijkstra famously opined in 1968 on the danger of Goto statements. New submitter Mei Nagappan writes with a mellower view, nearly 50 years later: By qualitatively and quantitatively analyzing a statistically valid random sample from almost 2 million C files and 11K+ projects, we find that developers limit themselves to using goto appropriately in most cases, and not in an unrestricted manner like Dijkstra feared, thus suggesting that goto does not appear to be harmful in practice. (Here's the preprint linked from above abstract.) -
Your Personal Data Is On Your Phone -- In the Form of Bacteria
jfruh (300774) writes "Yes, we all know that we have a lot of personally identifying information on our phones that maybe we shouldn't. But even if our data is locked down and encrypted, we're all leaving biological footprints on our phones, which are basically extensions of our personal bacterial ecosystem. A study has concluded that phones could be a less invasive source of information in studying individual microbiomes than current techniques." -
Study: Happiness Improves Developers' Problem Solving Skills
itwbennett writes "Researchers at the Free University of Bozen-Bolzano in Italy have found that happier programmers (or, more specifically, computer science students at the university) were significantly more likely to score higher on a problem solving assessment. The researchers first measured the emotional states of study participants using a measure devised by psychologists called the Scale of Positive and Negative Experience Affect Balance (SPANE-B) score. They then tested participants' creativity (ability to write creative photo captions) and problem-solving ability (playing the Tower of London game). The results: happiness didn't affect creativity, but did improve problem-solving ability." -
The Real Reason Journal Articles Should Be Free
Bennett Haselton writes "The U.S. government recently announced that academic papers on federally-funded research should become freely available online within one year of publication in a journal. But the real question is why academics don't simply publish most papers freely anyway. If the problem is that traditional journals have a monopoly on the kind of prestige that can only be conferred by having your paper appear in their hallowed pages, that monopoly can easily be broken, because there's no reason why open-access journals can't confer the same imprimatur of quality." Read on for the rest of Bennett's thoughts on the great free-access debate.Around the time of the tragic suicide of Aaron Swartz, who lobbied tirelessly for free access to academic articles (in his sometimes grey-hat manner, which ultimately got him in trouble), I admitted to some friends that I didn't understand how this became a problem. Why aren't all journal articles free, all the time?
I don't mean that I didn't know why the journal publishers charged exorbitant fees for their subscriptions. If academic researchers have to have access to journal articles in order to do their jobs, then you can expect the journals to gouge academic libraries on the prices. What I didn't understand was: Why do academics even publish in journals that demand exclusive publishing rights for their work, and then charge readers huge fees to read it?
Well actually, we know the answer to that too: academics want the prestige of publishing in big-name journals that have established reputations, and as a result, those well-known journals are in a position to dictate the terms of the contract. A professor might genuinely want to publish their paper in a journal where it can be read for free by all, but they can hardly be blamed for thinking of their own career path first.
Here's the question I really wanted answered: If "prestige" only exists in the minds of other academics within a field, then why don't the academics within a given field just agree to confer "prestige" on papers published in open-access journals, if they can see for themselves that the quality is equivalent to what would be published in the old-guard journals that charge an arm and a leg? And then make hiring, promotion, and tenure decisions accordingly?
I don't mean that the papers published in an open-access journal would bypass the peer-review process, and that everyone in the field would have to judge the papers for themselves without any prior certification of their quality. One of the points that Peter Suber makes repeatedly in his book Open Access is that open access is not about skipping peer review and dumping papers directly onto the web. Rather, the process would work similarly to peer review for a traditional journal:
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Author submits a paper to journal XYZ.
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Journal XYZ selects one or more peer reviewers from among their list of people they consider qualified to review the paper. The peer reviewers send back their usual suggestions and some consensus is reached as to whether or not to publish.
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If Journal XYZ publishes the paper, then they have certified that the paper passed the quality controls in step #2, and the author can now legitimately claim that they had a paper published in Journal XYZ.
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If people in the field know that Journal XYZ is not skimping on the quality controls in step #2 — that Journal XYZ is sending the papers to the same academics who would do peer review for one of the old-guard journals, and who are holding the papers to the same standard — then they should respect the paper just as much as if it were published in a traditional journal. If a person has never heard of Journal XYZ, then it should only take a minute to explain to them how it works (and crucially, that Journal XYZ is just as strict about quality as the old-guard journals that everybody has heard of).
Each step in this process should cost the journal virtually nothing. The "hard cost," the part that consumes the time of people with unique skills, is the peer review step, but peer reviewers are usually paid by universities and consider peer review for academic journals to be part of their job description. At a minimum, all the editors really have to do is maintain the list of people they consider qualified to do the peer review, and send the submitted papers off to them.
Moreover, the entire process should be fast. Again, the "hard cost" in time is the peer review, but there's no reason that the delays between submission and publication should be in the range of months or years.
(I'm assuming that the article authors would want their writings to be widely read, or at least would not be opposed to it. That may not be the case if, for example, the authors were commissioned by a pharmaceutical company for a study that cast their drug in a favorable light, but the authors realize that their research methods contained errors and want to minimize the number of eyes on their paper, to reduce the chances of their chicanery being caught. Ben Goldacre's Bad Pharma documents these types of problems very thoroughly, but I'm sidestepping that issue for now.)
So, with that in mind as the ideal, I asked my friends, including many current and former academics, why this essentially wasn't the model that was used. Several mentioned the Public Library of Science, which publishes all articles in its journals under a Creative Commons Attribution License (free for anyone to read and reproduce in full, as long as the original author is cited), and finances its operations through publication fees. These fees are in the $2,000-$3,000 range, heavily discounted for low-income countries and authors, and in any case most academic authors pay the fees out of their research grants and not out of their own pockets. That sounded much better than the traditional model, I thought, but I still didn't understand why the costs weren't even closer to zero. Another friend pointed out that PLOS costs cover the expenses for many of their other activities — which are all noble goals, to be sure, but at the same time, why isn't anybody operating a more bare-bones model which minimizes all expenses, and charges almost nothing for publication or subscription?
This, it turns out, appears to be the approach of the PeerJ project, which aims to let authors pay a one-time fee of $99 at article submission time for the right to publish one article per year — or, if you prefer to pay only if your article is accepted for publication, you can pay $129 "on acceptance" (explained here). And the author of the Techdirt piece mentions that he submitted a paper which was published in the inaugural edition of one of PeerJ's journals, 10 weeks after the submission date. This is cheap and fast enough that I'd call it a validation of the theoretical model which predicts the whole process should be able to be done for almost no cost in almost no time. In other words, I think PeerJ will succeed, but even if it does fail, it will only be because of some anomalous business snafu, not because the hard costs of the service they're providing are greater than the dirt-cheap price they're charging for it. If for any reason PeerJ doesn't happen to get it right the first time, they or some other company should keep trying until someone makes it work.
The basic algorithm at work here — taking a piece of content, submitting it to one or more suitably qualified reviewers, and then certifying the content based on the feedback of the reviewers — is something I've advocated in many contexts over the years, for many different types of problems. In one article I argued that we could make success in the music industry into much more of a meritocracy, with far less arbitrariness in determining who succeeds and fails, if a suitably popular site like Pandora simply took new submissions from artists, had the content "rated" by a random sample of listeners interested in that type of music, and if enough of them liked it, push the content out to all of the fans of that genre. In "Crowdsourcing the Censors" I suggested that Facebook's complaint review process should use the same principle: If a given page received enough complaints, have the page contents reviewed by a random subset of Facebook users who had signed up to be "abusive content" reviewers, and then only flag the page for removal if a high enough percentage of those users voted that the page had indeed violated Facebook's guidelines. This year I argued that "We The People", the White House's online petition-drive-organizing website, should rate ideas based on what a random subset of users think of each idea, rather than allowing users to organize mobs of their friends and followers to vote their own ideas to the top of the pile (which, in case you missed it, is how 4chan gave us this). Or, if you think the general public is not qualified to rate ideas according to how they should be prioritized by the White House (and I'd be inclined to agree), you could have the ideas rated by a random subset of, say, the nation's economics professors.
Of course, I haven't heard of any plans to implement this algorithm in any of those contexts. Not that I expected the key power players to be reading my articles, but it's a little surprising that none of them ever came up with this idea independently, either. (To this day, the only website I'm aware of that ever implemented random-sample voting correctly, was HotOrNot.com, where users could rate members' pictures by attractiveness — but each picture's rating was determined by showing it to a random subset of the site's visitors. That system is gone, since the site has made itself over into a date-finding service.)
But academia in general, and science specifically, is different from other arenas in a number of key ways which could help this algorithm succeed:
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Academia, uniquely, is comprised of many professionals whose love of knowledge and intellectual inquiry, is greater than their desire for money. That's not to say that I don't think the same algorithm could work just as well in a business like the music industry, where most of the stakeholders are in it for the money. But even if Pandora did successfully implement the algorithm, it would meet a lot of resistance from entrenched interests in the music industry, who make their money by finding and promoting and managing talent and would not be happy about a new system that threatened to make them irrelevant. In academia, by contrast, it's quite plausible that even the "entrenched interests" — the people who had become superstars under the old system — would see the new system's great potential for disseminating free knowledge, and would welcome it even if it gave scrappy new upstart academics a chance to dethrone them. Not everybody in academia loves knowledge more than they love their own prestige, but I know more people like that in academia than anywhere else.
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In academia, even among people who do care primarily about their own prestige, many of them have tenure and guaranteed job security, a situation that does not exist in most other industries. This gives them the freedom to experiment with new models, such as submitting papers to upstart PeerJ journals. But more importantly for our purposes, it means they can announce that in their department's hiring and promotion decisions, they will count PeerJ-published papers as legitimate professional accomplishments, for the benefit of non-tenured faculty members who do have to worry about their resume.
- Academics, particularly in maths and sciences, are more prone to the kind of thinking that would lead a person naturally in the direction of the kind of system that PeerJ embodies. First, think of a theoretical model (like the kind I described near the beginning of the article). This model predicts that, ideally, it should be possible to publish papers at very low cost with quick turnaround times, without sacrificing peer-review quality assurance. Now, try to approximate that model as closely as possible in the real world. (In most other industries that I've worked in, there's much more inertia around the existing way of doing things, and far less willingness to entertain any discussion about whether a theoretical model can show how we could accomplish the same thing with vastly less overhead.)
And that, in the end, is the real reason journal articles should be free. Not because the U.S. government is making it a condition for taxpayer-funded research, although that is a welcome development. But because there's no part of the process that should cost very much to begin with, if article authors and peer reviewers are already being paid by their employers. The last piece of the puzzle is that enough academics and faculty departments have to agree to confer "prestige" on articles published in open-access journals, equivalent to the level of prestige that they would accord for an article published in a traditional journal of the same quality. If they won't do that, then the old-guard journals will maintain their monopoly on conferring "prestige", and don't be surprised if journal prices keep growing to the point where even Harvard can't pay for them.
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PeerJ, A New Open Access Megajournal Launches
Mirk writes "Academic researchers want to make their papers open access for the world to read. If they use traditional publishers like Elsevier, Springer or Taylor & Francis, they'll be charged $3000 to bring their work out from behind the paywall. But PeerJ, a new megajournal launched today and funded by Tim O'Reilly, publishes open access articles for $99. That's not done by cutting corners: the editorial process is thorough, and they use rigorous peer-review. The cost savings come from running lean and mean on a born-digital system. The initial batch of 30 papers includes one on a Penn and Teller trick and one on the long necks of dinosaurs." $99 entitles you to publish an article a year, for life. $300 nets you unlimited articles published per year. -
PeerJ, A New Open Access Megajournal Launches
Mirk writes "Academic researchers want to make their papers open access for the world to read. If they use traditional publishers like Elsevier, Springer or Taylor & Francis, they'll be charged $3000 to bring their work out from behind the paywall. But PeerJ, a new megajournal launched today and funded by Tim O'Reilly, publishes open access articles for $99. That's not done by cutting corners: the editorial process is thorough, and they use rigorous peer-review. The cost savings come from running lean and mean on a born-digital system. The initial batch of 30 papers includes one on a Penn and Teller trick and one on the long necks of dinosaurs." $99 entitles you to publish an article a year, for life. $300 nets you unlimited articles published per year. -
PeerJ, A New Open Access Megajournal Launches
Mirk writes "Academic researchers want to make their papers open access for the world to read. If they use traditional publishers like Elsevier, Springer or Taylor & Francis, they'll be charged $3000 to bring their work out from behind the paywall. But PeerJ, a new megajournal launched today and funded by Tim O'Reilly, publishes open access articles for $99. That's not done by cutting corners: the editorial process is thorough, and they use rigorous peer-review. The cost savings come from running lean and mean on a born-digital system. The initial batch of 30 papers includes one on a Penn and Teller trick and one on the long necks of dinosaurs." $99 entitles you to publish an article a year, for life. $300 nets you unlimited articles published per year. -
Journal Offers Flat Fee For 'All You Can Publish'
ananyo writes "In what publishing experts say is a radical experiment, a new open-access venture is asking its authors for only a one-off fee to secure a lifetime membership that will allow them to publish free, peer-reviewed research papers. The venture, called PeerJ, formally announced its launch on 12 June. The model represents a big departure for science publishing, which has traditionally been dominated by two basic business models: either subscribers pay for access, or authors pay for each publication — often thousands of dollars — with access being free."