Saturday, December 28, 2013

If the code is not open, you're not doing science

This is a list of articles explicitly suggesting or tangentially indorsing Open Source Software in the context of academic publications. The list is far from complete and in no particular order, but it creates a strong defense of source code as an integral part of the scientific process (code is data after all!). 

Tuesday, December 10, 2013

And it is a kind of good deed to say well; And yet, words are no deeds.

After this year's Nobel prize winner and editor of glam mag eLife Randy Schekman announces a boycott to (other) glam magazines, several interesting comments appeared through twitter. This pursuit for glam hits close to home since I've seen first-hand the transition of arguments from "it's a sad necessity" to "that's how it should be done, space is limited" -- even without realizing that this scarcity is artificial. 

What is wrong with scientific publishing and how to fix it. : gg

Ok, so let’s assume tomorrow morning CNS cease to exist. They close down. How does this solve the issue? It doesn’t. CNS are not damaging Science. They are simply sitting on the very top of the ladder of scientific publishing and they receive more attention than any other journal. Remove them from the top and we have just moved the problem a bit down the ladder, next to whatever journal is following.

I think you might be a hypocrite | opiniomics

I wrote a blog post recently called “We didn’t ask for it”, and in case you missed the subtle nuance (!) of the post, what I was trying to say is that if you’re an established scientist, a tenured professor with hundreds of peer-reviewed papers behind you, and especially if you’re a man, you don’t get to tell people like me that the system is broken, because you’re the one who broke it!!!

I disgree with many ppoint of the text above, but the idea is sound. It's not about pointing fingers (seriously, man cannot complain about gender issues? by being born a man I'm at fault?), it's about talking the talk and not walking the walk. Which applies equally to politicians alike.

An Alternative to Schekman’s Boycott of Luxury Journals | Telliamed Revisited

Now let’s make a few small changes. I don’t think the words I’ve substituted are any less true than those that Prof. Schekman wrote.  I’ve changed only those words in italics:

“These luxury universities are supposed to be the epitome of quality, training only the best students. Because funding and appointment panels often use place of degree as a proxy for quality of science, obtaining degrees from these institutions often leads to fellowships and professorships. But the big universities’ reputations are only partly warranted. While they produce many outstanding scientists, they do not produce only outstanding scientists. Neither are they the only producers of outstanding scientists.”

So, will Prof. Schekman and his group also avoid luxury universities, and will he encourage others to do the same?

The problem is not the existence of glam journals, it's a system that gives disproportionate weight to them, and our even more unreasonable preference for such venues. So we cannot blame the overhyped magazines for making all kinds of arbitrary demands and creating schizophrenic standards. We crave for them, and we are willing to inflate our claims and to distort the narrative of our manuscripts, to divide our work's ouput into as many papers as we can, to avoid risky research and to follow bandwagon subjects, and to reject other people's manuscript for the quaintest disagreement (as e.g. their failure to inflate the claims and to distort etc.)

BTW, this discussion reminded me that it should be a concern that more and more scientists are not ashamed of parading their economic ignorance (instead of, let's say, recognizing our limitations as we should in all academic areas we have no first-hand expertise). It will certainly hurt us in the long term, first because we start to resemble creationists: refuse to study for fear of perceived consequences, reading instead excuses created by equally ignorant others; rejection of recognizing the field as a science, laying ground for an alternative but "inconvinent" version of the field; claim that knowledge of this 'deeper' version excuses the lack of familiarity with the field; lack of capacity to pass a first-year course on the discipline. Second, because people versed in the discipline may have less incentives to take us seriously (in the same way as we ignore claims made by quacks), and they will just stop listening.

To finish on a lighter tone, two nice tweets commenting on the boycott:

Friday, November 15, 2013

Some links about fisheries and the tragedy of the commons

(Just to complement our lunchtime discussion, I wanted to take a look at a few articles)

One solution to global overfishing found

One of the unexpected results of the study revealed that co-management benefits the wealthier people in the local community, although it is not detrimental to the poor. "In other words, the main benefits tend to trickle up to the wealthy, rather than trickle down to the poor," Dr Cinner added. "Nevertheless, most people felt that they benefitted." The team found that the institutional design of the fishery management arrangement was vital in determining whether or not people felt they benefited from co-management and were willing to work together to protect fish stocks by complying with the rules.

Ending the oceans' 'tragedy of the commons'

Fishers and scientists had been working together on the problem for some years, sharing knowledge and building trust. This led to the trialling of new co-operative models for fishery management, based on the latest that science can reveal about the state of the fish stock and the surrounding marine ecosystem. The result is a revolutionary national system of marine tenure that allocates user rights and responsibilities to collectives of fishers.

The tragedy of the commons in international fisheries: An empirical examination (Journal of Environmental Economics and Management Volume 57, Issue 3, May 2009, Pages 321–333)

The results of my ordered category estimation indicate that the probability of a fish stock being over- (under-)utilised rises (falls) with the number of countries sharing the stock. This negative effect of sharing is apparent when stocks are harvested from either large or small portions of nations’ waters, suggesting that access is all that is required to have an effect on stock status. In addition to the detrimental impact of international sharing, some economic and biological characteristics affect stock status, for example, higher valued and slower-growing stocks face further exploitation pressure.

The future of the sea: Fish food | The Economist

Trying to farm a fish just because there is an established market for it is a waste of time and money, argues Mr Greenberg. Farm animals were domesticated because they were suitable to begin with, and only got more so over time. Aquaculture will only work, environmentally and economically, with the right sort of fish. So far the search has turned up two good freshwater options—tilapia and the Vietnamese Pangasius or river cobbler. A marine version may still be out there. The prize is a form of protein that is far cheaper and more efficient to produce than meat.

Fisheries are Classic Example of the "Tragedy of the Commons" | PERC – The Property and Environment Research Center

Fisheries provide the classic example of the tragedy of the commons, which occurs when property rights are incomplete and access to a resource is open. The migratory nature of most fish species makes it difficult to establish and protect rights to fish in the sea, so the rule of capture prevails. The result is often overexploitation of the resource. Economists long have argued that the waste associated with this problem could be reduced if we "privatized the commons," that is, created individual private property rights for common-pool resources.

The tragedy of the commons in a fishery when relative performance matters (Ecological Economics Volume 81, September 2012, Pages 140–154)

This paper presents a simple model of a common access fishery where fishermen care about relative performance as well as absolute profits. Our model captures the idea that status (which depends on relative performance) in a community influences a person's well-being. In our main specification, relative performance depends on the absolute difference in after-tax profits. We show that overharvesting resulting from the tragedy of the commons problem is exacerbated by the desire for higher relative performance, leading to a smaller steady-state fish stock and smaller steady-state profit for all the fishermen. We also consider alternative specifications where status depends on the absolute difference in harvests or relative difference in profits, or where there is heterogeneity in the degree to which status matters, or allowing for the possibility of extinction. In all these specifications, status further reduces the steady-state fish stock. We examine taxes and an individual quota as policy alternatives and find support for using the direct quantity method to implement the socially efficient stock level.

Sunday, November 10, 2013

Brazilian rage at NSA was the sincerest form of flattery

Many people applauded the strong words Brazilian president Dilma Roussef directed at the US, but we should not forget that actions speak louder. And when politics is involved, we can give up any hope of coherence.

Brazil orders Google to hand over Street View data (here you can find the news in portuguese)

Brazilian judges have given US Internet search giant Google until Saturday to turn over private data collected through its Street View program, press reports said Thursday.

Bill Would Allow Brazil to Decree Local Internet Data Storage

Brazil is pushing ahead with legislation that would force global Internet companies such as Google and Facebook to keep data on Brazilian users inside the country, despite opposition from the companies and in Congress. A draft bill made public on Tuesday would grant President Dilma Rousseff decree powers to order companies to set up data centers in Brazil to store personal information on their users as a way of curbing U.S. spying.

The Statesman: Rousseff wants Web servers to be housed in Brazil

President Dilma Rousseff met earlier this week with the Bill's sponsor, Deputy Alessandro Molon of the governing Workers Party, and asked that he insert language into the Bill that would force Internet companies to keep their servers on Brazilian soil if they want to do business in the country, the lawmaker's office said. That would force companies to follow Brazilian privacy laws for the information on those servers.

A Molon spokesman, who would not allow his name to be used because he wasn't yet authorised to speak on the matter, said the legislator and his team were ironing out the exact language to be included in the Bill. The president’s office confirmed that Ms Rousseff met with Molon and Communications Minister Paulo Bernardo Silva on Tuesday, but referred all questions about the meeting to the legislator and the minister. After hours calls to the ministry rang unanswered.

Brazil Wants National 'Antisnoop' Email

The Brazilian government asked Correios (the Brazilian mail agency) to develop a national email system. Scheduled to be launched in the second half of 2014, it will be aimed at commercial security against "snooping." The plan is to create a Brazilian alternative to the popular Hotmail, of Microsoft, and Google's Gmail. The agency had been working on an electronic mailing system for commercial purposes which would include a delivery certification when read by the addressee. (...)

"When I send you an email and I want nobody to snoop. Last year, the U.S. made 311 requests (to companies). They aren't working in the retail market," Brazil's Communication Minister Paulo Bernardo told Folha. "It's necessary to encourage a safer email service." After the cases of espionage by the American government became public, Brazil's Communication Ministry requested the project be expanded into a national service. The government believes that the current services have proved to be vulnerable since Edward Snowden disclosed secret National Security Agency (NSA) documents, showing that American companies are obliged to supply their users' data.

Report - Brazil Monitored French Spies

Brazil's intelligence agency monitored French spies it suspected of involvement in the 2003 explosion at a satellite launch base, the Folha de S. Paulo newspaper said Tuesday, though it was finally determined they played no role. (...) When the explosion occurred, killing 21 engineers and technicians, suspicion fell on the French. Citing unnamed sources, the newspaper said the agency known as ABIN carried out at least three operations against what it called a "network of spies" from France's foreign intelligence agency and its activities in the French-Brazilian Technical and Scientific Cooperation Center and in Brazil's National Space Research Institute. But it said no evidence of sabotage was found and the explosion finally was blamed on poor maintenance and mechanical failures.

Report - Brazil Spied on Embassy Personnel

The Brazilian government confirmed Monday that its intelligence service targeted U.S., Russian, Iranian and Iraqi diplomats and property during spy activities carried out about a decade ago in the capital Brasilia. (...) Brazil's Institutional Security Cabinet, which oversees the Abin intelligence service, said in an emailed statement that all the operations cited in the Folha report "follow Brazilian law for the protection of national interests." (...)

In Monday's statement, Brazil's Institutional Security Cabinet said it planned to prosecute anyone who may have leaked the documents to the Folha newspaper. (...) The Folha report detailed at least 10 intelligence operations carried out in Brasilia in 2003-04, just as former President Luiz Inacio Lula da Silva was settling into office.

Other targets included diplomats from the Russian, Iranian and Iraqi embassies, who were followed and photographed as they came and went from embassies and official residences. In particular, Abin was interested in Russian officials involved in negotiating arms deals in Brazil, and followed Iran's ambassador to Cuba as he visited Brazil.

Brazil Says It Spied on U.S. and Others Inside Its Borders

Still, the report focuses new attention on Abin, an agency that has drawn scrutiny for being caught by surprise by the huge street protests that shook Brazilian cities in June and for quietly ousting an agent suspected of passing secrets to the Central Intelligence Agency. Active intelligence officials have also publicly criticized the agency for prioritizing surveillance of Brazilian social movements. (...) Brazilian intelligence officials insisted in their statement that Abin’s operations were intended to defend “national sovereignty.” Referring to the revelations in the newspaper report, they also said that the leaking of classified material was illegal and that those responsible for doing so would be held accountable under Brazilian law.

Abin espionou jornalistas durante governo Lula (in portuguese only. Iit describes how the Brazilian inteligence agency has been purportedly used to spy journalists and media companies since 2004. This other commentary raises the possibility of the spying in Brasil being much more widespread, waiting for another Snowden to uncover it):

Um documento da Agência Brasileira de Inteligência (Abin), que descreve detalhes de uma queda de braço travada entre um agente e seus superiores durante o governo Lula, tem valor histórico inestimável. Esse documento, hoje arquivado, é a evidência oficial mais forte até aqui de algo que agentes confidenciavam a jornalistas, mas não podiam provar: o governo Lula espionou a imprensa. O texto revela que houve uma “Operação Mídia”, ação clandestina de espionagem de jornalistas e donos de empresas jornalísticas. VEJA teve acesso ao documento de seis páginas no qual o tenente-coronel André Soares revela a existência da operação ilegal.

So, to "counter" international spying what Ms. Roussef and her government propose is to force internet companies to store data in Brazil (it wouldn't prevent said data from being also under NSA's reach, in the US) and to create a governent e-mail system (we know our data would be safe with them, right?). To me it looks like they are just seizing the moment to implement their own surveilance under the guise of "protection against international interests", their favorite enemy. The Brazilian government  has indeed a very poor relation with individual freedoms, being one of the worst offenders against google for instance (see below, or twitter info) and having a strong tendency to prohibit whatever might be considered offensive -- which encourages people to be offended very easily.

Some more links below.

Battle Over Biographies Rages in Brazil

Now, Veloso is taking a shellacking from the press and his fan base alike, who say he's endorsing censorship by leading the defense of a wide-ranging law that allows Brazilians to block or pull from the shelves any biographical work about them that was created without their consent.

With Brazil's publishers mobilizing to repeal the restrictions, Veloso, romantic crooner Robert Carlos and other singers who became famous under the dictatorship have banded together to defend the 2003 law, which empowers Brazilians to quash works they consider attacks on their "good name or respectability."

That means objections by a biography's subject are enough to get the books removed or even keep them from reaching stores, with many publishers not printing a book if it's not explicitly endorsed by a subject. The law also applies to films and other media, though the debate and legal actions have focused on books. Critics say it is possibly the most extreme law regulating privacy and intellectual property among democratic nations.

Why the NSA Watches Brazil

Not coincidentally some of the world's least free countries are President Rousseff's most important foreign-policy partners. In a September Miami Herald column titled "Why We Spy on Brazil," Cuban-born writer Carlos Alberto Montaner transcribed a conversation with an unnamed U.S. ambassador. The diplomat explained: "The friends of [Lula], of Dilma Rousseff and the Workers Party are the enemies of the United States: Chavist Venezuela, first with (Hugo) Chávez and now with (Nicolás) Maduro; Raúl Castro's Cuba; Iran; Evo Morales' Bolivia; Libya at the time of Gadhafi; Bashar Assad's Syria." He also noted that "in almost all conflicts, the Brazilian government agrees with the political lines of Russia and China." The Brazilian relationship with Cuba is especially troubling. Instead of showing solidarity with Cuba's victims of oppression, the diplomat noted, "former president Lula da Silva often takes investors to the island to fortify the Castros' dictatorship. The money invested by the Brazilians in the development of the superport of Mariel, near Havana, is estimated to be $1 billion."

Press Freedom in Brazil: Sound the Alarm

The recent increase in acts of censorship of and violence against journalists in Brazil underscores a disturbing trend of government apathy. While Brazilian journalists are being threatened, beaten, and even killed, Brazil’s leaders offer their condolences but do little to rectify the problem, sometimes even contributing to it. In more than 70 percent of the murders of journalists in Brazil in the past 20 years, the killer walked away without a jail sentence.[23] This troubling level of impunity could lead to self-censorship by frightened reporters, and demonstrates just how little has been done to protect journalists. Brazil’s press is still relatively free, especially compared to some of its neighbors, but Brazilian supporters of press freedom should definitely begin sounding the alarm.

Google transparency report about Brazil:

Why Rio’s ‘Favelas’ Disappeared On Google Maps

In the run-up to the 2014 World Cup and 2016 Olympic Games, Brazilian tourist boards and Rio’s city hall have been keen to maintain a squeaky-clean image not only in the real world but the digital one as well. So much so, that they asked Google to remove the word “favela” from its city maps. The term itself means slum or shantytown in Portuguese. Hundreds were previously identified as such on maps, but are now labeled as “morros” or hills. Officials believe the change will reduce the prominence given to the favela communities, which they said were given greater importance on maps than conventional neighborhoods like Humaita and Cosme Velho.

Brazil | Freedom House

In late 2012 and early 2013, a spate of legal cases concerning intermediary liability drew worldwide attention to Brazil’s internet policies. In September 2012, a Brazilian electoral court issued arrest warrants for two senior Google Brazil executives, Edmundo Luiz Pinto Balthazar and Fabio Jose Silva Coelho, for failure to remove content prohibited under electoral law. The executives were accused of violating a vague provision that bans campaign material which “offend[s] the dignity or decorum” of a candidate.

(Crossposted from my other blog, in portuguese -- by mistake, actually ;)

Saturday, August 17, 2013

When companies do it, shame on them. When politicians do it, that's the future.

The Next Frontier of Consumer Exploitation By Corporations
"So what if Google knows where I'm planning my next vacation and suggests hotels for me? Sure, it's creepy, but is there really any harm in companies tracking my info to target ads to me? Professor Ryan Calo (UW law) is out with a new paper that demonstrates the real harm behind these practices, making consumers vulnerable to making decisions that go against their self-interest (ie: predatory lending, price inflation, etc). The Atlantic has an article today that outlines the new research."
Obama, Romney Data Scientists Strike Out On Their Own
"The self-described nerds of President Obama's presidential campaign last year are back using big data analytics, this time to help Newark Mayor Cory Booker achieve a landside primary win Tuesday in the New Jersey Democratic primary for a vacant U.S. Senate seat. The data scientists from Obama and Romney campaigns recently formed their own consulting businesses within months of each other. The chief data scientist for Romney's campaign, Alex Lundry, co-founded Deep Root Analytics. He gives credit to the Obama campaign's data effort in 2012. But since last year's election, "what you are seeing is a flurry of activity on the right to make sure that we not only catch them, but surpass them," Lundry said. Meanwhile, the co-founder of BlueLabs, Chris Wegrzyn, a senior member of Obama's 2012 campaign analytics department, says last year was turning point for big data analytics in elections. "Usually the nerds in the back room don't warrant a great deal of attention, especially in politics," said Wegrzyn, "but the world is changing.""
Update 2014.03.01: I just realized that the same point (about neopopulism) has been made by Henry Kissinger at his talk at Google.

Tuesday, August 13, 2013

Do violent video games lead to real violence?

I have the impression that playing a (violent) video game has similar effects on real life as reading a violent book (or even the bible), a comics or watching a movie. After a tragedy in Brazil many people were quick to blame violent games (I was reminded of this), so I decided to refresh my memory about blog posts I have read (although I lost my RSS memory after google reader died), together with some commentaries new for me.

First are some blog posts at least marginally relevant.

Human-like opponents lead to more aggression in video game players |

“The Perception of Human Appearance in Video Games: Toward an Understanding of the Effects of Player Perceptions of Game Features,” published in the May 2013 issue of Mass Communication and Society, comes as lawmakers and the public are freshly debating the possible risks that violent games may pose to impressionable players. “

It’s important to think in terms of risk factors,” says Kirstie Farrar, associate professor of communication at UConn and the lead researcher on the study. “The research clearly suggests that, among other risk factors, exposure to violent video games can lead to aggression and other potentially harmful effects.” (...)

Participants who battled what they perceived as human-looking characters in the game were more likely to have aggressive thoughts and words than those who had shot down monstrous nonhuman characters.

Is the internet dangerous? Taking a closer look at Baroness Greenfield’s concerns — Risk Science Blog

People – including children and teens – are pretty sophisticated when it comes to distinguishing between fiction and reality.  I admit I worry still about the moral outlook that some games potentially instill in my teens.  But I have similar worries about many other influences.  When I was a kid, shooting each other with toy guns, or even sticks or our fingers, was all the rage.  Morally questionable?  Probably.  But did we all grow up thinking that there there are no consequences to our actions?  I don’t think so.  The relationship between video/gaming environments and personal/social interactions is an area of active research.  But to my knowledge those relationships are complex, and evidence for clear cause and effect when it comes to antisocial behavior is far from obvious. (...)

My two teens indulge in everything from complex puzzles to social simulation games to role playing to sports games to good old fashion shoot’em’ups.  And in many cases, these are social games.  My son will talk with friends in real time as he plays on his XBox.  He has friends over for tournaments, or arranges on-line competitions.  Gaming is part of his social community. Both my teens have rich social interactions around the on-line games they play.  Far from being socially isolating, they are socially enriching.

Guns don't kill people, video game players do | Martin Robbins | Science |

My point is so tediously obvious that I can scarcely be bothered to write it, but here I go anyway: if parents don't want their prepubescent progeny playing 18-rated video games, they shouldn't buy them 18-rated video games. (That many still do suggests Britain's breeders aren't quite as worried as the Daily Mail would like them to be.) Not that the 'research' cited says anything about violent video games to begin with. BAAM conducted a survey of 204 parents of children aged nine to eighteen, asking about their use of computer games: anything from Tetris to GTA IV via SimCity. This produced the following results:

"Forty-six per cent said their sons or daughters had become 'less co-operative' since they started playing video games. Forty-four per cent said they were more 'rude or intolerant towards others', 40 per cent said they were more impatient, 36 per cent reported an increase in 'aggressive behaviour', 29 per cent cited more mood swings and 26 per cent said their offspring had become more reclusive."

26% of parents thought their teen offspring had become more reclusive in the years since they started playing video games. No doubt pedantic nay-sayers will whine on about the other SEVENTY-BLOODY-FOUR PER CENT of kids who either didn't become more reclusive or became less reclusive, or ask how 'reclusive' is even defined or measured in the first place; but if that incredible correlation doesn't persuade you, well then by golly-gosh I don't know what will. Even the most 'persuasive' of those figures stands at just 46%. That, astonishingly, is the proportion of parents who think their teenaged children are becoming less cooperative with time.

Violent video games alter brain function in young men

A functional magnetic resonance imaging (fMRI) analysis of long-term effects of violent video game play on the brain has found changes in brain regions associated with cognitive function and emotional control in young adult men after one week of game play. The results of the study were presented today at the annual meeting of the Radiological Society of North America (RSNA). The controversy over whether or not violent video games are potentially harmful to users has raged for many years, making it as far as the Supreme Court in 2010. But there has been little scientific evidence demonstrating that the games have a prolonged negative neurological effect. "For the first time, we have found that a sample of randomly assigned young adults showed less activation in certain frontal brain regions following a week of playing violent video games at home," said Yang Wang, M.D., assistant research professor in the Department of Radiology and Imaging Sciences at Indiana University School of Medicine in Indianapolis. "These brain regions are important for controlling emotion and aggressive behavior."

Sandy Hook Shooting: Video Game Violence Isn't to Blame |

As a video game violence researcher and someone who has done scholarship on mass homicides, let me state very emphatically: There is no good evidence that video games or other media contributes, even in a small way, to mass homicides or any other violence among youth. Our research lab recently published new prospective results with teens in the Journal of Youth and Adolescence indicating that exposure to video game violence neither increased aggressive behaviors, nor decreased prosocial behaviors. (...)

At this point, we don’t know much about Adam Lanza’s media use history. Given that, as researchers Cheryl Olson and Lawrence Kutner note in their book Grand Theft Childhood, almost all young males play violent video games at least occasionally, it’s playing the odds to say Lanza did too.

Do violent video games reduce violent crime? | tvSmarter

The result would be that most people who play lots of violent video games would not have their aggression level increased to the point of committing a violent crime, but that a minority of players would indeed have their level of aggressiveness increased to the point of committing a violent crime. But is this what is actually happening? Has the enormous dedications of millions of players to violent video games actually lead to an increase in violent crime?

Apparently not. According to FBI Uniform Crime Reports, the homicide rate has gone down dramatically since the early 1990s. (...)

And the argument that the decrease in violent crime during the 1990s , which coincided with the introduction of violent video games, also during the 1990s, proves that violent video games do not cause real-life violence is also not proof-positive. 

Modern Technology is Making You Stupid. Sorry What? |

I was however, (not so) shocked to discover that the review is overwhelmingly positive, here are just a few of the many findings from studies cited in the review, none of which Professor Greenfield addressed:

  1. Owners of computers are seven percent more likely to graduate school (after controlling for confounding factors such as home environment)
  2. Interactive programming on television can improve language (whilst programmes like the “tellytubbies” damage language skills) 
  3. Playing action video games is associated with a number of enhancements in vision, attention, cognition, and motor control

Emotion, autonomy and psychopaths: a cyberpsychologist's take on video games | Technology |

The research suggests that human beings feel alienated from people who do not emote in the top half of their face, which correlates with how much video-game players relate to the facial animation in game characters. The research also suggests that the reason this might happen is that people who display psychopathic behaviour often are expressionless in the top half of their face, which sets off warning signals in people around them. In the same manner, if game developers were to deliberately not animate the facial expression in a character, it might transmit a significant feeling of alienation and fear to a player about a character, which could be used in horror games, for example.

Does violence in video games lead to real world violence? (Video) | by @mjrobbins | Science |

Can violent video games cause people to be violent in the real world? Cam Robinson investigates for Gamespot's What If Machine, including interviews with Guardian Science blogger Martin Robbins and Middlesex University psychologist Dr Mark Coulson.

Could Angry Birds lead to mass murder? | Martin Robbins | Science |

The research literature is just as vague. MIT's Professor Henry Jenkins has been a vocal critic of flaws in early studies, that hinted at a link between gaming and violence. He points out that children in studies are often exposed to violence in highly artificial contexts, that their supposed 'aggression' is measured in unrealistic ways (there are some obvious problems with "punching rubber dolls as a marker of real-world aggression" for example), that research fails to account for the ability of humans (and other apes) to "make basic distinctions between play fighting and actual combat", and that correlations in some studies could easily be explained by violent children choosing to play violent video games rather than video games causing children to become more violent.

BBC - Future - Science & Environment - Searching for a cure to violence

Weber, himself an avid gamer, initially thought the idea of using video games to test people’s reaction to violence was crazy, but then he and his colleagues eventually jury-rigged a way to do it: they placed a screen at the back of the functional MRI scanner, which the subject views through a mirror image reflected in the front, while using a joystick to control their avatar. As the subject hunts for innocent victims to kill off, researchers measure activation of the neural pathways. “We have a condition with full violence: They drive and run over little animals and pets,” Weber says. “They kill. It’s just terrible.” Six years ago, Weber and his colleagues demonstrated that violent video games activated the same neural pathways as real violence.

Violent video games: small causal link with aggression « Mind Hacks

There have been several similar studies in recent years which have come to different conclusions, based on whether the results have been thought to have been affected by publication bias or not. In other words, while the published studies suggest there is a small reliable effect of video games on aggression some reviews have suggested this is because fewer of the studies that don’t find a link actually get published.

Christopher Ferguson: Video Games Don't Make Kids Violent |


Our modern fears over VVGs appear to be in line with prior moral panics over media as diverse as jazz music, comic books and Harry Potter. Granted, too much passive activity, including video games, can contribute to obesity. Like anything else, gaming should be enjoyed in moderation, balanced with outdoor activity and allowing enough time for family and schoolwork. A very small number of kids, about 3%, exhibit signs of pathological gaming. But regarding concerns about aggression, it appears to be that, fairly early on, children learn to distinguish between fantasy and reality, and their brains don’t treat these phenomena the same. Santa Claus is a prime example.

And then some articles (some of them referred to in the posts above) -- as usual it's a very incomplete list:

1 -- Understanding the Effects of Violent Video Games on Violent Crime by Scott Cunningham, Benjamin Engelstätter, Michael R. Ward :: SSRN (alternative version here)

Video games are an increasingly popular leisure activity. As many of best-selling games contain hyper-realistic violence, many researchers and policymakers have concluded that violent games cause violent behaviors. Evidence on a causal effect of violent games on violence is usually based on laboratory experiments finding violent games increase aggression. Before drawing policy conclusions about the effect of violent games on actual behavior, these experimental studies should be subjected to tests of external validity. Our study uses a quasi-experimental methodology to identify the short and medium run effects of violent game sales on violent crime using time variation in retail unit sales data of the top 50 selling video games and violent criminal offenses from the National Incident Based Reporting System (NIBRS) for each week of 2005 to 2008. We instrument for game sales with game characteristics, game quality and time on the market, and estimate that, while a one percent increase in violent games is associated with up to a 0.03% decrease in violent crime, non-violent games appear to have no effect on crime rates.

2 -- A longitudinal study of the effects of Internet use and videogame playing on academic performance and the roles of gender, race and income in these relationships

In this research we examined the effects of Internet use and videogame playing on children’s academic performance. Gender, race, and income were also considered. Participants were 482 youth, average age 12 years old. One-third were African American and two-thirds were Caucasian American. All measures were completed twice, first in Year 1 and then one year later, Year 2. Results indicated that greater Internet use was associated with better reading skills, but only for youth initially low in reading skills. Videogame playing was associated with better visual-spatial skill but also with lower GPAs. Gender, race and income influenced Internet use, videogame playing and academic performance but not the relationships between using these technologies and academic performance. Implications of the results for increasing the benefits of technology use are discussed.

3 -- Evidence for publication bias in video game violence effects literature: A meta-analytic review

Violence in video games has come under increasing research attention over the past decade. Researchers in this area have suggested that violent video games may cause aggressive behavior among players. However, the state of the extant literature has not yet been examined for publication bias. The current meta-analysis is designed to correct for this oversight. Results indicated that publication bias does exist for experimental studies of aggressive behavior, as well as for non-experimental studies of aggressive behavior and aggressive thoughts. Research in other areas, including prosocial behavior and experimental studies of aggressive thoughts were less susceptible to publication bias. Moderator effects results also suggested that studies employing less standardized and reliable measures of aggression tended to produce larger effect sizes. Suggestions for future violent video game studies are provided.

4 -- Patents and Antitrust: Video Games and Violent Crime

Psychology studies of the effects of playing video games have found emotional responses and physical reactions associated with reinforced violent and anti-social attitudes. It is not clear, however, whether these markers are associated with increases in one's preferences for anti-social behaviors or whether virtual behaviors act to partially sate one's desire for actual antisocial behaviors. Violent or criminal behaviors in the virtual world and in the physical world could plausibly be either complements or substitutes. A finding of one versus the other would have diametrically opposing policy implications. I study the incidence of criminal activity as related to a proxy for increased gaming, the number of game stores, from a panel of US counties from 1994 to 2004. With fixed county and year effects, I can examine if changes relative increases in gaming in an area are associated with relative increases or decreases in criminal activity. For six of eight categories of crime, more game stores are associated with significant declines in crime rates. Proxies for other leisure activities, sports and movie viewing, do not have a similar effect. For confirmation, I also find that mortality rates, especially mortality rates stemming from injuries, also are negatively related to the number of game stores.

5 -- Video Games and Adolescent Fighting

Psychologists have found positive correlations between playing violent video games and violent and antisocial attitudes. However, these studies typically do not control for other covariates, particularly sex, that are known to be associated with both video game play and aggression. This study exploits the Youth Risk Behavior Survey, which includes questions on video game play and fighting as well as basic demographic information. With both parametric and nonparametric estimators, as there is accounting for more demographic covariates, the video game effects become progressively weaker. The overall link between video games and fighting is modest and not statistically significant. The remaining positive association appears only for individuals who play 4 or more hours per day.

6 -- Neuron - Children, Wired: For Better and for Worse

Children encounter technology constantly at home and in school. Television, DVDs, video games, the Internet, and smart phones all play a formative role in children's development. The term “technology” subsumes a large variety of somewhat independent items, and it is no surprise that current research indicates causes for both optimism and concern depending upon the content of the technology, the context in which the technology immerses the user, and the user's developmental stage. Furthermore, because the field is still in its infancy, results can be surprising: video games designed to be reasonably mindless result in widespread enhancements of various abilities, acting, we will argue, as exemplary learning tools. Counterintuitive outcomes like these, besides being practically relevant, challenge and eventually lead to refinement of theories concerning fundamental principles of brain plasticity and learning.

7 -- Causal or spurious: Using propensity score matching to detangle the relationship between violent video games and violent behavior

Throughout the past decade, numerous states have passed legislation to prohibit the sale of violent video games to children, usually in conjunction with an argument that exposure to violent media increases violent behavior. However, the link between video games and violence is not yet fully understood. This study uses propensity score matching as a method to more adequately address the underlying issue of causality. Using a sample of 6567 8th grade students, these analyses test whether there is a causal link between playing violent video games and violence, non-violent deviance and substance use. Results indicate a substantial decrease in the relationship between video games and these outcomes when a matched sample is used. This suggests that the strength of evidence supporting a relationship has likely been overestimated using other methodologies.

8 -- PsycNET - Comfortably numb or just yet another movie? Media violence exposure does not reduce viewer empathy for victims of real violence among primarily Hispanic viewers. (commented here)

Continued debate exists regarding the impact of media violence exposure on viewers' thoughts and behaviors. One facet of this debate has focused on the possibility that viewing media violence may desensitize viewers to the suffering of others and reduce their empathy. In the current study, 238 mostly Hispanic, young adults were randomized to watch either a violent or nonviolent TV show. Participants also watched clips of either fictional victims of violence (i.e., movie clips) or clips of actual people being injured or killed. Participants were significantly more empathic of victims' suffering when they knew they were watching real violence rather than fictional violence. However, previous exposure to a violent or nonviolent TV show did not reduce empathy. These results suggest that, at least among a primarily Hispanic audience, viewers' processing of media depends upon whether they understand it to be real or fictional, and media violence does not necessarily reduce empathy to real-life violence.

9 -- Not Worth the Fuss After All? Cross-sectional and Prospective Data on Violent Video Game Influences on Aggression, Visuospatial Cognition and Mathematics Ability in a Sample of Youth

The United States Supreme Court’s recent decision relating to violent video games revealed divisions within the scientific community about the potential for negative effects of such games as well as the need for more, higher quality research. Scholars also have debated the potential for violent games to have positive effects such as on visuospatial cognition or math ability. The current study sought to extend previous literature by using well-validated clinical outcome measures for relevant constructs, which have generally been lacking in past research. Cross-section data on aggression, visuospatial cognition, and math achievement were available for a sample of 333 (51.7 % female) mostly Hispanic youth (mean age = 12.76). Prospective 1-year data on aggression and school GPA were available for 143 (46.2 % female) of those youth. Results from both sets of analysis revealed that exposure to violent game had neither short-term nor long-term predictive influences on either positive or negative outcomes. A developmental analysis of the cross-sectional data revealed that results did not differ across age categories of older children, preadolescents or adolescents. Analysis of effect sizes largely ruled out Type II error as a possible explanation for null results. Suggestions for new directions in the field of video game research are proffered.

10 -- A longitudinal test of video game violence influences on dating and aggression: A 3-year longitudinal study of adolescents

Background In 2011 the field of video game violence experienced serious reversals with repudiations of the current research by the US Supreme Court and the Australian Government as non-compelling and fundamentally flawed. Scholars too have been calling for higher quality research on this issue. The current study seeks to answer this call by providing longitudinal data on youth aggression and dating violence as potential consequences of violent video game exposure using well-validated clinical outcome measures and controlling for other relevant predictors of youth aggression.

Method A sample of 165, mainly Hispanic youth, were tested at 3 intervals, an initial interview, and 1-year and 3-year intervals.

Results Results indicated that exposure to video game violence was not related to any of the negative outcomes. Depression, antisocial personality traits, exposure to family violence and peer influences were the best predictors of aggression-related outcomes.

Interpretation The current study supports a growing body of evidence pointing away from video game violence use as a predictor of youth aggression. Public policy efforts, including funding, would best be served by redirecting them toward other prevention programs for youth violence.

11 -- PsycNET - A longitudinal study of the association between violent video game play and aggression among adolescents

In the past 2 decades, correlational and experimental studies have found a positive association between violent video game play and aggression. There is less evidence, however, to support a long-term relation between these behaviors. This study examined sustained violent video game play and adolescent aggressive behavior across the high school years and directly assessed the socialization (violent video game play predicts aggression over time) versus selection hypotheses (aggression predicts violent video game play over time). Adolescents (N = 1,492, 50.8% female) were surveyed annually from Grade 9 to Grade 12 about their video game play and aggressive behaviors. Nonviolent video game play, frequency of overall video game play, and a comprehensive set of potential 3rd variables were included as covariates in each analysis. Sustained violent video game play was significantly related to steeper increases in adolescents' trajectory of aggressive behavior over time. Moreover, greater violent video game play predicted higher levels of aggression over time, after controlling for previous levels of aggression, supporting the socialization hypothesis. In contrast, no support was found for the selection hypothesis. Nonviolent video game play also did not predict higher levels of aggressive behavior over time. Our findings, and the fact that many adolescents play video games for several hours every day, underscore the need for a greater understanding of the long-term relation between violent video games and aggression, as well as the specific game characteristics (e.g., violent content, competition, pace of action) that may be responsible for this association.

12 -- PsycNET - Violent video games and the Supreme Court: Lessons for the scientific community in the wake of Brown v. Entertainment Merchants Association

In June 2011 the U.S. Supreme Court ruled that video games enjoy full free speech protections and that the regulation of violent game sales to minors is unconstitutional. The Supreme Court also referred to psychological research on violent video games as “unpersuasive” and noted that such research contains many methodological flaws. Recent reviews in many scholarly journals have come to similar conclusions, although much debate continues.

Given past statements by the American Psychological Association linking video game and media violence with aggression, the Supreme Court ruling, particularly its critique of the science, is likely to be shocking and disappointing to some psychologists. One possible outcome is that the psychological community may increase the conclusiveness of their statements linking violent games to harm as a form of defensive reaction.

However, in this article the author argues that the psychological community would be better served by reflecting on this research and considering whether the scientific process failed by permitting and even encouraging statements about video game violence that exceeded the data or ignored conflicting data. Although it is likely that debates on this issue will continue, a move toward caution and conservatism as well as increased dialogue between scholars on opposing sides of this debate will be necessary to restore scientific credibility. The current article reviews the involvement of the psychological science community in the Brown v. Entertainment Merchants Association case and suggests that it might learn from some of the errors in this case for the future.

13 -- Motion capture controls negate the violent video-game effect

Considerable research suggests that violent video game play increases players’ aggression. However, few studies have investigated this effect in the now ubiquitous context of motion-capture technology. Study 1 used a 2 × 2 design, with a violent (Soul Calibur) and non-violent (Lego Indiana Jones) game, played under analog (Playstation 3) and motion-capture (Nintendo Wii) conditions. Violent video game play led to less aggression when participants used motion-capture controls. Study 2 eliminated potential confounds by using the only game on the Wii system that can be played identically with or without motion capture (Punch-Out!!). Again, participants who used motion-capture were less aggressive. Study 3 looked for effects of cooperative vs. competitive play during 2-player motion-capture gaming (Soul Calibur, Wii). Participants using motion-capture controls in competitive and cooperative scenarios did not differ from baseline. These results run counter to standard models relating violent video game play to aggressive behavior, highlighting the difficulty in anticipating the effects of newer, more immersive technology

14 -- Studies in Media and Communications | A Futile Game: On the Prevalence and Causes of Misguided Speculation about the Role of Violent Video Games in Mass School Shootings

Purpose – Video game violence has historically been offered by policy-makers and some scholars as one contributing factor to mass homicides, particularly with shooters who are young, male, and white. However, the evidence for or against such beliefs has not been closely examined.

Approach – The current chapter examines the research exploring violent video game playing and its links with violent and aggressive behavior. Further, research regarding mass school shooters is also examined. The chapter also engages in a sociological analysis of structural factors within both the general society and scientific community by which media is often identified as a potential cause of social problems.

Findings – Current evidence cannot support proposed links between video game violence and aggressive or violent behavior, whether mild or mass homicides. Efforts to blame mass homicides on video games appear to be due to unfamiliarity with games among older adults, prejudicial views of young offenders, and a well-identified cycle of moral panic surrounding media as a scapegoat for social ills. Poor peer-reviewing within the scientific community allowed scholars to participate in this moral panic.

Social implications – Time focused on video games as a cause of mass school shootings is time wasted. Discussions of mental health issues and mental health care are likely to bear more fruit in relation to mass school shootings.

15 -- Virtually justifiable homicide: The effects of prosocial contexts on the link between violent video games, aggression, and prosocial and hostile cognition - Gitter - 2013 - Aggressive Behavior - Wiley Online Library

Previous work has shown that playing violent video games can stimulate aggression toward others. The current research has identified a potential exception. Participants who played a violent game in which the violence had an explicitly prosocial motive (i.e., protecting a friend and furthering his nonviolent goals) were found to show lower short-term aggression (Study 1) and show higher levels of prosocial cognition (Study 2) than individuals who played a violent game in which the violence was motivated by more morally ambiguous motives. Thus, violent video games that are framed in an explicitly prosocial context may evoke more prosocial sentiments and thereby mitigate some of the short-term effects on aggression observed in previous research. While these findings are promising regarding the potential aggression-reducing effects of prosocial context, caution is still warranted as a small effect size difference (d = .2–.3), although nonsignificant, was still observed between those who played the explicitly prosocial violent game and those who played a nonviolent game; indicating that aggressive behavior was not completely eliminated by the inclusion of a prosocial context for the violence.

16 -- Much ado about nothing: the misestimation and overinterpretation of violent video game effects in eastern and western nations: comment on Anderson et al. (2010). [Psychol Bull. 2010]

The issue of violent video game influences on youth violence and aggression remains intensely debated in the scholarly literature and among the general public. Several recent meta-analyses, examining outcome measures most closely related to serious aggressive acts, found little evidence for a relationship between violent video games and aggression or violence. In a new meta-analysis, C. A. Anderson et al. (2010) questioned these findings. However, their analysis has several methodological issues that limit the interpretability of their results. In their analysis, C. A. Anderson et al. included many studies that do not relate well to serious aggression, an apparently biased sample of unpublished studies, and a "best practices" analysis that appears unreliable and does not consider the impact of unstandardized aggression measures on the inflation of effect size estimates. They also focused on bivariate correlations rather than better controlled estimates of effects. Despite a number of methodological flaws that all appear likely to inflate effect size estimates, the final estimate of r = .15 is still indicative of only weak effects. Contrasts between the claims of C. A. Anderson et al. (2010) and real-world data on youth violence are discussed.

17 -- A Multivariate Analysis of Youth Violence and Aggression: The Influence of Family, Peers, Depression, and Media Violence

Objective To examine the multivariate nature of risk factors for youth violence including delinquent peer associations, exposure to domestic violence in the home, family conflict, neighborhood stress, antisocial personality traits, depression level, and exposure to television and video game violence.

Study design A population of 603 predominantly Hispanic children (ages 10-14 years) and their parents or guardians responded to multiple behavioral measures. Outcomes included aggression and rule-breaking behavior on the Child Behavior Checklist (CBCL), as well as violent and nonviolent criminal activity and bullying behavior.

Results Delinquent peer influences, antisocial personality traits, depression, and parents/guardians who use psychological abuse in intimate relationships were consistent risk factors for youth violence and aggression. Neighborhood quality, parental use of domestic violence in intimate relationships, and exposure to violent television or video games were not predictive of youth violence and aggression.

Conclusion Childhood depression, delinquent peer association, and parental use of psychological abuse may be particularly fruitful avenues for future prevention or intervention efforts. 

18 -- THE ROLE OF MEDIA VIOLENCE IN VIOLENT BEHAVIOR - Annual Review of Public Health, 27(1):393

Media violence poses a threat to public health inasmuch as it leads to an increase in real-world violence and aggression. Research shows that fictional television and film violence contribute to both a short-term and a long-term increase in aggression and violence in young viewers. Television news violence also contributes to increased violence, principally in the form of imitative suicides and acts of aggression. Video games are clearly capable of producing an increase in aggression and violence in the short term, although no long-term longitudinal studies capable of demonstrating long-term effects have been conducted. The relationship between media violence and real-world violence and aggression is moderated by the nature of the media content and characteristics of and social influences on the individual exposed to that content. Still, the average overall size of the effect is large enough to place it in the category of known threats to public health.

19 -- A meta-analysis of pathological gaming prevalence and comorbidity with mental health, academic and social problems

Background Mental health professionals, policy makers and the general public continue to debate the issue of pathological video gaming. Scholars disagree on the prevalence and diagnostic criteria for this potential new disorder. The current meta-analysis considers existing scholarship to examine how differing measurement methods influence prevalence rates and associations with other mental health problems.

Method Thirty three published studies and doctoral dissertations were analyzed in meta-analysis. Prevalence rates and comorbidity with other mental health problems were examined according to measurement method.

Results Prevalence estimates and comorbidity with other problems varied widely between studies. Measurement which attempted to replicate “pathological gambling” approaches produced higher prevalence estimates and lower comorbidity estimates than methods which focused on the interfering nature of pathological gaming. The most precise measures produce an overall prevalence rate of 3.1%.

Interpretation Diagnostic analogies with pathological gambling may produce spuriously high prevalence estimates, potentially over identifying non-pathological players as pathological. Diagnostic approaches focused on the interfering nature on other life needs and responsibilities may have greater validity and utility.

20 -- Just a game after all: Violent video game exposure and time spent playing effects on hostile feelings, depression, and visuospatial cognition

Research in the domain of video game violence continues to be contentious and debated. Scholars have examined both positive and negative effects of violent games, although results thus far have been inconclusive and systematic internal validity problems have been identified with past research. The current study adds to this growing literature by examining the effects of video game violence exposure and time spent playing on depression, hostility, and visuospatial cognition. This study improves upon previous research by matching game conditions carefully on confounding variables identified as problems by other scholars. In a laboratory setting, 100 participants were randomly assigned into one of six conditions based on two independent variables (time spent playing and type of video game). Results indicated that neither randomized video game play nor time spent playing a video game had any effect on depression, hostility, or, visuospatial cognition. Effect size estimates were below levels for practical significance. These results suggest that both positive and negative influences of violence in video games may be limited in scope.

21 -- Preference for Violent Electronic Games and Aggressive Behavior among Children: The Beginning of the Downward Spiral? - Media Psychology - Volume 14, Issue 3

A one-year longitudinal study with 324 German third and fourth graders was conducted in order to find out whether a preference for violent electronic games socializes children to become more aggressive or whether aggressive individuals tend to select this type of game. Cross-lagged panel analyses suggest that children who were rated as openly aggressive at Time 1 intensified their preference for violent electronic games over time. We determined that it could be ruled out that this selection effect was due to a number of underlying variables ranging from ecological variables (neighborhood) to family variables (migration status, older brother) and child variables (gender, self-esteem, level of achievement). Discussion focuses on the emerging preference for violent electronic games among children.

22 -- PLOS ONE: Failure to Demonstrate That Playing Violent Video Games Diminishes Prosocial Behavior

Background Past research has found that playing a classic prosocial video game resulted in heightened prosocial behavior when compared to a control group, whereas playing a classic violent video game had no effect. Given purported links between violent video games and poor social behavior, this result is surprising. Here our aim was to assess whether this finding may be due to the specific games used. That is, modern games are experienced differently from classic games (more immersion in virtual environments, more connection with characters, etc.) and it may be that playing violent video games impacts prosocial behavior only when contemporary versions are used.  
Methods and Findings Experiments 1 and 2 explored the effects of playing contemporary violent, non-violent, and prosocial video games on prosocial behavior, as measured by the pen-drop task. We found that slight contextual changes in the delivery of the pen-drop task led to different rates of helping but that the type of game played had little effect. Experiment 3 explored this further by using classic games. Again, we found no effect.  
Conclusions We failed to find evidence that playing video games affects prosocial behavior. Research on the effects of video game play is of significant public interest. It is therefore important that speculation be rigorously tested and findings replicated. Here we fail to substantiate conjecture that playing contemporary violent video games will lead to diminished prosocial behavior.

Thursday, June 20, 2013

Master in Biological Sciences (MBS) at the University of Vigo, SPAIN

We are pleased to announce the launch of the Master in Biological Sciences (MBS) of the University of Vigo (Spain) for the academic year 2013-2014. The MBS aims to provide future professionals in biology with the knowledge, skills and insights they will need to take on top science-based positions around the world (academic, research, environmental and biomedical applications, bioinformatics).

The official language of the MBS is English. Non-English speaking students must demonstrate that they have acquired the minimum language skills to study the Master. No additional proof is required, although holding a B1 or equivalent title would be desirable. In addition, personal interviews with members of the Academic Commission might be required before admission.

The staff teaching in this master cover a wide range of areas giving students contact with renowned researchers, specialists in developing professional skills and practitioners from industry. They all have long-term teaching experience.

For those students interested in doing a PhD, there are two Doctorate Programmes linked to the MBS, and rated as excellent from the Spanish Education Ministry

Master outline

The MSc programme comprises 120 ECTS in total distributed between 2 academic years (60 ECTS each one). During the 1st year, students will follow 4 general courses (Basic Module, 12 ECTS) on basic tools for designing and performing experimental tasks, analysing results and elaborating conclusions. This will be followed by the Elective Component (42 ECTS) where students will have the chance to follow specific tracks:

  1. Molecular Biology for Health and Life Sciences
  2. Environmental Sciences
  3. Bioinformatics and Computational Biology
  4. Green-Industries Management
The main part of the second year consists of a major project (Mandatory Major Project 48 ECTS), in which students will acquire advanced knowledge on different methodologies and techniques under the guidance of experienced experts to fulfil your professional requirements and possibly to gain a better position on the job market.
Finally, all students need to carry out a Master’s thesis (12 credits).

APPLICATION for academic year 2013-14
       First pre-registration period: 28 June to 4 July 2013
       Second pre-registration period: 27 August to 3 September 2013

DOCUMENTS that must accompany the application form:
       DNI, NIE or Passport
       Bachelor’s degree diploma
       Brief CV

María Jesús Iglesias Briones (coordinator)

Master in Biological Sciences
Facultad de Biología
Campus Lagoas-Marcosende
Universidad de Vigo
36310 Vigo, Spain.


Thursday, April 25, 2013

ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, Portugal, 29-30 April 2013

I just received the following info about the AES Conference:

ADVANCES IN ECOLOGICAL SPECIATION (AES) Conference, CIBIO/UP, Portugal, 29-30 April 2013

LIVE BROADCAST of the AES Conference!

We are happy to announce that the AES Conference can be followed Live on streaming from

If you want to join us please check out the program of the AES Conference from our website ( The Live broadcast will be on Portugal local time (UTC/GMT+1hour).

Invited Speakers:

Dolph Schluter (Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, Canada)
Felicity Jones (Friedich Miescher Laboratory of the Max Planck Society, Tubingen, Germany)
Walter Salzburger (Zoological Institute, University of Basel, Switzerland)
Sebastien Renaut (Botany Department, University of British Columbia, Vancouver, Canada)
Roger Butlin (Department of Animal and Plant Sciences, University of Sheffield, UK)

You can also follow the AES Conference on:

The conference videos will be available afterwards at the Campus do Mar website, and you can dowload the book of abstracts right now.

Saturday, April 20, 2013

Do as I say, not as I've been doing

Raising standards : Nature Immunology 14, 415 (2013) doi:10.1038/ni.2603 -- Nature journals' updated editorial policies aim to improve transparency and reproducibility:

. For example, authors will need to describe methodological parameters that may introduce bias or influence robustness and to provide precise characterization of key reagents, such as cell lines and antibodies, that may be subject to biological variability.
To help improve the statistical robustness of papers, the Nature journals will now employ statisticians as consultants on certain papers, at the editor's discretion and on the referees' suggestions. (...) Exploratory investigations often are not amenable to the same degree of statistical rigor as hypothesis-testing studies.
Those who would put effort into documenting the validity or irreproducibility of a published piece of work have little prospect of seeing their efforts valued by journals and funders; meanwhile, funding and efforts are wasted on false assumptions.

These are certainly much needed changes in NPG's policy, provided they are not just lip service while in practice neglecting valid statistical criticisms to their flagship papers. I remain skeptical. Would they put their money where their mouths are and demand openness for already published data or allow for retroactive post-review? (The infamous "your criticism won't add to the discussion" boilerplate reply?) Anyway, a few more links:

What We Have Here is a Failure to Replicate | Evolutionary Psychology:

Discussions of why replications aren’t more common – including Pashler’s remarks – focus extensively (but not exclusively) on incentives. If a researcher attempts to do an exact replication of published work, there are two possible results. If the result replicates successfully, it is likely to be difficult to publish because journals tend not to publish replications, though this is changing.(...) Other journals are proving more receptive to publishing replications – and failures to replicate – which will probably have some beneficial effect. In any case, my guess, though I don’t know, is that replications of results are cited relatively infrequently, especially compared to the original results. Publishing failures to replicate is likely no easier than publishing successes.

Authors, Don’t Call Us, We’ll Call You | Psychology Today:

Privileged access is only one of the many means by which political forces distort debates about evidence and select which conclusions are legitimized and which perspectives are marginalized. Because privileged access articles often escape rigorous peer review, the science is often flabby and grossly simplistic, and claims in privileged access articles can be extravagant.

Strategies for challenging inaccuracies and outright misrepresentations in privileged access articles are limited. Journals that grant privileged access also often restrict publishing of letters to the editor to only what authors indicate a willingness to respond. A refusal to respond is effective censorship, causing criticism to be barred from publishing. Even when letters are accepted, they often have severe restrictions on their length (often 400 - 600 words), are often published much later than the privileged access articles, fail to be indexed in ISI Web of science or other electronic bibliographic sources, or are limited to e-letters, not the paper editions of the Journal. It is notable that the webpages of the journals making the most use of privileged access articles do not link subsequent critiques with the original article, so that anyone in defining the critiques has to search for them separately.

Non-consensual replication | john hawks weblog:

You are building one assumption upon another. The disturbing part is that the discipline accepts that some researchers just have a "knack" for making a particular experimental design work, and other researchers may have trouble recreating the exact conditions. That very attitude enables fraud, as we have seen repeatedly during the last few years. In science, if no one else can make the experiment work, it didn't happen.

Opinion: Missing Methods | The Scientist Magazine®:

How has the requirement to share every iota of technical detail with the research community given way to “as described elsewhere,” elsewhere being Never Never Land?  First, I blame the journal editorial boards.  The push in recent years to shorten papers and limit the number of figures has never been clearly rationalized to the research public.
Next, I blame the authors. Failure to transmit clear and detailed technical details is not just a sin against the scientific community, it’s also indicative of poor internal mentoring skills. (...) This brings up the worst consequence to our increasingly lax eye for technical detail: faster publication of findings in higher impact journals will mean squat if the data will not stand the test of time, and in our field, this means experimental reproducibility.
The recent proliferation of smaller journals devoted solely to publishing novel methods and technologies is a great advance in this regard.

Actually this last conclusion is wrong -- the existence of journals devoted to these details is an incentive for the authors to hide the details from other manuscripts, in the (sometimes unfulfilled) hope that this slice of research will be a publication on its own. That is, you persuade authors to think about the method, software and data/conclusions as independent entities, and consequently it will become not more, but less likely for them to provide you with the other elements.

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