Tuesday, August 28, 2012

Transparency During Scientific Peer Review

F1000 Research is an Open Access publishing program which allows biomedical researchers to submit a scientific manuscript, which is subjected to a rapid in-house editorial review to confirm the appropriateness of the article:

Our editorial team will check the appropriateness of the article (including content, quality, tone and format), ensure it is intelligible and that it is written in good English. If a submission fails our initial checks, it will be returned to the authors to address the issues, and if they are not addressed satisfactorily, the article will not be accepted. If our in-house editorial team have concerns but are not completely sure whether to accept a submission, we will contact a relevant member of the Editorial Board for advice.  

The anonymous reviewer
(Photo from Wikimedia commons)
 If an article is thought to be appropriate during this rapid initial review, it is immediately published. This approach is in sharp contrast to current publishing approaches in most biomedical journals, where a manuscript is sent out to peer reviewers prior to publication. As many of us who routinely write such articles can attest, the traditional peer review approach can take months (or in some extreme cases even 1-2 years) of reviews, revisions and re-submissions, before an article is eventually published.

The F1000 Research approach avoids this lengthy pre-publication peer review, and instead focuses on a post-publication peer-review.  Selected reviewers first indicate if they approve, reject or approve the manuscript with reservations. They are then asked to comment the quality and strength of the scientific findings in the manuscript and their responses are then published alongside with the actual paper. The published manuscript can then be revised by the authors according to these comments by the reviewers. Additional researchers can also weigh in and write comments about the paper, even if they do not belong to the group of  reviewers that were specifically asked by the editorial team to review the paper. This allows the authors of a paper to take into account the comments of a broader group of fellow researcher and colleagues, especially when revising the paper. If a manuscript receives only negative reviews by the reviewers, it will be removed. It is only indexed by research databases such as PubMed if it receives two or more positive reviews. The editors of F1000 Research are still working with biomedical indexing databases to decide how to best index the multiple versions of the published manuscript as it is revised in this post-publication peer review process.
One of the most interesting aspects of this new, open review process is that the names of the reviewers are also made public. In the conventional pre-publication peer-review model,  anonymity of the reviewers is somewhat of a sacred corner-stone. It has the advantage that reviewers can be very frank in their comments, without fearing any repercussions or ill-will from the authors. The downside of this anonymity is that some peer-reviewers write scathing, non-constructive reviews and in some rare cases even abuse the anonymity to prevent the publication of manuscript by a competitor.
The obvious question is: Does such post-publication peer review work? It may be too early to tell since F1000 Research was only launched in July 2012. However, this early assessment by its publisher Rebecca Lawrence does sound very promising:

Many had predicted that our “publish first, peer review later” model would attract substandard work and that we would be inundated with poor quality articles, but we are very pleased to see that this has not been the case thus far.  Furthermore, the fact that our referees are clearly quite happy to openly criticize where they have concerns further supports our hunch that scientists will think twice before submitting sloppy articles as this will lead to open criticism of their work, which will be eternally linked to their paper by way of the article citation.

We obviously need more time to assess the scientific quality of the articles submitted as well as whether this novel post-publication peer review process actually improves the quality of the science presented in the paper as the paper is revised in accordance with the  reviewer comments. I have to admit that I am quite optimistic about this new peer-review approach because it is more similar to how we practice science. Most of the time, when scientific findings are presented at seminars or conferences, we receive feedback from non-anonymous colleagues and this feedback is extremely valuable. Most of us enjoy presenting our work to colleagues at conferences because we look forward to positive and negative comments. In the past, such feedback has been limited to the fellow researchers that happen to attend the conference. On the other hand, when articles are submitted for publication in the traditional model, we only receive feedback from 2-4 anonymous colleagues and it does not allow for a dialogue that is generally characteristic of good science. My hope is that this novel approach will allow the selected reviewers, fellow researchers and the authors of a scientific article to engage in a transparent and fruitful dialogue that will benefit all involved and help strengthen the quality of scientific research.

Sunday, August 26, 2012

Nostalgia: Popular 80's Hits in Germany Part 1

Duran Duran: The Wild Boys

Murray Head: One Night in Bangkok

Tears for Fears: Shout

Sandra: Maria Magdalena

Nena: 99 Luftballons

Saturday, August 25, 2012

Man on the Moon by R.E.M in honor of Neil Armstrong

The astronaut Neil Armstrong inspired millions by achieving a feat that for thousands of years had been deemed impossible: Walking on the moon. He unfortunately passed away today and here is the R.E.M song "Man on the Moon" in his honor:

Here is the video of the 1969 moon landing:

Friday, August 24, 2012

Speak Out Against the Blasphemy Laws

Place of Remembrance Martin Niemöller
From Wikimedia Commons, Berkan
I just read a Huffington Post article by Mehdi Hasan entitled: "Not in My Name: Islam, Pakistan and the Blasphemy Laws", which discusses the horrific blasphemy charges brought against a Christian girl in Pakistan.

You could not make it up. An 11-year old Christian girl in Pakistan with Down's Syndrome is in police custody, and could face the death penalty, for allegedly burning pages from the Quran.
The girl, who has been identified as Rifta Masih, was arrested on blasphemy charges and is being held in Islamabad pending a court appearance later this month. She was detained by police after an angry mob turned up at her family's single-roomed home in a poor district on the outskirts of the Pakistani capital.
"About 500-600 people had gathered outside her house in Islamabad, and they were very emotional, angry, and they might have harmed her if we had not quickly reacted," Pakistani police officer Zabi Ullah told reporters.
"Harmed her"? Really? I mean, really? What on Allah's earth is wrong with so many self-professed Muslims in the self-styled Islamic Republic of Pakistan? Have they taken leave of their morals as well as their senses? It beggars belief that they should want to hurt or attack a child in the name of a religion based on mercy, compassion and justice.

The article makes some very important points that counter ridiculous assertions by people defending the Pakistani blasphemy laws or the actions of the authorities. These defenders claim that the girl in question may not be 11 but is instead 16 years old; or that she may not have Down syndrome.

Hasan correctly points out: "SO WHAT?" It does not matter how old she is or whether she has Down syndrome. Arresting and prosecuting a child or an adult for "blasphemy" is simply wrong. Hasan's article ends with a very important message:

Denial is not an option, nor is turning a blind eye. We have to speak out against hate, intolerance and the bullying of non-Muslim minorities - otherwise we risk becoming complicit in such crimes. "Not in my name" has to be more than just an anti-war slogan.

Muslims need to take a clear stand here against the persecution and bullying of non-Muslim minorities. It reminds me of a famous quote by the German pastor Martin Niemöller when speaking about the Third Reich:

„Als die Nazis die Kommunisten holten, habe ich geschwiegen; ich war ja kein Kommunist.
Als sie die Sozialdemokraten einsperrten, habe ich geschwiegen; ich war ja kein Sozialdemokrat.
Als sie die Gewerkschafter holten, habe ich geschwiegen; ich war ja kein Gewerkschafter.
Als sie mich holten, gab es keinen mehr, der protestieren konnte.“

In English:

"First the Nazis came for the Communists, and I did not speak out--Because I was not a Communist.
Then they came for the Social Democrats, and I did not speak out-- Because I was not a Social Democrat.
Then they came for the trade unions, and I did not speak out-- Because I was not a member of a trade union.
Then they came for me--and there was no one left to speak for me."

There are many different versions of this quote and there is quite a bit of controversy as to how exactly Niemöller originally phrased it. However, the core message is pretty clear. Speak out for others and help protect their rights. Speak out as soon as possible, especially when they are being persecuted and you are not. Do not passively wait until you become the victim, because then it will be too late. 

Wednesday, August 15, 2012

How To Suck At Your Religion

Copyright © 2012 Matthew Inman.
A  really interesting comic entitled "How To Suck At Your Religion" can be found on "The Oatmeal" and forces you to ask yourself questions such as:

‎"Do you validate your beliefs by constantly trying to convince others to believe the same thing?"
‎"Do you mock other religions for believing crazy things.....?" 

Read more here

Why IQs are rising – and how to get better grades

Liz Else interviews James Flynn, professor of political science at the University of Chicago, for New Scientist:
Large Rubik's cube built on the
North Campus of the University of Michigan

Worldwide, IQs have risen by up to three points per decade over the past century. Known as the Flynn effect, the rise means IQ tests should be recalibrated regularly. At 78, James Flynn, the man it’s named after, explains how he’s still hard at work on its repercussions.
Are we getting smarter? 
Our ancestors were just as good as we are at practical intelligence, at dealing with everyday life. But our brains and minds have changed over the last century. That is when all these IQ gains have taken place, and we have developed the mental skills needed to deal with the demands of the modern world.
Read more here:

The Future of U.S. Health Care

Andrea Louise Campbell in the Boston Review:

Physician treating a patient.
Red-figure Attic aryballos, ca. 480–470 BC.

The Affordable Care Act is a monumental accomplishment. Thanks to its expansion of health care coverage and new regulations, tens of millions of Americans will feel more secure, knowing that they can seek medical attention when they need it and that they will be protected from the insurance industry’s most egregious practices.
But the reform was very much limited by the American terms of the debate, particularly the enduring belief that markets are always more efficient than government (even though our current private insurance system demonstrates otherwise) and the conviction that any changes to the arrangements of the insured cannot fly. The result is a sprawling, confusing, Gorgon-headed workaround, whose beneficial features are difficult for the typical consumer to discern.
Now that the Act has run the Supreme Court gauntlet, how will it affect the structure and politics of health care going forward? Assuming the ACA survives Republican repeal attempts, does it represent a large step toward a single-payer system? What will happen to the employer-provided sector of health insurance? Will health insurance in the United States settle into a pattern of competing private plans? And will some states really opt out of the ACA’s Medicaid expansion and forgo billions of federal dollars?

Continue reading here:

Do We Need Another Information Sharing Platform?

Diagram of a social network from Wikimedia Commons
Facebook, Twitter, Reddit, StumbleUpon, Blogger......We now have numerous ways to share information with each other and many of us already feel overwhelmed by the massive amount of information that we are presented with. When I read that the co-founders of Twitter Evan Williams and Biz Stone are creating a new information sharing platform, I asked myself: Is that really necessary? Aren't we already drowning in information? This new platform is called "Medium" and posting on this new platform is currently only available to selected individuals as it is being tested and developed. Soon, everyone who registers via their Twitter account will be able to post on it. Evan Williams gives us a preview of the nature and goals of "Medium" in an introductory post:
1999 was the year we launched Blogger. Ideas that seemed radical at the time--that anyone, anywhere could and should publish their thoughts to the global Internet audience (for free)--are now taken for granted.
This is definitely true. Anyone who has the sudden urge to publicly share their ideas or feelings can start a blog. Whether there is an audience that will read the blog is a separate question. Williams then writes:
Lots of services have successfully lowered the bar for sharing information, but there's been less progress toward raising the quality of what's produced.
This also is true. When we look at our Twitter feeds, Facebook updates or the millions of blog posts that are generated, it is difficult to claim that the quality of information being exchanged is improving. However, improving the quality of exchanged information seems to be a rather lofty goal and it is not clear that a new platform will necessarily achieve that. "Medium" will apparently rely on two key principles: Rating and Organizing.

 1. Rating:

Williams writes:
Medium is designed to allow people to choose the level of contribution they prefer. We know that most people, most of the time, will simply read and view content, which is fine. If they choose, they can click to indicate whether they think something is good, giving feedback to the creator and increasing the likelihood others will see it.
This will create a hierarchy of information, indicating which information is liked most. This does not seem too dissimilar from the rating that is currently achieved by existing platforms, such as Facebook, which allow one to "like" or "Share" articles, posts or images. Similarly, in Twitter the "Top Tweets" function shows the tweets that are most frequently re-tweeted or favorited.

  2. Organizing

A second key principle is the fact that posts will be organized in collections:
Posting on Medium (not yet open to everyone) is elegant and easy, and you can do so without the burden of becoming a blogger or worrying about developing an audience. All posts are organized into "collections," which are defined by a theme and a template.
Organizing information into collections may indeed be very helpful. When we, for example, look at our Twitter feeds to find information on specific topics, we usually depend on the hashtags or key words included in the tweets. Since a tweet only allows for a total of 140 characters and everyone can create new hashtags in a very subjective and arbitrary manner, it is very challenging to find information on a specific topic. Examples of the limited currently available "Medium" collections can be viewed and include "This Happened To Me" or "Look What I Made".
It is still not clear that "Medium" really represents a revolution in information exchange. One key difference between "Medium" and Twitter seems to be the fact that "medium" users will not be constrained by the 140 character limit. However, a lot of its success will depend on how the information on "Medium" will be organized and how users will be able to navigate the collections. If users will arbitrarily create new collections and generate millions of posts on a daily basis, we might still end up in an information jungle that does not represent the "evolutionary leap" the founders are aiming for. On the other hand, if "Medium" does create a way to organize the posts in collections that can be easily navigated or searched, it is likely to succeed, especially among Twitter users who feel they need more then 140 characters to express themselves.

Monday, August 13, 2012

The Desire to Regulate Desires

From Wikimedia Commons 

The lawyer and journalist Eric Berkowitz has written an excellent book entitled "Sex and Punishment: Four Thousand Years of Judging Desire" on how humanity devotes an extraordinary amount of time and effort to regulate human sexuality. 

Sara Wheeler has reviewed the book for the "Literary Review" and she points out:

What all this amounts to, in most of the human cultures that have ever existed, is the male fear of and wish to subjugate women.  
Continue reading Sara Wheeler's review here.

An excerpt of Berkowitz' book can be found on the Boing Boing website.

Sunday, August 12, 2012

Paul Ryan is a Blessing for American Democracy

The announcement that Paul Ryan would be Mitt Romney's running mate in the upcoming presidential election created ripples of joy among Democrats and Republicans. Democrats felt that President Obama's chances of winning the election had significantly improved because the majority of Americans will oppose the severe budget cuts that Paul Ryan has proposed in the past. Republicans were thrilled that they could energize their conservative base and re-activate the Tea Party enthusiasm that was so pervasive and successful in 2010. Only time will tell who should be celebrating the choice of Paul Ryan. What we do know is that this choice represents a big victory for democracy. The purpose of an election is to choose between candidates who present their distinct political goals and visions. For independent voters (who cast the deciding votes in American elections) the differences between Mitt Romney and President Obama may not have been that obvious. After all, Mitt Romney himself instituted a healthcare system as governor of Massachusetts that is quite similar to the one envisioned by President Obama. This has now changed with the choice of Paul Ryan as Romney's running mate. He can now offer something that Romney never could: A clear vision. What does Paul Ryan's vision consist of? In the past, he has articulated how strongly he has been influenced by Ayn Rand's philosophy. However, he then faced harsh criticism and push-back from American Catholics, who were not too enthusiastic about the atheism, pro-choice stance and laissez-faire capitalism that Ayn Rand stood for. An example of this criticism is this public letter, that was sent to Paul Ryan by members of the Georgetown University faculty:
"In short, your budget appears to reflect the values of your favorite philosopher, Ayn Rand, rather than the Gospel of Jesus Christ. Her call to selfishness and her antagonism toward religion are antithetical to the Gospel values of compassion and love."
Paul Ryan responded to such criticism by down-playing his admiration for Ayn Rand and even suggesting that he rejects Ayn Rand's philosophy. However, his proposals to aggressively cut government programs such as Medicaid and Medicare as well as curtail welfare spending constitute the center-piece of his political views. These proposed cuts have propelled his rise to stardom in the Republican Party and they are quite consistent with Ayn Rand's philosophy. Reneging on his goals to severely curtail government spending would diminish his credibility with the fiscal conservatives that see him as their champion. On the other hand, reducing government spending on the poor and the elderly appears antithetical to the Christian principles of compassion. This has created a dilemma for him, and forces him to find other ways to placate Catholics or other Christian voters who feel that his severe budget cuts are incompatible with Christian values. This may explain why Paul Ryan is emphasizing his religious conservatism by suggesting that he is anti-choice in matters of abortion and opposes same-sex marriage or adoption by gay couples. His positions on matters of abortion or gay marriage are quite inconsistent with the individualism of Ayn Rand and may thus help him distance himself from her views.
It therefore appears that Paul Ryan is generating a new hybrid philosophy: A reactionary vision for America which combines radical fiscal conservatism with selected "Christian values". Paul Ryan intends to roll back the progress made in the arena of providing affordable healthcare for the elderly and poor and diminish the social safety nets created over the past decades. The November ballot will tell whether American Christians will accept this hollowed version of Christianity, which has been stripped of its compassionate core. In this context, Paul Ryan's reactionary vision a blessing for American democracy. In recent years, the "everyone fend for themselves" philosophy of Ayn Rand has been taking hold in American culture and politics, gradually pushing the United States towards an "Ayn Rand Nation". This gradual process has been driven by selected activist groups such as the Tea Party, but there has been a much broader tacit approval. There has been lukewarm support for the Affordable Healthcare Act, which will provide healthcare of millions of uninsured Americans, even among those who would benefit from it. There is a growing American perception that European welfare programs should be blamed for the flailing European economies. These are all indicators that Ayn Rand's philosophy has been creeping into and taking hold of mainstream American culture. Discussion about how this creeping laissez faire capitalism and unhinged individualism is antithetical to Christian values has been rather scarce, which is surprising since the majority of Americans see themselves as Christians.
The November election will now force Americans to carefully think about their vision and their ideals. Do Americans really want an Ayn Rand Nation with a few cherry-picked "Christian values" as epitomized by Paul Ryan? This is the question that Americans will be asking themselves in the next months. Instead of just giving their tacit approval, Americans will have to actively vote on this question in November. This will require much soul-searching, but it is this type of soul-searching that makes a democracy vibrant.

Eric Kandel on the Intersection Between Neuroscience, Psychoanalysis and Art

Freud ca. 1900, from Wikimedia commons

The famous neuroscientist and Nobel Prize laureate Eric Kandel has written a new book on how science, psychoanalysis and art converged in Vienna around the 1900s and set in motion an exciting new integrative approach to understanding  the human mind and soul. The book is entitled "The Age of Insight: The Quest to Understand the Unconscious inArt, Mind, and Brain, from Vienna 1900 to the Present" and an excerpt of the book has been released:

Beauty does not occupy a different area of the brain than ugliness. Both are part of a continuum representing the values the brain attributes to them, and both are encoded by relative changes in activity in the same areas of the brain. This is consistent with the idea that positive and negative emotions lie on a continuum and call on the same neural circuitry. Thus, the amygdala, commonly associated with fear, is also a regulator of happiness.
For every evaluation of emotion, from happiness to misery, we use the same fundamental neural circuitry. In the case of art, we evaluate a portrait’s potential for providing new insights into another person’s psychological state. This discovery, by Ray Dolan and his colleagues at University College London, was based on a set of studies in which volunteers viewed faces whose expression of sadness, fear, disgust, or happiness was gradually changed from low to high intensity.

Continue reading the excerpt from the book here here....