Category Archives: Academia

Web breaks echo-chambers, or, ‘Echo-chamber’ is just a derogatory term for ‘community’ – my remarks at #AAASmtg

As you probably know, I was in D.C. last week, attending the annual AAAS meeting. This was my second one (funny, back when I was a member of AAAS I was still in grad school and I could never afford to go – now that I am out of science, invitations are finally happening). It is an enormous meeting (about 8200 people this year, I hear) and I missed even seeing some of the friends as the space was so enormous and the program so rich.

Unlike last year, when I was in a session that made quite a splash, this year I was a part of a much more academic panel on Social Networks and Sustainability.

Organized by Thomas Dietz of Michigan State University, the panelists were Mrill Ingram (University of Wisconsin), Ken Frank (Michigan State University) and Adam D. Henry (West Virginia University). These are people from areas like sociology, people who make graphs like this one and understand how to properly interpret it:

My role on the panel was as a ‘discussant’, i.e., someone who does not give a separate talk but comments, at the end, on what the other panelists have said.

I am glad I got the materials from the panelists in advance as this was quite dense stuff.

Every scientific discipline invents new words – the terminology (or jargon) with precise meaning that is necessary for practitioners to talk to each other. For the most part, natural sciences tend to stick to agreed definitions, and counter-examples are relatively rare thus usually quite well known (e.g., the different use of the term “gene” by population geneticists vs. molecular geneticists).

Social sciences, on the other hand, tend to appropriate words from the existing English vocabulary and give those words new, precise definitions. Thus, possibility of misunderstanding by non-experts is greater. Also, some of the terms are defined differently by different sub-disciplines, research communities or even individuals, which makes it even harder to be sure one got the meaning correctly.

This all made reading the materials, as well as listening to the panel, quite challenging for me, the outsider in this field. I am also not a researcher of social networks – I am a user and observer, perhaps an amateur student of them. My thoughts could not be supported by numbers and graphs, but had to, by necessity, be more impressionistic – what I learned from my experiences using, living in, and running online social communities.

As all the speakers went substantially over their allotted times all I had left was seven minutes. Fortunately for me, I had all seven (not 3.5) as the other discussant’s flight into D.C. was canceled. Also fortunately for me, this was the very last time-slot of the meeting, so nobody was in a rush to go to another session and thus everyone let me talk a few minutes longer and then remained in the room asking even more questions.

As I tend to do, and in this case particularly, I decided not to prepare too much (OK, at all) in advance. Instead, I listened to the panelists carefully and made the decision what to say only once I climbed onto the podium in the end and knew how much time I had at my disposal. I decided what to say in the first couple of sentences – the rest came out on its own, pure improvisational theater.

As I was reading the materials and listening to the talks, I realized that a couple of examples were clearly discussing real-world, meat-space, offline social networks, but that all the other examples were ambiguous: I could not figure out if those were online, offline, or combined/hybrid social networks.

So, I decided to use my seven minutes to compare and contrast online and offline social networks, how they differ (more important than how they are similar, which is the default thinking), and how they interact and potentially strengthen each other due to such differences.

This is, roughly, what I said – or at least what I meant to say but had to speed up, i.e., this is an (very) expanded version:

Social norms build and enforce echo-chambers

You want to remain in a friendly relationship with the people you see (or potentially can see) often: neighbors, family, colleagues and friends. Nothing makes for a more unpleasant interaction than discussion of politics, ideology or religion with the people you disagree with.

Thus, there is a social norm in place: politics and religion are taboo topics in conversation. It is considered bad manners to start such conversations in polite company.

This means that most people are not exposed to views other than their own in their day-to-day interactions with other people.

In a small tightly-knit community where everyone’s politics and religion are the same (and people tend to move to such places in order to feel comfortable, on top of most likely being born in such a community to begin with), there is no need to discuss these topics as everyone already agrees. If the topic is discussed, there are no other opinions to be heard – it’s just back-slapping and commiserating about the evil enemies out there.

In mixed communities, the taboo against discussing politics and religion is strongly enforced. Again, as a result, there is not much chance to hear differing opinions.

There is no more airtight echo-chamber than a small community which interacts predominantly within itself, and not so much with the outside world.

Mass media builds and enforces echo-chambers

If you are born and raised by parents with a particular set of beliefs, you will also inherit from them the notions of which media outlets are trustworthy. If you were raised in the reality-based community, you are unlikely to waste much time with the media of the fantasy-based community (and vice versa). If your parents read Washington Post, you are unlikely to read Washington Times. You’ll prefer New York Times and not New York Post. MSNBC rather than Fox News. NPR rather than Limbaugh show on the radio.

But it is even worse than that – the choice is really not as broad. The media shapes the public opinion by choosing what is and what is not respectable opinion, i.e., ‘sphere of legitimate debate’ – what opinions to cover as serious, what opinions to denigrate and what opinions to ignore. There are many ideas that people hold that you will never see even mentioned in the US mass media and some of those are actually very legitimate in the Real World.

Furthermore, the press then divides the ‘respectable opinion’ into two opposites, gives voice to each of the two, and will never actually tell you which of the two is more reasonable than the other – “we report, you decide”, aka, He Said She Said journalism.

By presenting every issue as a battle between two extremes (and the fuzzy, undefinable “middle” is reserved only for them, the wise men), the mainstream press makes every opinion something to be sneered at, both those they deem worthy of mentioning and the unmentionable ones.

By refusing to acknowledge the existence of many stands on any issue, by refusing to assign Truth-values to any, by looking down at anyone who holds any opinion that is not their own, the mainstream press fosters the atmosphere of a bipolar world in which enmity rules, and the wagons need to be circled – the atmosphere that is so conducive to formation and defense of echo-chambers and yet so devoid of airing of any alternatives.

The Web breaks echo-chambers

When an individual first goes online, the usual reaction is shock! There are people in the world who believe what!?!?

The usual first response is anger and strenuous attempts at countering all other ideas and pushing one’s own.

But after a while, unbeknown to the person, all those various novel ideas start seeping in. One is not even aware of changing one’s own mind from one year to the next. Many ideas take time to process and digest and may quietly get incorporated into one’s gradually enriching and more sophisticated worldview.

We all learn from encountering all those other opinions even if we vehemently disagree with them. And we cannot help bumping into them all the time. There are no taboo topics online, no social norms preventing people from saying exactly what they think.

Forming, finding or defending a vacuum-sealed echo-chamber online is extremely difficult, if at all possible.

Your Facebook friends will post stuff that reveals their politics is different than yours (and you did not even know that about them before – they seemed so nice in real life!). By the time you get around to blocking them…it’s too late – the virus has already entered your head [this one sentence added 2-27-11].

People you follow on Twitter because of some common interest (e.g., food or knitting or parenting or technology or geographic area) may be very different from you when concerning some other interest, e.g., religion, and will occasionally post links to articles that contain opinions you have never heard of before.

If you are, for example, a liberal and tend to read only liberal blogs, you will constantly see links to conservative sites that are being debunked by your favourite bloggers – thus you will be exposed to conservative ideas daily.

If your interest is science, you are even luckier. The mainstream media, if it links to anything at all, tends to link either to each other or to governmental sources (e.g., CDC, USDA, etc.). Political bloggers link a lot more, but again the spectrum of sources is pretty narrow – they link to MSM, to governmental pages, and to each other (including the “opposition” bloggers).

But science bloggers link to a vastly broader gamut of sources. If mass media is linked to at all, it is usually in order to show how bad the coverage was of a science story. Linking to each other is important (and that includes linking to anti-science sites when needed to counter them), but what science bloggers do that others do not is link to scientific papers, documents, databases, even raw data-sets (including some Open Notebook Science bloggers who pipe data straight from their lab equipment onto the web).

What echo-chamber? Contrary to what some uninformed op-eds in the mass media like to say, the Web breaks echo-chambers that the social norms and mass media have previously built.

The online and offline social networks can work synergistically to affect real change

Many curmudgeons like to say that the Web does not do anything on its own. They (unlike behavioral biologists) do not understand the distinction between Proximal Causes and Ultimate Causes. Web is a tool that allows, among other things, many more people in much shorter time to organize to do something useful in the real world.

Release of Tripoli 6 was an instance in which massive outpouring of support online forced the mainstream media to cover the story which then forced the hand of politicians to do something.

Likewise, in the case of resignation of George Deutsch from NASA, it was investigative work by a blogger, Nick Anthis, that energized the blogosphere, which pushed the MSM to finally report on the story, which forced the event to happen.

PRISM was an astroturf website built to counter the pro-open-access NIH bill in the US Senate. Outpouring of online anger at the tactics by the publishers’ lobby inundated the senatorial offices – as a result the bill passed not once, but twice (GW Bush vetoed the first version of the large omnibus bill it was a part of, then signed it with no changes in the language on this particular issue) and the Senate is now educated on this issue.

But probably the best example is the Dover Trial (Kitzmiller v. Dover Area School District) that made Intelligent Design illegal to teach in US public schools. The ruling by Judge Jones (pdf) is one of the most powerful texts in the history of judicial decisions I am aware of.

There are anti-evolution bills popping up somewhere in the country seemingly every week. But because of the Dover ruling, they are all illegal. Most don’t make it to the committee, let alone to the floor of the state legislatures. Others are soundly defeated.

Before Dover, both Creationist sites and pro-evolution sites, when linking to me, would bring approximately the same amount of traffic to my blog. After Dover, getting a link from PZ Myers, Richard Dawkins, Larry Moran or Jerry Coyne brings substantial new traffic. Links from Creationist sites? Essentially undetectable by traffic trackers – I discover them only when I search my blog URL to specifically see if there are new links out there. Creationism, while still popular with the people, is politically essentially dead. The Dover ruling castrated it.

But Dover Trial would not have gone that way, and would not result in such a gorgeously written document by the Judge, if it was not for a small army of bloggers who contribute to the blog Panda’s Thumb. A mix of scientists from different disciplines, lawyers, etc., this group has been online – first on Usenet, later on the blog – for a couple of decades before the trial.

This is a group of people who battled Creationists for many years, online and offline, in courtrooms and political campaigns, in classrooms and in print. They know all the characters, all the usual creationist “arguments” (and provided all the answers to them in one place), all the literature, etc.

It is one of them who discovered that the new Intelligent Design “textbook” is really just a reprint of an old Creationist book, in which the word “Creationists” was replaced by “Intelligent Design proponents” throughout the text….except in one place where they made a typo: “Cdesign proponentsists”.

Ooops – a huge piece of evidence that Intelligent Design Creationism is just a warmed-up version of the old-style Creationism masquerading as something new. The Panda’s Thumb bloggers were at the trial as expert witnesses who provided all the expert evidence that Judge Jones needed to make his decision. People who organized on the Web have helped a meatspace history come to pass.

The online and offline social networks can work synergistically if the ecology is right

When looking at the role of online communities and networks in meatspace events, counting the numbers of networked citizens (or ratio of networked to non-networked citizens) is not sufficient – one also needs to know their geographic distribution, and their connectiveness with non-networked citizens. The most fresh example are the so-called “Twitter revolutions” in the Arab world.

There are at least two possible scenarios (or thought experiments) that demonstrate the importance of ecological thinking about social networks:

1) There are 10 people on Twitter in a country. All in the same city, all in the same college dorm, good friends with each other. No communication with other people. No Twitterati in other cities. Nobody knows that other people in other cities have the same negative feelings toward the government.

2) There are 10 people on Twitter in a country. One each in 10 different cities. They communicate with each other via social networks continuously. Each is also a center of the local community of thousands of non-networked people using offline methods of communication. Through this connection, they become aware that there are millions of them, all over the country, and that a revolution is feasible.

In scenario 1, there are 10 buddies dreaming of revolution. In scenario 2, there are thousands of people in ten cities organizing revolution. In both, there are only 10 people on Twitter. Yet, the outcome is likely to be very different.

Thus, the ecology of the networkers, their spatial and temporal distribution, and their effectiveness in informing not just each other but many non-networked citizens, are important data one needs for this exercise.

‘Echo-chamber’ is just a derogatory term for ‘community’

I shamelessly stole this sub-heading from someone on Twitter (let me know who said it first if you know). Edit: Thank you – it was Chris Rowan,

A great example of a case where the Web produced a community (aka echo-chamber) but that was a good thing, is the case of American atheists.

Before the Web, each atheist in the USA thought he or she was the only one in the country. The social norms about the impoliteness of discussing religion, as well as the real fear of reprisals by the religious neighbors, made atheism completely invisible. No need to mention that the media never mentioned them – they were outside of the “sphere of legitimate debate”.

But then the Web happened, and people, often pseudonymously, revealed their religious doubts online. Suddenly they realized they are not alone – there are millions of atheists in the country, each closeted before, each openly so after! It is not a surprise that “no belief” is the fastest-growing self-description in questions about religion in various nation-wide polls and censuses.

President Bush Senior, himself not very religious, could say that atheists are not real American citizens. A decade later, his son GW Bush, himself a fundamentalist, could not say that any more – his speechwriters made sure he mentioned atheists in the listings of all the equally American religious groupings.

Not all online communities need to be politically active. Discovering people with the same interest in knitting is nice. Exchanging LOLcat pictures is fun. But such interactions also build ties that can be used for action in the real world if the need arises.

Without the Web, I would not know many people whose friendship I cherish. Without the Web I would not have this job. Without the Web, me and many of my friends would have never gone to a meeting like AAAS. There would be no such meetings as ScienceOnline, Science Online London, SciBarCamp, SciFoo, and others.

Every time I travel I make sure that people I know online – from blogs, Twitter, Facebook etc. – know I am traveling. I say on which date, at which time, I will be in which restaurant in which city. Twenty people show up. Most I have never met in real life before. But after sharing a meal, a beer, a handshake and a hug, our weak ties become strong ties. Superficial relationships become friendships. If there is a need to organize some real-world action – we can rely on each other to participate or help.

I have a separate Dunbar Number in each city I visited. And I try to connect them to each other even more than they are already connected via online communication. Which is one of the reasons we organize conferences and one of the reasons I am online all the time.


As Science Bloggers, Who Are We Really Writing For? by Emily Anthes.

Are science blogs stuck in an echo chamber? Chamber? Chamber? by Ed Yong.

UC Berkeley Genetic Testing Affair: Science vs Science Education – guest post by Dr.Marie-Claire Shanahan

Marie-Claire Shanahan is an Assistant Professor of Science Education at the University of Alberta, in Edmonton, Alberta, Canada. As a former science teacher, she was always surprised by the ways that students talked themselves out of liking science – and she decided to do something about it. She now researches the social and cultural aspects of science and science education, especially those related to language and identity.

Marie-Claire and I first met online, then also in Real World when she attended ScienceOnline 2010, after which I interviewed her for my blog. You can check out her website and follow her on Twitter. Very interested in her scholarly work, I asked her if she would write a guest-post on one of her topics, and she very graciously agreed. Here is the post about the Berkeley genetic testing affair.

Outside of issues related to teaching evolution in schools, the words controversy and science education don’t often come into close contact with one another. It would be even rarer to be reporting on legislative intervention aimed at halting science education activities. So what’s going on with the UC Berkeley genetic testing affair?

News started to surface in May that Berkeley was going to be asking incoming first year and transfer students to send in a DNA swab. The idea was to stimulate discussion between students as part of the yearly On the Same Page program. A heated debate ensued that has ultimately lead to proposed state legislation that would bar California’s post secondary institutions from making unsolicited requests for DNA samples from students. Both the controversy and the legislation are excellently reported by Ferris Jabr at Scientific American here and here.

It would be reasonable to assume that this seems controversial because it involves genetic testing and therefore personal information. But is there more to it than that?

I chatted informally with some friends about the issue. One expressed her divided feelings about it saying (roughly quoted) “It seems like they [university admin] have addressed the ethical concerns well by being clear about the use of the swabs and the confidentiality but something still just doesn’t feel right. There’s still a part of me that shivers just a little bit.”

What is the shiver factor? Genetic testing and the idea that institutions might have access to our DNA do conjure some imaginative science fiction possibilities. So that could be causing the shivers. But from my perspective as a science education researcher, I think there’s also an underlying issue that makes this particular situation feel controversial: despite having science education goals, this looks and feels a lot more like science. That look and feel leads to confusion about how this initiative should be judged both from an ethical perspective and an educational one.

Science and science education are not the same thing (nor should they be). One way to think of them is through activity analysis, paying attention to who is involved, what are their objectives and what are the artefacts (e.g., tools, language, symbols), actions, and rules that those involved generally agree are used to accomplish the goals of the activity. Studies in activity theory emphasize the importance of shared understanding for accomplishing and progressing in any activity. I would argue that science and science education are different (though obviously related) activities. They have, in particular, different objectives and different artefacts, rules and actions that guide and shape them. As participants in one or the other (or both), teachers, parents, students, researchers, administrators have both tacit and explicit understandings of what each activity entails – what are the rules, the acceptable tools and practices and the appropriate language.

This is where the Berkeley project places itself in a fuzzy area. The objectives of the project are clearly stated to be educational. From the On the Same Page website: “we decided that involving students directly and personally in an assessment of genetic characteristics of personal relevance would capture their imaginations and lead to a deeper learning experience.” Okay, that sounds like the same reasons teachers and professors choose to do many activities. Sounds like science education.

But what about the tools? Testing students’ blood type or blood pressure uses tools commonly available in high school labs (or even at the drug store). The tools used here though are not commonly available – these samples are being sent to a laboratory for analysis. Participants don’t therefore have a shared perspective that these are the tools of education. They seem like the tools of science.

What about the language? One of the main publically accessible sources of information is the On the Same Page website, in particular an FAQ section for students. It starts with the questions: What new things are going on in the scientific community that make this a good time for an educational effort focused on personalized medicine? and Why did Berkeley decide to tackle the topic of Personalized Medicine? These are answered with appeals to educational discourse – to academic strengths, student opportunities, and the stature of Berkeley as an educational center. The agent or actor in the answers to these questions is the university as an educational institutional: “This type of broad, scholarly discussion of an important societal issue is what makes Berkeley special. From a learning perspective, our goal is to deliver a program that will enrich our students’ education and help contribute to an informed California citizenry.”

Beside these educational questions, however, are questions that are part of the usual language and processes of science: Will students be asked to provide “informed consent” for this test of their DNA? What about students who are minors? How can you assure the confidentiality and privacy of a student’s genetic information? What will happen to the data from this experiment? Has this project been approved by Berkeley’s Human Subjects Institutional Review Board? These questions are the questions that appear in human subjects information letters. They make this sound like this is science. The answers to these questions take a different perspective to the ones above. The technical terms are not educational ones but scientific ones. The actor in these responses is neither the educational institution nor the student as an educational participant but the student as a research object: “All students whether they are minors or not will be asked to provide informed consent. They will read and sign a detailed form describing exactly what will be done with their DNA sample, how the information will be used and secured for confidentiality, how this information might benefit them, and what the alternatives are to submitting a sample.”

Anyone who has done human subjects research will recognize this language is almost word for word from typical guidelines for informed consent documents. My consent forms usually don’t deal with DNA samples (usually something much less exotic, such as student writing or oral contributions during class) but the intent is the same. This language sets out the individuals under consideration as the objects of scientific research.

The overall effect is one of a mixed metaphor – is this research or is it teaching? Are the students actually acting in the role of students or are they the objects of research? What standards should we be using to judge if this is an appropriate action. The materials posted by UC Berkeley suggest that they believe this should be judged as an educational project. But the reaction of bioethicists and advocacy groups (such as the Council for Responsible Genetics) suggests that it be judged by research standards.

Why does it matter? Because the ethical considerations are different. As I said above, I don’t usually deal with any materials that would be considered very controversial. I research the way people (including students) write, read, speak and listen in situations related to science. When dealing with students, many of the activities that I use for research could also be used for educational purposes. For example, in a project this year I distributed different versions of scientific reading materials. I asked students to read these in pairs. I tape recorded their conversations and collected their written responses to the text. As a classroom teacher, these are strategies that I have used for educational purposes. Tape recording students allows me to listen to the struggles they might have had while reading a text. Collecting their written responses allows me to assess their understanding. Parents would not object to their child’s teacher using these tools for these purposes. When I visit a classroom as a researcher though, I am judged differently. Parents often do not consent to me collecting their children’s writing. They object, especially frequently, to my requests to videotape or photograph their children. This is because they rightfully understand educational research as a different activity from education. They use different judgments and expect different standards.

From the sequence of events, it sounds as if Berkeley admin started this project with their own perspective that this was clearly educational without adequate consideration that, from an outside position, it would be judged from a research perspective. I don’t want to suggest that this whole thing is a simple miscommunication because there are serious ethical implications related to asking for DNA samples. As people try to figure out how an educational idea ended up in the state legislature, though, I just wanted to add my perspective that some of the controversy might come from that shiver factor – something just doesn’t feel right. One aspect of that feel might be that this challenges the boundaries of our understanding of the activities of science and science education. The language and the tools and the objectives are mixed, leading to confusion about exactly what standards this should be judged against. As tools that have traditionally been associated with laboratory science become more accessible (as genetic testing is becoming) this boundary is likely to be challenged more and more. Those making the decisions to use these tools for educational, rather than research, purposes need to understand that challenging peoples conceptions of the boundaries between science and science education can and will lead to conflict and that conflict should be addressed head on and from the beginning.

Seven Questions….with Yours Truly

Last week, my SciBling Jason Goldman interviewed me for his blog. The questions were not so much about blogging, journalism, Open Access and PLoS (except a little bit at the end) but more about science – how I got into it, what are my grad school experiences, what I think about doing research on animals, and such stuff. Jason posted the interview here, on his blog, on Friday, and he also let me repost it here on my blog as well, under the fold:

Continue reading

I got interviewed…

….by my SciBling, Jason Goldman at The Thoughtful Animal blog. But this time, it is very little about blogging or Open Access publishing or science journalism, except at the very end. This interview is more about my experience in the academia – how I got into grad school, how I survived it, how and why I left research, the How and Why questions of using animals in research, and more.
I know it’s long, but I hope you read and comment – go ahead and click right here and read it right now! 😉

‘Sexy’ science =| ‘good’ science, and all the fallacies that follow from misunderstanding this

Apparently, someone published a really curmudgeonly and regressive-thinking article about science publishing in The Chronicle of Higher Education, titled We Must Stop the Avalanche of Low-Quality Research. Commenters there are shredding it apart. But you should also see blog posts discussing it, by Female Science Professor, DrugMonkey, Orac and Geekmommyprof. If anything, they do not fisk it thoroughly enough 😉

What is the real purpose of a graduate education in science? (video)

Is starting a science career a risk? (video)

Science isn’t a business! (video)


The new issue of Journal of Science Communication is now published

The new issue of Journal of Science Communication is now online (Open Access, so you can download all PDFs for free). Apart from the article on blogging that we already dissected at length, this issue has a number of interesting articles, reviews, perspectives and papers:
Users and peers. From citizen science to P2P science:

This introduction presents the essays belonging to the JCOM special issue on User-led and peer-to-peer science. It also draws a first map of the main problems we need to investigate when we face this new and emerging phenomenon. Web tools are enacting and facilitating new ways for lay people to interact with scientists or to cooperate with each other, but cultural and political changes are also at play. What happens to expertise, knowledge production and relations between scientific institutions and society when lay people or non-scientists go online and engage in scientific activities? From science blogging and social networks to garage biology and open tools for user-led research, P2P science challenges many assumptions about public participation in scientific knowledge production. And it calls for a radical and perhaps new kind of openness of scientific practices towards society.

Changing the meaning of peer-to-peer? Exploring online comment spaces as sites of negotiated expertise:

This study examines the nature of peer-to-peer interactions in public online comment spaces. From a theoretical perspective of boundary-work and expertise, the comments posted in response to three health sciences news articles from a national newspaper are explored to determine whether both scientific and personal expertise are recognized and taken up in discussion. Posts were analysed for both explicit claims to expertise and implicit claims embedded in discourse. The analysis suggests that while both scientific and personal expertise are proffered by commenters, it is scientific expertise that is privileged. Those expressing scientific expertise receive greater recognition of the value of their posts. Contributors seeking to share personal expertise are found to engage in scientisation to position themselves as worthwhile experts. Findings suggest that despite the possibilities afforded by online comments for a broader vision of what peer-to-peer interaction means, this possibility is not realized.

The public production and sharing of medical information. An Australian perspective:

There is a wealth of medical information now available to the public through various sources that are not necessarily controlled by medical or healthcare professionals. In Australia there has been a strong movement in the health consumer arena of consumer-led sharing and production of medical information and in healthcare decision-making. This has led to empowerment of the public as well as increased knowledge-sharing. There are some successful initiatives and strategies on consumer- and public-led sharing of medical information, including the formation of specialised consumer groups, independent medical information organisations, consumer peer tutoring, and email lists and consumer networking events. With well-organised public initiatives and networks, there tends to be fairly balanced information being shared. However, there needs to be caution about the use of publicly available scientific information to further the agenda of special-interest groups and lobbying groups to advance often biased and unproven opinions or for scaremongering. With the adoption of more accountability of medical research, and the increased public scrutiny of private and public research, the validity and quality of medical information reaching the public is achieving higher standards.

Social network science: pedagogy, dialogue, deliberation:

The online world constitutes an ever-expanding store and incubator for scientific information. It is also a social space where forms of creative interaction engender new ways of approaching science. Critically, the web is not only a repository of knowledge but a means with which to experience, interact and even supplement this bank. Social Network Sites are a key feature of such activity. This paper explores the potential for Social Network Sites (SNS) as an innovative pedagogical tool that precipitate the ‘incidental learner’. I suggest that these online spaces, characterised by informality, open-access, user input and widespread popularity, offer a potentially indispensable means of furthering the public understanding of science; and significantly one that is rooted in dialogue.

Open science: policy implications for the evolving phenomenon of user-led scientific innovation:

From contributions of astronomy data and DNA sequences to disease treatment research, scientific activity by non-scientists is a real and emergent phenomenon, and raising policy questions. This involvement in science can be understood as an issue of access to publications, code, and data that facilitates public engagement in the research process, thus appropriate policy to support the associated welfare enhancing benefits is essential. Current legal barriers to citizen participation can be alleviated by scientists’ use of the “Reproducible Research Standard,” thus making the literature, data, and code associated with scientific results accessible. The enterprise of science is undergoing deep and fundamental changes, particularly in how scientists obtain results and share their work: the promise of open research dissemination held by the Internet is gradually being fulfilled by scientists. Contributions to science from beyond the ivory tower are forcing a rethinking of traditional models of knowledge generation, evaluation, and communication. The notion of a scientific “peer” is blurred with the advent of lay contributions to science raising questions regarding the concepts of peer-review and recognition. New collaborative models are emerging around both open scientific software and the generation of scientific discoveries that bear a similarity to open innovation models in other settings. Public engagement in science can be understood as an issue of access to knowledge for public involvement in the research process, facilitated by appropriate policy to support the welfare enhancing benefits deriving from citizen-science.

Googling your genes: personal genomics and the discourse of citizen bioscience in the network age:

In this essay, I argue that the rise of personal genomics is technologically, economically, and most importantly, discursively tied to the rise of network subjectivity, an imperative of which is an understanding of self as always already a subject in the network. I illustrate how personal genomics takes full advantage of social media technology and network subjectivity to advertise a new way of doing research that emphasizes collaboration between researchers and its members. Sharing one’s genetic information is considered to be an act of citizenship, precisely because it is good for the network. Here members are encouraged to think of themselves as dividuals, or nodes, in the network and their actions acquire value based on that imperative. Therefore, citizen bioscience is intricately tied, both in discourse and practices, to the growth of the network in the age of new media.

Special issue on peer-to-peer and user-led science: invited comments:

In this commentary, we collected three essays from authors coming from different perspectives. They analyse the problem of power, participation and cooperation in projects of production of scientific knowledge held by users or peers: persons who do not belong to the institutionalised scientific community. These contributions are intended to give a more political and critical point of view on the themes developed and analysed in the research articles of this JCOM special issue on Peer-to-peer and user-led science.
Michel Bauwens, Christopher Kelty and Mathieu O’Neil write about different aspects of P2P science. Nevertheless, the three worlds they delve into share the “aggressively active” attitude of the citizens who inhabit them. Those citizens claim to be part of the scientific process, and they use practices as heterogeneous as online peer-production of scientific knowledge, garage biology practiced with a hacker twist, or the crowdsourced creation of an encyclopedia page. All these claims and practices point to a problem in the current distribution of power. The relations between experts and non-experts are challenged by the rise of peer-to-peer science. Furthermore, the horizontal communities which live inside and outside the Net are not frictionless. Within peer-production mechanisms, the balance of power is an important issue which has to be carefully taken into account.

Is there something like a peer to peer science?:

How will peer to peer infrastructures, and the underlying intersubjective and ethical relational model that is implied by it, affect scientific practice? Are peer-to-peer forms of cooperation, based on open and free input of voluntary contributors, participatory processes of governance, and universal availability of the output, more productive than centralized alternatives? In this short introduction, Michel Bauwens reviews a number of open and free, participatory and commons oriented practices that are emerging in scientific research and practice, but which ultimately point to a more profound epistemological revolution linked to increased participatory consciousness between the scientist and his human, organic and inorganic research material.

Outlaw, hackers, victorian amateurs: diagnosing public participation in the life sciences today:

This essay reflects on three figures that can be used to make sense of the changing nature of public participation in the life sciences today: outlaws, hackers and Victorian gentlemen. Occasioned by a symposium held at UCLA (Outlaw Biology: Public Participation in the Age of Big Bio), the essay introduces several different modes of participation (DIY Bio, Bio Art, At home clinical genetics, patient advocacy and others) and makes three points: 1) that public participation is first a problem of legitimacy, not legality or safety; 2) that public participation is itself enabled by and thrives on the infrastructure of mainstream biology; and 3) that we need a new set of concepts (other than inside/outside) for describing the nature of public participation in biological research and innovation today.

Shirky and Sanger, or the costs of crowdsourcing:

Online knowledge production sites do not rely on isolated experts but on collaborative processes, on the wisdom of the group or “crowd”. Some authors have argued that it is possible to combine traditional or credentialled expertise with collective production; others believe that traditional expertise’s focus on correctness has been superseded by the affordances of digital networking, such as re-use and verifiability. This paper examines the costs of two kinds of “crowdsourced” encyclopedic projects: Citizendium, based on the work of credentialled and identified experts, faces a recruitment deficit; in contrast Wikipedia has proved wildly popular, but anti-credentialism and anonymity result in uncertainty, irresponsibility, the development of cliques and the growing importance of pseudo-legal competencies for conflict resolution. Finally the paper reflects on the wider social implications of focusing on what experts are rather than on what they are for.

The unsustainable Makers:

The Makers is the latest novel of the American science fiction writer, blogger and Silicon Valley intellectual Cory Doctorow. Set in the 2010s, the novel describes the possible impact of the present trend towards the migration of modes of production and organization that have emerged online into the sphere of material production. Called New Work, this movement is indebted to a new maker culture that attracts people into a kind of neo-artisan, high tech mode of production. The question is: can a corporate-funded New Work movement be sustainable? Doctorow seems to suggest that a capitalist economy of abundance is unsustainable because it tends to restrict the reach of its value flows to a privileged managerial elite.

Why it is important for media articles to link to scientific papers

You may be aware that, as of recently, one of my tasks at work is to monitor media coverage of PLoS ONE articles. This is necessary for our own archives and monthly/annual reports, but also so I could highlight some of the best media coverage on the everyONE blog for everyone to see. As PLoS ONE publishes a large number of articles every week, we presume that many of you would appreciate getting your attention drawn to that subset of articles that the media found most interesting.
So, for example, as I missed last week due to my trip to AAAS, I posted a two-week summary of media coverage this Monday. And that took far more time and effort (and some silent cursing) than one would expect. Why?
I don’t think I am a slouch at googling stuff. Some people joke that the entire Internet passes through my brain before it goes to the final audience. After all, I have been monitoring the Web for mentions of ‘PLoS’ and ‘Public Library of Science’ on blogs, Twitter, FriendFeed, Facebook and elsewhere for a few years now. If I don’t catch a mention within minutes of it being posted, you can bet one of my many online friends/followers/subscribers is bound to quickly let me know by e-mail or Direct Messaging somewhere. If someone says something nice about PLoS, I am quick to post a ThankYou note. If someone asks a question, I try to answer or to connect the person with the appropriate member of the PLoS staff. If someone is publicly musing about submitting a manuscript to one of our journals, I am right there to give encouragement. If someone makes a factual error, I gently correct it. It is very, very rare that I need to raise the Immense Online Armies because someone is wrong on the Internet 😉
So, why is it difficult then to compile a collection of weekly media coverage? Let me walk you through the process….
First, as you probably already know, PLoS makes no distinction between Old and New media. We have bloggers on our press list who apply/sign-up in the same way and abide by the same rules as traditional journalists (and, unlike mainstream media, bloggers NEVER break embargos, not once in the past three years since we started adding bloggers to our press list). For the kind of coverage we prefer to see, we point bloggers to the criteria. In return, bloggers can send trackbacks to our articles, their work is showcased side-by-side with the traditional outlets in our weekly posts, they can be discovered via Google Blogsearch, Postgenomic and links directly from each article, and one blogger per month wins a t-shirt and special recognition.
So, I start with blog posts first. The first thing I do is take a look at Those are the best of the best posts – not merely mentioning our articles, but adding analysis, commentary, critique, context and additional information. How do I find them? I just search the site for the phrase ‘journal.pone‘. That search brings up every single post that mentions a PLoS ONE article because that phrase is a part of every possible form of the URL of the article (including the shortest one, which includes just the DOI). If a post links to our article (and that is the only way to get aggregated on I will find it this way. Needless to say, this process takes just a few minutes per week.
Knowing that there are some good blogs out there that are not registered at (which is strange and unfathomable why – is a ‘stamp-of-approval’ place for science blogs recognized by the outside world of journals and media, as well as a nice way to get extra recognition and traffic, and even awards), I then repeat the same search – for ‘journal.pone‘ – on Google Blogsearch. This may bring up a few more posts that I did not catch yet. Occasionally, some of these are good. Another couple of minutes. Blogs are now done. Move on to traditional media….
And this is where the Hell starts. Try searching Google News for ‘journal.pone‘…?! All I get are a couple of prominent blogs that I have already counted, e.g., those blogs that are listed by Google News ( blogs, Ars Technica, Wired blogs, etc.). Where are the others?
The problem is, nobody in the mainstream media links to papers.
So I have to search for PLoS and for Public Library Of Science and then figure out which ones are covering specifically PLoS ONE articles (sometimes they don’t specify, sometimes they name the wrong journal – last week an article on PLoS Current-Influenza was reported to be in PLoS ONE by a number of outlets copying the error from each other). Then I have to search for keywords for individual articles I suspect may have received some coverage. Last week, for example, I searched for “swallows+antioxidants” and “St. Birgitta”, among many others. This lasts for hours! And at the end I am still not 100% sure I caught everything. How frustrating!
Not just is there a big difference in time and effort spent between finding blog posts and finding media articles, but there is an even bigger disparity when one considers what results come out of these searches. I have been doing this for a month now. I expected that there would be poor blog posts and poor media articles, that there would be good blog posts and good media articles, and that there would occasionally be some excellent blog posts and excellent media articles. So far, that is true…. except I have yet to discover an excellent media article. As a rule, the very best coverage of every paper in the past month was done by a blogger or two or three. Then there are some other, good pieces of coverage in both the New and Old media, and then there are some really bad pieces in both realms as well (not all blog posts I count here are really bad – they may just be too detailed, technical and dry for lay audience because the blogger is intentionally targeting scientific peers as audience, which is fair thing to acknowledge).
So, every week, it takes me a few minutes to find the very best coverage (which is on blogs, usually those aggregated on And then I spend hours looking for remnants, in the traditional media, which turn out to be so-so, some OK, some not so good, some horrible. If I wasn’t paid to do this, I would not do it – it cannot be good for my long-term mental health.
The resistance to post links is an atavism, a remnant of an old age before the Web. I know (because I asked many times) many good science journalists keep trying to add links, but the editors say No. The traditional media has still not caught on to the Ethic of the Link, which is an essential aspect of ethics of online communication.
I can think, off the top of my head, of three good reasons why everyone who publishes online should include a link to the scientific paper described in the article (just post the DOI link that comes with the press release if you are on the press list – if it does not resolve immediately, it is not your fault, you can always blame the journals for being slow on it – though this should never happen with PLoS articles):
Reason One: I will not go crazy every week. I am assuming that every scientific publisher has people on the staff whose task is to monitor media coverage and each one of these people is cussing and cursing YOU, the Media, every day. Try to make friends with people who provide you with source material on a regular basis.
Reason Two: Media coverage is one of the many elements of article-level metrics. Furthermore, links from the media affect the number of views and downloads of the article, and those are also elements of article-level metrics. Number of views/downloads then, in the future, affects the number of citations the work gets which is also and element of article-level metrics. Thus omitting the link skewes the ability of readers and observers to evaluate the papers properly.
The current ecosystem of science communication has a scientific paper at its core, additions to the paper (e.g., notes, comments and ratings, as well as Supplemental materials, videos posted on, etc) as a shell, and incoming and outgoing links – trackbacks, cited papers, citing papers, links to other papers in the same Collection, links to other papers with the same keywords, and yes, incoming links from the media – as connections building a network: the entire inter-connected ecosystem of scientific knowledge.
By not linking to scientific papers, traditional media is keeping itself outside of the entire ecosystem of empirical knowledge. By doing this, the traditional media is fast making itself irrelevant.
Reason Three: if an article in the media discusses a scientific study, that scientific paper is the source material for the article. If the link is missing, this is an automatic red flag for the readers. What is the journalist hiding? Why is the article making it difficult for readers to fact-check the journalist? Something does not smell good if the link is not provided (or worse, it is impossible to figure out even who are the authors and in which journal did they publish – yes, that is more common than you think).
The instant and automatic response of the readers is mistrust. Every time you fail to link to the paper, you further erode whatever trust and reputation you still may have with the audience. You soon cease to be a legitimate source of information. Sure, most readers will not go hunting for the paper to read it in order to fact-check you. But two or three will, and they will let everyone else know if your article is trustworthy or not, either in the comments under the article on your own site, or on their blogs which will be quickly picked up by Google (remember: Google loves blogs).
So please, media types, hurry up and catch up with the world. The 21st century is already a decade in – you really need to do some very fast learning. Right now. Or you’ll go extinct in a nanosecond. And despite my reputation, I never said that I’d consider that result to be a Good Thing. We are in this together, you just need to do your part. To begin with, start linking.

Not-so-self-correcting science: the hard way, the easy way, and the easiest way

Two recent events put in stark relief the differences between the old way of doing things and the new way of doing things. What am I talking about? The changing world of science publishing, of course.
Let me introduce the two examples first, and make some of my comments at the end.
Example 1. Publishing a Comment about a journal article
My SciBling Steinn brought to our collective attention a horrific case of a scientist who spent a year fighting against the editors of a journal, trying to have a Comment published about a paper that was, in his view, erroneous (for the sake of the argument it does not matter if the author of the original paper or the author of the Comment was right – this is about the way system works, er, does not work). You can read the entire saga as a PDF – it will make you want to laugh and cry and in the end scream with frustration and anger. Do not skip the Addendum at the end.
Thanks to Shirley Wu for putting that very long PDF into a much more manageable and readable form so you can easily read the whole thing right here:
See? That is the traditional way for science to be ‘self-correcting’….Sure, a particularly egregious example, but it is the system that allows such an example to be a part of that continuum somewhere on its edge – this is not a unique case, just a little bit more extreme than usual.
Janet wrote a brilliant post (hmmm, it’s Janet… was there ever a time I linked to her without noting it was a “brilliant post”? Is it even possible to do?) dissecting the episode and hitting all the right points, including, among others, these two:

Publishing a paper is not supposed to bring that exchange to an end, but rather to bring it to a larger slice of the scientific community with something relevant to add to the exchange. In other words, if you read a published paper in your field and are convinced that there are significant problems with it, you are supposed to communicate those problems to the rest of the scientific community — including the authors of the paper you think has problems. Committed scientists are supposed to want to know if they’ve messed up their calculations or drawn their conclusions on the basis of bad assumptions. This kind of post-publication critique is an important factor in making sure the body of knowledge that a scientific community is working to build is well-tested and reliable — important quality control if the community of science is planning on using that knowledge or building further research upon it.
The idea that the journal here seems to be missing is that they have a duty to their readers, not just to the authors whose papers they publish. That duty includes transmitting the (peer reviewed) concerns communicated to them about the papers they have published — whether or not the authors of those papers respond to these concerns in a civil manner, or at all. Indeed, if the authors’ response to a Comment on their paper were essentially. “You are a big poopyhead to question our work!” I think there might be a certain value in publishing that Reply. It would, at least, let the scientific community know about the authors’ best responses to the objections other scientists have raised.

Example 2: Instant replication of results
About a month ago, a paper came out in the Journal of the American Chemical Society, which suggested that a reductant acted as an oxidant in a particular chemical reaction.
Paul Docherty, of the Totally Synthetic blog, posted about a different paper from the same issue of the journal the day it came out. The very second comment on that post pointed out that something must be fishy about the reductant-as-oxidant paper. And then all hell broke lose in the comments!
Carmen Drahl, in the August 17 issue of C&EN describes what happened next:

Docherty, a medicinal chemist at Arrow Therapeutics, in London, was sufficiently intrigued to repeat one of the reactions in the paper. He broadcast his observations and posted raw data on his blog for all to read, snapping photos of the reaction with his iPhone as it progressed. Meanwhile, roughly a half-dozen of the blog’s readers did likewise, each with slightly different reaction conditions, each reporting results in the blog’s comment section.

The liveblogging of the experiment by Paul and commenters is here. Every single one of them failed to replicate the findings and they came up with possible reasons why the authors of the paper got an erroneous result. The paper, while remaining on the Web, was not published in the hard-copy version of the journal and the initial authors, the journal and the readers are working on figuring out exactly what happened in the lab – which may actually be quite informative and novel in itself.
Compare and contrast
So, what happened in these two examples?
In both, a paper with presumably erroneous data or conclusions passed peer-review and got published.
In both, someone else in the field noticed it and failed to replicate the experiments.
In both, that someone tried to alert the community that is potentially interested in the result, including the original authors and the journal editors, in order to make sure that people are aware of the possibility that something in that paper is wrong.
In the first example, the authors and editors obstructed the process of feedback. In the second, the authors and editors were not in a position to obstruct the process of feedback.
In the first example, the corrector/replicator tried to go the traditional route and got blocked by gatekeepers. In the second example, the corrector/replicator went the modern route – bypassing the gatekeepers.
If you had no idea about any of this, and you are a researcher in a semi-related field moving in, and you find the original paper via search, what are the chances you will know that the paper is being disputed?
In the first example – zero (until last night). In the second example – large. But in both cases, in order to realize that the paper is contested, one has to use Google! Not just read the paper itself and hope it’s fine. You gotta google it to find out. Most working scientists do not do that yet! Not part of the research culture at this time, unfortunately.
If the Comment was published in the first example, chances that a reader of the paper will then search the later issues of the journal seeking comments and corrections are very small. Thus even if the Comment (and Reply by authors) was published, nobody but a very small inner circle of people currently working on that very problem will ever know.
Back in grad school I was a voracious reader of the literature in my field, including some very old papers. Every now and then I would bump into a paper that seemed really cool. Then I would wonder why nobody ever followed up or even cited it! I’d ask my advisor who would explain to me that people tried to replicate but were not successful, or that this particular author is known to fudge data, etc. That is tacit knowledge – something that is known only by a very small number of people in an Inner Circle. It is a kind of knowledge that is transmitted orally, from advisor to student, or in the hallways at meetings. People who come into the field from outside do not have access to that information. People in the field who live in far-away places and cannot afford to come to conferences do not have access to that information.
Areas of research also go in and out of fashion. A line of research may bump into walls and the community abandons it only to get picked up decades later once the technological advances allow for further studies of the phenomenon. In the meantime, the Inner Circle dispersed, and the tacit knowledge got lost. Yet the papers remain. And nobody knows any more which paper to trust and which one not to. Thus one cannot rely on published literature at all! It all needs to be re-tested all over again! Yikes! How much money, time and effort would have to be put into that!?
Now let’s imagine that lines of research in our two Examples go that way: get abandoned for a while. Let’s assume now that 50 years from now a completely new generation of scientists rediscovers the problem and re-starts studying it. All they have to go with are some ancient papers. No Comment was ever published about the paper in the first Example. Lots of blogging about both afterwards. But in 50 years, will those blogs still exist, or will all the links found on Google (or whatever is used to search stuff online in 50 years) be rotten? What are the chances that the researchers of the future will be able to find all the relevant discussions and refutation of these two papers? Pretty small, methinks.
But what if all the discussions and refutations and author replies are on the paper itself? No problem then – it is all public and all preserved forever. The tacit knowledge of the Inner Circle becomes public knowledge of the entire scientific community. A permanent record available to everyone. That is how science should be, don’t you think?
You probably know that, right now, only BMC, BMJ and PLoS journals have this functionality. You can rate articles, post notes and comments and link/trackback to discussions happening elsewhere online. Even entire Journal Clubs can happen in the comments section of a paper.
Soon, all scientific journals will be online (and probably only online). Next, all the papers – past, present and future – will become freely available online. The limitations of paper will be gone and nothing will prevent publishers from implementing more dynamic approaches to scientific publishing – including on-paper commentary.
If all the journals started implementing comments on their papers tomorrow I would not cry “copycats!” No. Instead, I’d be absolutely delighted. Why?
Let’s say that you read (or at least skim) between a dozen and two dozen papers per day. You found them through search engines (e.g., Google Scholar), or through reference managers (e.g., CiteULike or Mendeley), or as suggestions from your colleagues via social networks (e.g, Twitter, FriendFeed, Facebook). Every day you will land on papers published in many different journals (it really does not matter any more which journal the paper was published in – you have to read all the papers, good or bad, in your narrow domain of interest). Then one day you land on a paper in PLoS and you see the Ratings, Notes and Comments functionality there. You shake your head – “Eh, what’s this weird newfangled thing? What will they come up with next? Not for me!” And you move on.
Now imagine if every single paper in every single journal had those functionalities. You see them between a dozen and two dozen times a day. Some of the papers actually have notes, ratings and comments submitted by others which you – being a naturally curious human being – open and read. Even if you are initially a skeptical curmudgeon, your brain will gradually get trained. The existence of comments becomes the norm. You become primed….and then, one day, you will read a paper that makes you really excited. It has a huge flaw. It is totally crap. Or it is tremendously insightful and revolutionary. Or it is missing an alternative explanation. And you will be compelled to respond. ImmediatelyRightThisMoment!!!11!!!!11!!. In the old days, you’d just mutter to yourself, perhaps tell your students at the next lab meeting. Or even brace yourself for the long and frustrating process (see Example 1) of submitting a formal Comment to the journal. But no, your brain is now primed, so you click on “Add comment”, you write your thoughts and you click “Submit”. And you think to yourself “Hey, this didn’t hurt at all!” And you have just helped thousands of researchers around the world today and in the future have a better understanding of that paper. Permanently. Good job!
That’s how scientific self-correction in real time is supposed to work.


A run-down of good recent stuff, highly recommended for your weekend reading and bookmarking:
PLoS One: Interview with Peter Binfield:

…In my view PLoS ONE is the most dynamic, innovative and exciting journal in the world, and I am proud to work on it.
In many ways PLoS ONE operates like any other journal however it diverges in several important respects. The founding principle of PLoS ONE was that there are certain aspects of publishing which are best conducted pre-publication and certain aspects which are best conducted post-publication. The advent of online publishing has allowed us to take a step back and re-evaluate these aspects of how we publish research, without the burden of centuries of tradition. In this way, we have been able to experiment with new ways of doing things which may result in dramatic improvements in the entire process of scholarly publication.
The most important thing which has come out of this premise is that unlike almost every other journal in the world, we make no judgment call whatsoever on the ‘impact’ or ‘significance’ or ‘interest level’ of any submission. What this means is that if an article appropriately reports on well-conducted science, and if it passes our peer review process (which determines whether it deserves to join the scientific literature) then we will publish it. In this way, no author should ever receive the message that their article is scientifically sound but ‘not interesting enough’ for our journal, or that their article is ‘only suited to a specialized audience’. As a result, we short circuit the vicious cycle of “submit to a ‘top tier’ journal; get reviewed; get rejected; submit to the next journal down the list; repeat until accepted” and we are therefore able to place good science into the public domain as promptly as possible, with the minimum of burden on the academic community….

The evolution of scientific impact (also a good FriendFeed thread about it):

What is clear to me is this – science and society are much richer and more interconnected now than at any time in history. There are many more people contributing to science in many more ways now than ever before. Science is becoming more broad (we know about more things) and more deep (we know more about these things). At the same time, print publishing is fading, content is exploding, and technology makes it possible to present, share, and analyze information faster and more powerfully.
For these reasons, I believe (as many others do) that the traditional model of peer-reviewed journals should and will necessarily change significantly over the next decade or so.

A threat to scientific communication (read excellent responses by Peter Murray-Rast and Bjoern Brembs and a thread on FriendFeed):

Sulston argues that the use of journal metrics is not only a flimsy guarantee of the best work (his prize-winning discovery was never published in a top journal), but he also believes that the system puts pressure on scientists to act in ways that adversely affect science – from claiming work is more novel than it actually is to over-hyping, over-interpreting and prematurely publishing it, splitting publications to get more credits and, in extreme situations, even committing fraud.
The system also creates what he characterises as an “inefficient treadmill” of resubmissions to the journal hierarchy. The whole process ropes in many more reviewers than necessary, reduces the time available for research, places a heavier burden on peer review and delays the communication of important results.

Why do we still publish scientific papers?:

I agree with the need to filter papers, but I want to be in control of the filter. I don’t want editors to control my filter and I definitely don’t want a monopolist like Thomson to muck up my filter. I don’t care where something is published, if it’s in my direct field I need to read it, no matter how bad it is. If a paper is in my broader field, I’d apply some light filtering, such as rating, comments, downloads, author institute, social bookmarks, or some such. If the paper is in a related field, I’d like to only read reviews of recent advances. If it’s in an unrelated field, but one I’m interested in nonetheless, I’d only want to see the news-and-views article, because I wouldn’t understand anything else anyway. For everything else, titles, headlines or newsreports are good enough for browsing. All of this can be done after publishing and certainly doesn’t require any artificial grouping by pseudo-tags (formerly called journals).

Science Jabberwocky (how to read/understand a scientific paper when you don’t know the technical terms):

I have to confess that in areas outside mine, there seems to be a terrible array of words no more obvious than ‘brillig’ and ‘slithy’. And words that look familiar, like ‘gyre and gimble’, but which don’t look like they are supposed to mean what I’m used to them meaning.

Media tracking:

The theropod behaviour paper that I have been boring you all with this last week or so has been the first time I have had decent control over the media access to my work and by extension the first time I have had a good idea of what happened to the original press release. I know what I sent to whom and when and thus can fairly easily track what happened afterwards to record the spread and exchange of information from that origin. In the past on the Musings I have targeted inaccuracies in news reports of scientific stories but without knowing the exact details of a story (I may have access to the press release but without knowing who it went to). Well, not so this time and as a result the pattern of reporting I can see is both interesting and informative both from understanding how the media works and knowing how to get your own work publicised.

Rapid evolution of rodents: another PLoS ONE study in the media:

Although media attention and coverage is not, and should certainly not be, the only criterion for scientific “quality” (whatever that is!), it is further testimony of the advantage to publish in “Open Acess”-journals in general, and PLoS ONE in particular. This study is also interesting because it shows the value of museum collections as a source for ecological and evolutionary research, a point that Shawn Kuchta has repeatedly emphasized in our lab-meetings (and which I completely agree with, of course).

20 Quick Points from ‘The World Is Open: How Web Technology Is Revolutionizing Education’:

9. Open Access Journals (Opener #5): The publishing world is increasing becoming open access. Open access journals in the healthcare area provide invaluable information to those in the developing world. The Public Library of Science (PLoS) offers free peer-reviewed scientific journals. Scientists who publish in PLoS journals might present their work in SciVee. SciVee allows the user to hear or see the scientist explain his or her research in what is known as pubcasts.

Pedagogy and the Class Blog:

I’ve been using blogs in my teaching for several years now, so I wanted to share a few ideas that have worked for me. I’m no expert and I’m still casting about for solutions to some of the more nagging problems, but after thirteen course blogs spread across seven semesters (I just counted!), I have obtained a small measure of experience. In other words, I keep making mistakes, but at least not the same ones over and over.

Practicing Medicine in the Age of Facebook:

In my second week of medical internship, I received a “friend request” on Facebook, the popular social-networking Web site. The name of the requester was familiar: Erica Baxter. Three years earlier, as a medical student, I had participated in the delivery of Ms. Baxter’s baby. Now, apparently, she wanted to be back in touch…..

Are young people of today Relationally Starved?:

The more I toss it around, I’m not so sure that our students are “relationally starved.” I just think that relationships look much different today than they have in generations past. Their relationships are more fluid and maybe a little more fragile. It is obvious that advances in technology have changed the way relationships are built and maintained (it has for me). This doesn’t mean that children aren’t in need of the same nurturing and love that we might have had, but there are other layers that we need to ask them about. And I think that might be the key, ASK THEM!

The New Yorker vs. the Kindle:

Now, let’s imagine for a moment that we are back in the 15th century, to be precise just shortly after 1439, when Johannes Gensfleisch zur Laden zum Gutenberg invented movable type printing. I can only imagine the complaints that Baker would have uttered in the local paper (which was, of course, copied by hand from the original dictation). What? Only one title on the catalog? (The Bible.) Oh, and the fonts are sooo boring compared to handwriting. And no colors! And the quality of the drawings, simply unacceptable. This movable type printing thing will never ever replace the amanuenses, it will simply die as yet another “modern invention” and things will keep being just the same as they have been throughout what they at the time didn’t yet call the Middle Ages.

The New Yorker & The News Biz:

After many years, I am finally subscribing to the New Yorker again. Not in print, but via their Digital Reader. I’m blogging about it because I like their model: the Digital Reader adds something I wouldn’t get from the library version, and I feel like this new model bears watching as we migrate from print to online.

The psychology of reading for pleasure:

According to a neurological study that Nell performed, processing demands are higher with books than other media (movies, television) but that also means that when you are absorbed in a book, you are more likely to block out distractions. While readers describe being absorbed in a book as “effortless,” their brains are actually intensely active. As one critic said, this is not an escape from thinking, it’s an escape into thinking – intensely, and without distraction.

How Twitter works in theory:

The key to Twitter is that it is phatic – full of social gestures that are like apes grooming each other. Both Google and Twitter have little boxes for you to type into, but on Google you’re looking for information, and expecting a machine response, whereas on Twitter you’re declaring an emotion and expecting a human response. This is what leads to unintentionally ironic newspaper columns bemoaning public banality, because they miss that while you don’t care what random strangers feel about their lunch, you do if its your friend on holiday in Pompeii.
For those with Habermas’s assumption of a single common public sphere this makes no sense – surely everyone should see everything that anyone says as part of the discussion? In fact this has never made sense, and in the past elaborate systems have been set up to ensure that only a few can speak, and only one person can speak at a time, because a speech-like, real-time discourse has been the foundational assumption.
Too often this worldview has been built into the default assumptions of communications online; we see it now with privileged speakers decrying the use of anonymity in the same tones as 19th century politicians defended hustings in rotten boroughs instead of secret ballots. Thus the tactics of shouting down debate in town halls show up as the baiting and trollery that make YouTube comments a byword for idiocy; when all hear the words of one, the conversation often decays.

Blogging Evolution (PDF):

I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a
user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

What Do Mathematicians Need to Know About Blogging?:

Steven Krantz asked me to write an opinion piece about math blogging in the Notices of the American Mathematical Society. I asked if I could talk about this column on my blog, and even have people comment on drafts of it before it comes out in the Notices. He said okay. So, just to get the ball rolling, let me ask: what do you think mathematicians need to know about blogging?

Five Key Reasons Why Newspapers Are Failing and Five Key Reasons Why Newspapers Are Failing, pt. 2:

Journalists are pretty good at working the scene of a disaster. They’ll tell you what happened, who did it, and why.
But when it comes to the disaster engulfing their own profession, their analysis is less rigorous. An uncharacteristic haze characterizes a lot of the reporting and commentary on the current crisis of the industry.
It could have been brought on by delicacy, perhaps romanticism. And since it is not just any crisis, but a definitive one–one that seems to mean an end to the physical papers’ role in American life as we have come to know it–perhaps there’s a little bit of shell-shock in the mix as well.

Online Community Building: Gardening vs Landscaping:

The Gardener creates an ecosystem open to change, available to new groups, and full of fresh opportunities to emerge naturally. The approach is focused on organic collaboration and growth for the entire community. The gardener is simply there to help, cultivate, and clear the weeds if/when they poke up.
The Landscaper creates an ecosystem that matches a preconceived design or pattern. The approach is focused on executing a preconceived environment, regardless of how natural or organic it may be for the larger area. The landscaper is there to ensure that everything stays just as planned.

Don’t Be Such a Scientist: Talking Substance in an Age of Style (book review):

So I end up feeling a bit torn. He’s telling us “Don’t be such a scientist”, and it’s true that there are many occasions when the scientific attitude can generate unnecessary obstacles to accomplishing our goals. At the same time, though, I want to say “Do be such a scientist”, because it’s part of our identity and it makes us stand out as unusual and, like Randy, interesting, even if it sometimes does make us a bit abrasive. But, you know, some of us revel in our abrasiveness; it’s fun.

This has also been in the news a lot last week:
Threats to science-based medicine: Pharma ghostwriting
Wyeth, ‘Ghost-Writing’ and Conflict of Interest
More On Ghostwriting, Wyeth and Hormone Replacement Therapy
Wyeth’s ghostwriting skeletons yanked from the closet
Ghostwriters in the sky
Quickie Must-Read Link … (probably the best commentary of them all).
Several recent posts on the topic dear to my heart – the so-called “civility” in public (including online) discourse:
How Creationism (and Other Idiocies) Are Mainstreamed:

One of the things that has enabled the mainstreaming of various idiocies, from altie woo, to creationism, to global warming denialism is mainstream corporate media’s inability to accurately describe lunacy. For obvious reasons, ‘family-friendly’ newspapers and teevee can’t call creationists, birthers, or deathers batshit lunatic or fucking morons. This is where ‘civility’ (beyond the basic norms of decency when dealing with the mentally ill) and pretensions of ‘balance’ utterly fail.

Weekend Diversion: How to Argue:

You are, of course, free to argue however you like. But if you want to argue on my site, you’re really best off remembering this hierarchy, and staying as high as possible on it. Most of you do pretty well, but this has served me well in general, and I hope it helps you to see things laid out like this. And if not, at least you got a great song out of it!

When an image makes an argument:

Along similar lines to a frequentist interpretation of the strata, maybe this pyramid is conveying something about the ease or difficulty inherent in different types of engagement. It doesn’t take a lot of effort to call someone an asshat, but understanding her argument well enough to raise a good counterexample to it may take some mental labor. If this is the rhetorical work that the pyramidal layout does here, it may also suggest a corresponding hierarchy of people who have the mental skills to engage in each of these ways — making the people at the tippy-top of the pyramid more elite than those using the strategies from lower strata.

How to Argue…:

White men are sufficiently privileged enough to demand that they be treated respectfully while white women, at best, can expect to be presented with contradiction and counterargument. When I saw the category “responding to tone” I thought of the “angry black man” who, although perhaps right, is castigated for his anger and lack of civility for not conforming to the norms of white society. If you’re a non-white woman? Then, the best you can do is hope to not be denied food and shelter if you don’t fuck your husband enough (h/t to Free-Ride for pointing this article out), but you only expect to be part of the discussion if you’re allowed to be.
The call to civility is a frequent tactic to derail the discussion and is as much of an ad hominem attack as calling someone a cocknozzle. It fails to recognize the perspective of the other party or appreciate why they might be angry.

More on the topic:
Dr. Isis Learns to Argue:

I am lucky to have such thoughtful commenters. When I wrote the previous post I had no idea that bleeding from my vagina was clouding my judgement. Then, just when I thought I had cleared enough of the estrogen from my girl brain to understand, I learned that this was all a carefully planned tactic to teach me a lesson. Damn! I hate when that happens!

Weekend Diversion: How to argue…and actually accomplish something:

Here we arrive at the meat of the matter. Once having accomplished more than about 300 ms worth of consideration of a given topic, people are highly resistant to the idea that their rationale, conclusions and evidence base might actually be wrong. And the wronger the consideration might be, the more resistant to acknowledgment is the individual. We might think of this as the intrapersonal Overton window.

A Tale of Two Nations: the Civil War may have been won by the North, but in truth the South never emotionally conceded.:

The Civil War may have been won by the North, but in truth the South never emotionally conceded.
The Town Hall mobs, the birthers, the teabaggers are all part of that long line of “coded” agitators for the notions of white entitlement and “conservative values.”
Of course, this conservative viewpoint values cheap labor and unabated use of natural resources over technological and economic innovation. It also – and this is its hot molten core – fundamentally believes that white people are born with a divine advantage over people of other skin colors, and are chosen by God to lead the heathen hordes.
That a Town Hall mob is itself a heathen horde would never occur to the economically stressed whites who listen to the lies of the likes of Glenn Beck, Sean Hannity, Rush Limbaugh and Lou Dobbs. Lies that confirm an emotionally reinforcing worldview – however heinous – become truths for those in psychological need of feeling superior and chosen.

I remember an America where black men didn’t grow up to be President.:

And all of them are asking for their America back. I wonder which America that would be?
Would that be the America where the Supreme Court picks your president instead of counting all the votes? Would that be the America where rights to privacy are ignored? Would that be the America where the Vice President shoots his best friend in the face? Or would that be the America where an idiot from Alaska and a college drop-out with a radio show could become the torchbearers for the now illiterate Republican party?
I fear that would not be the America they want back. I fear that the America they want back is the one where black men don’t become President.
I remember that America. In that America people screaming at public gatherings were called out for what they were – an angry mob. Of course, they wore sheets to cover up their bad hair. Let’s be clear about something: if you show up to a town hall meeting with a gun strapped to your leg, the point you are trying to make isn’t a good one. Fear never produced anything worthwhile.

In America, Crazy Is a Preexisting Condition:

The tree of crazy is an ever-present aspect of America’s flora. Only now, it’s being watered by misguided he-said-she-said reporting and taking over the forest. Latest word is that the enlightened and mild provision in the draft legislation to help elderly people who want living wills — the one hysterics turned into the “death panel” canard — is losing favor, according to the Wall Street Journal, because of “complaints over the provision.”

Two oldies but goodies:
Atheists and Anger:

One of the most common criticisms lobbed at the newly-vocal atheist community is, “Why do you have to be so angry?” So I want to talk about:
1. Why atheists are angry;
2. Why our anger is valid, valuable, and necessary;
And 3. Why it’s completely fucked-up to try to take our anger away from us.

Atheists and Anger: A Reply to the Hurricane:

Now my replies to the critics. I suppose I shouldn’t bother, I suppose I should just let it go and focus on the love. But I seem to be constitutionally incapable of letting unfair or inaccurate accusations just slide. So here are my replies to some of the critical comments’ common themes.

The Privilege of Politeness:

One item that comes up over and over in discussions of racism is that of tone/attitude. People of Color (POC) are very often called on their tone when they bring up racism, the idea being that if POC were just more polite about the whole thing the offending person would have listened and apologized right away. This not only derails the discussion but also tries to turn the insults/race issues into the fault of POC and their tone. Many POC have come to the realization that the expectation of politeness when saying something insulting is a form of privilege. At the core of this expectation of politeness is the idea that the POC in question should teach the offender what was wrong with their statement. Because in my experience what is meant by “be polite” is “teach me”, teach me why you’re offended by this, teach me how to be racially sensitive and the bottom line is that it is no one’s responsibility to teach anyone else. And even when POC are as polite as possible there is still hostility read into the words because people are so afraid of being called racist that they would rather go on offending than deal with the hard road of confronting their own prejudices.

The exciting history of history of science. And mammoths!

Scientific facts are fun. But probably to a limited number of people.
It’s more fun to know how scientists got those facts – their thoughts, motivations and methods. How they did it. Why they did it. Where did they get the idea to do it in the first place.
It’s even more fun, for a broader number of people, if that finding is placed in a historical context – how work of previous generations of scientists, meandering around various age-specific ideas, led to the work of this particular group.
But it is even more fun watching the historians of science at work. Most recent science is pretty easy to figure out. But going into the past, it gets harder and harder. The unit of information today is the peer-reviewed scientific paper in a journal that is for the most part easily obtainable online. But in the past, books were more important. The standards of evidence were not as stringent. The various pseudoscientific and borderline scientific ideas were mainstream. Many scientific findings were made by adventurous explorers, not people with long and sophisticated scientific training. The line between science and fiction was not very clear. While today English is the language of science, in the past many languages were used, and not everyone could read all of them. Transport of books around the world was slow and difficult. Plagiarism was harder to detect, thus rampant. History of science, and even more the work of science historians, reads like a detective thriller! Now that’s exciting!
Which is why I regularly read John McKay at Archy, who is a professional historian, slowly working on his book. And occasionally putting some of the essays on his blog for the commenters to help with corrections, ideas and additional information. See his latest output – all riveting reads:
Fragments of my research – VIII
A mammoth literary mystery
A very brief history of plagiarism
The intellectual dishonesty of Allan Quist
Quist, Antarctica, and all that
Mammoth on ice
Mammoth illustrations

Why or why not cite blog posts in scientific papers?

As the boundaries between formal and informal scientific communication is blurring – think of pre-print sites, Open Notebook Science and blogs, for starters – the issue of what is citable and how it should be cited is becoming more and more prominent.
There is a very interesting discussion on this topic in the comments section at the Sauropod Vertebra Picture of the Week blog, discussing the place of science blogs in the new communication ecosystem and if a blog post can be and should be cited. What counts as a “real publication”? Is the use of the phrase “real publication” in itself misleading?
You may remember that I have touched on this topic several times over the past few years (as two of my blog posts got cited in scientific papers), most recently in the bottom third (after the word “Except…”) of this post, where I wrote:

National Library of Medicine even made some kind of “official rules for citing blogs” which are incredibly misguided and stupid (and were not changed despite some of us, including myself, contacting them and explaining why their rules are stupid – I got a seemingly polite response telling me pretty much that my opinion does not matter). Anyway, how can anyone make such things ‘official’ when each journal has its own reference formatting rules? If you decide to cite a blog post, you can pretty much use your own brain and put together a citation in a format that makes sense.
The thing is, citing blogs is a pretty new thing, and many people are going to be uneasy about it, or ignorant of the ability and appropriateness to cite blogs, or just so unaware of blogs they would not even know that relevant information can be found on them and subsequently cited. So, if you see that a new paper did not cite your paper with relevant information in it, you can get rightfully angry, but if you see that a new paper did not cite your blog post with relevant information in it, you just shrug your shoulders and hope that one day people will learn….
One of the usual reasons given for not citing blog posts is that they are not peer-reviewed. Which is not true. First, if the post contained errors, readers would point them out in the comments. That is the first layer of peer review. Then, the authors of the manuscript found and read a blog post, evaluated its accuracy and relevance and CHOSE to use it as a reference. That is the second layer of peer-review. Then, the people who review the manuscript will also check the references and, if there is a problem with the cited blog post, they will point this out to the editor. This is the third layer of peer-review. How much more peer-review can one ask for?
And all of that ignores that book chapters, books, popular magazine articles and even newspaper articles are regularly cited, not to mention the ubiqutous “personal communication”. But blogs have a bad rep, because dinosaur corporate curmudgeon journalists think that Drudge and Powerline are blogs – the best blogs, actually – and thus write idiotic articles about the bad quality of blogs and other similar nonsense. Well, if you thought Powerline is the best blog (as Time did, quite intentionally, in order to smear all of the blogosphere by equating it with the very worst right-wing blathering idiotic website that happens to use a blogging software), you would have a low of opinion of blogs, too, wouldn’t you?
But what about one’s inability to detect relevant blog posts, as opposed to research papers to cite? Well, Google it. Google loves blogs and puts them high up in searches. If you are doing research, you are likely to regularly search your keywords not just on MedLine or Web Of Science, but also on Google, in which case the relevant blog posts will pop right up. So, there is no excuse there.

But, some will say, still….a blog post is not peer-reviewed!
Remember that the institution of peer review is very recent. It developed gradually in mid-20th century. None of the science published before that was peer reviewed. Yup, only one of Einstein’s papers ever saw peer review.
Much of the science published today is not peer reviewed either as it is done by industry and by the military and, if published at all, is published only internally (or on the other extreme: citizen science which is published on Flickr or Twitter!). But we see and tend to focus only on the academic research that shows up in academic journals – a tip of the iceberg.
If you think that the editorial process is really important, remember that manuscripts, in their final version, need to be submitted by the authors in the form and format ready for publication. It is not the job of editors to rewrite your poorly written manuscript for you. Thus, scientific papers, even those that went through several rounds of peer review on content are, just like blog posts, self-edited on style, grammar and punctuation (and comprehensibility!). What is the difference between peer reviewers and blog commenters? There are more commenters.
Then, think about the way gradual moving away from the Impact Factor erodes the importance of the venue of publication. This kind of GlamorMagz worship is bound to vanish as article-level metrics get more broadly accepted – faster in less competitive areas of research and in bigger countries, slower in biomedical/cancer research and in small countries.
As the form of the scientific paper itself becomes more and more dynamic and individuals get recognized for their contributions regardless of the URL where that contribution happens, why not cite quality blog posts? Or quality comments on papers themselves?

Support the UCLA Pro-Test tomorrow and get educated about the use of animals in research

The UCLA Pro-Test is tomorrow. If you live there – go. If not, prepare yourself for inevitable discussions – online and offline – by getting informed. And my fellow science bloggers have certainly provided plenty of food for thought on the issue of use of animals in research.
First, you have to read Janet Stemwedel’s ongoing series (5 parts so far, but more are coming) about the potential for dialogue between the two (or more) sides:
Impediments to dialogue about animal research (part 1).:

Now, maybe it’s the case that everyone who cares at all has staked out a position on the use of animals in scientific research and has no intentions of budging from it. But in the event that there still exists a handful of people who are thinking the issues through, or are interested in understanding the perspectives of those who hold different views about research with animals — in the event that there are still people who would like to have a dialogue — we need to understand what the impediments to this dialogue are and find ways to work around them.

Impediments to dialogue about animal research (part 2).:

Research with animals seems to be a topic of discussion especially well-suited to shouting matches and disengagement. Understanding the reasons this is so might clear a path to make dialogue possible. Yesterday, we discussed problems that arise when people in a discussion start with the assumption that the other guy is arguing in bad faith. If we can get past this presumptive mistrust of the other parties in the discussion, another significant impediment rears its head pretty quickly: Substantial disagreement about the facts.

Impediments to dialogue about animal research (part 3).:

As with yesterday’s dialogue blocker (the question of whether animal research is necessary for scientific and medical advancement), today’s impediment is another substantial disagreement about the facts. A productive dialogue requires some kind of common ground between its participants, including some shared premises about the current state of affairs. One feature of the current state of affairs is the set of laws and regulations that cover animal use — but these laws and regulations are a regular source of disagreement: Current animal welfare regulations are not restrictive enough/are too restrictive.

Impediments to dialogue about animal research (part 4).:

As we continue our look at ways that attempted dialogues about the use of animals in research run off the rails, let’s take up one more kind of substantial disagreement about the facts. Today’s featured impediment: Disagreement about whether animals used in research experience discomfort, distress, pain, or torture.

Impediments to dialogue about animal research (part 5).:

Today we discuss an impediment to dialogue about animals in research that seems to have a special power to get people talking past each other rather than actually engaging with each other: Imprecision about the positions being staked out. Specifically, here, the issue is whether the people trying to have a dialogue are being precise in laying out the relevant philosophical positions about animals — the position they hold, the position they’re arguing against, the other positions that might be viable options.

Also check Janet’s older posts on the topic.
Mark C. Chu-Carroll:
Can simulations replace animal testing? Alas, no.:

I don’t want to get into a long discussion of the ethics of it here; that’s a discussion which has been had hundreds of times in plenty of other places, and there’s really no sense repeating it yet again. But there is one thing I can contribute to this discussion. One of the constant refrains of animal-rights protesters arguing against animal testing is: “Animal testing isn’t necessary. We can use computer simulations instead.”
As a computer scientist who’s spent some time studying simulation, I feel qualified to comment on that aspect of this argument.
The simplest answer to that is the old programmers mantra: “Garbage in, Garbage out”.
To be a tad more precise, like any other computer program, a simulation can only do what you tell it to. If you don’t already know how something works, you can’t simulate it. If you think you know how something works but you made a tiny, miniscule error, then the simulation can diverge dramatically from reality.

Tilting at Animal Rights Activist Windmills:

As we are in the midst of a traditional week-o-ARA-wackaloonery and two days away from the first US Pro-Test rally (at UCLA) this is all highly topical. Why not take some time to do a little bit of reading and thinking about these issues? After all, it is only the continued health and well being of yourself, your family, your friends and neighbors that is at stake.

Virtual IACUC: Reduction vs. Refinement:

One of the thornier problems in thinking about the justification of using animals is when two or more laudable goals call for opposing solutions. For today’s edition of virtual IACUC we will consider what to do when Refinement calls for the use of more animals, in obvious conflict with Reduction.

FBI Places Alleged ARA Terrorist on Most Wanted List:

The important thing is the setting of priority. These acts, like the March 2009 bombing of neuroscientist J. David Jentsch’s car, are fundamental crimes against our rule of law as well as being a specific attack on scientific progress and the development of life-saving medical advances. With this announcement, and all of the publicity and news surrounding the UCLA Pro-Test rally in support of animal research scheduled for tomorrow…well, at the very least the wind has been taken out of the ARA sails during one of their big PR weeks.

Also check older posts on the topic on the DrugMonkey blog.
Why are we marching?:

At a banner making session today (Monday) I decided to ask a few people why they were planning on attending Wednesday’s rally. Here are a handful of responses I got:

Scientists dare to defend research:

As students and scientists at UCLA stand up to support lifesaving medical research, researchers at other institutions are offering their support for the cause. From Wake Forest University to the University of Arizona, from UC Davis to the University of South Dakota, researchers from across the United States have been united in their support for UCLA Pro-Test.

Nick Anthis:
New UCLA Pro-Test Chapter Announces April 22nd Rally:

Unfortunately, researchers at UCLA have become a major target of animal rights extremists over the last few years. This has included various incidents of destruction of property aimed at specific scientists, and this has coincided with a general rise in animal rights extremist activity in the US.

Also check Nick’s older posts on the topic.
You can also see what I have written in the past on this topic.
Here is the official NIH Statement Deploring Terrorism Against Researchers:

It is important that everyone know that all animals used in federally-funded research, are protected by laws, regulations, and policies to ensure they are used in the smallest numbers possible and with the greatest commitment to their comfort and welfare. The search for cures for devastating diseases depends on cumulative evidence gained from quality research. The appropriate use of animals in medical research has enabled the development of successful therapies and preventive measures for a wide- range of human diseases such as polio, Parkinson’s disease, and hepatitis A and B.

Check out the UCLA Pro-Test page and show yoru support (and get informed) by joining the UCLA Pro-test Facebook group and the more general Pro-Test – Supporting Animal Research group.

ScienceOnline’09 – Saturday 4:30pm and beyond: the Question of Power

I know it’s been a couple of months now since the ScienceOnline’09 and I have reviewed only a couple of sessions I myself attended and did not do the others. I don’t know if I will ever make it to reviewing them one by one, but other people’s reviews on them are under the fold here. For my previous reviews of individual sessions, see this, this, this, this and this.
What I’d like to do today is pick up on a vibe I felt throughout the meeting. And that is the question of Power. The word has a number of dictionary meanings, but they are all related. I’ll try to relate them here and hope you correct my errors and add to the discussion in the comments here and on your own blogs.
Computing Power
Way back in history, scientists (or natural philosophers, as they were called then), did little experimentation and a lot of thinking. They kept most of their knowledge, information and ideas inside of their heads (until they wrote them down and published them in book form). They could easily access them, but there was definitely a limit to how much they could keep and how many different pieces they could access simultaneously.
A scientist who went out and got a bunch of notebooks and pencils and started writing down all that stuff in an organized and systematic manner could preserve and access much more information than others, thus be able to perform more experiments and observations than others, thus gaining a competitive advantage over others.
Electricity and gadgets allowed for even more – some degree of automation in data-gathering and storage. For instance, in my field, there is only so much an individual can do without automation. How long can you stay awake and go into your lab and do measurements on a regular basis? I did some experiments in which I did measurements every hour on the hour for 72 hours! That’s tough! All those 45min sleep bouts interrupted by 15min times for measurements, even as a couple of friends helped occasionally, were very exhausting.
But using an Esterline-Angus apparatus automated data-gathering and allowed researchers to sleep, thus enabling them to collect long-term behavioral data (collecting continuous recordings for weeks, months, even years) from a large number of animals. This enabled them to do much more with the same amount of time, space, money and manpower. This gave them a competitive advantage.
But still, Esterline-Angus data were on paper rolls. Those, one had to cut into strips, glue onto cardboard, photograph in order to make an actograph, then use manual tools like rulers and compasses and protractors to quantify and calculate the results (my PI did that early in his career and kept the equipment in the back room, to be shown to us whenever we complained that we were asked to do too much).
Having a computer made this much easier: automated data-collection by a computer, analyzed and graphed on that same computer, inserted into manuscripts written on that same computer. A computer can contain much more information than a human brain and, in comparison to notebooks, it is so much easier and quicker to search for and find the relevant information. That was definitely a competitive advantage as one could do many more experiments with the same amounts of time, space, money and manpower.
Enter the Web: it is not just one’s own data that one can use, but also everyone else’ data, information, ideas, publications, etc. Science moves from a collection of individual contributions to a communal (and global) pursuit – everyone contributes and everyone uses others’ contributions. This has a potential to exponentially speed up the progress of scientific research.
For this vision to work, all the information has to be freely available to all as well as machine-readable – thus necessity of Open Access (several sessions on this topic, of course) and Open Source. This sense of the word Power was used in sessions on the ‘Semantic Web in Science’, the ‘Community intelligence applied to gene annotation’, and several demos. Also, in the session on ‘Social Networking for Scientists’, this explains why, unlike on Facebook, it is the information (data) that is at the core. Data finds data. Subsequently, people will also find people. Trying to put people together first will not work in science where information is at the core, and personalities are secondary.
Power Relationships
In the examples above, you can already see a hierarchy based on power. A researcher who is fully integrated into the scientific community online and uses online databases and resources and gives as much as he/she takes, will have an advantage over an isolated researcher who uses the computer only offline and who, in comparison, has a competitive advantage over a person who uses mechanical devices instead of computers, who in turn does better than a person who only uses a pencil and paper, who beats out the guy who only sits (in a comfy armchair, somewhere in the Alps) and thinks.
Every introduction of new technologies upsets the power structure as formerly Top Dogs in the field may not be the quickest to adopt new technologies so they bite the dust when their formerly lesser colleagues do start using the new-fangled stuff. Again, important to note here, “generation” is a worldview, not age. It is not necessarily the young ones who jump into new technologies and old fogies do not: both the people who are quick to adopt new ways and the curmugeons who don’t can be found in all age groups.
Let’s now try to think of some traditional power relationships and the way the Web can change them. I would really like if people would go back to my older post on The Shock Value of Science Blogs for my thought on this, especially regarding the role of language in disrupting the power hierarchies (something also covered in our Rhetorics In Science session).
People on the top of the hierarchy are often those who control a precious resource. What are the precious resources in science? Funding. Jobs. Information. Publicity.
Funding and Jobs
Most of the funding in most countries comes from the government. But what if some of that funding is distributed equally? That upsets the power structure to some extent. Sure, one has to use the funds well in order to get additional (and bigger) funds, but still, this puts more people on a more even footing, giving them an initial trigger which they can use wisely or not. They will succeed due to the quality of their own work, not external factors as much.
Then, the Web also enables many more lay people to become citizen scientists. They do not even ask for funding, yet a lot of cool research gets done. With no control of the purse by government, industry, military or anyone else except for people who want to do it.
Like in Vernon Vinge’s Rainbows End, there are now ways for funders and researchers to directly find each other through services ranging from Mechanical Turk to Innocentive. The money changes hands on per-need basis, leaving the traditional purse-holders outside the loop.
As more and more journals and databases go Open Access, it is not just the privileged insiders who can access the information. Everyone everywhere can get the information and subsequently do something with it: use it in own research, or in application of research to real-world problems (e.g., practicing medicine), or disseminating it further, e.g., in an educational setting.
In a traditional system, getting publicity was expensive. It took a well-funded operation to be able to buy the presses, paper, ink, delivery trucks etc. Today, everyone with access to electricity, a computer (or even a mobile device like a cell phone) and online access (all three together are relatively cheap) can publish, with a single click. Instead of pre-publication filtering (editors) we now have post-publication filtering (some done by machines, some by humans). The High Priests who decided what could be published in the first place are now reduced to checking the spelling and grammar. It is the community as a whole that decides what is worth reading and promoting, and what is not.
In a world in which sources can go directly to the audience, including scientists talking directly to their audience, the role of middle-man is much weakened. Journal editors, magazine editors, newspaper editors, even book editors (and we had a separate session on each one of these topics), while still having power to prevent you from publishing in elite places, cannot any more prevent you from publishing at all. No book deal? Publish with No magazine deal? Write a blog. No acceptance into a journal? Do Open Notebook Science to begin with, to build a reputatiton, then try again. If your stuff is crap, people will quickly tell you and will tell others your stuff is crap, and will vote with their feet by depriving you of links, traffic, audience and respect.
You can now go directly to your audience. You can, by consistently writing high quality stuff, turn your own website or blog into an “elite place”. And, as people are highly unlikely to pay for any content online any more, everything that is behind a pay wall will quickly drop into irrelevance.
Thus, one can now gain respect, reputation and authority through one’s writing online: in OA journals, on a blog, in comment threads, or by commenting on scientific papers. As I mentioned in The Shock Value of Science Blogs post, this tends to break the Old Boys’ Clubs, allowing women, minorities and people outside of Western elite universities, to become equal players.
Language is important. Every time an Old Boy tries to put you down and tell you to be quiet by asking you to “be polite”, you can blast back with a big juicy F-word. His aggressive response to this will just expose him for who he is and will detract from his reputation – in other words, every time an Old Boy makes a hissy fit about your “lack of politeness” (aka preserving the status quo in which he is the Top Dog), he digs himself deeper and becomes a laughingstock. Just like Jon Stewart and Stephen Colbert do to politicians with dinosaur ideas and curmudgeon journalists who use the He Said She Said mode of reporting. It is scary to do, but it is a win-win for you long-term. Forcing the old fogies to show their true colors will speed up their decline into irrelevance.
Another aspect of the Power on the Web is that a large enough group of people writing online can have an effect that were impossible in earlier eras. For instance, it is possible to bait a person to ruin his reputation on Google. It is also possible to affect legislation (yes, bloggers and readers, by calling their offices 24/7, persuaded the Senators to vote Yes). This is a power we are not always aware of when we write something online, and we need to be more cognizant of it and use it wisely (something we discussed in the session about Science Blogging Networks: how being on such a platform increases one’s power to do good or bad).
The session on the state of science in developing and transition countries brought out the reality that in some countries the scientific system is so small, so sclerotic, so set in their ways and so dominated by the Old Boys, that it is practically impossible to change it from within. In that case one can attempt to build a separate, parallel scientific community which will, over time and through use of modern tools, displace the old system. If the Old Boys in their example of Serbia are all at the University of Belgrade, then people working in private institutes, smaller universities, or even brand new private universities (hopefully with some consistent long-term help from the outside), can build a new scientific community and leave the old one in the dust.
Teachers used to be founts of knowledge. This was their source of power. But today, the kids have all the information at their fingertips. This will completely change the job description of a teacher. Instead of a source of information, the teacher will be a guide to the use of information: evaluation of the quality of information. Thus, instead of a top-down approach, the teachers and students will become co-travellers through the growing sea of information, learning from one another how to navigate it. This is definitely a big change in power relationship between teachers and their charges. We had three sessions on science education that made this point in one way or another.
And this is a key insight, really. Not just in education, but also in research and publishing, the Web is turning a competitive world into a collaborative world. Our contributions to the community (how much we give) will be more important for our reputation (and thus job and career) than products of our individual, secretive lab research.
Yet, how do we ensure that the change in the power-structure becomes more democratic and now just a replacement of one hierarchy with another?
Coverage of other sessions under the fold:

Continue reading

Why eliminate the peer-review of baseline grants?

ResearchBlogging.orgAbout a week ago, my brother sent me a couple of interesting papers about funding in science, one in Canada, the other in the UK. I barely had time to skim the abstracts at the time, but thought I would put it up for discussion online and come back to it later. So I posted the link, abstract and brief commentary a few days ago to the article: Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant:

Abstract: Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money. We anticipate that the net result would be more and better research since more research would be conducted at the critical idea or discovery stage. Control of quality is assured through university hiring, promotion and tenure proceedings, journal reviews of submitted work, and the patent process, whose collective scrutiny far exceeds that of grant peer review. The greater efficiency in use of grant funds and increased innovation with baseline funding would provide a means of achieving the goals of the recent Canadian Value for Money and Accountability Review. We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation.

A long and interesting discussion ensued in the comments, with the author of the paper himself showing up and offering to send reprints to those who are interested. More discussion also happened on FriendFeed here and here.
Several other bloggers also posted about it, and discussions happened on their posts as well. T. Ryan Gregory posted about it both on his Nature Network blog Pyrenaemata and on his indy blog Genomicron.
Larry Moran was largely in agreement with the article, but some commenters were not, including Rosie Redfield whose comment motivated T. Ryan Gregory to post again, just to explain his disagreement with Rosie.
Jonathan Eisen pointed out to a related post of his and Cameron Neylon to a related post of his. Finally, Zen Faulkes used it as a starting point for three posts here,
here and here.
I have finally managed to find time to read the paper myself so I think I can say something semi-intelligent about it. It became obvious that many who commented have not actually read the paper, just the Abstract, and thus were not in the position to respond to it intelligently (the paper actually answers, clearly and in detail, all the questions and complaints voiced by the commenters). The abstract is just, …well, an abstract. The paper is full of thought-provoking ideas and really needs to be read in its entirety.
Finally, my brother showed up in the comments and I would like to use his comment as a starting point today. That is – once you read the actual paper (ask for a reprint if you cannot access it), the linked blog posts and comment threads. I’ll be right here, waiting for you to come back….
I am assuming that the Canadian funding system is not very dissimilar to that in many other countries, including the USA – there is a central governmental body that gets its budget from the government and uses committees of unpaid peer-reviewers to decide how the money will be allocated to the researchers. The paper explains in detail at least a dozen reasons why and how this system is flawed: how it stifles truly innovative science, repels students from entering science, disproportinately pushes women out of science, encumbers students and postdocs with tasks they are not supposed to be doing (e.g., clerical, or technical), introduces an element of uncertainty about one’s livelihood, gives universities excuses to completely get out of research funding, shafts teaching and outreach as criteria for promotion, etc. But the clincher, for politicos at least, is that this system costs more than if a set sum of about $30,000 (Canadian) was given to every academic employed by a Canadian university who asks in any given year.
Yes, giving every Canadian scientist who already has a job and a lab this small amount of money no-questions-asked, geared toward innovative exploratory research, costs the government less than going through the peer-review system that gives money to some and no money to others (not to mention the reinforcement of the Old Boys Club this way).
This does not mean, in their proposal, that all of the Canadian money earmarked for science would be given this way – this is still just a small part of it. If you have a big lab or do expensive research and need to apply for much bigger grants, that would be done by the traditional peer review. But in order to get to the point where you have a good proposal, you need to have some neat stuff done (the “preliminary data”). With the proposed system, that preliminary data can be really exciting or revolutionary, something that, as an initial proposal, would never fly by peers.
Would people send out proposals for crap? Some would, I’m sure, but that doesn’t matter. Most would not. Scientists are curious about nature and would like to test their hunches. Some will flop, some will be amazing – it is the latter that this new system is worth doing for, as they may never be done otherwise. Anyway, how many $5,000,000 grants produced amazing stuff? All? I.Don’t. Think.So.
Where does quality control come from? First, it already came from universities who hired these researchers out of hundreds of applicants for each position. Aren’t they going to trust those best-of-the-best they hired? Second, the research itself will be judged after it is done – at conferences, in journal articles, and in post-publication metrics (citations, downloads, online chatter, etc., including perhaps a Nobel Prize here and there). If it is not up to standards, $30,000 Canadian dollars is not a big price to pay, and even the negative or inconclusive results can be useful to others if the thinking is original. If it is up to standards or more, that person will now have something exciting to base a bigger grant proposal on.
This also goes back to something I like to rant about (oh yes, go read that again!) – the bandwagon of Big Science. Biology, for example, does not equal running gels (hmmm, that’s chemistry, isn’t it?). But many people are given that appearance. “No gels – no grants, no papers, no career” (yup, I was told that a few years ago). Unless you already have a big molecular lab, this small grant will not build you one. Instead, you can do some really cool stuff at other levels – from tissues up to ecosystems and everything in-between, including computer modeling. You can use it to travel to some jungle that has never seen a Westerner and see what species live there – not hypothesis-testing, exploratory and exciting, definitely useful, but not something that is easily funded with a current system. If your proposal includes research on live vertebrates, you first have to get an IACUC proposal, something that will take 6-9 months of extremely frustrating fighting and proposal-modification – getting an IACUC proposal is the toughest peer-review known to science: if they say Yes to your proposal, no other committee of peers can add any more wisdom to it. And if you decide to work on invertebrates – it is much cheaper.
Another paper looks at this from another perspective – four stages of science. The grants, especially the big ones, disproportionately target science in Stage 3. The small baseline grants would target primarily Stage 1, the exciting, innovative stage – and this is a Good Thing. They could also more easily fund research in Stage 2 and Stage 4, also a Good Thing – from the article:

In this article I propose the classification of the evolutionary stages that a scientific discipline evolves through and the type of scientists that are the most productive at each stage. I believe that each scientific discipline evolves sequentially through four stages. Scientists at stage one introduce new objects and phenomena as subject matter for a new scientific discipline. To do this they have to introduce a new language adequately describing the subject matter. At stage two, scientists develop a toolbox of methods and techniques for the new discipline. Owing to this advancement in methodology, the spectrum of objects and phenomena that fall into the realm of the new science are further understood at this stage. Most of the specific knowledge is generated at the third stage, at which the highest number of original research publications is generated. The majority of third-stage investigation is based on the initial application of new research methods to objects and/or phenomena. The purpose of the fourth stage is to maintain and pass on scientific knowledge generated during the first three stages. Groundbreaking new discoveries are not made at this stage. However, new ways to present scientific information are generated, and crucial revisions are often made of the role of the discipline within the constantly evolving scientific environment. The very nature of each stage determines the optimal psychological type and modus operandi of the scientist operating within it. Thus, it is not only the talent and devotion of scientists that determines whether they are capable of contributing substantially but, rather, whether they have the ‘right type’ of talent for the chosen scientific discipline at that time. Understanding the four different evolutionary stages of a scientific discipline might be instrumental for many scientists in optimizing their career path, in addition to being useful in assembling scientific teams, precluding conflicts and maximizing productivity. The proposed model of scientific evolution might also be instrumental for society in organizing and managing the scientific process. No public policy aimed at stimulating the scientific process can be equally beneficial for all four stages. Attempts to apply the same criteria to scientists working on scientific disciplines at different stages of their scientific evolution would be stimulating for one and detrimental for another. In addition, researchers operating at a certain stage of scientific evolution might not possess the mindset adequate to evaluate and stimulate a discipline that is at a different evolutionary stage. This could be the reason for suboptimal implementation of otherwise well-conceived scientific policies.

Now, the proposal in this paper is quite definitive about allowing only researchers employed by universities to apply for such grants. But my mind instantly started thinking about those outside. How about amateur scientists? How about people not affiliated with the academia? How about distributed citizen science projects? Those are usually Stage 1 or Stage 2 projects, attractive to a particular kind of researcher (myself included – don’t try to lure me into a big Stage 3 lab). If I wanted to get some crayfish or spiders (or even birds, if a local IACUC would let me) and do experiments at home, this kind of a small grant would be just ideal. Could I have a local University, or some peers, write a letter in support of my proposal? Would that fly?
The paper also mentions, in a couple of places, similarities and differences between peer-review of grants and peer-review of manuscripts, including the importance of Openness to science. In one place, it mentions new journals “where ideas may be published initially unreviewed, but anyone may append public discussions to each article”. I am hoping this refers to arXiv and Nature Precedings, or even the concept of Open Notebook Science, but it smells too much like one of the pernicious myths spread by the enemies of Open Access about PLoS ONE which is, as readers of this blog are aware, stringently peer-reviewed.
One thing that the article mentions is that the current granting system allows researchers to buy time for research away from their teaching time. They note this as bad for teaching, true, but there is another angle to it. As danah writes in regard to the new proposed NSF funding of qualitative research, this kind of work does not require much in terms of equipment, but much in terms of time. It is essential for people, especially in social sciences, who do qualitative research, to be able to buy the time they need to do their research correctly.
Oh, and I mentioned at the beginning that my brother sent me two papers, yet we talked here only about one of them. The other one, if you are interested in starting a whole new discussion, is this one: Life after death? The Soviet system in British higher education

Recent studies of British higher education (HE) have focused on the application of the principles of the ‘new managerialism’ in the public sector, ostensibly aimed at improving the effectiveness of research and teaching, and also on the increasing commercialisation of HE. This article examines HE management in the light of the historical experience of the Soviet system of economic planning. Analogies with the dysfunctional effects of the Soviet system are elaborated with regard to financial planning and the systems of quality control in academic research and teaching. It is argued that Soviet-style management systems have paradoxically accompanied the growing market orientation of HE, undermining traditional professional values and alternative models of engagement between HE institutions and the wider society.

A FriendFeed discussion has started. Read the entire paper before chiming in, of course – we are scientists here!
Gordon, R., & Poulin, B. (2009). Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant Accountability in Research, 16 (1), 13-40 DOI: 10.1080/08989620802689821

Eliminate peer-review of baseline grants entirely?

This is very interesting, referring to Canadian system:
Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant:

Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money. We anticipate that the net result would be more and better research since more research would be conducted at the critical idea or discovery stage. Control of quality is assured through university hiring, promotion and tenure proceedings, journal reviews of submitted work, and the patent process, whose collective scrutiny far exceeds that of grant peer review. The greater efficiency in use of grant funds and increased innovation with baseline funding would provide a means of achieving the goals of the recent Canadian Value for Money and Accountability Review. We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation.

I don’t know how that would work in the USA, and certainly would not work for big $million grants, but this is quite an interesting idea – skipping the peer-review of small grants entirely and just giving all the applicants a Baseline Grant. If they use the money well and are lucky with the result, they will have publications and data they can then use to apply for bigger grants. Some really cool and unusual, non-band-waggony stuff would get done that way. What do you think?

Are solo authors less cited?

Daniel Lemire asks this question when observing a fallacy voiced in an editorial:

…..only a small fraction of the top 100 papers ranked by the number of citations (17 of 100) were published by single authors…..a published paper resulting from collaborative work has a higher chance of attracting more citations.

You can discuss the fallacy if you want, but I am much more interested in the next question that Daniel asks – are solo authors and groups of authors inherently attracted to different kinds of problems, or if solo vs. group dynamics make some projects more conducive for solo work and others for group collaboration:

But the implication is that solo authors are less interesting. Instead, I believe that solo authors probably work on different problems. (Hint: This could be the subject of a study of its own!)
Because of something I call problem inertia. For collaboration to occur, several people must come together and agree to a joint project. Sometimes money is required to pay the assistants or the students. All of these factor means that small problems or risky problems will be ignored in favor of safe bets. To put it bluntly, Microsoft will not sell PHP plugins! Hence, statistically, teams must be deliberate and careful. Also, fewer problems can be visited: even if the selected problem is a bad one, changing the topic in mid-course might be too expensive.
An autonomous author can afford to take more risks. Even more so if he has a permanent position. This may explain why Peter Turney seems to believe that researchers lack ambition. They may simply be rational: if it takes you three weeks to even get started on a project, you cannot afford many false starts!

And he than quotes Seth Roberts:

One reason my self-experimentation was effective was it didn’t depend on grants. No matter what I found, no matter how strange or upsetting or impossible or weird the results might be, I could publish them and continue to investigate them.

So, what I think he means is that groups jump on bandwagons, and bandwagoners are more common, thus bandwagoners will cite other bandwagoners more. Solo authors can do weird stuff and only very few other people will work on the same stuff, or similar enough stuff to warrant a citation.
If thousands are studying process X in rats, they will tend to cite each other and easily get grants for collaborative work. They have little incentive to cite your work on that same process X that you study in the Platypus, and nobody else in the world studies it in the Platypus so there’s not a large group (or anyone) out there to cite your stuff. But if you find something really revolutionary in Platypus that cannot be discovered in the rat – then your high risk resulted in a huge payoff (not to mention you will get lots of invitations to give talks at meetings as the organizers will like to have someone ‘weird’ – “that Platypus guy, snicker” – attract their audience).
But for the progress of science, both types of research need to be done. And the lack of citations for risky single-author work should not be used as a measure of quality of that work or as impediment to career advances.
Agree or disagree?
Also, a discussion of this happened on FriendFeed.

Why are scientists so HARD to move!?

The unmovable movers! Or so says Bill Hooker:

For instance: I use Open Office in preference to Word because I’m willing to put up with a short learning curve and a few inconveniences, having (as they say here in the US) drunk the Open Kool-Aid. But I’m something of an exception. Faced with a single difficulty, one single function that doesn’t work exactly like it did in Word, the vast majority of researchers will throw a tantrum and give up on the new application. After all, the Department pays the Word license, so it’s there to be used, so who cares about monopolies and stifling free culture and all that hippy kum-ba-yah crap when I’ve got a paper to write that will make me the most famous and important scientist in all the world?
Researchers have their set ways of doing things, and they are very, very resistant to change — I think this might be partly due to the kind of personality that ends up in research, but it’s also a response to the pressure to produce. In science, only one kind of productivity counts — that is, keeps you in a job, brings in funding, wins your peers’ respect — and that’s published papers. The resulting pressure makes whatever leads to published papers urgent and limits everything else to — at best — important; and urgent trumps important every time. Remember the old story about the guy struggling to cut down a tree with a blunt saw? To suggestions that his work would go faster if he sharpened the saw, he replies that he doesn’t have time to sit around sharpening tools, he’s got a tree to cut down!
I think that’s true, but like the guy with the saw, scientists are caught up in short-term thinking. Put the case to most of them, and they’ll agree about the advantages of Open over closed — for instance, I’ve yet to meet anyone who disagreed on principle that Open Access could dramatically improve the efficiency of knowledge dissemination, that is, the efficiency of the entire scientific endeavour. I’ve also yet to meet more than a handful of people willing to commit to sending their own papers only to OA journals, or even to avoiding journals that won’t let them self-archive! “I have a job to keep”, they say, “I’m not going to sacrifice my livelihood to the greater good”; or “that’s great, but first I need to get this grant funded”; or my personal favourite, “once I have tenure I’ll start doing all that good stuff”. (Sure you will. But I digress.)
When it comes to scientists, you don’t just have to hand them a sharper saw, you have to force them to stop sawing long enough to change to the new tool. All they know is that the damn tree has to come down on time and they will be in terrible trouble (/fail to be recognized for their genius) if it doesn’t.

A vigorous discussion ensued. What do you think? Is it true that for scientists to adopt any new way of doing things, Carrots don’t work, only Big Sticks?

The Profzi Scheme

Yes, this is how the academia works:
Profzi Scheme.gif

Meetings I’d like to go to….Part VIII

The Two Cultures in the 21st Century:

A full-day symposium sponsored by: Science & the City, ScienceDebate2008, Science Communication Consortium
At the 50th anniversary of C.P. Snow’s famous Rede Lecture on the importance to society of building a bridge between the sciences and humanities, this day-long symposium brings together leading scholars, scientists, politicians, authors, and representatives of the media to explore the persistence of the Two Cultures gap and how it can be overcome. More than 20 speakers will cover topics including science in politics, education, film and media, and science citizenship.

Exciting schedule and list of speakers/panelists!

World’s Biggest Scientific Fraud?

Wow! This is massive!
From Anesthesiology News:

Scott S. Reuben, MD, of Baystate Medical Center in Springfield, Mass., a pioneer in the area of multimodal analgesia, is said to have fabricated his results in at least 21, and perhaps many more, articles dating back to 1996. The confirmed articles were published in Anesthesiology, Anesthesia and Analgesia, the Journal of Clinical Anesthesia and other titles, which have retracted the papers or will soon do so, according to people familiar with the scandal (see list). The journals stressed that Dr. Reuben’s co-authors on those papers have not been accused of wrongdoing.

There is more about it in New York Times and the Wall Street Journal.
My SciBlings Orac, Janet and Mike have more details, thoughts on ethics and implications.
This case is Big!

Diversity in Science – Women’s History Month Edition

The next edition of this fantastic carnival will be hosted by Zuska:

The first Diversity in Science carnival, created and hosted by DNLee of Urban Science Adventures as a Black History Month Celebration, was a great success. Thanks to everyone who contributed!
Now it’s time for our second round, which will be hosted right here at Thus Spake Zuska. Naturally, since it is March, our focus this time around will be a Women’s History Month Celebration! The theme is “Women Achievers in STEM – Past and Present” and we are asking you to profile a woman in some field of science – your own or maybe one you wish you’d chosen! Tell us something about her life, her work, why you find her interesting.

A very brief history of plagiarism

Archy does an amazing detective job on who stole what from whom in the old literature on mammoths, going back all the way to Lyell!
Then, as much of that literature is very old, he provides us with a history and timeline of the ideas of copyright and plagiarism so we could have a better grasp on the sense of the time in which these old copy+paste jobs were done.

Nature Methods: It’s good to blog

Another editorial about science blogging today, this time in Nature Methods: Lines of communication:

The public likes science stories it can easily relate to, and we have to admit that most science, including that published in Nature Methods, is unlikely to get more than a snore from nonscientists. In contrast, science stories that have a human interest or other emotionally charged angle require the concerted efforts of both journalists and scientists to ensure that the public understands the story well enough to make an informed personal decision. A failure in this regard can lead to a crisis that is difficult to resolve.
A powerful aspect of blogs is their capacity to put a human face on science and related health issues by allowing scientists to discuss how these things affect them personally in a format in which regular readers feel as though they know the writer. Analysis of the MMR vaccine incident suggests that emotional arguments like a scientist talking about vaccinating his or her own children might be more powerful than the rational arguments that form the basis of normal scientific discourse. The public’s emotional response to genetically modified food in some countries might also have been very different if people could see numerous online blog entries from scientists discussing why they were not concerned about the scenarios being promulgated in the press. But can enough scientists be convinced of the potential benefits of blogging to make this a reality?
Conferences such as Science Blogging 2008: London, organized by Nature Network, and ScienceOnline’09 are exploring the role of blogging in science and trying to get more scientists involved. Nature Network just concluded their Science Blogging Challenge 2008–won by Russ B. Altman–where the goal was to get a senior scientist to start blogging. Altman’s colleague Steve Quake also just started blogging in a guest stint for the New York Times. One hopes that examples of prominent scientists blogging will convince others of the benefits. When a blog author is not a prominent scientist with a reputation to maintain, the quality of information on the blog can be a concern, but scienceblog tracking sites such as can help alleviate this problem.

w00t for the mention of ScienceOnline09! I wish they also mentioned as a means to track good science blogging (mention of carnivals would be too much to expect from a short article like this, I understand).

In the spirit of leading by example, Nature Methods will convert its online commenting site, Methagora, into a proper blog in preparation for later this year when commenting capabilities will be incorporated into published papers. Methagora will allow us to highlight and comment on papers that we feel are of interest to a larger readership and discuss the impact we see them having on science and hopefully society. We invite you, our readers–scientists and nonscientists alike–to share your thoughts and concerns, including your thoughts on this editorial. See you in the blogosphere!

I am happy to hear this. I guess the PLoS ONE example is emboldening others to start the experiment as well. This is a Good Thing. More journals allow the commenting on the papers, more ‘normal’ this will appear to scientist, more quickly it will become normal for scientists to use this. You remember when Nature tried this experiment a couple of years ago, then quit and proclaimed the experiment to be a failure after only six months? When they did that, I was, like, WTF? Who ever expected such a big shift in the entire scientific culture to happen in six months?! But give it another five years and it will start getting there. And remember that a scientific paper is not a blog post – do not expect a bunch of comments over the first 24 hours: they will slowly accumulate over the years and decades.
Finally, let me just notice that both Nature and Nature Methods published pro-blog editorials on the same day. And they also interviewed me this week for a topical issue on the state of science journalism/communication they are planning for a couple of weeks from now. I don’t think this is a coincidence – Nature group is cooking something and we’ll have to wait and see what that is.

Nature: It’s good to blog

In today’s Nature you can read an editorial that says, right there in the title, It’s good to blog:

Is blogging a part of science, journalism or public discourse? In fact it may be all of these — an ambiguity that can sometimes leave scientists feeling uncertain about the rules of the game.
The blogosphere differs from mass media and specialized media in many respects, but the same considerations apply in disseminating new scientific results there. Authors of papers in press have the right to correct misrepresentations and to point to results that will appear in a paper. But a full discussion should await the paper’s publication.
Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.
Moreover, there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

Read the whole thing, then go over to the Nature Opinion forum to discuss it.
There are also related threads there, see here and here..

Meetings I’d like to go to….Part IV

SLEEP 2009:

23rd Annual Meeting of the Associated Professional Sleep Societies, LLC (APSS) will be held June 6-11, 2009, at the Washington State Convention and Trade Center in Seattle, Washington. The SLEEP meeting attracts the largest audience of sleep specialists in the nation. It is the only five and a half day meeting in the nation with scientific sessions and an exhibition hall focused solely on sleep medicine and sleep research.

Hmmm, always wanted to visit Seattle. And this sounds like a very bloggable conference. And I’d get to finally meet Archy….

Diversity in Science Carnival #1 is amazing!

The very first, inaugural, and absolutely amazing edition of the Diversity in Science Carnival is now up on Urban Science Adventures. Wow! Just wow! Totally amazing stuff.
And what a reminder of my White privilege – a couple of names there are familiar to me, as I have read their papers before, never ever stopping to think who they were or how they looked like! What a wake-up call!
For instance, I have read several papers by Chana Akins, as she works on Japanese quail. And I am somewhat familiar (being a history buff and obsessive reader of literature in my and related fields) with the work of Charles Henry Turner, covered in this carnival not once but twice – both by Danielle Lee and by Ajuan Mance!
It also did not escape my notice that several of the posts are eligible for the next editions of Scientiae and The Giant’s Shoulders – double your readership by submitting those posts there as well!

Meetings I’d like to go to….Part III

The 2009 Gordon Conference on Chronobiology is all molecular, and it is tough to get in anyway. It would be nice to go, but I don’t see how I can get invited and/or funded.

Meetings I’d like to go to….Part I

XI Congress of the European Biological Rhythms Society, organized in association with the Japanese Society for Chronobiology
Hmmmm, Strasbourg in August. Fun for the family to do stuff while I chat with fellow chronobiologists, and just a short flight away from Belgrade…. Have to investigate if there’s a way for me to go….
And the program looks interesting…

‘The Art and Politics of Science’ – Harold Varmus on NPR Science Friday

That was last week, but I had no time to listen until now – check out the podcast (in the upper left corner of the page):

In 1989, Dr. Harold Varmus won a Nobel Prize for his cancer research. He was director of the National Institutes of Health during the Clinton administration, and now heads the Memorial Sloan-Kettering Cancer Center. Recently, President Obama named him to co-chair his Council of Advisers on Science and Technology. And he’s written a new book, “The Art and Politics of Science.” In this segment, Ira talks with Harold Varmus about his work, biological research, and the intersection between politics and science.

‘University professors turn to the blogosphere, for classes and recognition’

From Michigan Daily: University professors turn to the blogosphere, for classes and recognition:

In recent years, academics across the country have started using blogs to relay information and ideas. Many are now incorporating the medium into their classes, asking students to take to their keyboards and post thoughts or resources on course material.
The time commitment means professors need to prioritize when it comes to blogging. Those who write personal blogs do so outside of their teaching requirements, but as blogs become more popular, the question of their role in academic research and publishing becomes more complex.
“It’s so new that (universities) haven’t quite incorporated it yet into the three areas that we’re responsible for — teaching, research and service,” Perry said. “But it really kind of overlaps in all those areas.”
Perry said he believes that blogging could be considered applied research.
But in an interview, University Provost Teresa Sullivan said that blogging lacks an important element, which generally elevates the credibility of a publication: peer review.
“Peer review is an important quality marker,” said Sullivan. “With electronic media now, anybody can publish anything.”
While the University doesn’t view blogs as a form of official research or publishing, Sullivan said she encourages professors to use them, even if they express controversial opinions or ideas.
“That’s what universities are about,” Sullivan said. “The university is the place where you’re free to put ideas out there, and we’re tolerant of other people’s ideas but it also means you’ve got to be ready for somebody to go after you and attack your ideas.”
Blogs considerably raise the profile of University professors, which is good for the University. Through their archive of posts, professors advertise their expertise in a given field. Establishing that authority leads calls from the media — and the University’s name appearing in print.

A good, positive article, including quotes from some well-known academic bloggers. Except for the very first sentence:

The booming blogosphere is a world dominated by celebrity gossip, confessionals and radical opinions.

But we know that corporate journalists have to say something offensive whenever they mention blogs, as a loyalty test, lest they be expelled from their guild.

Bruce Alberts, next Friday at Duke

From Center for Science Education:

When: Friday, January 30, 2009 1:30 PM – 2:30 PM
Where: LSRC B101 Love Auditorium
Description: Bruce Alberts, a prominent biochemist strongly commited to the improvement of science education, began service as Editor-in-Chief of Science in March 2008. He is a professor in the Department of Biochemistry and Biophysics at the University of California, San Francisco. Alberts has been instrumental in developing the National Science Education standards implemented in school systems nationwide. He is a major proponent of “science as inquiry” teaching that emphasizes logical, hands-on problem solving. Alberts is committed to the promotion of the “creativity, openness and tolerance that are inherent to science”. Alberts believes that scientists everywhere must help create more rational, scientifically-based societies.For More information on Dr. Alberts and his guest seminar, please click on More Info above.
Sponsor: Center for Science Education

Praxis Blog Carnival – Your Graduate Guide To Succeeding In 2009

Praxis #6 is up on Podblack Cat

On Peer-Review

Michael Nielsen posted today the first part of his look at peer-review: Three myths about scientific peer review:

What’s the future of scientific peer review? The way science is communicated is currently changing rapidly, leading to speculation that the peer review system itself might change. For example, the wildly successful physics preprint arXiv is only very lightly moderated, which has led many people to wonder if the peer review process might perhaps die out, or otherwise change beyond recognition.
I’m currently finishing up a post on the future of peer review, which I’ll post in the near future. Before I get to that, though, I want to debunk three widely-believed myths about peer review, myths which can derail sensible discussion of the future of peer review.
A brief terminological note before I get to the myths: the term “peer review” can mean many different things in science. In this post, I restrict my focus to the anonymous peer review system scientific journals use to decide whether to accept or reject scientific papers.

The article immediately sparked a fiery debate, which also yielded some good links, e.g., The purpose of peer review and Peer Review: The View from Social Studies of Science (pdf).
What do you think?

Academic Evolution

Academic Evolution is Gideon Burton’s blog, intended as a playground for posting drafts and eliciting feedback while he is writing a book of the same title. You can see the rough outline of the proposed contents of the book here:

This blog is intended to become Academic Evolution, the book. My model is Chris Anderson, whose Long Tail blog helped bring about his seminal book of the same name. Similarly, I am beta testing my ideas, developing them in keeping with the principle of transparency and with the goal of inviting public review and collaboration. I’m smart enough to know others are often much smarter, and I firmly believe that publishing one’s thinking process improves it. So, here’s the working table of contents for the book. Obviously I will be making each of these proposed chapters the subject of my various blog posts. Let’s figure this out together! I welcome your suggestions:

In the introduction to the blog, Gideon writes:

Academic Evolution is a blog dedicated to discussing where the new media is leading higher education, publishing, and teaching as the traditional institutions for producing and communicating knowledge are both enhanced and challenged in the digital age.
Knowledge is evolving in step with communication. What counts as knowledge, who controls it, where it is generated and consumed, how it is revised and developed–all of this is at stake and in question due to democratized media creation, social networking, broadened access, new modes of representing knowledge, new discovery methods, the crossover between entertainment and information, and emerging economic models. What is “the book” or “the press” or even “the university” in the age of Open Access, social knowledge, and the semantic web? These revered institutions no longer monopolize the circulation, creation, or authentication of knowledge.
So much is in flux right now in how we find, develop, communicate, validate, teach, use, and re-use knowledge, and so much is at stake–intellectually, economically, pedagogically, academically. The institutions that we have relied upon to produce, organize and communicate authoritative knowledge (in other words, traditional scholarship, libraries, academic publishing, and classroom teaching) are all competing now with the vibrant and abundant media culture that inundates us. It is a phenomenon that alternately dazzles and threatens us with its splendors and grotesques, and this genie isn’t going to go back into his bottle.
Everyone knows something very big is in play. Some have embraced the new media culture with abandon; others dismiss it as digital detritus. Some see the electronic world as a playground; others, as the opening gambit of a technological apocalpyse. Somewhere between the extremes there must be a way to make the best of our electronic evolution, a way to preserve order amid change as well as change amid order (as Whitehead so aptly put it).
And so I launch this blog–a spinoff from my more general personal blog (where I’d begun discussing these issues enough to merit a more focused blog). I’m preparing a wiki to accompany this, a place to organize my own evolving thoughts along with the feedback I hope to receive. Thanks for reading, and please join me in the conversation.
What do you think? Are we in an academic evolution? What are the key issues from your perspective?

It will be fun to watch as this progresses. Go there and post some feedback as the posts keep coming in.

The Shock Value of Science Blogs

There was a good reason why the form and format, as well as the rhetoric of the scientific paper were instituted the way they were back in the early days of scientific journals. Science was trying to come on its own and to differentiate itself from philosophy, theology and lay literature about nature. It was essential to develop a style of writing that is impersonal, precise, sharply separating data from speculations, and that lends itself to replication of experiments.
The form and format of a scientific paper has evolved towards a very precise and very universal state that makes scientist-to-scientist communication flawless. And that is how it should be, and at least some elements of style and form (if not format) will remain once the scientific paper breaks down spatially and temporally and becomes a dynamic ongoing communication – clarity and precision will always be important.
But that is strictly technical communication between scientists in the same research field. How about communication between scientists in far-away fields, between scientists and lay audience, or among the educated lay-people? How about communication between scientific colleagues outside of peer-reviewed papers? This is where we are seeing the biggest changes right now and not everyone’s happy. And the debate is reminiscent of the debate in mainstream journalism.
Until pretty recently, the informal communication between scientists was limited to Letters To The Editor of scientific journals, conferences and invited seminars. In all three of those venues, the formal rhetoric of science remained. Fine, but….
Part of training in the academia is training in rhetoric. As you go up the ladder of academic science, you are evaluated not just by the quality of your research (or teaching, in some places), but also in how well you mastered the formalized kabuki dance of the use of Scientese language. The mastery of Scientese makes one part of the Inside club. It makes one identifiable as the Member of this club. The Barbarians at the Gate are recognizable by their lack of such mastery – or by refusal to use it. And it is essential for the Inside Club to make sure that the Barbarians remain at the Gate and are never allowed inside.
Academic science is a very hierarchical structure in which one climbs up the ladder by following some very exact steps. Yes, you can come into it from the outside, class-wise, but you have to start from the bottom and follow those steps “to the T” if you are to succeed. But those formal steps were designed by Victorian gentlemen scientists, thus following those steps turns one into a present-time Victorian gentleman scientist. But not everyone can or wants to do this, yet some people who refuse are just as good as scientists as the folks inside the club. If you refuse to dance the kabuki, you will be forever kept outside the Gate.
The importance of mastery of kabuki in one’s rise through the hierarchy also means that some people get to the top due to their skills at glad-handling the superiors and putting down the competitors with formalized language, not the quality of their research or creativity of their thought. Those who rose to the top due to being good at playing the game know, deep inside, they do not deserve that high position on merit alone. And they will be the loudest defenders of the system as it has historically been – they know if the changes happen, and people get re-evaluated for merit again, they will be the first to fall. This is the case in every area (mainstream journalism, business, politics, etc.), not just academic science.
Insistence on using the formalized kabuki dance in science communication is the way to keep the power relations intact. Saying “don’t be angry” is the code for “use the rhetoric at which I excel so I can destroy you more easily and protect my own spot in the hierarchy”. It is an invitation to the formal turf, where those on the inside have power over those who cannot or will not use the kabuki dance. This has always been the way to keep women, minorities and people from developing countries outside the club, waiting outside the Gate. If, for reasons of your gender, race, nationality or class you are uncomfortable doing the kabuki dance, every time you enter the kabuki contest you will lose and the insider will win. The same applies outside science, e.g., to mainstream journalism and politics.
This is why some people in the academic community rant loudly against science bloggers. If they cannot control the rhetoric, they fear, often rightly, that they will lose. Outside their own turf, they feel vulnerable. And that is a Good Thing.
The debates about “proper” language exist on science blogs themselves. See this and this for recent examples (the very best discussion was on this post which is now mysteriously missing). In response I wrote:

We here at Sb are often accused of being cliquish and insular. But if you look at our 70+ blogs and dig through the archives, you will see that we rarely comment on each other’s blogs – most (99%?) of the comments come from outside readers. Also, most of our links point to outside of Sb. On the other hand, NN [Nature Network] is specifically designed to be a community (not a platform for independent players) and almost all of the comments there are from each other. Thus, it is easy for them to maintain a high level of politeness there (this is not a bad thing – this is how they designed it on purpose). It is much harder to harness the hordes of pharyngulites that spill over to all of our blogs – and I do not mind them at all, I think they make the debate spirited and in a way more honest by bypassing superficial niceness and going straight to the point. This may also have something to do with NN bloggers mainly being in the academia, while a large proportion of SciBlings are ex-academia, journalists, artists, etc. with a different rhetoric. The rhetoric of academia is a very formalized kabuki dance, while the rhetoric of the blogosphere has shed all formalities and is much more reminiscent to the regular everyday oral conversation.

Remember the Roosevelts on Toilets saga? The biggest point of contention was the suggestion by the authors of the paper to the bloggers to move the discussion away from blogs to a more formal arena of letters to the editor. We, the bloggers, fiercely resisted this, for the reasons I spelled above – in the letters to the editor, the Insiders have power over the Outsiders because it is their turf. No, if we want to have a non-kabuki, honest discussion, we will have it out here on the blogs, using our rhetoric, because the honest language of the modern Web places everyone on the even ground – it does not matter who you are, what degrees you have, or how well you’ve learned to dance the kabuki: it is what you say, the substance, that counts. This is why being pseudonymous online works, while academia requires full names and degrees. The Web evaluates you directly, by what you write. The academia uses “tags” – your name and degree – to evaluate you. The academia is in the business of issuing credentials, the stand-ins for quality. The credentials are rough approximations of quality – more often then not they work fine, but they are not 100% foolproof. And if one is insecure about one’s own quality, one would insist on using credentials instead of quality. The use of “proper” rhetoric is, as I said above, a good quick-and-dirty way to recognize credentials.
During the Roosevelt saga, I wrote this post very, very carefully, with a specific purpose in mind. First, I went to great effort to explain the science at length and as simply, clearly and conclusively as possible. This performed several functions for me: first, to establish my own credentials, second, to make my readers understand the science and thus be on “my side” in the comments, and third, to make sure I was as complete about science as possible so as to not have to talk about science at all in the comments. Apart from science, I also included several snarky comments about the authors which served as bait – I wanted them to come and post comments. And they bit. Go read the comment thread there to see what was happening. The author insisted on discussing science. I insisted on refusing to talk about science (to him, I did respond a little bit to some other commenters) and to talk about rhetoric instead.
But first, in a comment I posted even before the authors showed up, in order to set the stage for what I wanted, I wrote this:

In an earlier post, burried deep inside, is this thought of mine:

The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.

What happened on Dr.Isis’ blog is very similar – a clash of two cultures. I think that the picture of the Teddy Bear on the potty was a clever and funny shorthand for your point. If you did it about something I published, I’d laugh my ass off. But I can see how the uptight strain of the scientists would balk at it. It is them, though, who need to get up to speed on the changed rhetoric of science. The straight-laced, uber-formal way of writing in science is on its way out.
The rhetoric, even after it completely modernizes, will still have four concentric circles: the paper itself will always be more formal, especially the Materials/Methods and Results sections due to the need for precision; the letters to the editor will remain pretty formal, but not as formal as they are now; the comments on the paper itself will be still less formal but still polite; the commentary on the trackbacked blogs will be freewheeling, funny and to-the-point, just like yours was, not mealy-mouthing with politeness on the surface and destructive hatred underneath, but honest and straightforward. So, if it is crap, what better way to say it than with a picture of a Teddy Bear on a potty – much more lighthearted and polite than saying it politely, and less devastating for the paper’s authors as it takes their mistake lightly instead of trying to destroy their reputation forever.
The point that both Dr.Isis and I made is that the paper is neat, experimental method sound, data are good, but the interpretation is crap. Now, having a couple of crappy paragraphs in an otherwise good paper is not the end of the world. A paper is not some kind of granite monument with The Truth writ in stone. It is becoming a living document (with comments on the paper and tracbacked blogs), and it has always been a part of a greater living document – the complete literature of a field. That is how science works.
It is hard to know which paper will persist and which one will perish in the future, what sentence will turn out to be a gem of prophetic wisdom, and which one is crap. People publish a lot of stuff, some better than other.
Making a mistake in one paper is not the end of one’s career. But many people perceive criticism as if they are just about to be sent out to join a leper colony. This is, in part, due to the formal rhetoric of science: outwardly polite, but underneath it is an attempt to destroy the person. In comparison, a light-hearted joke with a Teddy Bear acknowledges the failability of humans, allows for everyone to make a mistake and move on (we all shit, don’t we?). It is actually much more normal, and much less dangerous for one’s career to receive such a funny form of criticism than a formal-looking destruction of all our work and our personna.

In the next comment I did the one and only hat-tip to science, then moved onto the territory I wanted – rhetoric (many comments, so go and read them all now). As a result, Dr. Janszky grokked it – and we’ll probably see more of him in the blogosphere in the future. The reason he grokked it is because he is confident in his own qualities – he can change the rhetoric and tone and still not lose the debate because he knows what he’s talking about. Those who know they do not have the quality, would just have ranted harder and harder, complaining about the tone. Dr. Janszky adopted the bloggy tone in the comments right then and there. Which was a victory for everybody.
The informal rhetoric of blogs is a form of subversion – breaking the Gate and letting the Barbarians in (while not allowing quacks and Creationist to hitch a ride inside as well – which is why so many science bloggers focus on those potential free-riders and parasites). What we are doing is leveling the playing field, pointing out the inherent dishonesty of the formalized rhetoric, and calling a space a spade. This is a way to make sure that smart, thoughtful people get heard even if they did not have a traditional career trajectory, or refuse to play the Inside club games. If some of the insiders fall down in the process, that’s a good thing – they probably did not deserve to be up in the first place.
Different bloggers do this in different ways. We can use a brilliant, but snarky use of English (PZ Myers), or texting/LOLCat snark (Abbie), or awe and reverence for the great scientists of old (Mo), or sexual innuendo (SciCurious), or shoes (Dr.Isis), or a light-hearted sense of humor (Ed or Darren), or excessive use of profanity (PhysioProf). What we all do is write in unusual, informal ways. We want to shock. We feel there are many people out there who need a jolt, an injection of reality. We do it by using informal language. And this can be very powerful – just see how the dinosaurs squirm when they read some of our posts! But that’s the point. We are testing them: if, like Dr. Janszky, you “get it”, this means that you have the balls, which means you are confident about your own qualities independent from your credentials. If you keep ranting about “dirty, angry bloggers”….what are you so insecure about? Why are you so afraid of being shown a fraud if you are not? Or, are you?
Another point about blogs, which I alluded above already, is the time-frame. This is a very important point that is often forgotten in the scientists vs. bloggers “let’s be polite” debates. In the formal arenas (Letters, conferences, etc.), where formal language is used, the game some people play is to use an outwardly seemingly polite language to write or say something that is designed to destroy a career. Often in multiple places over a stretch of time. On blogs, when we snarkily attack you, our purpose is to teach a lesson (more to our readers than the scientists in question who may not even know the blog post was written). In other words, it is a one-time thing that is designed to correct a single error, not an attempt at destroying a career.
For good recent examples of the way scientists use the formal venues as well as formal language to destroy each other, see this and this (I have seen more on PLoS ONE, but don’t want to draw your attention to those right now, for professional reasons – keeping my job).
I post 8.2 posts per day on this blog, on a large variety of topics. Do you really think I have the time, energy and interest to study in great detail the life-time achievements of everyone who did something wrong on the Internet? Of course not. I see an article that says something stupid and I shoot a post that shows how stupid it is, so the readers, especially if the deconstruction of stupidity requires some expertise I may have and most people don’t, can see why that particular argument is wrong. Then I move on to the next post on some completely different topic. I have forgotten about your existence in about a nanosecond after publishing that post. I have no interest in destroying your career, but I understand that you are touchy – the life in academia, with its poisonous kabuki game, has trained you to defend yourself against every single little criticism because, underneath the veneer of civility is the career-damaging attack by someone powerful who is hell-bent on destroying you. We don’t do that on blogs. We don’t care enough to do that (unless you are a dangerous peddler of pseudoscience or medical quackery). We want to educate the lay audience and have fun doing it. I have no idea if everything else you have written before and after is brilliant and I don’t care – I think that this one stupid paragraph you wrote is good blogging material, amusing, edifying and useful to use to educate the lay audience. You are NOT the target personally. Your stupid argument is. And I don’t care if that was your one-off singular mistake in life, or an unusually bad moment for you. So, don’t take it personally. This is not academia. We are, actually, honest here on the intertubes, and you need to learn to trust us.
The attempts at character assassinations within academia, by using the formalized kabuki language by the powerful and forcing the powerless to adopt the same and thus be brought to slaughter, do not happen only in print. They also happen in person. Read this and this for a recent example of a senior researcher trying to publicly destroy a younger, female colleague at a meeting. And he was wrong. But he was powerful and intimidating. I wish the young woman responded by going outside of formal kabuki dance, shocking the audience in one way or another, giving all the present colleagues a jolt, making them listen and perhaps notice what is happening. Or, if she was shy, I wish some senior male colleague did the same for her and put the old geezer in his place. I wrote a comment:

“Tone it down” and “Why are you so angry?” are typical sleazy tactics used by a person in power over a person not in power. It was used against people of other races, against women, against gays, against atheists – this is the way to make their greivances silent and perpetuate the status quo, the power structure in which they are on the top of the pecking order. The entire formal, convoluted, Victorian-proper discourse one is supposed to use in science is geared towards protecting the current power structure and the system that perpetuates it. Keeping the dissenters down and out. Bur sometimes, anger, or snark, or direct insult, are the jolt that the system needs and it will have to come from the people outside the power structure, and it would have to occur often and intensely until they start paying attention.

And then, there is the area in between scientists and lay audience. The job of translating Scientese into English (or whatever is the local language) has traditionally been done by professional science journalists. Unfortunately, most science journalists (hats off to the rare and excellent exceptions) are absolutely awful about it. They have learned the journalistic tools, but have no background in science. They think they are educated, but they only really know how to use the language to appear they are educated. Fortunately for everyone, the Web is allowing scientists to speak directly to the public, bypassing, marginalizing and pushing into extinction the entire class of science “journalists” because, after all, most scientists are excellent communicators. And those who are, more and more are starting to use blogs as a platform for such communication.
The problem is, the professional science journalists also love to put down the blogs and use the paternalistic “tone it down” argument. But, unlike the political journalists who are incapable of seeing the obvious (stuck too far inside Cheney’s rectum to see what we all could see?), the science journalists have the added problem of not having the expertise for their job in the first place. In politics, everyone with the brain, not just journalists, could see that excuses for going to Iraq were lame. But in science journalism, there exist out there people with real expertise – the scientists themselves – who now have the tools and means to bypass you and make you obsolete because you cannot add any value any more.
To the list that includes MSM “journalists” aka curmudgeouns like Richard Cohen, Sarah Boxer, Andrew Keen, Lee Siegel, Michael Skube, Neil Henry and many others, we can now add curmudgeounly science journalists George Johnson and John Horgan as well – just listen to this!!!!! Yes go an listen before you come back. If you can stand it. But if I suffered through it, you can, too. I am a pretty calm kind of guy, but listening to that “dialogue” filled me with rage – I felt insulted, my intelligence insulted, and my friends insulted. Frankly, I’ve heard smarter science-related conversations from the drunks in rural Serbian bars.
I’ve been in this business (both science and science communication) for a long time, but I have never heard of George Johnson until today. From what I saw in that clip, I have not missed anything. Where does his smugness come from then? As for John Horgan, I’ve heard of him – he earned his infamy when he published – and was instantly skewered and laughed at by anyone with brains – his book “The End of Science”, arguably one of the worst and most misguided books about science (outside of Creationist screeds) ever. Where is his humbleness after such a disaster? Why is he not hiding in the closet, but instead shows up in public and appears – smug. Some people just have no self-awareness how stupid they appear when they behave as if they have authority yet they don’t and it’s obvious. What is it about professional journalists that makes them have illusions they are educated? “No, I am not a scholar but I play one on TV” turns into “Since I can transcribe and read smart stuff I must be really smart myself”.
Luckily, bloggers have no qualms about defending themselves – please read this gorgeous smack-down by Abbie, this older post by Ed in which he explains exactly what he meant, and perhaps this old post of mine which also, in a circuitous way, predicts the extinction of science journalistic dinosaurs.
But perhaps I shouldn’t be that nasty to Johnson and Horgan? After all, my blogging schtick is niceness. This makes it very easy for me to destroy someone – on those rare occasions when someone like me, renowned for endless patience, flies off the handle, people sit up and pay attention. If I use profanity to describe someone, that one probably richly deserves it. I know I have to use this power with prudence. If I attack someone full-blast, people will tend to believe me, as I rarely do that kind of stuff. And if you subsequently Google that name, my blogpost about him/her is likely to be the #1 hit on the search, or in the top ten.
Perhaps Johnson and Horgan are actually nice and smart guys. They may be nice to their wives and kids. Perhaps they wrote, 30 years ago, something really smart. But I have no interest in digging around for that. I want to finish this post and move on. And after watching this movie, I really have no motivation to search for anything else by these two guys as it appears to be a waste of my time. It does not appear to me like a bad-day, one-off mistake that everyone sometimes makes. It is 30 minutes of amazing ignorance and arrogance at display – probably sufficient material to make me doubt I’d ever find anything smart penned by them in the past, so why should I bother with them at all? I can probably evaluate their qualifications quite accurately from these 30 minutes and safely conclude they equal zero. Their “angry bloggers” shtick was the first give-away they know deep inside they are irrelevant and on their way out. Their subsequent chat about science was amateurish at best, no matter how smug their facial expressions at the time.
Perhaps if we remove those middle-men and have scientists and the public start talking to each other directly, then we will have the two groups start talking to each other openly, honestly and in an informal language that is non-threatening (and understood as such) by all. The two sides can engage and learn from each other. The people who write ignorant, over-hyping articles, the kinds we bloggers love to debunk (by being able to compare to the actual papers because we have the background) are just making the entire business of science communication muddled and wrong. Please step aside.
Update: Brian, Greg, Ed, Dr.Isis, Mike Brotherton, Hank and Larry chime in on this discussion as well. More: Alex, Chris Mooney, Mike, Chad, Eric Wolff, Stephanie and Tom Levenson, Sabine and Tom again.

Undergraduate science research journals

I did not know there were so many of them:
Student science publishing: an exploratory study of undergraduate science research journals and popular science magazines in the US and Europe:

Science magazines have an important role in disseminating scientific knowledge into the public sphere and in discussing the broader scope affected by scientific research such as technology, ethics and politics. Student-run science magazines afford opportunities for future scientists, communicators, politicians and others to practice communicating science. The ability to translate ‘scientese’ into a jargon-free discussion is rarely easy: it requires practice, and student magazines may provide good practice ground for undergraduate and graduate science students wishing to improve their communication skills.

National Academy of Sciences Survey

I get mail:

The National Academies want to identify the topics in science, engineering, and medicine that matter most to the public and that people have the greatest interest in learning more about. Once the topics have been selected, we plan to create a suite of educational materials (in both print and web formats) about each subject, with the goal of offering objective, reliable resources about complex topics.
We developed a 2-minute survey that we’d like to distribute to our key audiences. Readers of your blog are one of those key audiences and we would love to hear what topics matter most to them. Please note that this survey is just one component of the research we are conducting to inform our selection process for the topics.

Sounds like a great idea to me. So, read this:

What topics in science, engineering, and medicine matter most to you? The National Academies are interested in developing useful and engaging print and web-based educational materials on the topics that you’d like to learn more about. They invite you to participate in a brief survey. You can find that survey here.
In the 2-minute survey you’ll be presented with a list of topics and asked to select the five that matter most to you. At the end, you can see how your answers compare with the results so far. And you can enter a drawing to receive a National Academies tote bag!
Let the National Academies know what topics you think they should focus on so they can be sure to provide you with materials that are informative and useful. Your participation is greatly appreciated.

Go do the survey.

Who Bears the Growing Cost of Science at Universities?

From EconPapers:

Scientific research has come to dominate many American universities. Even with growing external support, increasingly the costs of scientific research are being funded out of internal university funds. Our paper explains why this is occuring, presents estimates of the magnitudes of start-up cost packages being provided to scientists and engineers and then uses panel data to estimate the impact of the growing cost of science on student/faculty ratios, faculty salaries and undergraduate tuition.We find that universities whose own expenditures on research are growing the most rapidly, ceteris paribus, have had the greatest increase in student faculty ratios and, in the private sector, higher tuition increases. Thus, undergraduate students bear part of the cost of increased institutional expenditures on research.

RNA wiki

Publish in Wikipedia or perish:

Wikipedia, meet RNA. Anyone submitting to a section of the journal RNA Biology will, in the future, be required to also submit a Wikipedia page that summarizes the work. The journal will then peer review the page before publishing it in Wikipedia.
The RNA wiki is a subset of a broader project, the WikiProject Molecular and Cellular Biology, which has marshalled hundreds of scientists to improve the content of biology articles in Wikipedia. It, in turn, is collaborating with the Novartis Research Foundation on GeneWiki 3, an effort to create Wikipedia articles describing every human gene. Beyond Wikipedia itself, scientists are also increasingly using wiki technology to get scientists to help curate other biological databases.

Did a Drug Company ‘Buy’ One of This Year’s Nobel Prizes?

Probably not:

Rumors swirl, but a Swedish prosecutor will only confirm a “preliminary investigation” into allegations that pharma giant AstraZeneca fixed the Nobels for financial gain.
As for the Nobels, as scurrilous as the charges may sound, there is little evidence to support them. First off, AstraZeneca’s ties to the anti-HPV vaccine are tenuous at best: In 2007 it purchased a company called MedImmune, which had developed the viruslike particle (VLP) technology licensed for use in Merck’s Gardasil and GlaxoSmithKline’s Cervarix vaccines — both designed to prevent HPV infection. The technology, however, is not specific to HPV and companies are working to adapt VLPs and similar techniques for a variety of vaccines, including influenza….

Read the rest…

Scientific Red Cards: a good idea or opening a hornet’s nest?

From The Scientist: Flagging fraud:

A team of French life sciences grad students has launched an online repository of fraudulent scientific papers, and is calling on researchers to report studies tainted by misconduct.
The website — called Scientific Red Cards — is still in a beta version, but once it’s fully operational it should help the scientific community police the literature even when problems slip past journal editors, the students claim.
The database might also prevent researchers from citing papers that they don’t even realize are fraudulent, said Claire Ribrault, a PhD student in neurobiology at the Ecole Normale Superieure in Paris, who unveiled the new website last month at a workshop in Madrid, Spain, organized by the European Science Foundation’s Research Integrity Forum.
After misconduct is detected in a published paper, “sometimes the paper is not retracted, depending on the policy of the journal, and even if the paper is retracted sometimes it’s still cited after the retraction,” Ribrault said in a press release.
The website color-codes misconduct into three categories: red for data-related misconduct, including fabrication, falsification, and plagiarism; blue for publication-related misconduct, such as when editorial policies are not followed; and green for research practice misconduct, including problems with consent forms.
Each problematic paper in the register includes a full bibliographic reference, a link to published accounts of the misconduct, and a discussion board for users to leave their comments. So far, only around 30 papers have been listed.
Scientific Red Cards received a cautious thumbs-up from the meetings’ attendees, although some voiced concerns over legal problems and the site being used for scientific smear campaigns. Other countered that it provides a transparent way to patrol the literature.

Co-Researching spaces for Freelance Scientists?

Pawel tried, for a year, to be a freelance scientist. While the experiment did not work, in a sense that it had to end, he has learned a lot from the experience. And all of us following his experience also learned a lot about the current state of the world. And I do not think this has anything to do with Pawel living in Poland – I doubt this would have been any different if he was in the USA or elsewhere.
You all know that I am a big fan of telecommuting and coworking and one of the doomsayers about the future existence of the institution of ‘The Office’. And you also know that I am a scientist, so it is no surprise that I have been also thinking how to connect these two – is there a way to have a coworking (or co-researching) facility for freelance scientists?
If you work 9-5 for The Man, it is understandable that you should strive mightily to sharply delineate work from the rest of your life, and to measure your worth in dollars (or place of employment, e.g., Harvard). But if you are lucky (and work to make it happen), you will do what you like to do, what you’d do for free anyway. Thus, you express your person through your work, you are what you do and your job is you, and it is perfectly fine to completely blur that distinction. If that is the case, your worth is not measured in dollars – you can say you “made it” if you can live wherever you want on the planet (or even off of it if you are adventurous), surrounded by people you like, doing what you like, and having lots of friends. You will be measured by the size of your network – who is your (mutual – it has to be mutual!) friend.
Sure, you can make many mutual friends online, through blogs, Facebook, LinkedIn, Twitter, FriendFeed, etc. But, as a human being, you also need physical proximity to some of the people you really like a lot. What are blogs but means to find each other in order to organize a Blogger Meetup or BloggerCon?
So, if you have that luck and freedom, you will choose where on Earth to live both by the criterion of climate and natural beauty and by unusual concentration of people you really like and want to be surrounded with.
But what about your work – how can you transport your work wherever you want to live? This depends, of course, on the nature of your work. If your job is to think, read, write, communicate, publish or do stuff with computers, you can do that everywhere as long as there is electricity and internet access. You can work at home, or a corner cafe, or a nice local coworking space.
But what if you are a scientist? How can you do that?
Remember World 2.0 at Rainbows End? In that plausible world, which will cease to be Science Fiction in mere years, some scientists obviously work at universities or at institutes that may or may not be associated with universities. They are presumably hired to teach and train the new generations of scientists there. But most of scientific research is apparently happening elsewhere – in the virtual world, on the “boards”.
When I read about those “boards”, I was reminded of sites like Innocentive, Innovation Exchange, Nine Sigma or even 2collab – places where funders and researchers find each other and exchange money for discoveries – a free-market type of funding. As an alternative, it sound pretty good, though big basic science would probably still have to be funded by the government agencies.
But, Vinge never tells where those scientists live and where they actually do their research. They may pick up jobs online, but they still have to do wet work in some lab somewhere. Where? Some may be at universities, supplementing their income in this way. But many are likely freelancers (many of those perhaps without any formal degrees in science, just talented people who learned by themselves and through their thoughts, words and actual discoveries, built their reputations in the scientific community). Where do those freelancers do their research?
Perhaps in a scientific equivalent of a coworking place – perhaps something like a Science Hostel. I have been thinking about this for quite a while, but I did not know that Garret Lisi also came up with this concept. Apart from being on the cutting edge of science publishing, he is also apparently thinking innovatively about the way science in the future will be done. In his interview on Backreaction, Garett says:

I’ve been thinking about what the ideal scientific work environment would be, and the best thing I’ve been able to come up with is a Science Hostel. I envision a large house where theorists could live and work on their stuff alone or in groups while having their meals and living space provided. The idea is to give researchers time, with an easily accessible but undemanding social atmosphere, and as little responsibility as possible. And, of course, it would have to be somewhere beautiful — with good hiking and other things to do outside. For the past year I’ve been living near Lake Tahoe — a great environment for thinking and playing. Anywhere in the mountains would probably be good for a Science Hostel — even better if it’s next to a good ski hill. 🙂

Now that is all very nice if you are a theorist – all you need is an armchair. Or if your only scientific tool is a computer, you can do it there. But what if you need more?
A coworking space has three important components: the physical space, the technological infrastructure, and the people. A Science Hostel that accommodates people who need more than armchairs and wifi, would need to be topical – rooms designed as labs of a particular kind, common equipment that will be used by most people there, all the people being in roughly the same field who use roughly the same tools.
But this is not such a new idea. Remember Entwicklungsmechanik from the late 19th and early 20th century? The winters in Germany are cold, so the developmental biologists spent a lot of their time at Stazione Zoologica in Naples, where they made their discoveries by studying eggs and embryos of sea urchins. That was a Science Hostel. How about Woods Hole? Cold Spring Harbor? Perimeter Institute? Those are all Science Hostels.
But in the modern world, there can be more of those. There will be vast differences in size, type and economics. Some will be built and funded by large, rich institutions. Others will be cooperative projects. Some will be free, but by invitation only. Others will be open, but charging for space and use of the facilities. While most of the past and existing institutes of this sort only cater to people who are already associated with other academic institutions, some of the new hostels will cater to freelancers as well (needless to say, Open Access to literature is essential to development of such spaces).
And people will choose to live where the appropriate Science Hostel is located because this is where they can do their work and live their lives surrounded by like-minded people. There will be a lot of physicists living in the village that has a Physics Hostel. A lot of molecular biologists surrounding a Hostel equipped for them. Perhaps there will be a Hostel specifically geared towards research on whole animals with its own IACUC, facilities and staff.
We’ll wait and see….


Praxis #5 is up on Effortless Incitement

Advice on designing scientific posters

This one is good and thorough – by Colin Purrington, Department of Biology, Swarthmore College. Short excerpt from the beginning:

Why a poster is usually better than a talk
Although you could communicate all of the above via a 15-minute talk at the same meeting, presenting a poster allows you to more personally interact with the people who are interested in your research, and can reach people who might not be in your specific field of research. Posters are more efficient than a talk because they can be viewed even while you are off napping, and especially desirable if you are terrible at giving talks. And once you have produced a poster, you can easily take it to other conferences. If you don’t like to travel far, or are broke, many college and university science departments sponsor poster sessions that welcome students from nearby institutions. For all of the above, session organizers typically have a “Best Poster Prize Committee,” which awards fame and often cold hard cash to deserving posters. And when you’re ready to retire your poster from active duty, you can hang it in your dorm room to impress your friends, or display it in your departmental hallway so that faculty can show off your hard work to visitors for years to come. You can also submit your final product to, which promises to keep a PDF version of your poster in perpetuity (for free) and allows people to send you comments about your poster.

The structure of scientific collaboration networks

On arXiv, by M. E. J. Newman (Santa Fe Institute):

We investigate the structure of scientific collaboration networks. We consider two scientists to be connected if they have authored a paper together, and construct explicit networks of such connections using data drawn from a number of databases, including MEDLINE (biomedical research), the Los Alamos e-Print Archive (physics), and NCSTRL (computer science). We show that these collaboration networks form “small worlds” in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances. We further give results for mean and distribution of numbers of collaborators of authors, demonstrate the presence of clustering in the networks, and highlight a number of apparent differences in the patterns of collaboration between the fields studied.


DOCTOR Eva Amsen!

Interview with Michael Nielsen

Sam Dupuis (yes, the son of John) contacted Michael Nielsen and posted a nice, smart, long blog interview. Check it out.