Category Archives: Open Science

The line between science and journalism is getting blurry….again

 

Human #1: “Hello, nice weather today, isn’t it?”

Human #2: “Ummm…actually not. It’s a gray, cold, windy, rainy kind of day!”

Many a joke depends on confusion about the meaning of language, as in the example above. But understanding the sources of such confusion is important in realms other than stand-up comedy, including in the attempts to convey facts about the world to one’s target audience.

In the example above, Human #1 is using Phatic language, sometimes referred to as ‘small talk‘ and usually exemplified, at least in the British Isles, with the talk about the highly unpredictable weather. (image: by striatic on Flickr)

Phatic language

Phatic discourse is just one of several functions of language. Its role is not to impart any factual information, but to establish a relationship between the people. It conveys things like emotional state, relative social status, alliance, intentions and limits to further conversation (i.e., where the speaker “draws the line”).

If a stranger rides into a small town, a carefully chosen yet meaningless phrase establishes a state of mind that goes something like this: “I come in peace, mean no harm, I hope you accept me in the same way”. The response of the local conveys how the town looks at strangers riding in, for example: “You are welcome…for a little while – we’ll feed you and put you up for the night, but then we hope you leave”. (image: Clint Eastwood in ‘Fistful of Dollars’ from Squidoo)

An important component of phatic discourse is non-verbal communication, as the tone, volume and pitch of the voice, facial expression and body posture modify the language itself and confirm the emotional and intentional state of the speaker.

It does not seem that linguistics has an official term for the opposite – the language that conveys only pure facts – but the term usually seen in such discussions (including the domain of politics and campaigning) is “Conceptual language” so this is what I will use here. Conceptual language is what Human #2 in the joke above was assuming and using – just the facts, ma’am.

Rise of the earliest science and journalism

For the sake of this article, I will use two simplified definitions of science and journalism.

Journalism is communication of ‘what’s new’. A journalist is anyone who can say “I’m there, you’re not, let me tell you about it.”

Science is communication of ‘how the world works’. A scientist is anyone who can say “I understand something about the world, you don’t, let me explain it to you”.

Neither definition necessitates that what they say is True, just what they know to the best of their ability and understanding.

Note that I wrote “science is communication”. Yes, science is the process of discovery of facts about the way the world works, but the communication of that discovery is the essential last step of the scientific process, and the discoverer is likely to be the person who understands the discovery the best and is thus likely to be the person with the greatest expertise and authority (and hopefully ability) to do the explaining.

For the greatest part of human history, none of those distinctions made any sense. Most of communication contained information about what is new, some information about the way the world works, and a phatic component. Knowing how the world works, knowing what is happening in that world right now, and knowing if you should trust the messenger, were all important for survival.

For the most part, the information was local, and the messengers were local. A sentry runs back into the village alerting that a neighboring tribe, painted with war-paints, is approaching. Is that person a member of your tribe, or a stranger, or the well-known Boy Who Cried Wolf? What do you know about the meaning of war-paint? What do you know about the neighboring tribe? Does all this information fit with your understanding of the world? Is information coming from this person to be taken seriously? How are village elders responding to the news? Is this piece of news something that can aid in your personal survival?

For the longest time, information was exchanged between people who knew each other to some degree – family, neighbors, friends, business-partners. Like in a fishing village, the news about the state of fishing stocks coming from the ships at sea is important information exchanged at the local tavern. But is that fish-catch information ‘journalism’ (what’s new) or ‘science’ (how the world works)? It’s a little bit of both. And you learn which sailors to trust by observing who is trusted by the locals you have already learned to trust. Trust is transitive.

Someone in the “in-group” is trusted more than a stranger – kids learned from parents, the community elders had the authority: the trust was earned through a combination of who you are, how old you are, and how trustworthy you tended to be in the past. New messengers are harder to pin down on all those criteria, so their information is taken with a degree of skepticism. The art of critical thinking (again, not necessarily meaning that you will always pick the Truth) is an ancient one, as it was essential for day-to-day survival. You trust your parents (or priests or teachers) almost uncritically, but you put up your BS filters when hearing a stranger.

Emergence of science and of journalism

The invention of the printing press precipitated the development of both journalism and science. But that took a very long time – almost two centuries (image: 1851, printing press that produced early issues of Scientific American). After Gutenberg printed the Bible, most of what people printed were political pamphlets, church fliers and what for that time and sensibilities went for porn.

London Gazette of 1666 is thought to be the first newspaper in the modern sense of the word. (image: from DavidCo) Until then, newspapers were mostly irregular printings by individuals, combining news, opinion, fiction and entertainment. After this, newspapers gradually became regular (daily, weekly, monthly) collections of writings by numerous people writing in the same issue.

The first English scientific journal was published a year before – the Philosophical Transactions of the Royal Society of London in 1665 (image: Royal Society of London).

Until then, science was communicated by letters – those letters were often read at the meetings of scientists. Those meetings got formalized into scientific societies and the letters read at such meetings started getting printed. The first scientific journals were collections of such letters, which explains why so many journals have the words “Letters”, “Annals” or “Proceedings” in their titles.

Also, before as well as for a quite a long time after the inception of first journals, much of science was communicated via books – a naturalist would spend many years collecting data and ideas before putting it all in long-form, leather-bound form. Those books were then discussed at meetings of other naturalists who would often respond by writing books of their own. Scientists at the time did not think that Darwin’s twenty-year wait to publish The Origin was notable (William Kimler, personal communication) – that was the normal timeline for research and publishing at the time, unusual only to us from a modern perspective of 5-year NIH grants and the ‘publish or perish’ culture.

As previously oral communication gradually moved to print over the centuries, both journalistic and scientific communication occured in formats – printed with ink on paper – very similar to blogging (that link leads to the post that served as a seed from which this article grew). If born today, many of the old writers, like Montaigne, would be Natural Born Bloggers (‘NBBs’ – term coined by protoblogger Dave Winer). A lot of ship captains’ logs were essentially tweets with geolocation tags.

People who wanted to inform other people printed fliers and pamphlets and books. Personal letters and diaries were meant to be public: they were as widely shared as was possible, they were publicly read, saved, then eventually collected and published in book-form (at least posthumously). Just like blogs, tweets and Facebook updates today….

The 18th century ‘Republic of Letters’ (see the amazing visualization of their correspondence) was a social network of intellectual leaders of Europe who exchanged and publicly read their deep philosophical thoughts, scientific ideas, poetry and prose.

Many people during those centuries wrote their letters in duplicate: one copy to send, one to keep for publishing Collected Letters later in life. Charles Darwin did that, for example (well, if I remember correctly, his wife made copies from his illegible originals into something that recipients could actually read), which is why we have such a complete understanding of his work and thought – it is all well preserved and the availability of such voluminouos correspondence gave rise to a small industry of Darwinian historical scholarship.

What is important to note is that, both in journalism and in science, communication could be done by anyone – there was no official seal of approval, or licence, to practice either of the two arts. At the same time, communication in print was limited to those who were literate and who could afford to have a book printed – people who, for the most part, were just the wealthy elites. Entry into that intellectual elite from a lower social class was possible but very difficult and required a lot of hard work and time (see, for example, a biography of Alfred Russell Wallace). Membership in the worlds of arts, science and letters was automatic for those belonging to the small group of literate aristocracy. They had no need to establish formalized gatekeeping as bloodlines, personal sponsorship and money did the gatekeeping job quite well on their own.

As communication has moved from local to global, due to print, trust had to be gained over time – by one’s age, stature in society, track record, and by recommendation – who the people you trust say you should trust. Trust is transitive.

Another thing to note is that each written dispatch contained both ‘what’s new’ and ‘how the world works’ as well as a degree of phatic discourse: “This is what happened. This is what I think it means. And this is who I am so you know why you should trust me.” It is often hard to tell, from today’s perspective, what was scientific communication and what was journalism.

Personal – and thus potentially phatic – communication was a norm in the early scientific publishing. For example, see “A Letter from Mr J. Breintal to Peter Collinfoxl, F. RXS. contairnng an Account of what he felt after being bit by a Rattle-fnake” in Philosophical Transactions, 1747. – a great account of it can be found at Neurotic Physiology. It is a story of a personal interaction with a rattlesnake and the discovery leading from it. It contained “I was there, you were not, let me tell you what happened” and “I understand something, you don’t, let me explain that to you” and “Let me tell you who I am so you can know you can trust me”.

Apparently, quite a lot of scientific literature of old involved exciting narratives of people getting bitten by snakes – see this one from 1852 as well.

The anomalous 20th century – effects of technology

The gradual changes in society – invention of printing, rise of science, rise of capitalism, industrial revolution, mass migration from rural to urban areas, improvements in transportation and communication technologies, to name just a few – led to a very different world in the 20th century.

Technology often leads societal changes. If you were ever on a horse, you understand why armies that used stirrups defeated the armies that rode horses without this nifty invention.

Earlier, the speed of spreading news was much slower (see image: Maps of rates of travel in the 19th century – click on the link to see bigger and more). By 1860 Telegraph reached to St. Louis. During its short run the Pony Express could go the rest of the way to San Francisco in 10 days. After that, telegraph followed the rails. First transcontinental line was in 1869. Except for semaphores (1794) information before the telegraph (1843) could only travel as fast as a rider or boat (Thanks to John McKay for this brief primer on the history of speed of communication in Northern America. I am assuming that Europe was slightly ahead and the rest of the world somewhat behind).

The 20th century saw invention or improvement of numerous technologies in transportation – cars, fast trains, airplanes, helicopters, space shuttles – and in communication – telephone, radio, and television. Information could now travel almost instantly.

But those new technologies came with a price – literally. While everyone could write letters and send them by stagecoach, very few people could afford to buy, run and serve printing presses, radio stations and television studios. These things needed capital, and increasingly became owned by rich people and corporations.

Each inch of print or minute of broadcast costs serious money. Thus, people were employed to become official filters of information, the gatekeepers – the editors who decided who will get access to that expensive real estate. As the editors liked some people’s work better than others, those people got employed to work in the nascent newsrooms. Journalism became professionalized. Later, universities started journalism programs and codified instruction for new journalists, professionalizing it even more.

Instead of people informing each other, now the few professionals informed everyone else. And the technology did not allow for everyone else to talk back in the same medium.

The broadcast media, a few large corporations employing professional writers informing millions – with no ability for the receivers of information to fact-check, talk back, ask questions, be a part of the conversation – is an exception in history, something that lasted for just a few decades of the 20th century.

The anomalous 20th century – industrialization

Industrial Revolution brought about massive migration of people into big cities. The new type of work required a new type of workforce, one that was literate and more educated. This led to the invention of public schools and foundation of public universities.

In the area of science, many more people became educated enough (and science still not complex and expensive yet) to start their own surveys, experiments and tinkering. The explosion of research led to an explosion of new journals. Those too became expensive to produce and started requiring professional filters – editors. Thus scientific publishing also became professionalized. Not every personal anecdote could make it past the editors any more. Not everyone could call oneself a scientist either – a formal path emerged, ending with a PhD at a university, that ensured that science was done and published by qualified persons only.

By the 1960s, we got a mass adoption of peer-review by scientific journals that was experimentally done by some journals a little earlier. Yes, it is that recent! See for example this letter to Physical Review in 1936:

 

Dear Sir,

We (Mr. Rosen and I) had sent you our manuscript for publication and had not authorized you to show it to specialists before it is printed. I see no reason to address the — in any case erroneous — comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere.

Respectfully,

Albert Einstein

Or this one:

 

John Maddox, former editor of Nature: The Watson and Crick paper was not peer-reviewed by Nature… the paper could not have been refereed: its correctness is self-evident. No referee working in the field … could have kept his mouth shut once he saw the structure…

Migration from small towns into big cities also meant that most people one would meet during the day were strangers. Meeting a stranger was not something extraordinary any more, so emergence and enforcement of proper proscribed conduct in cities replaced the need for one-to-one encounters and sizing up strangers using phatic language. Which is why even today phatic language is much more important and prevalent in rural areas where it aids personal survival than in urban centers where more general rules of behavior among strangers emerged (which may partially explain why phatic language is generally associated with conservative ideology and conceptual language with politicial liberalism, aka, the “reality-based community“).

People moving from small hometowns into big cities also led to breaking up of families and communities of trust. One needed to come up with new methods for figuring out who to trust. One obvious place to go was local media. They were stand-ins for village elders, parents, teachers and priests.

If there were many newspapers in town, one would try them all for a while and settle on one that best fit one’s prior worldview. Or one would just continue reading the paper one’s parents read.

But other people read other newspapers and brought their own worldviews into the conversation. This continuous presence of a plurality of views kept everyone’s BS filters in high gear – it was necessary to constantly question and filter all the incoming information in order to choose what to believe and what to dismiss.

The unease with the exposure to so many strangers with strange ideas also changed our notions of privacy. Suddenly we craved it. Our letters are now meant for one recepient only, with the understanding it will not be shared. Personal diaries now have lockets. After a century of such craving for privacy, we are again returning to a more historically traditional notions, by much more freely sharing our lives with strangers online.

The anomalous 20th century – cleansing of conceptual language in science and journalism

Until the 20th century we did not see the consolidation of media into large conglomerates, and of course, there were no mass radio or TV until mid-20th century. Not until later in the century did we see the monopolization of local media markets by a single newspaper (competitors going belly-up) which, then, had to serve everyone, so it had to invent the fake “objective” HeSaidSheSaid timid style of reporting in order not to lose customers of various ideological stripes and thus lose advertising revenue.

Professionalising of journalism, coupled with the growth of media giants serving very broad audiences, led to institutionalization of a type of writing that was very much limited to “what’s new”.

The “let me explain” component of journalism fell out of favor as there was always a faction of the audience that had a problem with the empirical facts – a faction that the company’s finances could not afford to lose. The personal – including phatic – was carefully eliminated as it was perceived as unobjective and inviting the criticism of bias. The way for a reporter to inject one’s opinion into the article was to find a person who thinks the same in order to get the target quote. A defensive (perhaps cowardly) move that became the norm. And, once the audience caught on, led to the loss of trust in traditional media.

Reduction of local media to a single newspaper, a couple of local radio stations and a handful of broadcast TV channels (that said esentially the same thing), left little choice for the audience. With only one source in town, there was no opportunity to filter among a variety of news sources. Thus, many people started unquestioningly accepting what 20th-century style broadcast media served them.

Just because articles were under the banners of big companies did not make them any more trustworthy by definition, but with no alternative it is still better to be poorly informed than not informed at all. Thus, in the 20th century we gradually lost the ability to read everything critically, awed by the big names like NYT and BBC and CBS and CNN. Those became the new parents, teachers, tribal elders and priests, the authority figures whose words are taken unquestioningly.

In science, explosion in funding not matched by explosion of job positions, led to overproduction of PhDs and a rise of hyper-competitive culture in academia. Writing books became unproductive. The only way to succeed is to keep getting grants and the only way to do that is to publish very frequently. Everything else had to fall by the wayside.

False measures of journal quality – like the infamous Impact Factor – were used to determine who gets a job and tenure and who falls out of the pipeline. The progress of science led inevitably to specialization and to the development of specialized jargon. Proliferation of expensive journals ensured that nobody but people in highest-level research institutions had access to the literature, so scientists started writing only for each other.

Scientific papers became dense, but also narrowed themselves to only “this is how the world works”. The “this is new” became left out as the audience already knew this, and it became obvious that a paper would not be published if it did not produce something new, almost by definition.

And the personal was so carefully excised for the purpose of seeming unbiased by human beings that it sometimes seems like the laboratory equipment did all the experiments of its own volition.

So, at the close of the 20th century, we had a situation in which journalism and science, for the first time in history, completely separated from each other. Journalism covered what’s new without providing the explanation and context for new readers just joining the topic. Science covered only explanation and only to one’s peers.

In order to bridge that gap, a whole new profession needed to arise. As scientists understood the last step of the scientific method – communication – to mean only ‘communication to colleagues’, and as regular press was too scared to put truth-values on any statements of fact, the solution was the invention of the science journalist – someone who can read what scientists write and explain that to the lay audience. With mixed success. Science is hard. It takes years to learn enough to be able to report it well. Only a few science journalists gathered that much expertise over the years of writing (and making mistakes on the way).

So, many science journalists fell back on reporting science as news, leaving the explanation out. Their editors helped in that by severely restricting the space – and good science coverage requires ample space.

A good science story should explain what is known by now (science), what the new study brings that is new (news) and why does that matter to you (phatic discourse). The lack of space usually led to omission of context (science), shortening of what is new (news) and thus leaving only the emotional story intact. Thus, the audience did not learn much, Certainly not enough to be able to evaluate next day’s and next week’s news.

This format also led to the choice of stories. It is easy to report in this way if the news is relevant to the audience anyway, e.g., concerning health (the “relevant” stories). It is also easy to report on misconduct of scientists (the “fishy” stories) – which is not strictly science reporting. But it was hard to report on science that is interesting for its own sake (the “cool” stories).

What did the audience get out of this? Scientists are always up to some mischief. And every week they change the story as to what is good or bad for my health. And it is not very fun, entertaining and exciting. No surprise that science as endeavour slowly started losing trust with the (American) population, and that it was easy for groups with financial, political or religious interests to push anti-science rhetoric on topics from hazards of smoking to stem-cell research to evolution to climate change.

At the end of the 20th century, thus, we had a situation in which journalism and science were completely separate endeavors, and the bridge between them – science journalism – was unfortunately operating under the rules of journalism and not science, messing up the popular trust in both.

Back to the Future

It is 2010. The Internet has been around for 30 years, the World Wide Web for 20. It took some time for the tools to develop and spread, but we are obviously undergoing a revolution in communication. I use the word “revolution” because it is so almost by definition – when the means of production change hands, this is a revolution.

The means of production, in this case the technology for easy, cheap and fast dissemination of information, are now potentially in the hands of everyone. When the people formerly known as the audience employ the press tools they have in their possession to inform one another, we call that ‘citizen journalism.’ And some of those citizens possess much greater expertise on the topics they cover than the journalists that cover that same beat. This applies to science as well.

In other words, after the deviation that was the 20th century, we are going back to the way we have evolved as a species to communicate – one-to-one and few-to-few instead of one-to-many. Apart from technology (software instead of talking/handwriting/printing), speed (microseconds instead of days and weeks by stagecoach, railroad or Pony Express, see image above) and the number of people reached (potentially – but rarely – millions simultaneously instead of one person or small group at a time), blogging, social networking and other forms of online writing are nothing new – this is how people have always communicated. Like Montaigne. And the Republic of Letters in the 18th century. And Charles Darwin in the 19th century.

All we are doing now is returning to a more natural, straightforward and honest way of sharing information, just using much more efficient ways of doing it. (Images from Cody Brown)

And not even that – where technology is scarce, the analog blogging is live and well (image: Analog blogger, from AfriGadget).

What about trustworthiness of all that online stuff? Some is and some isn’t to be trusted. It’s up to you to figure out your own filters and criteria, and to look for additional sources, just like our grandparents did when they had a choice of dozens of newspapers published in each of their little towns.

With the gradual return of a more natural system of communication, we got to see additional opinions, the regular fact-checks on the media by experts on the topic, and realized that the mainstream media is not to be trusted.

With the return of a more natural system of communication, we will all have to re-learn how to read critically, find second opinions, evaluate sources. Nothing new is there either – that is what people have been doing for millennia – the 20th century is the exception. We will figure out who to trust by trusting the judgment of people we already trust. Trust is transitive.

Return of the phatic language

What does this all mean for the future of journalism, including science journalism?

The growing number of Web-savvy citizens have developed new methods of establishing trustworthiness of the sources. It is actually the old one, pre-20th century method – relying on individuals, not institutions. Instead of treating WaPo, Fox, MSNBC and NPR as the proxies for the father, teacher, preacher and the medicine man, we now once again evaulate individuals.

As nobody enters a news site via the front page and looks around, but we all get to individual articles via links and searches, we are relying on bylines under the titles, not on the logos up on top. Just like we were not born trusting NYTimes but learned to trust it because our parents and neighbors did (and then perhaps we read it for some time), we are also not born knowing which individuals to trust. We use the same method – we start with recommendations from people we already trust, then make our own decisions over time.

If you don’t link to your sources, including to scientific papers, you lose trust. If you quote out of context without providing that context, you lose trust. If you hide who you are and where you are coming from – that is cagey and breeds mistrust. Transparency is the new objectivity.

And transparency is necessarily personal, thus often phatic. It shows who you are as a person, your background, your intentions, your mood, your alliances, your social status.

There are many reasons sciencebloggers are more trusted than journalists covering science.

First, they have the scientific expertise that journalists lack – they really know what they are talking about on the topic of their expertise and the audience understands this.

Second, they link out to more, more diverse and more reliable sources.

Third, being digital natives, they are not familiar with the concept of word-limits. They start writing, they explain it as it needs to be explained and when they are done explaining they end the post. Whatever length it takes to give the subject what it’s due.

Finally, not being trained by j-schools, they never learned not to let their personality shine through their writing. So they gain trust by connecting to their readers – the phatic component of communication.

Much of our communication, both offline and online, is phatic. But that is necessary for building trust. Once the trust is there, the conceptual communication can work. If I follow people I trust on Twitter, I will trust that they trust the sources they link to so I am likely to click on them. Which is why more and more scientists use Twitter to exchage information (PDF). Trust is transitive.

Scientists, becoming journalists

Good science journalists are rare. Cuts in newsrooms, allocation of too little space for science stories, assigning science stories to non-science journalists – all of these factors have resulted in a loss of quantity and quality of science reporting in the mainstream media.

But being a good science journalist is not impossible. People who take the task seriously can become experts on the topic they cover (and get to a position where they can refuse to cover astronomy if their expertise is evolution) over time. They can become temporary experts if they are given sufficient time to study instead of a task of writing ten stories per day.

With the overproduction of PhDs, many scientists are choosing alternative careers, including many of them becoming science writers and journalists, or Press Information Officers. They thus come into the profession with the expertise already there.

There is not much difference between a research scientist who blogs and thus is an expert on the topic s/he blogs about, and a research scientist who leaves the lab in order to write as a full-time job. They both have scientific expertise and they both love to write or they wouldn’t be doing it.

Blog is software. A medium. One of many. No medium has a higher coefficient of trustworthiness than any other. Despite never going to j-school and writing everything on blogs, I consider myself to be a science writer.

Many science journalists, usually younger though some of the old ones caught on quickly and became good at it (generation is mindset, not age), grok the new media ecosystem in which online collaboration between scientists and journalists is becoming a norm.

At the same time, many active scientists are now using the new tools (the means of production) to do their own communication. As is usually the case with novelty, different people get to it at different rates. The conflicts between 20th and 21st style thinking inevitably occur. The traditional scientists wish to communicate the old way – in journals, letters to the editor, at conferences. This is the way of gatekeeping they are used to.

But there have been a number of prominent cases of such clashes between old and new models of communication, including the infamous Roosevelts on toilets (the study had nothing to do with either US Presidents or toilets, but it is an instructive case – image by Dr.Isis), and several other smaller cases.

The latest one is the Arsenic Bacteria Saga in which the old-timers do not seem to undestand what a ‘blog’ means, and are seemingly completely unaware of the important distinction between ‘blogs’ and ‘scienceblogs’, the former being online spaces by just about anyone, the latter being blogs written by people who actually know their science and are vetted or peer-reviewed in some way e.g., at ResearchBlogging.org or Scienceblogging.org or by virtue of being hand-picked and invited to join one of the science blogging networks (which are often run by traditional media outlets or scientific publishers or societies) or simply by gaining resepect of peers over time.

Case by case, old-time scientists are learning. Note how both in the case of Roosevelts on toilets and the Arsenic bacteria the initially stunned scientists quickly learned and appreciated the new way of communication.

In other words, scientists are slowly starting to get out of the cocoon. Instead of just communicating to their peers behind the closed doors, now they are trying to reach out to the lay audience as well.

As more and more papers are Open Access and can be read by all, they are becoming more readable (as I predicted some years ago). The traditional format of the paper is changing. So they are covering “let me explain” portion better, both in papers and on their own blogs.

They may still be a little clumsy about the “what’s new” part, over-relying on the traditional media to do it for them via press releases and press conferences (see Darwinius and arsenic bacteria for good examples) instead of doing it themselves or taking control of the message (though they do need to rely on MSM to some extent due to the distinction between push and pull strategies as the media brands are still serving for many people as proxies for trustworthy sources).

But most importantly, they are now again adding the phatic aspect to their communication, revealing a lot of their personality on social networks, on blogs, and even some of them venturing into doing it in scientific papers.

By combining all three aspects of good communication, scientists will once again regain the trust of their audience. And what they are starting to do looks more and more like (pre-20th century) journalism.

Journalists, becoming scientists

On the other side of the divide, there is a renewed interest in journalism expanding from just “this is new” to “let me explain how the world works”. There are now efforts to build a future of context, and to design explainers.

If you are not well informed on an issue (perhaps because you are too young to remember when it first began, or the issue just started being relevant to you), following a stream of ‘what is new’ articles will not enlighten you. There is not sufficient information there. There is a lot of tacit knowledge that the writer assumes the readers possess – but many don’t.

There has to be a way for news items to link to some kind of collection of background information – an ‘explainer’. Such an explainer would be a collection of verifiable facts about the topic. A collection of verifiable facts about the way the world works is….scientific information!

With more and more journalists realizing they need to be transparent about where they are coming from, injecting personality into their work in order to build trust, some of that phatic language is starting to seep in, completing the trio of elements of effective communication.

Data Journalism – isn’t this science?

Some of the best journalism of the past – yes, the abominable 20th century – was done when a reporter was given several months to work on a single story requiring sifting through boxes and boxes of documents. The reporter becomes the expert on the topic, starts noticing patterns and writes a story that brings truly new knowledge to the world. That is practically science! Perhaps it is not the hardest of the hard sciences like physics, but as good as well-done social science like cultural anthropology, sociology or ethnography. There is a system and a method very much like the scientific method.

Unfortunately, most reporters are not given such luxury. They have to take shortcuts – interviewing a few sources to quote for the story. The sources are, of course, a very small and very unrepresentative sample of the relevant population – from a rolodex. Call a couple of climate scientists, and a couple of denialists, grab a quote from each and stick them into a formulaic article. That is Bad Science as well as Bad Journalism. And now that the people formerly known as audience, including people with expertise on the topic, have the tools to communicate to the world, they often swiftly point out how poorly such articles represent reality.

But today, most of the information, data and documents are digital, not in boxes. They are likely to be online and can be accessed without travel and without getting special permissions (though one may have to steal them – as Wikileaks operates: a perfect example of the new data journalism). Those reams of data can be analyzed by computers to find patterns, as well as by small armies of journalists (and other experts) for patterns and pieces of information that computer programs miss.

This is what bioinformaticists do (and have already built tools to do it – contact them, steal their tools!).

Data journalism. This is what a number of forward-thinking journalists and media organizations are starting to do.

This is science.

On the other hand, a lot of distributed, crowdsourced scientific research, usually called Citizen Science, is in the business of collecting massive amounts of data for analysis. How does that differ from data journalism? Not much?

Look at this scientific paper – Coding Early Naturalists’ Accounts into Long-Term Fish Community Changes in the Adriatic Sea (1800–2000) – is this science or data journalism? It is both.

The two domains of communicating about what is new and how the world works – journalism and science – have fused again. Both are now starting to get done by teams that involve both professionals and amateurs. Both are now led by personalities who are getting well-known in the public due to their phatic communication in a variety of old and new media.

It is important to be aware of the shortness of our lives and thus natural tendency for historical myopia. Just because we were born in the 20th century does not mean that the way things were done then are the way things were ‘always done’, or the best ways to do things – the pinnacle of cultural and social development. The 20th century was just a strange and deviant blip in the course of history.

As we are leaving the 20th century behind with all of its unusual historical quirks, we are going back to an older model of communicating facts – but with the new tools we can do it much better than ever, including a much broader swath of society – a more democratic system than ever.

By the way, while it’s still cold, the rain has stopped. And that is Metaphorical language…

This article was commissioned by Science Progress and will also appear on their site in 24 hours.

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:

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Open Laboratory – old Prefaces and Introductions

One difference between reading Open Laboratory anthologies and reading the original posts included in them is that the printed versions are slightly edited and polished. Another difference is that the Prefaces and Introductions can be found only in the books. They have never been placed online.
But now that four books are out and we are halfway through collecting entries for the fifth one, when only the 2009 book is still selling, I think it is perfectly OK to place Prefaces and Introductions that I wrote myself online. I wrote Prefaces for the 2006, 2007 and 2008 book, as well as the Introduction for the 2006 one. The introductions for the subsequent editions were written by the year’s guest editor, i.e., Reed Cartwright in 2007, Jennifer Rohn in 2008, and SciCurious in 2009.
So, under the fold are my three Prefaces and one Introduction. See how the world (and my understanding of it) of the online science communication has changed over the last few years:

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Good article about the history and current state of Open Access

US seeks to make science free for all by Declan Butler:

The push to open up scientific knowledge to all looks set to go into overdrive. Over the past decade, the accessibility offered by the Internet has transformed science publishing. Several efforts have already tried to harness the web’s power to make research papers available for free. Now two parallel efforts from the US government could see almost all federally funded research made available in free, publicly accessible repositories…..

Read the whole thing….

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 ResearchBlogging.org 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 ResearchBlogging.org 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 ResearchBlogging.org. 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 ResearchBlogging.org) 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 ResearchBlogging.org (which is strange and unfathomable why – RB.org 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 (scienceblogs.com 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 ResearchBlogging.org). 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 Scivee.tv, 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.

AAAS 2010 meeting

In San Diego this week. Check it out. I’ll be there – see my session. If you will be there, let me know. Let’s have coffee or lunch, etc. My session is on 21st in the morning, and there is a lot of social stuff I agreed to on the 19th in the afternoon and evening, and of course I want to see a lot of other sessions, but I am generally flexible. Just ping me over e-mail or Twitter or phone (if you have my number) or post a comment here.

Aves 3D

Aves 3D is a ‘three dimensional database of avian skeletal morphology’ and it is awesome!
Aves3D logo.pngThis is an NSF-funded project led by Leon Claessens, Scott Edwards and Abby Drake. What they are doing is making surface scans of various bones of different bird species and placing the 3D scans on the website for everyone to see and use. With simple use of the mouse or arrow buttons, one can move, zoom and rotate each image any way one wants.
The collection is growing steadily and already contains some very interesting bones from a number of species, both extinct and extant. You can see examples of bones of the dodo or the Diatryma gigantea (aka Gaston’s Bird), as well as many skulls and sternums and various limb bones of currently existing species.
The database is searchable by
Cladogram, Scientific Name, Common Name, Skeletal Element, geological era, Geographical Location or Specimen Number.
Most of the actual scanning is done by undergraduate students and the database is already being use for several scientific projects. You can get involved and help build the database, you can use the scans for teaching and research, or you can just go and have fun rotating the cool-looking bird bones.

ResearchBlogging.org posts now a part of Article-Level-Metrics at PLoS

Two years ago, at the 2008 Science Blogging Conference, Dave Munger introduced to the world a new concept and a new wesbite to support that concept – ResearchBlogging.org. What is that all about?
Well, as the media is cuttting science out of the newsroom and the science reporting is falling onto institutional press information officers and science bloggers, more and more people are looking for scientific information on science blogs, especially as the expertise of the blogger is likely to provide a more accurate assessment of a freshly published study than the mainstream media can usually do.
But many new readers of science blogs were put off by the fact that a blog is a personal platform. In other words, not every post was about pure science news. There may be a beautiful nature picture, a personal story, a YouTube video, a comic strip, an aggressive defence of science from the latest attack by the politically motivated anti-science groups, etc. They were asking “where is science on science blogs?”. Well, it’s there if one looks around for more than a few seconds. But not everyone has patience to look around. So Dave came up with the idea….
And the idea was to a) come up with a method for approving science bloggers, b) give such bloggers tools to tag their posts that are specifically covering peer-reviewed literature, and c) use the tags to aggregate links to all such posts in one place. Thus, the ResearchBlogging.org was born.
In the two years since its inception, ResearchBlogging.org has grown and improved and gained quite a lot of respect. A few languages other than English were added. Weekly ‘editors’ picks’ in various disciplines started getting posted. Seed Media Group became a partner. I use it as the only source of posts when considering the entries for my PLoS ONE Blog Pick Of The Month (only 13 days to go in December, folks, keep blogging!).
Yesterday, a new milestone was reached. Coverage of a PLoS article (in any of the seven PLoS journals) by a blog post that gets aggregated on ResearchBlogging.org was added to the article-level-metrics found on each PLoS article (under the “Metrics” tab) so it can be discovered by a single click from the article itself. Here is a short video demonstrating how it works:

Sure, PLoS articles can receive (and showcase) trackbacks from blogs which we encourage you to do, but some blogging platforms cannot send trackbacks, some trackbacking posts are just lists of links without additional explanations, or may even come from spam blogs. The advantage of linking only to blog posts aggregated at ResearchBlogging.org is that there is a vetting mechanism for blog authors, minimal criteria for inclusion of a post, and ability to flag and potentially remove inappropriate posts from it. Thus, only those blog posts that add value to the article are included. A one-stop shopping place for the best blog coverage of the article.
You can read in more detail about the news at ResearchBlogging.org news blog and on everyONE blog.

New issue of Journal of Science Communication

The December 2009 edition of the Journal of Science Communication is now online with some intriguing articles – all Open Access so you can download all the PDFs and read:
Control societies and the crisis of science journalism:

In a brief text written in 1990, Gilles Deleuze took his friend Michel Foucault’s work as a starting point and spoke of new forces at work in society. The great systems masterfully described by Foucault as being related to “discipline” (family, factory, psychiatric hospital, prison, school), were all going through a crisis. On the other hand, the reforms advocated by ministers throughout the world (labour, welfare, education and health reforms) were nothing but ways to protract their anguish. Deleuze named “control society” the emerging configuration.

Science cafés. Cross-cultural adaptation and educational applications:

Tokyo Institute of Technology (TokyoTech) has been developing a number of methodologies to teach graduate students the theory and practice of science communication since 2005. One of the tools used is the science café, where students are taught about the background based primarily on theoretical models developed in the UK. They then apply that knowledge and adapt it the Japanese cultural context and plan, execute and review outcomes as part of their course. In this paper we review 4 years of experience in using science cafés in this educational context; we review the background to the students’ decision-making and consensus-building process towards deciding on the style and subject to be used, and the value this has in illuminating the cultural influences on the science café design and implementation. We also review the value of the science café as an educational tool and conclude that it has contributed to a number of teaching goals related to both knowledge and the personal skills required to function effectively in an international environment.

Science comics as tools for science education and communication: a brief, exploratory study:

Comics are a popular art form especially among children and as such provide a potential medium for science education and communication. In an attempt to present science comics in a museum exhibit I found many science themed comics and graphic books. Here I attempt to provide an overview of already available comics that communicate science, the genre of ‘science comics’. I also provide a quick literature review for evidence that comics can indeed be efficiently used for promoting scientific literacy via education and communication. I address the issue of lack of studies about science comics and their readers and suggest some possible reasons for this as well as some questions that could be addressed in future studies on the effect these comics may have on science communication.

Science on television: how? Like that!:

This study explores the presence of science programs on the Flemish public broadcaster between 1997 and 2002 in terms of length, science domains, target groups, production mode, and type of broadcast. Our data show that for nearly all variables 2000 can be marked as a year in which the downward spiral for science on television was reversed. These results serve as a case study to discuss the influence of public policy and other possible motives for changes in science programming, as to gain a clearer insight into the factors that influence whether and how science programs are broadcast on television. Three factors were found to be crucial in this respect: 1) public service philosophy, 2) a strong governmental science policy providing structural government support, and 3) the reflection of a social discourse that articulates a need for more hard sciences.

Often overlooked: formative evaluation in the development of ScienceComics:

Formative evaluation should play a key role in the development of a science communication project or initiative. Such research is vital to understanding the needs and interests of the audience or participants; meeting these needs and interests helps ensure the project’s success. However, there can be a temptation to plough ahead without undertaking adequate formative evaluation. Using ScienceComics (www.sciencecomics.uwe.ac.uk) as a case study, this article explores both the challenges and benefits of using formative evaluation to guide project development. It focuses on the actors involved in the formative stages and the impacts these actors had on the final outputs. This evidence is used to develop practical guidance on integrating formative evaluation right from the start.

Socialization of scientific and technological research: further comments:

Research systems are increasingly required to be more practically oriented and to address issues which appear more promising in economic and social results, with special reference to trans-disciplinary research fields, such as nanotechnology or ICTs; policy makers show a sharp tendency to establish research priorities and to drive research systems; universities and research institutions are asked to be more transparent and open to dialogue with social actors on contents, impacts, ethical implications and practical applications of scientific and technological research. These transformations affecting both the ways in which science and technology are produced and their relationships with society pose new challenges to European research. All the aspects of research activities are concerned, including the life of the research groups, the approaches to scientific evaluation, the development of European research policies and the interaction between researchers with their social environment. Continuing a reflection started in the last issue of JCOM, Luisa Prista, Evanthia Kalpazidou-Schmidt, Brigida Blasi, Sandra Romagnosi and Miguel Martínez López offered their contribution in identifying some of the key implications and risks which these changes are bringing about, mainly in the perspective of the construction of the European Research Area.

Too much power to the networks:

In his latest book titled “Communication power”, the famous sociologist of information society Manuel Castells focuses on the way in which power takes shape and acts in information societies, and the role of communication in defining, structuring, and changing it. From the rise of “mass self-communication” to the role of environmental movements and neuropolitics, the network is the key structure at play and the main lens used to analyse the transformations we are witnessing. To support his thesis Castells links media studies, power theory and brain science, but his insistence on networks puts in danger his ability to give to his readers a comprehensive and coherent interpretative framework.

The brain seduction: the public perception of neuroscience:

The increasing number of magazine covers dedicated to brain studies and the success of magazines and scientific journals entirely dedicated to brain and mind indicate a strong interest on these themes. This interest is clearly surpassing the boundaries of scientific and medical researches and applications and underlines an engagement of the general public, too. This phenomenon appears to be enhanced by the increasing number of basic researches focusing on non-health-related fMRI studies, investigating aspects of personality as emotions, will, personal values and beliefs, self-identity and behaviour. The broad coverage by the media raises some central questions related to the complexity of researches, the intrinsic limits of these technologies, the results’ interpretative boundaries, factors which are crucial to properly understand the studies’ value. In case of an incomplete communication, if those fundamental interpretative elements are not well understood, we could register a misinterpretation in the public perception of the studies that opens new compelling questions. As already observed in the past debates on science and technologies applications, in this case, too, we assist to a communicative problem that set against scientific community on one side and media, on the other. Focusing our attention, in particular, on the debate on fMRI, taken as a good model, in the present letter we will investigate the most interesting aspects of the current discussion on neuroscience and neuroscience public perception. This analysis was performed as one of the bid – brains in dialogue – activities (www.neuromedia.eu). bid is a three year project supported by the European Commission under the 7th Framework Program and coordinated by Sissa, the International School for Advanced Studies of Trieste, aimed at fostering dialogue between science and society on the new challenges coming from neuroscience.

Help the Obama Administration devise a healthy Open Access policy

As many of you, my readers, are interested in Open Access publishing and have given it quite some thought over time, I think you are the right kind of people to contribute to this in a thoughtful and persuasive manner. Please do it.
From everyONE blog:

The White House Office of Science and Technology Policy has invited comment on broadening public access to publicly funded research and they want to hear from you. Please post your contributions to this blog.
Their Request for Information (RFI) lasts for just 30 days and expires on 7 January 2010, so we’d like to encourage you to get involved sooner rather than later. This is an opportunity for us to shape a broader public access policy – how it should be implemented, what type of technology and features are needed, and how to manage the process.
Adding your thoughts to the blog will help ensure that the administration form a balanced (the comment thread is moderated) view of stakeholders’ interest. E-mail comments will also be accepted and will be posted to the blog by the moderators.
There are 3 main topics where the administration would appreciate your input (they also welcome general comments) and each one is open for a set period of time:
1. Implementation – expires 20 December 2009. Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release?
2. Features and Technology – 21-31 December 2009. In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?
3. Management – 1-7 January 2010. What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Interview (in Serbian)

I know there is a nice subset of my readers who can read Serbian language. If you are one of those, you may be interested in the last issue of ‘Pancevacko Citaliste’. Along with several interesting articles about science publishing and librarianship, there is also an interview with me by Ana Ivkovic, librarian at the Oncology Institute in Belgrade. The journal is Open Access, so you can download and read the PDF here.

It’s so easy to re-use Open Access stuff (video)

It’s barely been a day since PLoS ONE published the article Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila when a video appeared on YouTube mashing up images and text from the press release:

Of course, as this is Open Access, nobody needs to worry about copyright and stuff….though a direct link to the paper would have been nice (or, considering the infamous YouTube commenters, perhaps better not!).
See the related blog post as well.

Open Access Week in Serbia

Open Access Week is in full swing and there is a lot of blogging about its various events in many countries.
OA week was marked in Serbia this year as well. As you may remember, I went to Belgrade twice in the past two years – in 2008 and 2009 and gave a total of four lectures, one brief TV interview, four long radio interviews and a print interview. I am now writing a paper about Open Access for one of their journals as well.
This effort has paid off.
I have remarked before how difficult it is to make changes in smaller countries – the scientific community is small, everyone knows everybody else and there is usually an entrenched hierarchy that resists changes from below.
But, the small community may also be susceptible to a “founder effect” of sorts: if the small group of people with influence starts changing the system, then it is likely to spread very rapidly and get fixed in the entire country.
So, for example in Serbia, there is one enormous university – Belgrade University – and only a small number of smaller schools in other cities. Those smaller universities are almost certain to adopt whataver changes the BU adopts – it is a matter of survival for them. So if Belgrade University adopts some kind of Open Access rule, or decides to give Impact Factor a smaller role in hiring and promotion decisions, then all the other schools will be quick to follow and the entire system of the country will change rapidly.
But how does one change the system in such an enormous and buraucratic entity as Belgrade University? The change will happen if the new rules are first adopted and pushed by university librarians and by the Medical School – the rest of the university will then follow their lead.
So I was particularly happy to see that the OA week event in Belgrade was attended by several of those people who are in positions of influence – Medical School professors and university librarians. You can see the announcements here, here and here.
The meeting was opened by Dr.Simic, the Dean for Research at Medical School at the University of Belgrade. This is her opening address (you can download the MP3 files by clicking on the links – of course, you need to understand Serbian):
http://www.mediafire.com/?b1h0dvzmydm
Here is the rest of the program:
1.Zoran Zdravkovic (Senior Librarian and Library Manager at Belgrade City Library): Access to Information
http://www.mediafire.com/?zmeovyghgdy

2.Sanja Antonic (Biomedical and Biotechnology librarian at the University Library in Belgrade): Impact Factor and the future of Open Access
http://www.mediafire.com/?0lhzdoomthz

3.Vedran Vucic (President of the GNU Linux Center): RSS Feed Aggregators of Medical Information
http://www.mediafire.com/?2mylmunzijn

4.Ana Ivkovic (Senior Librarian at Institute for Oncology and Radiology of Serbia, National Cancer Research Center): Social Media and Scientific Information
http://www.mediafire.com/?a2zm2myjedu

5.Dr Vera Zdravkovic (Professor of Medicine, Child Clinic, Belgrade University): Open Access and the User
http://www.mediafire.com/?kyzkdcmzyy2

6.Nada Arbutina (Belgrade’s City Library): Where does the Scientific Path Begin?
http://www.mediafire.com/?a2zm2myjedu
Ana Ivkovic has also blogged about the event, with some pictures.
Afterwards, they told me that 6 out of 6 presentations mentioned PLoS, two of them going into details of Article-Level Metrics, particularly in the context of reducing the influence of Impact Factor in hiring and promotion decisions. I was also told that 5 out of 6 presentations mentioned me by name, with those who could say “Bora told me” winning over those who could only say “as Bora said when he was here” ;-)
Now I have to sit down and write that paper for them – of course, this is the craziest week on record with OA Week, ScienceOnline2010 finalization, anti-Ida paper to monitor media reactions, a manuscript to review for JOMC, galley proofs of another paper of mine to proofread, and more….but I’ll do it this weekend for sure.

Open Access Week

OAWeek.jpg
This week – 19th-23rd October 2009 – is the Open Access week around the world – fitting nicely with the 5th birthday of PLoS Medicine. And when I say ‘around the world’ I really mean it. Just check out all the global events happening this week.
The OA Week is co-organized by Open Access Directory, PLoS, SPARC, Students for Free Culture, eIFL (Electronic Information for Libraries) and OASIS.
Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in Germany (there are 67 events in that country alone!), Netherlands, China and Japan.
You can get all the information and follow the events on the Open Access Week blog. There is also a nice round-up on the SPARC site.
As the week unfolds, I will blog more about it here. In the meantime, you can follow the news of the OA week on Facebook or by following PLoS on Twitter.You may also want to sign up to participate in the OASPA webinar (locationless – sign up to participate online).
I love this video in which Jennifer McLennan and Heather Joseph of SPARC explain what the OA week is all about:

And in this video, Walter H. Curioso, M.D., M.P.H., talks a bit about his views of Open Access and how it can help in developing countries.

Open Access 101 (video)

Open Access 101, from SPARC from Karen Rustad on Vimeo.

The Swedish Research Council mandates Open Access

Press release (in Swedish – translation from the Swedish by Ingegerd Rabow):

The Swedish Research Council requires free access to research results.
In order to receive research grants the Research council requires now that researchers publish their material freely accessible to all.
The general public and other researchers shall have free access to all material financed by public funding,
The thought behind the so called Open Access is that everybody shall have free and unlimited access to scientifically refereed articles, The Research Council has now decided, that researchers who are granted research funding from the Council shall publish their refereed texts in journals and at conferences in this way.
“We are of the opinion that texts presenting research funded by public funds shall be freely available to all,” says professor Pär Omling Director General of the Swedish Research Council. “Open Access is an important prerequisite for the dissemination of research results to the benefit of society.”
Researchers are required to guarantee that everything published shall be freely available according to to Open Access not later than six months after publication.
The Council’s decision regarding Open Access has been taken in close cooperation with SUHF, the Association of Swedish Higher Education. To promote free dissemination of research results is not and isolated Swedish occurrence, The so called Berlin Declaration aiming to implement Open Access has been signed by several large, mainly European research funders.
The Open Access-mandate covers so far only refereed journal articles and conference reports, not monographs and book chapters. The mandate will be included in the new grant conditions from 2010..
For more information, contact
Håkan Billig, main secretary for the Medical Council, tel +46 8-546 44 294, e-post hakan.billig@vr.se
Pär Omling, Director General the Swedish Research Council, tel +46 8-546 44 185, e-post par.omling@vr.se

The PLoS ONE Blog Pick of the Month for September 2009 is…

….to be found on the everyONE blog.

Article-Level Metrics at PLoS – Download Data (updated with links)

If you are a regular reader of this blog, you are certainly aware that PLoS has started making article-level metrics available for all articles.
Today, we added one of the most important sets of such metrics – the number of times the article was downloaded. Each article now has a new tab on the top, titled “Metrics”. If you click on it, you will be able to see the numbers of HTML, XML and PDF downloads, a graph of downloads over time and a link to overall statistics for the field, the journal, and PLoS as a whole.
Mark Patterson explains (also here and here), what it all means:

We believe that article-level metrics represent an important development for scholarly publishing. While some publishers are providing limited data, we are not aware of any publisher that has gone as far as PLoS in providing such a broad range of indicators and metrics, and in making the data openly available. We invite you to visit our journal sites and seek out the Metrics tab for each article.
It’s also important to emphasize that online usage should not be seen as an absolute indicator of quality for any given article, and such data must be interpreted with caution. To provide additional context and to aid interpretation, we have provided a series of summary tables indicating the average usage of categories of article (grouped by age, journal and topic area). Users will also notice that a number of articles do not have any usage data, because of problems with the log files. We are working hard to add data for these articles, and we also encourage readers to let us know if they find any anomalies or have any questions about the data.

You can also download the entire dataset for all seven PLoS Journals. If you click on this you can download a ZIP folder that contains an Excel file that lists all the metrics for all the articles. Please play with the data – let us know what you find, or blog about your impressions.
You can find more information (with lots of detail about the methodology, caveats, etc) about all article-level metrics on the pages of individual journals (here is the example for PLoS ONE) or specifically about download data here.
There is also a FAQ page and an entire new website devoted to explaining the new metrics. Take some time and explore. And experiment with the data and let the world know what you found.
As you may be aware, download statistics strongly correlate with subsequent citations. And just like researchers have perfected ways to game the citation numbers, of course the downloads can be gamed as well. Which is why we provide all the raw data and methods we used to get them. So you can figure out everything for yourself. It is all transparent.
The first reactions are in. Christina Pikas wrote on her blog:

So I’m very excited to hear that PLOS is offering article download information. So no begging of your acquisitions folks, no looking at the “top downloads” listing to see if your article is there. You can get it right at the article if you happen to get your article accepted into a PLOS journal. Oh, and even cooler, you can download the whole shebang in a spreadsheet! (Quick, find me a research question using this data!) You can also get how many times things are cited from a couple different sources.
If you’re a scientist, this is also one way to filter for articles that are worthy of more attention when there are so many new articles coming out. (things will have more downloads if they have press releases, etc., but still). Read more about the PLOS article level metrics here.

One of PLoS authors, Jamie Sundsbak, says:

I have written before on how impact factors of journals and their publications are being rethought. I believe that by providing the data on how scientific publications are disseminated into the world, we will truly be able to judge an article on its individual scientific worth, not just on the authors’ reputatons or where it is published.

And this from Karen Grepin:

As academic research is increasingly disseminated through new media channels, I think this is a very important improvement in measuring the impact of work. Old metrics, such as just the number of citations, may miss the importance of many academic publications. Here’s to hoping that more journals begin to report such data.

Duncan Hull took a look at the some of the articles and said:

So all the usual caveats apply when using this bibliometric data. It is more revealing than the useful (but simplistic) “highly accesssed” papers at BioMedCentral, which gives little or no indication what “highly” actually means without the raw data to back it up. It will be interesting to see if other publishers now follow the lead of PLoS and also publish their usage data. For authors publishing with PLoS, this data has an added personal dimension too, it is interesting to see how many views your paper has.
As paying customers of commercial publishers, should scientists and their funders be demanding more of this kind of information in the future? I reckon they should.

And Andrew Farke wrote a longer post:

So what’s to like here? Well, an author gets an immediate sense if someone is paying attention to a publication. Page views and PDF downloads are a valuable tool for gauging community interest. In concert with citation data, it’s probably a far better gauge of a paper’s worth than the impact fact[or] that the publication happens to show up in. The data are also freely available, transparent, and frequently updated. The latter is particularly important because it may be years before a paper’s full impact is known. An open-access metric for an open-access world.
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I suspect that other journals will follow suit – it may not happen tomorrow, but it will happen. We may be seeing the death of the traditional, sometimes tyrannical, “impact factor.” Let’s hope we don’t replace it with a new despot!

And on the Small Gray Matters blog:

You can now see the number of citations, blog mentions, article views and PDF downloads for every PLoS article, so if you’ve published in one of the PLoS journals, you’re free to go find out just how many times your article’s been viewed compared to everyone else’s. And then you of course you’re free to make up all sorts of convenient excuses for the fact that your stats suck and your paper’s only been viewed seventeen times in the last three years.
What’s even cooler is the PLoS editors have collated all of that information and released it as one monstrous Excel spreadsheet. So you can now run off and do a quick regression analysis to determine whether or not having longer paper titles leads to more citations, if you’re so inclined.

Other mentions:
NeuroTechnica
Library Stuff
Greg Laden
UBC Library eResources: Service Bulletins
Pimm – Partial immortalization
The Tree of Life
LiLoLe
And check out A.J.Cann on his blog and on YouTube

The Public Library of Science (PLoS), announced the release of an expanded set of article-level metrics on its scientific and medical journal articles (some 14,000 articles across 7 journals). The article-level metrics program was launched in March 2009, and with this addition of online usage data, PLoS is providing an unprecedented set of information on every published article. Such information will be of value to researchers, readers, funders, administrators and anyone interested in the evaluation of scientific research. The PLoS article metrics include the new online usage data (HTML page views, PDF downloads and XML downloads), as well as citation counts, comments, ratings, social bookmarks and blog coverage. Usage data will be updated daily and currently include more than four years of statistics from all seven peer-reviewed PLoS journals. With this growing and detailed set of metrics on every article, PLoS aims to demonstrate that individual articles can be judged on their own merits rather than on the basis of the journal in which they are published. Because very few data have previously been made public by scholarly publishers, visitors to the journal sites will need help to understand these data. For example, it is clear from the PLoS data that online usage is dependent on the age of the article, as well its subject area. In order to place the new usage data in context, PLoS is therefore providing summary tables to allow users to see how an article compares with various average measures. For anyone wishing to examine the data in detail the complete raw data set is also available as a download. PLoS is still in the early stages of the article-level metrics program, but this is the first attempt by a major publisher to place such a broad range of data on each article. PLoS therefore hopes that the provision of these data will encourage other publishers to make such data available, which will lead ultimately to broader improvements in scholarly communication and research assessment.

drdrA over on Blue Lab Coats has this to say:

One of these tabs is the ‘metrics’ tab. If you click on it it takes you to a page that shows the metrics – things like article views, and downloads, for that particular article. Here is an example from that article that I posted on the other day. That article was just published, but you can also see metrics on older articles that were collected prior to the appearance of this feature-… like for this article for example. I love this feature because it reflects reality to the level of readership of a given article better and more immediately than the traditional pre-electronic media age measures such as citation rate or total citation number could. And, I’ve gotten quite used to looking at readership data in terms of hits and page views- running this blog and whatnot… so I’ve kind of got a feeling for this kind of data anyway.
And see that ‘Related Content’ tab up at the top there too. From that page you are set up to quickly search for related articles, bookmark things in CiteULike (which I need to become more savvy with), AND LOOK FOR RELATED BLOG POSTS!!! How awesome is that!!?? Now you are immediately connected to related scientific literature, and to the immediate response to a given article in the blogosphere, with all the commentary that brings with it.

Cameron Neylon (guest post on the PLoS blog):

Actual public interest in your paper? Real educational value being gained from it? These are things that you want to know about. It would be even better if we could separate these out, and I find the prospects of using download versus citation metrics in the future quite exciting. But in the meantime, it gives us a new measure that we can compare with what we already have available.
And, at the end of the day, that is how I think we should see these new metrics–it is more information. It isn’t yet clear how best to use these measures, but it is up to us as scientists, who, after all, make our living out of measurement and analysis, to figure out how best to use them. The approach PLoS is taking of simply presenting the data, and as much of it as is possible, is to me exactly the right approach. It is not the responsibility of journals to tell us how to measure and report things–it is up to us.
In the end, there is only one way of determining whether a particular paper is important and relevant to you personally, and that is to read it, digest the information, critically analyze it, and come to your own conclusions. You can’t avoid this and you shouldn’t. Where download and other article-level metrics can help is in making that decision about how much time you want to invest in a given paper. We need better ways of making that decision, and more data can only help.

Interview with Dr.Derya Unutmaz, Section Editor for Immunology at PLoS ONE…

….is now posted on everyONE blog.

PLoS Medicine’s 5th anniversary competition

On Speaking of Medicine:

PLoS Medicine turns 5 years old on October 19th, 2009. To highlight the crucial importance of open access in medical publishing we’re holding a competition to find the best medical paper published under an open-access license anywhere (not just in PLoS) since our launch.
Vote for your choice from the 6 competing papers, detailed below — nominated and then shortlisted by our editorial board. Winners will be announced during Open-Access week (19-23rd October 2009). If you’re interested in how we came up with this shortlist of top-quality open-access medicine papers, please read on below the poll.

Go vote!

Now THIS is Open Science!!!

OpenDinosaurProject logo.jpgDinosaur fossils have been dug out for a couple of centuries now. They have been cleaned up and mounted in museums and described in papers and monographs. The way this is all done has evolved over time – the early techniques were pretty crude compared to what palaeontologists do today. One of the important techniques is actually quite simple: making measurements of bones. And yes, many such bones have been measured and the measurements reported in the literature. And that literature is scattered all over the place in many different formats in many different journals. Nobody has put all the measurements in one place where one could do statistics with the numbers and perhaps learn something from the exercise.
Now Andy Farke, Matt Wedel and Mike Taylor want to do just that:

We want to put together a paper on the multiple independent transitions from bipedality to quadrupedality in ornithischians, and we want to involve everyone who’s interested in helping out. We’ll get to the details later, but the basic idea is to amass a huge database of measurements of the limb bones of ornithischian dinosaurs, to which we can apply various statistical techniques. Hopefully we’ll figure out how these transitions happened — for example, whether ceratopsians, thyreophorans and ornithopods all made it in the same way or differently.

So, in order to accomplish this enormous project, they founded the Open Dinosaur Project – you can be a co-author of the resulting paper if you contribute! What is the idea? To crowdsource the effort. Published measurements need to be all copied into a single place for analysis. Bones not yet measured as well – if you are at a museum or university or in some other ways have access to the fossils, you can take your measuring tools and go down to the vaults and send in the numbers. They explain:

Constructing the Database
A huge, virtually untapped resource of skeletal measurements resides in the published scientific literature. In order to put these measurements to good use, it is necessary to place the data into a form that can be analyzed mathematically. Essentially, we aim to construct a giant spreadsheet with as many measurements for ornithischian dinosaur limb bones as possible. For simplicity, we will focus on bone lengths and maximum diameters along the shaft. From the forelimb, we will look at the scapula, coracoid, sternal plates, humerus, radius, ulna, and manus (“hand”). Within the hind limb, we will look at the femur, tibia, fibula, and pes (“foot”).
In the old days, this would require a lot of time in the library stacks. Some aspects of the project may still require this. But, a number of scientific papers are now freely available to the general public! So, anyone with an internet connection can help out.
Who Can Participate?
Anyone! We do not care about your age, education, previous paleontological experience, or geographic location. You don’t have to be a professional paleontologist – just a person who is willing to act professionally in the accurate and ethical collection, analysis, and interpretation of real scientific data.
What Can I Do?
It’s simple! Just locate the necessary scientific papers, and start entering data into our spreadsheet. If you have access to real specimens, you may enter these data.
What Do I Get Out of This?
Two things – 1) the thrill of participating in real scientific research; and 2) an opportunity for authorship on a scientific paper. Yes, you read that correctly. All contributors to the database are given the option of joining us as authors for the final published paper. If you opt out of authorship, you will still be listed in the acknowledgments (unless you request otherwise).
How Do I Sign Up?
Simply drop an email to project head Andy Farke – andrew.farke@gmail.com – with your name and preferred email address. If you have an institutional affiliation, please include that also. . .but remember that a formal academic affiliation is not required! In all aspects of the project, we ask that you use your real name rather than an on-line handle or other pseudonym. This is important both for personal accountability, as well as a professional standard. We may not all be professionals, but we will certainly conduct ourselves professionally!
Help! I’m Lost!
Never fear. . .we’re going to publish a series of tutorials in the next few days outlining how to search for scientific literature, what measurements to look for, and other important introductory pieces for those new at the research game.

So if you can, participate. And if the analysis uncovers a new species – there’s a little paper right there as well. And if the project works well for ornithischians, then future projects may turn to theropods or whatever else strikes the paaleontologists’ fancy.
Also nice – the resulting paper(s) will be published in Open Access venues. I am salivating at the prospect of seeing these things published in PLoS ONE and joining the fast-growing Paleontology Collection….

PLoS & Mendeley live on the Web! Science Hour with Leo Laporte & Dr. Kiki (video)

Leo Laporte and Kirsten Sanford (aka Dr.Kiki) interviewed (on Twit.tv) Jason Hoyt from Mendeley and Peter Binfield from PLoS ONE about Open Access, Science 2.0 and new ways of doing and publishing science on the Web. Well worth your time watching!

Introducing PLoS Currents: Influenza

Yesterday PLoS and Google unveiled PLoS Currents: Influenza, a Google Knol hosted collection of rapid communications about the swine flu.
In his blog post A new website for the rapid sharing of influenza research (also posted on the official Google blog), Dr.Harold Varmus explains:

The key goal of PLoS Currents is to accelerate scientific discovery by allowing researchers to share their latest findings and ideas immediately with the world’s scientific and medical communities. Google Knol’s features for community interaction, comment and discussion will enable commentary and conversations to develop around these findings. Given that the contributions to PLoS Currents are not peer-reviewed in detail, however, the results and conclusions must be regarded as preliminary. In time, it is therefore likely that PLoS Currents contributors will submit their work for publication in a formal journal, and the PLoS Journals will welcome these submissions.

The response from the community has been overwhelmingly positive so far. For example, Frederic Lardinois writes, on ReadWriteWeb – Finally a Good Use for Google Knol: Sharing Information About Flu Research:

Overall, we think this is a great project. Knol is a good, easy-to-use platform for these kinds of publications, and given that the articles are also archived on other servers, this project also doesn’t rely on Google to keep Knol’s servers running indefinitely.
PLoS, being a non-profit, is also the right organization to give this project a try. Commercial publishers are still wary of the Internet, and while the open access movement has been gathering some support over the last few years, a lot of research in most scientific fields will still be hidden behind paywalls for a long time.

On Tech Babble: PLOS Currents : Influenza:

PLOS Currents : Influenza is built utilizing Google Knol and a new service from the National Center for Biotechnology Information (NCBI) called Rapid Research Notes. This service allows the user an easy way to follow current research and search for relevant scientific information.
As we approach influenza season, expect greater levels of concern and interest in H1N1.

Steven Salzberg, one of the moderators of PLoS Currents: Influenza, wrote on his blog – Opening up influenza research with a new kind of journal:

What’s the difference between this and a regular journal? Well, first of all, submissions won’t be thoroughly reviewed, which means they don’t “count” as journal papers, but it also means you can publish them later in a peer-reviewed journal. The Public Library of Science has already bought into this model – they’re sponsoring PLoS Currents, after all – and we expect other journals to do so also. So why publish, you might ask? That’s easy: in a highly competitive field such as influenza research, different scientists are often racing to answer the same question. By publishing super-rapidly in PLoS Currents, you will get a citable, time-stamped reference that establishes your discovery, and most importantly, establishes when you made it.
The big win here, we hope, is that scientists will be empowered to announce their results to the world without worrying about being “scooped” – a common fear that leads to many results being kept secret for months while papers are prepared and revised. This in turn will speed up scientific progress overall, which is the real goal behind PLoS Currents.

Eddie Holmes, Chief Moderator of PLoS Currents: Influenza, wrote in a guest-post on the PLoS Blog – Welcome to PLoS Currents: Influenza:

The central idea of PLoS Currents: Influenza is to rapidly disseminate data and ideas in the realm of influenza research, stimulated by the ongoing epidemic of swine-origin influenza virus (H1N1pdm). Given this backdrop, it is no surprise that some of first contributions consider important aspects of the H1N1pdm epidemic.
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Although PLoS Currents: Influenza was inspired by H1N1pdm, it will cover all types of research on all types of influenza virus. Indeed, the emergence of H1N1pdm brings into focus the need for basic research into many fundamental aspects of influenza biology.
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These initial contributions have given PLoS Currents: Influenza an excellent start. The next few months should prove to be very exciting. I therefore encourage all of you working in the area of influenza to send a contribution to PLoS Currents: Influenza, however preliminary, so that your data and ideas are rapidly distributed to a wide audience.

Iddo Friedberg, on ByteSizeBio: PLoS Currents: Influenza. Because knowledge should travel faster than epidemics:

So here we have all chief elements of scientific communication: credibility (by the moderators), timeliness (immediate online publishing) and attribution (by public archiving). PC:I is heavily skewed towards timeliness. The rationale being that in Influenza research and monitoring, time is of essence. After all, a report going through the usual peer review mill can take months: which is exactly the time required for a full-blown pandemic.
Not that other scientific fields are not in need of timeliness. Physicists and mathematicians have known that for almost two decades now. Nature Precedings are also providing an outlet for rapid communication in life sciences. But the combination of speed, accessibility and credibility offered by PC:I is indeed something new and welcome.

Vincent Racaniello on Watching The Watchers: Rapid Sharing of Influenza Research:

Contributions that will be welcome at PLoS Currents: Influenza include research into influenza virology, genetics, immunity, structural biology, genomics, epidemiology, modeling, evolution, policy and control. The manuscripts will not be subject to peer-review, but unsuitable submissions will be screened out by a board of expert moderators. This policy will enable rapid publication of research.
The path to publishing original scientific research is often long and tortuous. A manuscript describing the findings is prepared and submitted to a scientific journal (such as Nature, Cell, Journal of Virology). The manuscript is assigned to two or three expert reviewers, generally scientists involved in the same area of research. If their reviews are favorable, the paper is published. Usually additional experiments are called for, which may require additional time to complete. Many months to a year may pass before the paper is published, although some manuscripts (e.g. those on 2009 pandemic influenza) may be expedited. The point is that PLoS Currents: Influenza will allow everyone – including non-scientists – to read about research soon after the authors have prepared the paper.
PLoS Currents: Influenza is a terrific idea, and I welcome this venture with great enthusiasm. I hope that PLoS Currents will grow to include other areas of science.

David Bruggeman on Pasco Phronesis blog – PLoS Currents – An ArXiv for the Rest of Us?:

Presently in beta, Currents is accepting “new scientific data, analyses, and ideas” and encouraging the discussion and analysis of this information. The material is not peer reviewed as it would be for a regular PLoS publication, but is screened by moderators who are experts in the field at issue. The idea is that the work posted and discussed in Currents would lead to papers in peer reviewed journals at a later date.
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So policy research could find its way into a science journal – excellent.
While the material is hosted by Google, as the PLoS explains on its blog, it is also archived at the National Center for Biotechnology Information. Hopefully the Currents topics will not be simply reactive, but consider a number of different topics that aren’t breathing down our collective neck.
As the ScienceInsider article suggests, this is not the first time a preprint collection has been suggested for biomedical topics. Apparently when PLoS co-founder (and current PCAST co-chair) Harold Varmus tried this when he was leading the National Institutes of Health, some scientific societies raised a ruckus and the effort was discontinued. Hopefully history won’t repeat itself.

Glyn Moody, on his blog ‘Open….’, writes – PLoS Reinvents Publishing and Saves the World:

As someone who has been writing about open access for some years, I find myself returning again and again to the Public Library of Science. That’s because, not content with pioneering open access, PLoS has time and again re-invented the broader world of scientific publishing. Now, it’s done it again.
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The current system of publishing papers is simply too slow to deal with pandemics, where speed is of the essence if we’re to have a chance of nipping them in the bud. It’s good to see PLoS stepping in to help address this major problem.
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This is really exciting from many viewpoints. It’s pushing the ideas behind open access even further; it’s reshaping publishing; and it may even save humanity.

So, what do you think?

The Future of Online (Academic) Publishing

Talk given by Peter Binfield at the ISMTE meeting (slides and audio):

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:
null
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.
———-snip———-
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.

Praxis

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.
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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.
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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.

Science Online London 2009 – now in Second Life

Science Online London is next week. I really wanted to go this year, but hard choices had to be made….eh, well.
For those of you who, like me, cannot be there in person, there are plenty of ways to follow the meeting virtually. Follow @soloconf and the #solo09 hashtag on Twitter. Join the FriendFeed room. Check out the Facebook page. And of course there will be a lot of blogging, including in the Forums at Nature Network.
And for those of you who have computers with enough power and good graphics cards, another option is to follow the conference in Second Life – check that link to see how.

Making the Web Work for Science (video)

Making the Web Work for Science – Full from Jordan Mendelson on Vimeo.

From left to right: Tim O’Reilly, Jimmy Wales, Stephen Friend and John Wilbanks – via Jonathan (there is also a shorter summary version here)

Open Access, Achievements and Looking Forward (video)

Ginny Barbour, Part 5: Open Access, Achievements and Looking Forward from PLoS on Vimeo.

PLoS Medicine’s Fifth Anniversary and Future Plans (video)

Ginny Barbour, Part 4: PLoS Medicine’s Fifth Anniversary and Future Plans from PLoS on Vimeo.

Open Access to Health Information (video)

Ginny Barbour, Part 3: PLoS Medicine Open Access to Health Information from PLoS on Vimeo.

Future of science publishing interview

A few weeks ago in Lindau, Lars Fischer (remember his guest post here?) sat me down with the digital audio recorder and conducted an interview – we talked for about an hour about Open Access, future of scientific publishing/papers/communication, etc.
The article based on that interview is now online – you can read it here, but only if you can read German. Then you can tell me what is it that I actually said ;-)
Update: the translation is now here.
Update 2: The entire transcript is now available online/

Cameron Neylon on Article Level Metrics

On Vimeo:

Article-level Metrics from PLoS on Vimeo.

Praxis

Open Access and the divide between ‘mainstream’ and ‘peripheral’ science (also available here and here) by Jean-Claude Guédon is a Must Read of the day. Anyone have his contact info so I can see if he would come to ScienceOnline’10?
There is a whole bunch of articles about science publication metrics in the latest ESEP THEME SECTION – The use and misuse of bibliometric indices in evaluating scholarly performance. Well worth studying. On article-level metrics, there are some interesting reactions in the blogosphere, by Deepak Singh, Bjoern Brembs, Duncan Hull, Bill Hooker and Abhishek Tiwari. Check them out. Of course, all of those guys are also on FriendFeed where more discussion occured.
Can someone use FOIA to sneak a peak into your grant proposal and check-out your preliminary data? See the discussion on DrugMunkey blog, on Dr.Isis’ blog and on Heather Etchevers’ blog. My beef: don’t use the term “Open Access” for this as it is not related. This is not even Open Notebok Science – which, and I am on record in several places about this – MUST be voluntary and does not fit everyone.

Gavin Yamey, the Senior Magazine Editor of PLoS Medicine, is currently on sabbatical from the journal after being awarded a “mini-fellowship” from the Kaiser Family Foundation to undertake a project as a reporter in East Africa and Sudan.

His first two posts about this: Reporting from East Africa and Sudan and Far from the reach of global health programs.
The “article of the future” by Cell/Elsevier, analyzed by DrugMonkey, Kent Anderson, Marshall Kirkpatrick and Martin Fenner.

Measuring scientific impact where it matters

Everyone and their grandmother knows that Impact Factor is a crude, unreliable and just wrong metric to use in evaluating individuals for career-making (or career-breaking) purposes. Yet, so many institutions (or rather, their bureaucrats – scientists would abandon it if their bosses would) cling to IF anyway. Probably because nobody has pushed for a good alternative yet. In the world of science publishing, when something needs to be done, usually people look at us (that is: PLoS) to make the first move. The beauty of being a path-blazer!
So, in today’s post ‘PLoS Journals – measuring impact where it matters’ on the PLoS Blog and everyONE blog, PLoS Director of Publishing Mark Patterson explains how we are moving away from the IF world (basically by ignoring it despite our journals’ potential for marketing via their high IFs, until the others catch up with us and start ignoring it as well) and focusing our energies in providing as many as possible article-level metrics instead. Mark wrote:

Article-level metrics and indicators will become powerful additions to the tools for the assessment and filtering of research outputs, and we look forward to working with the research community, publishers, funders and institutions to develop and hone these ideas. As for the impact factor, the 2008 numbers were released last month. But rather than updating the PLoS Journal sites with the new numbers, we’ve decided to stop promoting journal impact factors on our sites all together. It’s time to move on, and focus efforts on more sophisticated, flexible and meaningful measures.

In a series of recent posts, Peter Binfield, managing editor of PLoS ONE, explained the details of article-level metrics that are now employed and displayed on all seven PLoS journals. These are going to be added to and upgraded regularly, whenever we and the community feel there is a need to include another metric.
What we will not do is try to reduce these metrics to a single number ourselves. We want to make all the raw data available to the public to use as they see fit and we will all watch as the new standards emerge. We feel that different kinds of metrics are important to different people in different situations, and that these criteria will also change over time.
A paper of yours may be important for you to be seen by your peers (perhaps for career-related reasons which are nothing to frown about) in which case the citation numbers and download statistics may be much more important than the bookmarking statistics or the media/blog coverage or the on-article user activity (e.g., ratings, notes and comments). At least for now – this may change in the future. But another paper you may think would be particularly important to be seen by physicians around the world (or science teachers, or political journalists, etc.), in which case media/blog coverage numbers are much more important for you than citations – you are measuring your success by how broad an audience you could reach.
This will differ from paper to paper, from person to person, from scientific field to field, from institution to institution, and from country to country. I am sure there will be people out there who will try to put those numbers into various formulae and crunch the numbers and come up with some kind of “summary value” or “article-level impact value” which may or may not become a new standard in some places – time will tell.
But making all the numbers available is what is the most important for the scientific community as a whole. And this is what we will provide. And then the others will have to start providing them as well because authors will demand to see them. Perhaps this is a historic day in the world of science publishing….

Open Access in Belgrade

As you know, I gave two lectures here in Belgrade. The first one, at the University Library on Monday, and the second one at the Oncology Institute of the School of Medicine at the University of Belgrade. As the two audiences were different (mainly librarians/infoscientists at the first, mainly professors/students of medicine at the second) I geared the two talks differently.
You can listen to the audio of the entire thing (the second talk) here, see some pictures (from both talks) here and read (in Serbian) a blog post here, written by incredible Ana Ivkovic who organized my entire Belgrade “tour” this year.
The second talk was, at the last minute, moved from the amphitheater to the library, which was actually good as the online connection is, I hear, much much better in the library. Library got crowded, but in the end everyone found a chair. What I did, as I usually do, was to come in early and open up all the websites I wanted to show in reverse chronological order, each in a separate window. Thus, the site I want to show first is on top at the beginning. When I close that window, the second site is the top window, then the third, etc. Thus I do the talk by closing windows instead of opening them (and hoping and praying that would not take too much time).
Knowing how talks usually go in the States, I prepared to talk for about 50 minutes. But, when I hit the 50 minute mark, I realized that nobody was getting restless – everyone was looking intently, jotting down URLs of sites I was showing, nodding….so I continued until I hit 60 minutes as which time I decided to wrap up and end. Even then, nobody was eager to get up and leave. I was hoping I’d get a question anyway….and sure, I got 45 minutes of questions. Then another 20 minutes or so of people approaching me individually to ask questions….
I used the Directory of Open Access Journals as the backdrop to give a brief history of the Open Access movement, the difference between Free Access and Open Access and the distinction between Green OA and Gold OA.
Then I used the PLoS.org site to explain the brief history of PLoS and the differences between our seven journals. Of course, this being medical school, I gave some special consideration to PLoS Medicine.
Then I used the Ida – Darwinius massillae paper to explain the concept of PLoS ONE, how our peer-review is done and to show/demonstrate the functionalities on our papers, e.g., ratings, notes, comments, article-level metrics and trackbacks.
Then I used the Waltzing Matilda paper to enumerate some additional reasons why Open Access is a Good.Thing.
Trackbacks were also a good segue into the seriousness by which the scientific and medical community is treating blogs these days. I showed Speaking of Medicine and EveryONE blog as examples of blogs we use for outreach and information to our community.
I showed and explained ResearchBlogging.org (which they seemed to particularly be taken with and jotted down the URL), showed and explained the visibility and respect of such blogging networks as Scienceblogs.com and Nature Network and then Connotea as an example of various experiments in Science 2.0 that Nature is conducting.
I put in a plug for ScienceOnline conferences and the Open Laboratory anthologies as yet another proof how seriously Science 2.0 and science blogging is now being taken in the West. Then showed 515 scientists on Twitter, The Life Scientists group and Medicine 2.0 Microcarnival on FriedFeed as examples of the ways scientists are now using microblogging platforms for communication and collaboration. I pointed out how Pawel Szczesny, through blogging and FriendFeed, got collaborations, publications, and in the end, his current job.
Then I described Jean-Claude Bradley’s concept (and practice) of Open Notebook Science and showed OpenWetWare as a platform for such work. I pointed out that Wikipedia and wiki-like projects are now edited by scientists, showing the examples of A Gene Wiki for Community Annotation of Gene Function, BioGPS and ChemSpider and ended by pointing out a couple of examples of the ways the Web allows citizen scientists to participate in massive collaborative research projects
But probably the most important part of the talk was my discussion of the drawbacks of Impact Factor and the current efforts to develop Article-level metrics to replace it – something that will be particularly difficult to change in developing countries yet is essential especially for them to be cognizant of and to move as fast as they can so as not to be left behind as the new scientific ecosystem evolves.

Waltzing Matilda – why were the three Australian dinosaurs published in PLoS ONE?

As I was traveling, I only briefly mentioned the brand new and exciting paleontology paper in PLoS ONE – New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton, Queensland, Australia that was published on Thursday. Bex has written an introduction and will post a Media/Blog coverage (of which there was a lot!) summary probably tomorrow.
The fossils were discovered, cleaned and analyzed by the Australian Age Of Dinosaurs non-profit organization, with a help of thousands of volunteers – the ‘citizen scientists’. You can learn more from their press release.
The importance of the publication of this paper from the angle of its scientific significance has been covered by several bloggers already. Also, several notice how good it is that the paper was published in an Open Access online-only journal. For example, Andy Farke writes:

This paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a “waste” of precious space – but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages – and this doesn’t include the supplementary information!

The lead author Scott Hocknull, in an interview for us, said:

“One of my major motivations for submitting to PLoS ONE was the fact that my research will reach a much wider community, including the hundreds of volunteers and public who gave their time and money to the development of natural history collections. They are the backbone of our work (excuse the pun) and they usually never get to see their final product because they rarely subscribe to scientific journals.”

In the comment on the post at Sauropod Vertebra Picture of the Week, Scott Hocknull said:

This project is almost a 100% volunteer effort, with thousands of volunteer preppers working endlessly to get the bones ready for publication. This was one of my main reasons for choosing PLoS ONE to publish in. One of my others was the opportunity to provide detail images and descriptions (as best I can).
Most of our volunteers have no access to scientific journal subscriptions, therefore having it online and free for them to look at meant that they could see for themselves the fruits of their labours. They need more credit for the beautiful bones than I.

And all of you can read it for free as well – all 51 pages of it, plus all the great images and supplemental information. And you can add ratings, notes, comments and trackbacks on the paper as well.

On my last scientific paper, I was both a stunt-man and the make-up artist.

From the ArchivesThis is a repost of an November 6, 2007 post (as always, click on the icon to see the original and its comments):

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Why does Impact Factor persist most strongly in smaller countries

From the ArchivesA repost of a November 28, 2008 post:

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The Scientific Paper: past, present and probable future

From the ArchivesA post from December 5, 2007:

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Journal Clubs on PLoS ONE articles

What does it mean – a Journal Club? Read here and, if you want to do one, contact me.

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?

Open Access panel at Lindau

When I go to the Lindau Nobel meeting in Germany in a few weeks, I will not only report from there as a blogger. I was also asked to participate on a panel about Open Access publishing:

“Beatrice Lugger, German science journalist (and founder of Scienceblogs Germany), will moderate this panel. The panelists are: Nobel Laureates Aaron Ciechanover and Sir Harold Kroto, Bora Zivkovic of PLoS, and Dr Jason Wilde, publisher for the physical sciences at Nature Publishing Group.”

Science & Technology Parks – what next?

As you may have noticed if you saw this or you follow me on Twitter/FriendFeed/Facebook, I spent half of Tuesday and all of Wednesday at the XXVI International Association of Science Parks World Conference on Science & Technology Parks in Raleigh. The meeting was actually longer (starting on Sunday and ending today), but I was part of a team and we divided up our online coverage the best we could do.
IASP2009 001.jpgChristopher Perrien assembled a team (including his son) to present (and represent) Science In The Triangle, the new local initiative. They manned a booth at which they not only showcased the website, but also had a big screen with TweetDeck showing the livetweeting of the conference by a few of us (e.g., @maninranks, @mistersugar, @IASP2009 and myself), gave out flyers explaining step-by-step how to start using Twitter, and gave hands-on instruction helping people get on Twitter and see what it can do for them.
You can look at the coverage by seaching Twitter for IASP or #IASP or #IASP2009 (in some of my first tweets I misspelled it as IESP). You can search FriendFeed for all the same keywords as well, as most of the tweets got imported there.
IASP2009 002.jpgScience In The Triangle is an online portal for news (and stories about news) about scientific research happening in the Triangle region of North Carolina. This is a way to keep the researchers in the Triangle informed about each other’s work and local science-related events, as well as a way to highlight the local research efforts for the outside audience. It is in its early stages but we’ll work on developing it more. It will be interesting to compare it to other similar portals, like NSF Science Nation and The X-Change Files (neither one of which is regional in character).
Apart from that, what was I doing at this kind of conference? Frankly, I never really thought about science/technology parks much until now. I have spent the last 18 or so years inside the sphere of influence of the Research Triangle Park and was blissfully unaware of the existence of any others. I did not know that there were dozens, perhaps hundreds of such parks around the world (including – and I should have known about it – the Technology Park Ljubljana in Slovenia). I did not know they had an official international association. I did not know that there are specified criteria as to what makes a park a park. Or that, for instance, the NCSU Centennial Campus is considered a science/technology park and is itself a member of the Association, outside of its proximity to RTP. Just learning these things was enlightening in itself, besides the actual susbtance of the talks.
IASP2009 003.jpgThis was also an interesting cultural experience for me. For the past several years, my conference experiences were mainly unconferences or very laid back and friendly science conferences. This was not it. This was a formal, old-style business conference with about a thousands businessmen (and very few women) wearing business suits. Even I felt compelled to wear a coat and tie and uncomfortable shoes to fit in. I also forgot that the program itself was bound to be much more formal. A session called a “panel” does not mean that 3-4 people on the stage will vigorously discuss a topic between themselves and with the vocal audience, but that 3-4 people will give PowerPoint presentations in rapid succession.
But I am not complaining – I know that the business world is even slower to evolve than the science world and that the tech world is light years ahead – as some of those talks were quite interesting and enlightening (see all the Tweets from the various sessions), and some of the people I met (and I knew almost nobody there in the beginning) were interesting as well. For example, Will Hearn prospects the sites for potential corporate (or industrial park) development around the world, from Peru to Macedonia. He runs Site Dynamics and has developed software – SiteXcellerator – that provides important information about the population, education and economics of any place on earth the company may be interested in moving into.
So, what is a science/technology/industrial park? It is a place. Seriously, and importantly, it is a place, in a geographical sense. It is a piece of land which houses a collection of science, technology, business and industrial companies and organizations, all placed together because they can potentially collaborate.
IASP2009 004.jpgThe location of the Park is chosen for being conducive to business (nice tax breaks by the state, for instance) and for containing well-educated and skilled workforce in abundance (thus usually close to a big university). In some cases, the companies go where the skilled potential employees already are. In other cases, the Park members build educational institutions needed to produce skilled workforce out of the local population (so, for example, if biotech moves into a place abandoned by the textile industry, a college needs to be built to re-train the local workers for the new and more high-tech jobs). Some parks are focused on a single industry (e.g., pharmaceutical, or even defense in some places) or even a single product (e.g., solar panels), while other parks are drawing together a variety of different fields.
More than 20 Parks received silver medals last night for existing 25 or more years. So this is not a new fad in any way. Research Triangle Park got a gold medal as it celebrated 50 years of existence this year. It is the largest and the oldest of the science/technology parks in the world, at least among the members of the Association.
But I had a nagging thought in the back of my head. Is RTP really the oldest?
IASP2009 005.jpgSo last night when I got home I went online and started searching for “science cities” or Naukograds of the old Soviet Union. The most famous is Akademgorodok which is possibly a couple of years older than RTP as the Wikipedia page states “in the 1950s” (RTP was founded in 1959) and this NYTimes article from 1996 says “four decades ago” which places its foundation at around 1956.
By the way, that NYTimes article (I actually remember reading it at the time – the heady old days of reading newspapers on paper!) is quite interesting. But take it with a big grain of salt – remember the source and the time: the New York Times in the 1990s was essentially Clinton’s Pravda, especially in the area of foreign politics, so any article about a foreign country is automatically suspicious. I’d love to see a blog post on the topic by a respected Russian blogger, either as an antidote or as a confirmation of that NYTimes article.
I would love to see someone cover the history and evolution of Naukograds, their strengths and weeknesses, ups and downs, during the Soviet era, during Perestroika, and in modern Russia, as well as the science cities that are now located in other countries that gained independence from USSR during the 1990s. That would be quite a teaching moment for everyone involved, I’m sure. If I am reading it correctly, these science cities conform to the criteria of being science/technology parks as the Association of Science Parks defines them. I wonder if any one of them actually became members of the Association since then?
IASP2009 006.jpgBack to the RTP now. Plenary talk by the Duke University President Richard Brodhead confirmed some of the history and some thoughts I had about the importance of RTP in North Carolina history (I missed the talk by Andrew Witty, but Anton blogged it and it appears to have been along similar lines).
UNC-Chapel Hill is the oldest state university in the country. NCSU and Duke are also very old. There are a couple of dozen smaller universities and colleges (and a couple of amazing high schools for kids with math and science talent) in the Triangle. And other science-related organizations. Then, there are many more schools around the state. From what I gather, each one of those schools was on its own, pretty isolated from each other. Researchers at one school were not aware of the researchers at another.
Then, some enlightened people in the state decided that with all those schools churning out all those educated graduates, the jobs for those graduates should also be in North Carolina. Why teach them here, just to see them leave for the greener pastures? And thus the RTP was born.
IASP2009 007.jpgIt took a while for the park to grow, but it attracted or spawned some powerful and creative organizations, from RTI and Glaxo and NIEHS, through IBM and SAS, to Sigma Xi and NESCENT and Lulu.com. Instead of educated people leaving the state in search of jobs, the companies started bringing jobs to where the educated people are – and there was one place to move to: the Research Triangle Park or as close to it as possible.
But that was not the end of the story. All those companies and organizations started collaborating with (or hiring) the researchers from local universities and….this brought people from different Universities together! People from NCSU and Duke and UNC and other schools got introduced to each other this way and started collaborative research with each other. Soon formal and informal collaborations between schools and departments were put in place. As a result, science in the state boomed. Instead of isolated nodes, there was now a network.
And I still think this network is pretty unique in the USA. In other places known for top-level science all of it is concentrated in one big city (e.g., New York City, Boston, Atlanta, or San Francisco) while the countryside of the state has nothing of the sort. And if one adds the historical rivalries between those old Universities in these cities, there is not much network effect there. Much more competitive than collaborative. But in North Carolina there are long-term ongoing collaborations between researchers, departments and schools all across the state, from Wilmington and Greenville, to Triangle, Winston-Salem and Greensboro, to Charlotte, Davidson, Cullowhee, Boone and Asheville (which is why I argued that the Nature Network Triangle Group should be renamed North Carolina Group which you should join if you are in NC and interested in science). Just look at how geographically dispersed the NC science bloggers are, if that is any indication.
IASP2009 008.jpgThus RTP, besides bringing together researchers and industry (which some of us purist scientists may not like that much) also inadvertently spurred on the advancement of pure, basic research. RTP provided the central place that connected all the schools and then people in those schools could make their own connections and do whatever kind of research they liked, even the most basic kind that does not have an obvious and immediate application (of course, long-term, all that basic knowledge ends up being applied to something, it is just impossible to predict at the time what the application could be).
There are other effects of this rise in science and technology in the state. Instead of graduates leaving the state, people from other places started coming in (look at licence plates on cars on I-40, or parked on campuses – you can see everything from Ohio and Michigan and Georgia to New York and California and Alaska), further increasing the concentration of highly educated people. The knowledge and education and expertise are regarded quite highly. Thus, the reality-based party has been in charge of state politics for a long time and last year even the national offices were deemed important enough for locals to vote out the anti-science party.
But that was last 50 years. That is 20th century world. How about today and tomorrow, now that everything about the world is changing: economics, communication, environmental awareness, even the mindset of the new generations?
You know that the rapid changes in the workplace are one of my ‘hot’ topics here. How will the information revolution affect parks (and the domino effect downstream from parks – universities, jobs, infrastructure)?
This is the moment to introduce the most interesting presentation at the meeting, by Anthony Townsend. Anthony is the Research Director at The Institute for the Future, focusing on Science In Action as well as coworking. I tried to get him in touch with Brian Russell of Carrboro Creative Coworking (and if you are in the Triangle area, but Carrboro is too far for you, fill out this survey about the potential need for coworking spaces in other parts of the Triangle), but I am not sure if they found time to meet this week. For this meeting, Anthony wrote a booklet – Future Knowledge Ecosystems: The Next Twenty Years of Technology-Led Economic Development – which you can download as a PDF for free, and I think you should.
His talk was a firehose – I tried live-tweeting it, but even the speed of Twitter was not fast enough for that. I am sure happy that he mentioned PLoS (and showed the homepage of PLoS Genetics on one of his slides) as an example of the new global, instantenuous mechanism of dissemination of scientific information. But I digress…
The main take-home message I got from his talk is that the world has fundamentaly changed over the past decade or so and that science/technology parks, old or new, need to adapt to the new world or die. He provided three possible scenarios. In the first scenario, parks evolve gradually, adapting, with some delay, to fast but predictable changes. In the second scenario, the physical space of the park becomes obsolete as research and connections move online – the park dies. In the third scenario, the parks are forced to adapt quickly and non-incrementally – inventing whole new ways of doing research combining physical and virtual worlds.
A traditional Park is a place where different companies occupy different buildings. The interaction is at the company-to-company level.
A new Park may become a giant coworking space, where the interactions are at the individual-to-individual level. Anthony actually showed a slide of a Park in Finland where a building (or a large floor of a large building) was completely re-done and turned into a coworking space.
As more and more people are turning to telecommuting and coworking, the institution of a physical office is becoming obsolete. What does that mean?
Employees are happy because they can live where they like. They get to collaborate with who they find interesting and useful, not who their corporation also decided to employ. They don’t have to see their bosses or coworkers every day (or ever). Everything else can be done in cyberspace.
What does the company gain from it? Happy productive employees. No echo-chamber effect stemming from employees only talking to each other. Ability to hire employees who are the best in what they do and, knowing that, unwilling to move from the place on Earth they like to live in. Employees who are always up to the latest trends and industry gossip due to constant mingling with the others. Free PR wherever the employees are located – they all meet the locals and answer the inevitable question “What do you do?”
The phenomenon of company loyalty is quickly fading. Most people do not expect to work for a single employer all their lives. They will work several jobs at a time, changing jobs as needed, sometimes jumping from project to project. Getting together with other people in order to get a particular job done, then moving on.
This will actually weaken the corporation – making everyone but controlling CEOs and CFOs happy. Corporations will have to become fluid, somewhat ad hoc, very flexible and adaptable, as their people will be constantly circulating in and out.
In such a world, a sci/tech Park will have to be where the people want to live – a nice place, with nice climate, nice culture, good school systems, safe, etc.
In such a world, single-payer health-care system that is not disbursed via the employer will become a necessity.
Sure, there is the production part of companies that actually produce ‘stuff’ and they will also be in such Parks so their own (and other’s) blue-collar and white-collar employees can routinely interact (Anthony showed a slide of a production line literally weaving through the offices, forcing workers, bureacrats and R&D personel to get to know each other and watch each other at work, thus coming to creative solutions together).
As for science itself, a Park may be something like a Science Motel, a place where both affiliated and freelance scientists can come together, exchange ideas and information, work together, use common facilities and equipment, regardless of who their official employers are and where those are located geographically.
Sounds like something out of science fiction? That kind of future is right around the corner.
The interaction at the organization-to-organization level, the cornerstone of Parks and the local economic growth in the 20th century, has been discussed quite a lot at the meeting, as expected. Especially collaboration between Universities and industry (and sometimes government).
The park-to-park level of interaction, essential in the global economy, and the reason the Association of Science Parks exists, was discussed quite a lot, of course.
IASP2009 009.jpgBut I did not get the vibe that the level of individual-to-individual was on many people’s minds. The idea that the corporation will have to get less coherent and/or hiererchical because the new generations will insist on the individual-to-individual collaboration did not get much air play. The time when people realize that information wants to be free and that, with current technology, it can be set free, is a challenge to corporations, especially for keeping trade secrets. Perhaps there will be less trade secrets as the new mindset sets in – a network can do more and better than competing units.
This was brought splendidly to us all last night, at the end of the Gala (no, not the amazing Tri-chocolate mousse dessert!), by theCarolina Ballet dancers, each bringing his or her own individual skills and talent (and it was visible that they all differ – some are more athletic, some more elegant, the #1 ballerina is top-world-class) and working together to produce a collective piece of beauty.

Caryn Shechtman: A Blogger Success Story (an interview with Yours Truly)

You may have noticed a couple of days ago that Caryn Shechtman posted an interview with me on the New York blog on Nature Network. Then, Caryn and Erin and I thought it might be a good idea to have the entire interview reposted here, for those who missed it. So, proceed under the fold:

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Science Online London 2009

You have proven your fitness, evolutionarily speaking, not when you have babies, but when your babies have babies. So I am very excited that my babies – the three science blogging conferences here in the Triangle so far – have spawned their own offspring. Not once, but twice. The London franchise will happen again this year. And just like we changed the name from Science Blogging Conference into ScienceOnline, so did they.
scienceonlinelondon logo.gifScience Online London 2009 will take place on Saturday August 22, 2009 at the Royal Institution of Great Britain in London, co-hosted by Nature Network, Mendeley and the Royal Institution of Great Britain. The organizers are Matt Brown (Nature Network), Martin Fenner (Hannover Medical School), Richard P. Grant (F1000), Victor Henning (Mendeley), Corie Lok (Nature Network) and Jan Reichelt (Mendeley).
To help build the program, suggest speakers/sessions, to register and organize your trip, or to participate virtually, you should join the Nature Network forum and the FriendFeed room. Follow @soloconf and the #soloconf_09 hashtag on Twitter.
There will probably be a registration fee to cover the costs, likely in the range of £10, so nothing really expensive. They are also looking for sponsors. And if anyone wants to sponsor my trip, I’ll go ;-)

If research papers had a comment section….

It appears that Jorge Cham has been reading some of these posts or associated FriendFeed threads, because today’s PhDcomics strip is this one:
phdcomic comments.gif
I am wondering how many of ‘weissberg’s’ comments have been removed by the moderators over the years.
Also, if duplicate comments are posted 14 years apart, is it because MoveableType stalled that long? Do they even count as duplicates any more?
And why did the reviewer take so long to post the review? And how does one get scooped by a 14-year old paper? Just the lack of habit of reading historical literature?
Task: identify the paper this is attached to (I see Miguel Nikolelis in the References, so it will be some kind of multi-electrode brain monitoring, most likely)?

Creative reuse of OA materials

Last week also demonstrated another benefit of Open Access. Not just that everyone could re-use the images from the Ida paper without wondering “is this too much for Fair Use principles?” (yes, I have seen people re-post every single image from the paper into their articles/posts, plus lengthy excerpts of text), but people could do fun stuff to them as well, and even use it for commercial endeavors.
And I am not talking just about the Google logo last Wednesday!
First to make a creative reuse of an article image was Ed Yong in his brilliant and hilariously funny post Darwinius changes everything in which Ida appears on toast:
Darwinius-on-toast.jpg
Richard Carter was next, depicting Ida playing saxophone:
darwinius-sax.jpg
But then, there is also a way to use the hype to counteract hype…and make some money in the process. The first store I saw that is selling t-shirts and other merchandise with Ida on it was this one. You can get This Mug Which is Not Missing:
Darwinius mug.jpg
Or you can choose one of the t-shirts for which the proceeds go to a good cause, the Beagle Project, with a good message “There is no such thing as a missing link”:
Darwinius nomissinglink shirt.jpg
And you can find other t-shirt designs in this shop and this shop and this shop – perhaps walking around wearing one of these will be a conversation starter, or will get a kid to want to become a palaeontologist when s/he grows up, who knows.
Now, if I were a palaeontologist and got my hands on such a spectacular, one-in-a-lifetime fossil, I’d milk it for all it’s worth, too. I’d certainly not put all of the analysis in one paper – then what, retire? I’d also publish the description first, with a lot of fanfare if I could get it. Then I would spread all sorts of other analyses over several more papers – as it appears they are planning to do – including the cladistic analysis for those who think science without numbers is not scientific enough (forgetting the GIGO law and that every single thing input into the cladistic analysis programs is an assumption – I was astonished when I took a dinosaur class with Dale Russell some 10 years ago how the palaeontologists’ assumptions about traits – which are hard to evolve, thus likely to show up only once, and which are easy to evolve, thus could re-appear in independent lineages over and over again – differed dramatically from my thinking of developmental switches; who knows who was right about any trait – we both had our assumptions).
Now, I really hope they choose Open Access venues (perhaps PLoS ONE again) for the subsequent papers so the entrepreneurs in the future can print t-shirts with cladograms – imagine the street-fights inevitably breaking out between t-shirt wearing palaeontologists arguing the correctness of the depicted tree! Can’t do that if the journal holds the copyright to the images!

Article-Level Metrics (at PLoS and beyond)

Pete Binfield, the Managing Editor of PLoS ONE, presented a webinar about article-level metrics to NISO – see also the blog post about it:

Commenting on scientific papers

There have been quite a few posts over the last few days about commenting, in particular about posting comments, notes and ratings on scientific papers. But this also related to commenting on blogs and social networks, commenting on newspaper online articles, the question of moderation vs. non-moderation, and the question of anonymity vs. pseudonymity vs. RL identity.
You may want to re-visit this old thread first, for introduction on commenting on blogs.
How a 1995 court case kept the newspaper industry from competing online by Robert Niles goes back into history to explain why the comments on the newspaper sites tend to be so rowdy, rude and, frankly, idiotic. And why that is bad for the newspapers.
In Why comments suck (& ideas on un-sucking them), Dan Conover has some suggestions how to fix that problem.
Mr. Gunn, in Online Engagement of Scientists with the literature: anonymity vs. ResearcherID tries to systematize the issues in the discussion about commenting on scientific papers which has the opposite problem from newspapers: relatively few people post comments.
Christina Pikas responds in What happens when you cross the streams? and Dave Bacon adds more in Comments?…I Don’t Have to Show You Any Stinkin’ Comments!
You should now go back to the analysis of commenting on BMC journals and on PLoS ONE, both by Euan Adie.
Then go back to my own posts on everyONE blog: Why you should post comments, notes and ratings on PLoS ONE articles and Rating articles in PLoS ONE.
Then, follow the lead set by Steve Koch and post a comment – break the ice for yourself.
Or see why T. Michael Keesey posted a couple of comments.
You may want to play in the Sandbox first.
I am watching all the discussions on the blog posts (as well as on FriendFeed) with great professional interest, of course. So, what do you think? Who of the above is right/wrong and why? Is there something in Conover’s suggestions for newspapers that should be useful for commenting on scientific papers? What are your suggestions?