A Blog Around The Clock

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Category: Housekeeping

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A Farewell to Scienceblogs: the Changing Science Blogging Ecosystem

Category: Blogging • Housekeeping • Media • Personal

It is with great regret that I am writing this. Scienceblogs.com has been a big part of my life for four years now and it is hard to say good bye.

Everything that follows is my own personal thinking and may not apply to other people, including other bloggers on this platform. The new contact information is at the end of the post, but please come back up here and read the whole thing - why I feel like I must leave now.

Sb beginnings

Scienceblogs.com started back in January 2006. On that day, several of my favourite science bloggers moved to this new site, posting the URL on their farewell posts on their old blogs. I took one look at the homepage - which at the time was a simple, black-on-white version of the current Last 24 Hours page - and said to myself: this is where I want to be. My instant feeling was that whoever does not get on this site will bite the dust - become invisible in the shadow of the network. I e-mailed several of the original 14 bloggers with a simple question: "How do I get on?" They all assured me that the site will add more bloggers and that my name is already 'in the hat'. In June of that year, I was one of the 20+ bloggers in the "second wave" of migrants to Scienceblogs.com.

How the move to Sb changed my blogging

You can hide on your own little Blogspot blog. You cannot hide on a network. My first instinctive and unconscious change, something I only became of aware later, was that I changed the way I made factual statements in my posts. What does that mean?

I started thoroughly fact-checking the statements before posting instead of learning the hard way that readers will do it for you.

Of course, I started (in 2003/4) in political blogging where much is a matter of opinion, stakes are high, tempers are short, speed of blogging is important, and stating things confidently and even ferociously is important as a persuasion method. If I have heard some useful factoid somewhere, I would often boldly claim it as true without checking first.

But then I gradually switched to blogging about science. This is the domain of verifiable facts. The goal is education, not so much political action. I wrote about my area of expertise, and I wrote in a way that built on that expertise and made it accessible to the lay public. I wrote about things I knew a lot about and was very familiar with the literature. So I referenced, cited and linked to a lot of supporting documents - peer-reviewed scientific papers.

When I moved to Scienceblogs, I doubled up on that effort, even when writing on other topics. Sometimes I wrote purposefully provocative posts, stating extreme positions and playing Devil's advocate. Such posts were written as mind experiments, or as "let's see how far the blind following of the logic can take us, even if it sounds crazy" and I hoped that nobody would mistake them for my real positions. But I tried not to make statements of fact if I was not sure they were actually facts. I became a better blogger. My place here requires I be trusted. For that, I needed to trust myself first.

Getting invited to blog here is an honor, and the only correct response is to blog with maximal integrity, even during online fights and kerfuffles that alight in every corner of the blogosphere, including the science blogosphere, with predictable regularity. Every single blogger on scienceblogs.com, even those who I may disagree with 99% of the time, blogs here with strong personal integrity (yes, human beings sometimes make mistakes, but they correct them once the onslaught dies down and it is possible to do it without losing face). And that is one of the greatest strengths of this network - just wander around the Web randomly for a while and you'll see some interesting contrasts to this.

How getting hired by PLoS changed my blogging

Most of you probably know that I got the job with PLoS in the comments section of my blog. It is the support for my application for the role at PLoS voiced by my commenters that sealed the deal in the eyes of PLoS. Would I have that kind of support if I was not on Scienceblogs.com?

As an Online Community Manager at PLoS, I try to model myself and learn from the experiences of people like Robert Scoble, one of the first "corporate bloggers" (and everyone who thinks there is anything new or wrong with being paid to blog, should read Say Everything by Scott Rosenberg, a definitive history of blogging which will open your eyes). I have been a supporter (and promoter) of Open Access model of scientific publishing well before I got this job and I often blogged about PLoS papers because I - and everyone esle - have access to them. PLoS is a fabulous organization to work for. Its goals match my own. And I love all the individual people working there. Working with them is a blast, and I am proud of it. It is unfortunate that, in this economic situation (and my own personal economic situation), I can only work there part-time.

I assume that many of my readers are also interested in Open Access and may also be interested in what PLoS does. So, I blog (and tweet, etc,) about news from PLoS. As I see which new papers are coming out in PLoS ONE (and other PLoS journals) a couple of days in advance, I pick those that catch my attention, that I personally find interesting, and post links to them here once they are published. Nobody at PLoS has ever asked me to blog (or not blog) anything work-related on my own individual blog (that is what everyONE blog is for). I do it because I am genuinely excited about some of the papers, or am proud of what the PLoS team at the HQ has accomplished - new functionalities or benchmarks, etc. Like everyone else, I am promoting a cause I believe in, and I am blogging what I want and like.

One of the things that changed in my blogging comes from self-awareness that I am an online public face of PLoS. I need to behave in ways that are appropriate for this role. Thus I try to avoid (as much as that is possible) getting into big online fights and I am more careful about my use of language, especially profanity. The fact that I am much less likely today to blog on very controversial topics reflects much more my own tiredness of such topics and the endless flame-wars and troll-hunting that always follow such posts. It gets really boring after a while. I just don't have much appetite and energy for that any more (if you think battling Creationists is nasty, try debating nationalists of various stripes from the Balkans on Usenet during the wars there - those people WOULD really kill you if they could physically get at you). I want my blog to be a positive force (while fully understanding that would be impossible if others were not doing the dirty trench warfare at the same time, providing the environment in which a positive blog can exist) and I want it to be a creative place, an informative place, and a peaceful and welcoming place for everyone interested in science and in science communication. And for my Mom. Hi, Mom!

So, while this is supposed to be my individual blog, I think of it as such, and it is seen by others as such, it is impossible to completely separate the personal from the professional. I am one of the lucky few for whom life and work are perfectly integrated - I do what I love, with great support (emotional and financial) from my wife. One of the things I am is a promoter of Open Access and PLoS, so this part of my persona is bound to find its way onto my personal blog - it would be self-censorship NOT to allow that stuff onto my blog.

Metcalf's Law, or why are we here at scienceblogs.com

It appears that many commenters during the recent l'affair Pepsi did not understand the difference between blogging on Scienceblogs.com and blogging independently on Blogspot or Wordpress. It is not so much about the direct traffic. It is not so much about payment (I earned through Blogads, back on my old blog in 2006, the same amount as I am getting here today). It is the 'network effect'.

Let's say I keep blogging my usual stuff day after day. I get some regular readers, some people coming from searches, some people coming from external links, etc. I also get a lot of traffic from other blogs here, from the homepage, Last24H page, from the various widgets (e.g., Reader's Choice, Editor's Choice, top page banner), multiple kinds of RSS feeds (e.g., Select Feed), etc. But if I have to say something really important, something that may require action, or something that many people need to know, or an important question that I may ask, there is a group of people that I can rely on much more than just my usual daily readership - the SciBlings (the name given to my fellow bloggers on Scienceblogs.com). I know they will pick up an item, link to it on their own blogs, and dramatically increase my reach for that one particular item. I don't need to beg, or e-mail anyone, this happens spontaneously by the virtue of me being piece. Remember that still very few people read blogs through RSS feeds - they come via searches and links. These days, some of those links are posted by my SciBlings also in other places like Twitter, FriendFeed and Facebook. Then others, outside the network, start linking to it and blogging/tweeting about it, spreading my message far and wide. This is something that would be much more difficult on an independent blog. This is what I call "indirect traffic" - a potential instant reach that I get just by virtue of being on this network.

This kind of network effect resulted in an explosive rise in the online reputation and ranking of Scienceblogs.com. Technorati does not count Sb as a single entity (it used to), but ranks each blog independently. The most high-trafficked blog here, Pharyngula, is ranked at number 68 today. The 68th most influential blog in the world right now. Even if Pharyngula accounts for as much as half of the traffic here (I think it is at around 40%...OK, just checked, it is 42.15%) and half of the number of incoming links to the site, the site as a whole is probably up around top 30th of all the blogs in the world. That is serious visibility and influence for all of us.

All that interlinking between us, as well as links from outside, result in all of us having Google Ranks of about 6 or 7. That is huge. Much of my traffic comes from searches (of course - I have more than 10,000 posts on many topics, some very long, using many different words and phrases). If I click to see a particularly interesting set of search keywords that brought someone to my blog, I discover that my blog is one of the top ten hits for that search string. And studies have shown that most people only check the top ten results when they do a search.

Furthermore, such a significant rise in traffic and rank of scienceblogs.com resulted in all sorts of other deals. Choice posts of ours are linked from the New York Times science page. Likewise with the National Geographic site. Our blogs are sold on Amazon.com for Kindle. And the site is indexed not just in Google but also on Google News.

This means not only that each one of us gets more direct traffic, and more potential indirect traffic from our SciBlings due to being on the network, but also an even larger and more powerful indirect traffic and visibility outside of the network. We are being closely watched, both by thousands of other bloggers and by the mainstream media. Whenever Scienceblogs.com explodes with a story, MSM takes note. It is not by chance that some of the first reactions to the Pepsi scandal, even faster than on individual's blogs, appeared in places like The Guardian and the Columbia Journalism Review. As Jay Rosen and Dave Winer noted in their weekly podcast, the distance between us at Sb and the global media is very small. We are not just a loose collection of individuals blogging just for fun any more.

That is huge power. I keep mentioning this power every now and then (see this, this, this and this for good examples) because it is real. Sustained and relentless blogging by many SciBlings (and then many other bloggers who followed our lead) played a large role in the eventual release of 'Tripoli Six', the Bulgarian medical team imprisoned in Libya. Sustained blogging by SciBlings (and others who first saw it here) played a large part in educating the U.S.Senate about the importance of passing the NIH open access bill with its language intact. Blogging by SciBlings uncovered a number of different wrongdoings in ways that forced the powers-that-be to rectify them. Blogging by SciBlings brings in a lot of money every October to the DonorsChoose action. Sustained blogging by SciBlings forced SEED to remove the offending Pepsi blog within 36 hours. And if a bunch of SciBlings attack a person who did something very wrong, that person will have to spend years trying to get Google to show something a little bit more positive in top 100 hits when one googles their name (which is why I try to bite my tongue and sleep over it when I feel the temptation to go after a person). The power of the networks of individuals affects many aspects of the society, including the media.

With great power comes great responsibility, and I am not sure that all of my SciBlings are aware of the extent of this power. A Scienceblog is not a personal diary or a hobby any more.

Scienceblogs.com is Media

Scienceblogs.com has always been the project of the Seed Media Group, thus at least a self-designated media organization. But since the moment our blogs got indexed in Google News we de facto became writers for a media organization. I am not sure some of my SciBlings really understood the importance of that day and how that changed who we are and what we do.

Most of us here do not consider ourselves to be journalists or even have goals of wanting to become journalists. A few of us are. And a few of us are not sure what we are any more. But by virtue of being searchable on Google News we are journalists, whether we want it or not.

Do we write news? Some of us sometimes do. But videos, cartoons, quotes, linkfests, etc. are considered not not to be News only if one adopts a very narrow and traditional sense of the term - reporting on an event that just happened. If you open a newspaper, you will see much more than News in that sense - there are obituaries, comic strips, classifieds, horoscopes, quotes, photos, poems, crossword puzzles....all of that is News in a sense that most consumers of news think: News is what comes in the Media.

I think it is much more productive to think of media in a different way. Media is a means to disseminate and exchange information. Some of that information is important, some is informative, some is entertaining, some is educational, some is aesthetic, some is comic, some is analytic, some is opinionated, some is relevant to many people, some is relevant to just a handful, and yes, some of it may actually report on "what event just happened". Some of it is distributed by legacy media companies, some is distributed by individuals to each other.

We here at Scienceblogs, by virtue of moving from our individual blogs to the network, have largely left the realm of "distributed by individuals to each other". We are the Media. Which means we need to be aware of it, and behave accordingly. This does not mean we have to change anything about our blogging. After all, we were picked and hired in the hope we would continue to do exactly what we were doing with our blogs before the move to Sb. But the same picture of a cat posted on Wordpress just for fun, as a hobby, becomes News once posted on Scienceblogs.com. Gotta keep that in mind at all times.

We have built an enormous reputation, and we need to keep guarding it every single day. Which is why the blurring of lines between us who are hired and paid to write (due to our own qualities and expertise which we earned), and those who are paying to have their material published here is deeply unethical. Scientists and journalists share some common ethical principles: transparency, authenticity and truth-telling. These ethical principles were breached. This ruins our reputation, undermines our work, and makes it more unpalatable for good blogger to consider joining Sb in the future. See also Jennifer's post on this issue for a clear-headed take.

Seed is not in magazine business any more

Seed Media Group was founded in order to publish Seed Magazine. And it was a very nice magazine, glossy, lush, filled with awesome visualizations. Some articles were awesome, others a little flakier, but nothing nearly as bad as some other (don't make me name it again) popular science magazines managed to publish under their own banners. I liked Seed Magazine. My kids liked it. It was a cool, modern and novel way to design a pop-sci publication.

In a happier time, before the meltdown of the media industry and then a general meltdown of the economy, Seed Magazine would have survived. But it was not meant to be. About a year ago, the last issue of Seed Magazine appeared on the newsstands. Its brand was not big enough, with enough longevity and reader loyalty, for any other corporation to step in and buy it out. It's gone.

But if you think you are in the magazine business, if you think that your main product is a magazine, and if you have an office full of writers, editors and graphic designers, what do you do? You retain the mindset of a magazine publisher. Instead of rethinking the mission of the organization as a whole, Seed was only rethinking how to repackage Seed Magazine. They did not let the magazine die. They moved it online instead, retaining most or all of the editorial and writing staff. As Jay Rosen likes to quip about Washington Post, "the print guys won". The print mindset won.

Yet, at the same time, Seed had a bunch of "side-projects", including some cool visualization stuff and yes, Scienceblogs.com. Some of those projects, including the magazine itself, fell by the wayside. But Scienceblogs.com was going from strength to strength:

Looking at the graph (I know, PageRank measures one thing, other services measure it differently, but the take-home message is the same), it is obvious that the main product of the Seed Media Group is Scienceblogs.com.

One could argue that traffic is not the proper measure, but I cannot think of a better one. If it was a scientific journal, having a middling traffic would not be so bad if other metrics, e.g., citations, media coverage, incoming links, proportion of visits that result in a PDF download, etc., are high. But there is no such thing to measure for a magazine. Impact of an article in a magazine is measured only by traffic, and traffic is also an important metric for advertisers.

What used to be a fun side-project, Scienceblogs, became the centerpiece. Or so you'd think. But remember that the print guys won. Seed never realized that they were not in the magazine business any more. It is telling that some commenters during last week's fiasco said they never heard of Seed Magazine until now (I had not heard of it before I moved to Scienceblogs either). It is squirreled away on its obscure website, with miniature traffic, no brand recognition, not even much linking from Scienceblogs.com to it to drive at least some traffic there. We do not hear about new articles there to help promote them (except when Dave Munger writes one and tweets the link). If we are not aware that there are new articles in the magazine, how are others going to be?

Several months ago (in the wake of a loss of a couple of our top bloggers) I suggested they move the magazine onto Scienceblogs as an "editor's blog" and let us pitch stories for it and use the existence of in-house editors to make our stories more polished than a usual blog post. It did not happen.

What Seed Media Group is doing right now is trying to run a magazine, while treating Scienceblogs.com as a source of revenue. What Seed Media Group should be doing, what every media group should be doing, is become a tech-oriented company (one of the reasons PLoS is successful is that it is essentially a technology-rich publishing company, with an incredible and visionary IT/Web team working with the editorial team in driving innovation). Instead of trying to produce content in-house, which is expensive (all those salaries!), Seed should realize that they already have 80 (now more like 60 and getting smaller every day) producers of content. Barely paid producers of content. I know, it is really hard to fire all those wonderful people - but keeping them can just speed up the end-point so everyone ends up jobless in the end. If Seed Media Group (SMG) has money for employing twenty people, fifteen of those should be tech folks, driving innovation, serving Scienceblogs.com, making it bigger, better, more powerful.

Everything at Seed should be set up to be in service of Scienceblogs: administrators, legal staff, editors, and most importantly a large, powerful, innovative technical staff. The experiment was run, the results are in, scienceblogs.com was shown to be a successful endeavor, and the rest of the experiments, magazine included, were failures and need to be thrown out and forgotten. I guess that many people in the office are emotionally invested in the magazine, but tough luck - the thing is a corpse. Mourn for a while, and move on.

Who gets to be on Scienceblogs.com?

A couple of years ago I heard the statistic that Seed got an average of seven applications per day to blog here. That is thousands of bloggers over the years to date!

The network had a succession of several excellent Community Managers who made decisions on who to invite next. As the site grew and changed, their visions also changed, which determined what kinds of blogs they were looking for. Sometimes, they would accept a new blog, and let us know about it only about a day in advance. But in most cases they consulted with us. They would ask us to recommend who we thought were the best bloggers in a particular area, e.g., technology, infoscience, art, food, chemistry, etc., whatever they thought we lacked and needed more of at any particular time. And they would usually consider our recommendations and invite bloggers we respected. There were even times when we ganged up on them and relentlessly lobbied for a particular blogger to get invited and they would have to agree eventually.

Not everybody who was invited said yes, either, but most did. And over the years there was a natural cycle - as new blogs got added, some of the older ones shut down or left. Often life and work interfered and people decided they could not continue blogging any more. Or just got tired of blogging. Some felt too much pressure to blog more frequently than they were comfortable with. Some bloggers fused their blogs into a single multi-author blog. Some invited co-bloggers to help. Some got better-paying gigs elsewhere. Some left due to personal conflicts with other bloggers. And now several have left due to the damaged reputation of the network that started with a sale of a blogging spot to a corporate entity.

And more are leaving, and will be leaving, due to "Bion's effect":

"You are at a party, and you get bored. You say "This isn't doing it for me anymore. I'd rather be someplace else. I'd rather be home asleep. The people I wanted to talk to aren't here." Whatever. The party fails to meet some threshold of interest. And then a really remarkable thing happens: You don't leave. You make a decision "I don't like this." If you were in a bookstore and you said "I'm done," you'd walk out. If you were in a coffee shop and said "This is boring," you'd walk out.

You're sitting at a party, you decide "I don't like this; I don't want to be here." And then you don't leave. That kind of social stickiness is what Bion is talking about.

And then, another really remarkable thing happens. Twenty minutes later, one person stands up and gets their coat, and what happens? Suddenly everyone is getting their coats on, all at the same time. Which means that everyone had decided that the party was not for them, and no one had done anything about it, until finally this triggering event let the air out of the group, and everyone kind of felt okay about leaving.

This effect is so steady it's sometimes called the paradox of groups. It's obvious that there are no groups without members. But what's less obvious is that there are no members without a group. Because what would you be a member of?"

Yes, suddenly everyone is getting their coats on, all at the same time. This party is not as fun as it once was. Time to go.

Scienceblogs.com - The Good

Four years is eternity on the Web. But try to think back to early 2006 and understand how revolutionary that concept was at the time: grabbing a bunch of already popular bloggers, putting them all on the same site, paying them a little bit, and giving them complete editorial freedom. Anything goes! The editorial hand is in the initial choice of bloggers. Once you choose the people whose work you like, just let them lose.

The existence of Scienceblogs.com as a one-stop shopping place for all things science resulted in the high visibility of science and of science blogging and spurred the explosive growth of the science blogosphere. In 2006, I could read every post by every science blogger in the world. Today, there are thousands out there that I don't even know about. And there are many other media companies who tried to emulate Seed and build their own networks, with, to be generous, mixed success so far.

The Seed motto, "Science Is Culture", also contributed to opening science for the lay audience. Many of our readers are not scientists. The stereotypical image of scientists as socially inept recluses who speak in incomprehensible lingo was dispelled.

In many ways my feeling that "who is not here will bite the dust" was not realized. Instead of building an isolated elitist community, we felt the responsibility to be generous, to constantly look for, seek out, link to and promote bloggers who are not on the network. Instead of acting as "we are elite bloggers producing elite content", we acted as "we are elite filters, finding and choosing the best content on the Web and showcasing it to everybody".

Thus, much of what we did as SciBlings had, as a goal, the building of the science blogging community that is much broader than just our own internal network community. Nobody got rich from, and many put a lot of work into, the Open Laboratory anthologies which not only showcase the best of science blogging to the audience outside of the Web, but also promote new and upcoming bloggers outside the network. The ScienceOnline conferences (now a full-time job to organize, but still done for free on our own time) also contribute to a similar effort to get people on and off networks together. The DonorsChoose action every year brings us all together, as well as many other such actions. Scienceblogs.com was definitely a key player in the emergence and building of the science blogging community.

Scienceblogs.com - The Bad

The network has evolved over time. The initial offering was composed of bloggers who were already popular - they brought their readership with them. They just happened to be mostly bloggers - and this is probably why they were popular in the first place - whose blogging covered those aspects of "science is culture" that are quite controversial, from beating up on pseudoscience and medical quackery, to the relationship between science and religion, to the politics and politicization of science. This made for quite a lively discourse on the network, bringing up discussion topics that were important to have yet were considered taboo before. This did not sit well with all of the audience, many still squeamish about breaking of such cultural taboos (especially bold defenses of atheism), and the network got somewhat of a bad reputation in some circles, as a hotbed of godless, pinko-commie, liberal whateverwhatever people. That reputation, even during the most recent period when only about five out of 80 bloggers focused much on politics and/or religion, seems to persist.

Since the continuous additions of popular bloggers did not add many new readers and traffic (they were all already reading here anyway), and as the erroneous perception which Sb-haters promulgated that "there is no science on scienceblogs.com" needed to be countered, Seed invited many bloggers who never touch controversial topics and only blog about science. They also invited a couple of bloggers who are openly religious and a couple of conservatives. More recently, several bloggers who joined were reputable science writers and journalists. A new idea was to try and pick up some very new and not-yet-established bloggers, especially very young ones with talent, and bring them here and help them grow.

But none of this helped dispel the nefarious myths about Sb being an atheism network. In this effort to dilute politico-religious content with science content, Sb grew, in my opinion, too big. I think 80-something blogs with 90+ bloggers is too big. Internal rifts and formation of cliques was inevitable in such a large group, which led to some hidden and some very public fights, and resulted in some of our prominent bloggers leaving in a huff. This did not look good from the outside, I'm sure. And it did not work well for the bloggers' morale either.

The chronic inability of the Seed management to communicate to and with bloggers did not help either (I feel the Overlords who tried to represent our interests were sidelined in the Seed newsroom). As a result, there is not much loyalty to the Seed brand. We are here for the network effect and traffic (and even the little money we get is important grocery money for some of us, including me), not because we are in love with Seed.

This is not about Pepsi

Two weeks ago, as most of you probably know, Seed started a new blog on Scienceblogs.com. It was to be not just sponsored, but authored by people from PepsiCo, a continuation of their Food Frontiers blog (go take a look). It was to be hosted, I believe, for three months, for a fee that PepsiCo would pay Seed (out of which, I guess, we bloggers would also get paid, perhaps even get up to date on payments - I just got my April check).

We have hosted a few corporate-sponsored blogs before, but the main bloggers on them were either independent journalists or some of our own bloggers. Those blogs were introduced to us in the backchannels in advance, we were consulted, changes were made as needed, and some of us still protested on our blogs or wrote posts that are quite damning to those corporations, their shady corporate behavior, and their products.

It is not well known - at least I did not see anyone mention it - that Seed tried to hire an outside freelance science journalist to host the Pepsi blog. Apparently, they could not find anyone. So, when the date came when they promised Pepsi they would start, they launched the blog without an independent host, with just Pepsi employees blogging. Huge mistake! They should have quickly asked some of us to pitch in that role, but instead they did not even tell us about it - the appearance of the blog was a total surprise to us all. Orac was the first one to spot it on the Last24Hour page and alerted the rest of us. Understandably, we all went berserk (and if you think our anger was strongly worded on our blogs, can you imagine what it looked like in the backchannels!?). This is a flagrant breach of the wall between content and advertising. A huge no-no in any kind of media. We are Media and this was the (un)ethical straw that broke the camel's back.

Greg Laden was not the first one to think of it, but explained it the best the other day how the blog could have been made much more palatable to us and readers, if Seed just thought to ask us (even if that meant a delay of a couple of days before launching) to blog there. We have many bloggers here who could have contributed their expertise on various aspects of food. We have bloggers who could write with authority on obesity from physiological, medical, public health and sociological perspectives, on the chemistry of food, on poisons, on neuroscience of appetite, on nutrition, on raising one's own food, on evolution of food plants and domesticated animals, on endangered seafood, on the economics and politics of the food industry, on useless dietary supplements, on the reason why a piece of bread always falls on the buttered side, how to desecrate crackers, and even how to roast a zebra and share it with locals in Africa. Not to mention pie recipes! That could have been fun and informative. And if Pepsi scientists contributed as themselves, not as frontmen for the company, their perspective would have been interesting as well.

Instead, we got an infomercial posing as one of us.

It is completely irrelevant that it was Pepsi.

It is completely irrelevant that it was about food.

It is completely irrelevant that they never got to post anything on the blog before it was removed under the storm of criticism by us, readers and the media.

It is completely irrelevant if their content was going to be good or bad.

What is relevant is that a corporation paid to have a seat at the table with us. And that Seed made that happen.

What is relevant is that this event severely undermined the reputation of all of us. Who can trust anything we say in the future?

Even if you already know me and trust me, can people arriving here by random searches trust me? Once they look around the site and see that Pepsi has a blog here, why would they believe I am not exactly the same, some kind of shill for some kind of industry?

Even if you know me and trust me, would you be able to trust any new addition to the network? All those thousands of bloggers who applied to Sb and did not get invited to join? What are they all thinking now about someone paying to blog here? Do you think anyone will ever apply again?

Is Scienceblogs reputation permanently damaged?

In the wake of the Pepsi scandal, other things started coming to light. Things like this and this and this and this, all adding up to the realization that Seed is not what it makes out itself to be. So yes, I think the reputation of Seed is permanently damaged. The quick reversal, under pressure, and removal of the Pepsi blog is not enough.

Will it survive? I don't know. Probably it will, but smaller (this also depends on the biggest-traffic bloggers remaining). But the scienceblogs.com stable is shrinking rapidly, and I do not see it growing in size or reputation again any time soon. Without it - the only profitable enterprise in the SMG - I am not sure the company can survive. We won many big races, but our racing career is now over, and we should retire to some pleasure riding in the meadows now (not ready for the slaughterhouse yet, not me).

Where will bloggers go?

Some of the most prominent bloggers who have left - or will leave - can quite easily go solo. Since 2006, the Web ecosystem has evolved and now has mechanisms, including social networking sites, that can keep an already popular site from fading into oblivion by going solo. One's blog is now only one part of one's online presence.

Others have been approached or will be approached (as soon as they make their leaving Sb official) by many other existing or incipient newtorks out there. Field Of Science is a new network, GenomesUnzipped is a new group-blog for people interested in genomics, All Geo may try to collect geobloggers, and Southern Fried Science new network may accumulate more ocean bloggers. Panda's Thumb offered evolution bloggers defecting from Scienceblogs.com to post there (I am not sure how to think about the division by topic - does it mean that general science networks can never attract a geoblogger and an ocean blogger any more?).

SciBlogs NZ is a wonderful network, but limited by geography to New Zealand bloggers only. There are German Scienceblogs and Scienceblogs Brazil (in Portuguese). There is a growing North Carolina group science blog.

Ira Flatow offered to host bloggers on Science Friday. And so did Wired UK (and US?) and apparently The Guardian as well. Scientific American is bound to jump into the fray, picking up defecting SciBlings. National Geographic has a blog network - I guess they are watching these developments as well. These media-run blogs/networks may well be changing their technological architecture as we speak in order to absorb multiple new bloggers they are trying to attract.

Blogging on Huffington Post is an instant loss of credibility - a day of a Pepsi blog is nothing compared to years of pseudoscience, medical quackery, Creationism and Deepak Chopra's posts there. Nobody in their right mind would want to be associated with such a cesspit of anti-science.

There are awesome blog/news networks for students of science journalism at NYU (Scienceline) and their counterparts in the UK, mainly at City University (Elements).

Nature Network whose target audience are primarily scientists rather than lay public, and Science 2.0 (formerly Scientificblogging.org, not to be confused with the similarly named but very new and interesting Science 2.0 network that does more than just blogging) seem to be pretty open and approachable and have nice internal communities, but are essentially invisible from the outside. Likewise for Discovery Networks Blogs. The Psychology Today blogs is a very big network, but they do not seem to have anything like a community, and seem to be pretty unselective as to who they accept. I have heard of at least three new networks still in the making.

But going to any of these is potentially a step down and a big loss of visibility and traffic. The only network that has recently started to come close to the clout of Scienceblogs.com is Discover blogs, but they have a specific type of blogger in mind and do not appear to have an appetite at this point to suddenly invite dozens of new bloggers - they seem to be building the network as a small, but highly elite place for people with some existing journalistic and professional writer cred. Definitely ones to watch!

New scienceblogging ecosystem

The potential step down and loss of visibility by leaving Sb may be an illusion. It makes sense in the existing ecosystem in which Scienceblogs.com is The Borg and everyone else is biting the dust. But the ecosystem is changing. Scienceblogs.com is rapidly losing reputation and bleeding bloggers. A number of other networks are absorbing these bloggers and adding more, growing in size and visibility very rapidly. Very soon - and I mean SOON as in weeks - instead of one big place to watch, there will be two dozen medium-sized places to watch. Instead of one site that everyone reads, there will be a number of sites that will have to read each other instead. Networks that get too large will be viewed, perhaps, with suspicion they are not selective enough. Networks that are too small will get lost and invisible in such a crowded ecosystem. The trick is to find the Goldilocks solution - just the right size.

Many science bloggers are personal friends, and many are also heavy users of social networks like Twitter, FriendFeed and Facebook, so the ties will remain. The popularity of blog carnivals may come back up, at least temporarily, due to their well-established effect of building and maintaining the community. ResearchBlogging.org, apart from building respect for science bloggers in the outside world, is also beginning to serve as a center of the blogging community (and I hope it survives, funded by Seed or, if that becomes impossible at some point in the future, by whoever else can be lured to do so).

Instead of one big network, there will be a network of networks. Nobody can afford now to ignore or be ignored by others. I bet we will see aggregators springing up that link to all the networks, perhaps networks will carry each other's RSS Feed widgets on sidebars to facilitate cross-linking and traffic between networks, and thus raise visibility of all. And the legacy media will have to adjust to the new ecosystem as well, and instead of just watching Scienceblogs.com, find a way to monitor all of the networks at the same time.

When science blogosphere was young, existence of Scienceblogs.com was a boon - it lifted all the boats with it, made both the science and the science blogging visible and prominent. Today, having only one overgrown site so visible is toxic - it takes the oxygen out of the system, and makes the other networks and independent bloggers invisible. With the current process of Sb being cut to size, and concomitant process of other networks growing in size, visibility and relevance (as well as brand new networks springing up), we are reaching a point where being on Sb is not the pinnacle of one's potential science blogging career - it is one of many places where it is good to be.

Many who are, for now, deciding to stay on Sb, are doing so because they are terrified of becoming invisible by going solo. But in the new emerging ecosystem, going solo is not necessarily going to mean invisibility. People who go solo will still be a part of the community - yes, the same science blogging community that Scienceblogs.com was a key to building in the first place.

Going solo also makes one "fair game". Other networks will not approach Sciblings who are not officially leaving as they do not want to tread on Adam Bly's territory or be seen as poaching. But they will approach people who go solo. And they will also approach independent bloggers who were never on a network before - because those bloggers are really good and have been left out so far, because there are not enough Sb defectors to build sufficiently large networks just out of them, and because they do not want the perception that they are growing and building networks entirely on the ashes of Seed.

A growing number of networks and growing visibility of all the networks, also means that bloggers will have many choices. Seed is not the only game in town any more. Some networks pay bloggers, others don't. Some have advertising, some don't. Some have posting frequency requirements, others don't. Some are run by for-profit organizations, others by non-profits, and others are bloggers' cooperatives. Some have complete editorial freedom, some have limited restrictions. Some have excellent tech support, some lousy or none at all. Some are smaller and highly selective as to who they invite, others are big and also accept bloggers who are not really up to par. Thus, each blogger has a range of choices and the ability to choose according to what each individual finds important for their own goals. And those bloggers who think of this as a hobby and do not want to be seen as Media, can easily go solo and remain connected to the ecosystem in a variety of ways.

What will I do?

My first impulse when Pepsi blog suddenly and surprisingly showed up on the homepage was to bail out immediately.

But I decided instead to take some time to think and decide. My wife also told me to wait and watch the events unfold instead of saying anything myself. Wise.

Not saying anything publicly also made me open to others - I was approached by many with questions, fears, confusions, and their own plans. I have heard a whole lot from various people - who is courting them, where they are going to go, what new networks are being secretly built, etc. which gives me a pretty good lay of the land. I have a pretty good grasp of what is going on out there, I think (though I can be surprised, I'm sure). Most people are quite secretive about their plans, and I will NOT reveal anything that anybody told me until they themselves go public, but I am also not ready to completely reveal my own plans just yet.

After agonizing for almost two weeks, I finally made a decision. I will leave Scienceblogs.com, effective today.

I am not making this decision lightly. A number of factors played a part in this. On one hand there are negative factors - the loss of reputation by Sb, the complete lack of technical support here, the deflated morale of bloggers here, and the indications that all the recent changes at Seed are not a sign of losing the print mindset, which makes it unlikely that meaningful changes will happen. There is also a feeling that SMG is financially a sinking ship. On the other hand are positive factors - I am excited by the swift evolution of the new science blogging ecosystem and want to position myself well within it. I feel that this is also an opportunity to make something better once the dust settles. But the main reason I am leaving is the ethical breach that has seriously placed our reputation in jeopardy.

Unlike some others, I have nothing personal against Adam Bly. We have met once and he seems to be a really nice guy. We loved going to the New York City meetups in the early years and meeting with him there and being hosted at his house. He has interesting ideas and I think his goals are quite in sync with my own - increasing the prominence and relevance of science in our society. I just think that he is consulting with (and sometimes hiring) people with the old legacy media mindset, getting outdated ideas from them, and not being aware how the world has changed even in the past four years and how those changes require a much more dramatic change in direction.

I also want to acknowledge how much being on Scienceblogs.com has meant to me both personally and professionally. This is where I got my job, many other gigs, invitations to give talks, preview copies of books, and a general prominence and reputation in the worlds of science, publishing and the Web. Without Scienceblogs.com, there probably would never be Open Laboratory and ScienceOnline. I have made many fast friends here, both SciBlings and readers, and I am optimistic that these friendships will continue, wherever any one of us end up blogging.

Though many other solutions are possible for me, I have decided that I want to be solo for a little while - I want to see who approaches me and with what kinds of offers. Perhaps something great comes out of it. With my wife on disability leave our finances are shot, and I need to find a way to get paid for all the things I do so I can support my family. And even if no good offers come about, at least when I make up (and announce) my final decision, I will be sure I had all the necessary information I need to make the best decision for myself.

So, farewell, Scienceblogs, it was honor to be a part of this community for so long.

You can find me, in the meantime, at http://coturnix.wordpress.com/. I will continue blogging at everyONE blog and Science in the Triangle blog as well. And you can follow me on Twitter, FriendFeed and Facebook, so you will know when I make other moves in the future.

Posted by Coturnix at 12:00 PM • 89 Comments • 0 TrackBacks

Open Laboratory 2010 - submissions so far

Category: OpenLab10

The list is growing fast - check the submissions to date and get inspired to submit something of your own - an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Read on »

Posted by Coturnix at 7:40 AM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

At bottom every man know well enough that he is a unique being, only once on this earth; and by no extraordinary chance will such a marvelously picturesque piece of diversity in unity as he is, ever be put together a second time.

- Friedrich Wilhelm Nietzsche

Posted by Coturnix at 3:54 AM • 1 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

Love makes the time pass. Time makes love pass.

- French proverb

Posted by Coturnix at 3:59 AM • 2 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

The sentiment of justice is so natural, so universally acquired by all mankind, that it seems to be independent of all law, all party, all religion.

- Francois Marie Arouet (Voltaire)

Posted by Coturnix at 4:00 AM • 2 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

It's a great advantage not to drink among hard-drinking people. You can hold your tongue and, moreover, you can time any little irregularity of your own so that everybody else is so blind that they don't see or care.

- F. Scott Fitzgerald

Posted by Coturnix at 4:14 AM • 1 Comments • 0 TrackBacks

New and Exciting in PLoS this week

Category: Science News

There are new articles in four PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Read on »

Posted by Coturnix at 11:43 PM • • 0 TrackBacks

ScienceOnline2010 - interview with Anne Frances Johnson

Category: SO'10 • Scio10 Interviews

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years' interviews as well: 2008 and 2009.

Today, I asked Anne Frances Johnson to answer a few questions. Anne is a freelancer and grad student at the University of North Carolina at Chapel Hill.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?

When I was a kid, I, like all 8-year-old girls, wanted to be a marine biologist and ride around on dolphins. A couple decades later, I'm still into science and nature, but I don't actually ride wild animals. I'm a freelance science writer and master's student in the Medical & Science Journalism program at UNC. I like to think it's as fun as riding dolphins, but probably better for the environment.

I'm originally from Raleigh, NC, and I've recently come full circle back to the Triangle after more than ten years away with stops in New Mexico, New England, New Zealand and Washington, DC (I lived there even though it doesn't have "new" in its name). I have a B.A. in biology from Smith College, where I spent lots of time cutting open fish stomachs for my thesis on lobster predation (What Eats Lobsters besides People?).

I always liked learning about science, but in college I found actually doing it to be rather gooey and tedious, and decided I probably didn't have the endurance for it as a career. I found myself gravitating instead toward the edges of science, where it interacts with society. I worked at a marine reserve in New Zealand, patrolled Costa Rican beaches for would-be sea-turtle-egg poachers, and tended persimmons, goats and alpacas on various farms here and abroad. But it wasn't until my first "real" job--at the National Academy of Sciences--that I discovered science writing. Instantly smitten, I've been a ravenous science reader and writer ever since.

Tell us a little more about your career trajectory so far: interesting projects past and present?

My first science communications piece was an educational booklet on stem cells. Most of the stem cell information available at the time followed either the science community's party line (embryonic stem cells are more useful than adult stem cells so we should use them) or the conservative/political party line (scientists want to kill babies and we should stop them). Since I was working for a scientific organization, it would have been simple to take the usual tack, but we decided it was really time to go beyond that. I spent a lot of time talking to people ethically opposed to human embryonic stem cell research and tried to craft the booklet so it could reach those folks on their terms, while still being true to the science. Dealing with both the scientific and ethical issues head-on ultimately made it a more useful product for people, and tens of thousands of the booklets found their way into schools and doctors' offices. It was very rewarding.

After that, I had the pleasure of developing a whole slew of other booklets (and posters and gadgets and websites) on topics including how to plant a pollinator-friendly garden, why microbes are cool and what the new science of "metagenomics" can tell us, and how climate change might affect ecosystems across the U.S. It's been a constant learning experience.

What is taking up the most of your time and passion these days? What are your goals?

Last year I decided to go back to school to pick up some additional communications skills I wasn't sure I could learn on the job. So now I'm a science journalism grad student. Perhaps the most exciting aspect of the curriculum is the multimedia work I'm doing. I know "multimedia" is a silly buzzword, but it really is useful to be able to apply whatever combination of media--text, sound, video, graphics, animations--is right for the topic at hand. I'm enjoying learning to wield all those tools and figuring out how to leverage the strengths of each to communicate in an engaging way.

Although teamwork is incredibly powerful, it's also useful to be able to function as a "one-woman-band," with a complete suite of skills to produce everything from documentaries to press releases myself. Wherever I end up after I graduate in 2011, I hope I'll be able to apply all my fun new skills and continue to learn and adapt to the changing communications landscape.

What's up with going to journalism school? No offense, but isn't that a dying industry?

I get that a lot. Journalism school is actually alive and well, even in the current climate. The journalism business model is in a period of adjustment that's leaving a lot of traditional journalists out of work, and that's too bad. But I think people are hungrier than ever for information, and for the most part they know the difference between bad information and good information. I think there will always be a role for good journalistic work--especially when it comes to science topics.

Career-wise, I'm more interested in communications than traditional journalism, but I think going through this experience of learning to write more like a journalist makes me a stronger communications person. I also just love being in journalism school because I'm surrounded by really creative thinkers from all different backgrounds, which challenges me to go beyond the obvious and try different approaches.

What aspect of science communication and/or particular use of the Web in science interests you the most?

I love that there's this vast array of genuinely interesting science content online that teachers can use as part of science education. Science education has had a terrible reputation for a long time. The Web gives teachers and parents opportunities to engage children in ways that have never existed before. Kids can interact with the scientific world on their terms and keep following the leads that interest them most. It sure beats those awful textbooks and cheesy videos I remember from childhood.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I have a healthy skepticism about using blogs and social networking in science communications. Organizations pour so much into getting their content out in all these different ways. They're available and "free," so why not? And sometimes they're really effective at amplifying your reach and visibility. But they're not magical. Sometimes, you're better off simply producing more or better actual content, and your resources would be better spent focusing on the dissemination avenues that are most effective for your specific target audiences. There's always a trade-off between quantity and quality, between producing new content and promoting your existing content. You have to hit the right balance, and I think blogs and social networking can be distracting if you don't keep them in perspective. I try to use 'em when they're right for the task, and leave 'em when they're not.

What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference - a session, something someone said or did or wrote - that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

One of my favorite experiences was getting to hold these really old dead birds they keep in the bowels of the NC Museum of Natural Sciences. There were just racks and racks of them. We got to pass them around, and they were so astoundingly light and beautiful. It was fun to connect with nature in the way that taxonomists have for years and years, where you can take note of the tiniest differences among species. I loved that behind-the-scenes tour, and would be thrilled to be able do more of the tours next year.

On blogging, the conference perhaps counterintuitively convinced me that it's okay not to blog about science. Seeing all those people blogging and tweeting so passionately, I thought, you know, there's room for all types here. And if daily blogging isn't my thing, it's okay. People are blogging about science, and people are writing involved, long-form articles and books about science, and folks will continue to be engaged with science on whatever basis is useful for them--whether it's monthly, daily or by the second. There are so many possibilities, so many ways for people to talk about science. With all those opportunities, you can really shop around and focus on what you can do best.

Thank you so much for the interview. I hope you will come to the meeting again next January.

Posted by Coturnix at 2:47 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

Time is a dressmaker specializing in alterations.

- Faith Baldwin

Posted by Coturnix at 3:52 AM • • 0 TrackBacks

New World-Science Forum - The Origins of Kindness

Category: Psychology • Science Education

The Origins of Kindness:

Listen to our interview with science historian Oren Harman. He's our guest in this Science Forum discussion.

Harman is a professor at Bar Ilan University in Israel.

If evolution favors the survival of the fittest, how did kindness and selflessness evolve? The search for that answer is the subject of Harman's new book, The Price of Altruism.

It tells the story of George Price, a scientist who developed an equation that explains how natural selection can favor altruistic behaviors.

As Harman writes, George Price's life and work were full of contradictions.

Disappointed by his findings, because they implied that seemingly selfless behaviors are in fact selfish, Price decided to prove his own science wrong. He became an evangelical Christian and gave away everything he owned to the poor and homeless.

Price took his own life in 1975.

Oren Harman is taking your comments and questions. Come join the conversation. It's just to the right.

Posted by Coturnix at 10:35 PM • • 0 TrackBacks

New and Exciting in PLoS ONE

Category: Science News

There are 29 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Read on »

Posted by Coturnix at 5:20 PM • • 0 TrackBacks

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

Category: Academia • Education • Genetics • SO'10 • Science Education • Science Practice

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Posted by Coturnix at 3:13 PM • 5 Comments • 0 TrackBacks

RSA Animate - Smile or Die (video)

Category:

Posted by Coturnix at 2:34 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

If only we'd stop trying to be happy we could have a pretty good time.

- Edith Wharton

Posted by Coturnix at 3:56 AM • 1 Comments • 0 TrackBacks

Oxygen (video)

Category: Fun • Science Education

Posted by Coturnix at 11:40 PM • • 0 TrackBacks

New and Exciting in PLoS this week

Category: Science News

There are many new articles in four PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Barcoding Life to Conserve Biological Diversity: Beyond the Taxonomic Imperative:

In the 250 years since the Swedish scientist Carl Linnaeus first started classifying organisms, taxonomists have formally described roughly 1.7 million species. Although seemingly large, this number represents only a small fraction of the estimated tens of millions of species on the planet. Moreover, human activities are causing the extinction of species hundreds of times faster than the natural rate of extinction found in the fossil record. Fully one-third of all species on the planet may be gone by the end of this century--many without ever having been studied or, more importantly, protected [1].

DNA barcoding, developed in 2003 to identify species, has helped to rejuvenate taxonomic research. The science of taxonomy is key to understanding and monitoring biodiversity [2]. The technique is based on a simple but powerful observation: that sequence diversity, in short, standardized gene regions (i.e., DNA barcodes), can serve as a tool to identify known species and potentially discover new ones. Moreover, DNA barcoding allows researchers to develop a system for species identification based on digital characters, eventually allowing for automated identifications, thereby promising to improve the capacity to identify, monitor, and manage biodiversity, with profound societal and economic benefits. It also raises the possibility of identifying the vectors of zoonotic diseases as well as the disease organisms themselves.

Left to Their Own Devices: Breakdowns in United States Medical Device Premarket Review:

Medical devices encompass nearly every medical product that does not achieve its intended purpose through chemical action, from the simple (tongue blades) to the complex (MRI machines), and from the safe (stethoscopes) to the risky (artificial hearts) [1],[2]. Certain drug-device combinations, such as drug-eluting coronary stents, are also regulated as devices.

The number and complexity of medical devices have increased dramatically over the past several decades, often to the betterment of patients' health. Between 1997 and 2006, the value of device sales roughly doubled to US$123 billion, representing a fairly consistent 6% of the nation's health care expenditures [3].

The Center for Devices and Radiological Health (CDRH) at the Food and Drug Administration (FDA) is charged with ensuring the safety and effectiveness of medical devices. While a number of serious safety problems with devices have emerged--the Dalkon Shield [4], the Bjork-Shiley heart valve [5], and the Sprint Fidelis defibrillator lead [6], to name a few--problems with effectiveness are not as readily apparent once a device is on the market, in part because postmarket efficacy trials of approved devices are rare. Thus, the burden of ensuring device effectiveness is heavily weighted toward premarket evaluation.

Phylogenetic and Morphologic Analyses of a Coastal Fish Reveals a Marine Biogeographic Break of Terrestrial Origin in the Southern Caribbean:

Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world. Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a ~2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by ~150 km at the Santa Marta Massif (SMM) in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated ~0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at ~0.78 my. Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of additional Southern Caribbean taxa, particularly those with varying life history traits and dispersal capabilities, will determine the extent by which the SMM has influenced marine phylogeography in the region.

Efficient Mitigation Strategies for Epidemics in Rural Regions:

Containing an epidemic at its origin is the most desirable mitigation. Epidemics have often originated in rural areas, with rural communities among the first affected. Disease dynamics in rural regions have received limited attention, and results of general studies cannot be directly applied since population densities and human mobility factors are very different in rural regions from those in cities. We create a network model of a rural community in Kansas, USA, by collecting data on the contact patterns and computing rates of contact among a sampled population. We model the impact of different mitigation strategies detecting closely connected groups of people and frequently visited locations. Within those groups and locations, we compare the effectiveness of random and targeted vaccinations using a Susceptible-Exposed-Infected-Recovered compartmental model on the contact network. Our simulations show that the targeted vaccinations of only 10% of the sampled population reduced the size of the epidemic by 34.5%. Additionally, if 10% of the population visiting one of the most popular locations is randomly vaccinated, the epidemic size is reduced by 19%. Our results suggest a new implementation of a highly effective strategy for targeted vaccinations through the use of popular locations in rural communities.

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity:

"The enigma of soil animal species diversity" was the title of a popular article by J. M. Anderson published in 1975. In that paper, Anderson provided insights on the great richness of species found in soils, but emphasized that the mechanisms contributing to the high species richness belowground were largely unknown. Yet, exploration of the mechanisms driving species richness has focused, almost exclusively, on above-ground plant and animal communities, and nearly 35 years later we have several new hypotheses but are not much closer to revealing why soils are so rich in species. One persistent but untested hypothesis is that species richness is promoted by small-scale environmental heterogeneity. To test this hypothesis we manipulated small-scale heterogeneity in soil properties in a one-year field experiment and investigated the impacts on the richness of soil fauna and evenness of the microbial communities. We found that heterogeneity substantially increased the species richness of oribatid mites, collembolans and nematodes, whereas heterogeneity had no direct influence on the evenness of either the fungal, bacterial or archaeal communities or on species richness of the large and mobile mesostigmatid mites. These results suggest that the heterogeneity-species richness relationship is scale dependent. Our results provide direct evidence for the hypothesis that small-scale heterogeneity in soils increase species richness of intermediate-sized soil fauna. The concordance of mechanisms between above and belowground communities suggests that the relationship between environmental heterogeneity and species richness may be a general property of ecological communities.

How Normal Cells Can Win the Battle for Survival Against Cancer Cells:

During the early stages of tumorigenesis, cancerous cells undergo rapid and uncontrolled cell division as they invade the surrounding tissue. How tumors create space around them to accomplish this invasion is not well understood. A recent study showed that cancerous cells in fruit flies manage this feat by inducing neighboring cells to spontaneously destroy themselves and then filling the vacated space left behind in a process known as cell competition. In this issue of PLoS Biology, Yoichiro Tamori et al. provide evidence that this battle also occurs in mammalian tissues and uncover what determines the winners and losers when cells compete.

Limbs Made to Measure:

This year marks the 150th anniversary of the birth of D'Arcy Thompson, the British biologist, classicist, and all round polymath (For more information on D'Arcy Thompson see www.darcythompson.org). Like many, he was fascinated by the appearance and structure of living matter, and in his influential book, On Growth and Form [1], he set out to describe and explain the principles of morphogenesis--the way living things grow and acquire their forms. Using a vast range of examples, from the honeycomb in beehives to the spirals in a snail's shell, he emphasized that form should be studied in the context of growth and that to explain shape it was essential to understand the underlying mechanisms. This led to the central thesis of the book: biological forms are the result of mechanical and physical processes that should be described with mathematical precision.

Posted by Coturnix at 8:00 PM • • 0 TrackBacks

The Vaccine Song (video)

Category: Medicine

Posted by Coturnix at 12:44 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

Apparent failure may hold in its rough shell the germs of a success that will blossom in time, and bear fruit throughout eternity.

- Frances Watkins Harper

Posted by Coturnix at 4:18 AM • 2 Comments • 0 TrackBacks

New and Exciting in PLoS ONE

Category: Science News

There are 26 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

The Clock Genes Period 2 and Cryptochrome 2 Differentially Balance Bone Formation:

Clock genes and their protein products regulate circadian rhythms in mammals but have also been implicated in various physiological processes, including bone formation. Osteoblasts build new mineralized bone whereas osteoclasts degrade it thereby balancing bone formation. To evaluate the contribution of clock components in this process, we investigated mice mutant in clock genes for a bone volume phenotype. We found that Per2Brdm1 mutant mice as well as mice lacking Cry2−/− displayed significantly increased bone volume at 12 weeks of age, when bone turnover is high. Per2Brdm1 mutant mice showed alterations in parameters specific for osteoblasts whereas mice lacking Cry2−/− displayed changes in osteoclast specific parameters. Interestingly, inactivation of both Per2 and Cry2 genes leads to normal bone volume as observed in wild type animals. Importantly, osteoclast parameters affected due to the lack of Cry2, remained at the level seen in the Cry2−/− mutants despite the simultaneous inactivation of Per2. This indicates that Cry2 and Per2 affect distinct pathways in the regulation of bone volume with Cry2 influencing mostly the osteoclastic cellular component of bone and Per2 acting on osteoblast parameters.

Locomotor Adaptation versus Perceptual Adaptation when Stepping Over an Obstacle with a Height Illusion:

During locomotion, vision is used to perceive environmental obstacles that could potentially threaten stability; locomotor action is then modified to avoid these obstacles. Various factors such as lighting and texture can make these environmental obstacles appear larger or smaller than their actual size. It is unclear if gait is adapted based on the actual or perceived height of these environmental obstacles. The purposes of this study were to determine if visually guided action is scaled to visual perception, and to determine if task experience influenced how action is scaled to perception. Participants judged the height of two obstacles before and after stepping over each of them 50 times. An illusion made obstacle one appear larger than obstacle two, even though they were identical in size. The influence of task experience was examined by comparing the perception-action relationship during the first five obstacle crossings (1-5) with the last five obstacle crossings (46-50). In the first set of trials, obstacle one was perceived to be 2.0 cm larger than obstacle two and subjects stepped 2.7 cm higher over obstacle one. After walking over the obstacle 50 times, the toe elevation was not different between obstacles, but obstacle one was still perceived as 2.4 cm larger. There was evidence of locomotor adaptation, but no evidence of perceptual adaptation with experience. These findings add to research that demonstrates that while the motor system can be influenced by perception, it can also operate independent of perception.

Identification and Characterization of Full-Length cDNAs in Channel Catfish (Ictalurus punctatus) and Blue Catfish (Ictalurus furcatus):

Genome annotation projects, gene functional studies, and phylogenetic analyses for a given organism all greatly benefit from access to a validated full-length cDNA resource. While increasingly common in model species, full-length cDNA resources in aquaculture species are scarce. Through in silico analysis of catfish (Ictalurus spp.) ESTs, a total of 10,037 channel catfish and 7,382 blue catfish cDNA clones were identified as potentially encoding full-length cDNAs. Of this set, a total of 1,169 channel catfish and 933 blue catfish full-length cDNA clones were selected for re-sequencing to provide additional coverage and ensure sequence accuracy. A total of 1,745 unique gene transcripts were identified from the full-length cDNA set, including 1,064 gene transcripts from channel catfish and 681gene transcripts from blue catfish, with 416 transcripts shared between the two closely related species. Full-length sequence characteristics (ortholog conservation, UTR length, Kozak sequence, and conserved motifs) of the channel and blue catfish were examined in detail. Comparison of gene ontology composition between full-length cDNAs and all catfish ESTs revealed that the full-length cDNA set is representative of the gene diversity encoded in the catfish transcriptome. This study describes the first catfish full-length cDNA set constructed from several cDNA libraries. The catfish full-length cDNA sequences, and data gleaned from sequence characteristics analysis, will be a valuable resource for ongoing catfish whole-genome sequencing and future gene-based studies of function and evolution in teleost fishes.

Socioeconomic Inequality in the Prevalence of Autism Spectrum Disorder: Evidence from a U.S. Cross-Sectional Study:

This study was designed to evaluate the hypothesis that the prevalence of autism spectrum disorder (ASD) among children in the United States is positively associated with socioeconomic status (SES). A cross-sectional study was implemented with data from the Autism and Developmental Disabilities Monitoring Network, a multiple source surveillance system that incorporates data from educational and health care sources to determine the number of 8-year-old children with ASD among defined populations. For the years 2002 and 2004, there were 3,680 children with ASD among a population of 557 689 8-year-old children. Area-level census SES indicators were used to compute ASD prevalence by SES tertiles of the population. Prevalence increased with increasing SES in a dose-response manner, with prevalence ratios relative to medium SES of 0.70 (95% confidence interval [CI] 0.64, 0.76) for low SES, and of 1.25 (95% CI 1.16, 1.35) for high SES, (P<0.001). Significant SES gradients were observed for children with and without a pre-existing ASD diagnosis, and in analyses stratified by gender, race/ethnicity, and surveillance data source. The SES gradient was significantly stronger in children with a pre-existing diagnosis than in those meeting criteria for ASD but with no previous record of an ASD diagnosis (p<0.001), and was not present in children with co-occurring ASD and intellectual disability. The stronger SES gradient in ASD prevalence in children with versus without a pre-existing ASD diagnosis points to potential ascertainment or diagnostic bias and to the possibility of SES disparity in access to services for children with autism. Further research is needed to confirm and understand the sources of this disparity so that policy implications can be drawn. Consideration should also be given to the possibility that there may be causal mechanisms or confounding factors associated with both high SES and vulnerability to ASD.

Posted by Coturnix at 6:24 PM • 1 Comments • 0 TrackBacks

Suggest sessions for ScienceOnline2011

Category: SO'11

We'll probably set up the new website and organizing wiki for ScienceOnline2011 at some point over the next couple of weeks. But in the meantime, I am having trouble keeping up with all the ideas people are sending me by e-mail or via Twitter. So I have started a new page on the last year's wiki (thus old login will work for people who registered to edit the wiki over the past couple of years). Please log in and edit the page to add your ideas - sessions you'd volunteer to moderate: ScienceOnline2011 Program Suggestions.

Posted by Coturnix at 2:54 PM • 3 Comments • 0 TrackBacks

Open Laboratory 2010 - submissions so far

Category: OpenLab10

The list is growing fast - check the submissions to date and get inspired to submit something of your own - an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Read on »

Posted by Coturnix at 2:35 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

He that will not apply new remedies must expect new evils; for time is the greatest innovator.

- Francis Bacon

Posted by Coturnix at 3:58 AM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

"Cats are smarter than dogs. You can't get eight cats to pull a sled through snow."

- Jeff Valdez

Posted by Coturnix at 3:53 AM • 2 Comments • 0 TrackBacks

Another interesting graph....

Category: Blogging • Media

Click on image to check stats, play around...

Posted by Coturnix at 12:22 AM • 15 Comments • 0 TrackBacks

The PepsiGate linkfest

Category: Blogging • Media

I will not be saying anything about PepsiCo thing myself yet. I do have opinions (and decisions that come from them), but I am not revealing anything until I am ready (and it may end up being one of those horribly long posts, who knows).

But in the meantime I can put together this linkfest, so you can have a one-spot-shopping place for all the key posts about the event. I don't think this is a complete collection, and I could not order them in a chronological order (too much work, so the order is random) but close enough - the key posts/articles are here, and the comment sections are very informative as well on all of the posts.

Jennifer Ouellette

John Rennie
John Rennie

Martin Robbins

Abel PharmBoy
Abel PharmBoy
Abel PharmBoy

Columbia Journalism Review

The National Association of Science Writers blog

The Guardian
The Guardian

Gaia Vince

Rebecca Skloot
Rebecca Skloot

David Dobbs
David Dobbs

Brian Switek

Scicurious

Pal MD
Pal MD

Janet Stemwedel

Page 3.14
Page 3.14

Alex Wild

Pamela Ronald

Skulls in the Stars

Carl Zimmer

Knight Science Journalism Tracker
Knight Science Journalism Tracker
Knight Science Journalism Tracker

Colin Schultz

PZ Myers

Martin Rundquist

Orac

Grrrlscientist
Grrrlscientist

Mike Dunford
Mike Dunford

Jason Goldman
Jason Goldman
Jason Goldman

Chad Orzel

Chris Clarke
Chris Clarke
Chris Clarke

Chris Rowan and Anne Jefferson

Christie Wilcox
Christie Wilcox

DrugMonkey

Maryn McKenna

Sharon Astyk:
Sharon Astyk

Deborah Blum

John Wilbanks

Dr.Isis

James Hrynyshyn

Zuska
Zuska

Mike the Mad Biologist
Mike the Mad Biologist

Josh Rosenau
Josh Rosenau
Josh Rosenau

John Dupuis

Greg Laden
Greg Laden
Greg Laden

Dave Winer

The Dog Zombie

John Wilkins
John Wilkins

PhysioProf

David Colquhoun

Slashdot

Mark Chu-Carroll

DailyKos
DailyKos

skeptifem

Grant Jacobs
Grant Jacobs

Lab Lemming

Jonathan Eisen

Consumerist

Hank Campbell
Hank Campbell
Hank Campbell

Southern Fried Scientist

Forbes.com blog

Scholarly Kitchen

Metafilter

ERV
ERV
ERV

Adam Bly

More:

John Pavlus

Eric Michael Johnson

Liz Borkowski

DrugMonkey

Chris Rowan and Anne Jefferson

Andrew Gelman

Jay Rosen and Dave Winer

Michael Welland

Watching the Watchers

OmegaMom

Jason Rosenhouse

John Dupuis

Jennifer Jacquet

Brian Switek

DrugMonkey

Posted by Coturnix at 10:08 PM • 9 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

Courage is sometimes frail as hope is frail: a fragile shoot between two stones that grows brave toward the sun though warmth and brightness fail, striving and faith the only strength it knows.

- Frances Rodman

Posted by Coturnix at 4:10 AM • • 0 TrackBacks

An interesting chart....

Category: Blogging

From here

Posted by Coturnix at 11:53 PM • 3 Comments • 0 TrackBacks

MSM Orientation (video)

Category: Media

Posted by Coturnix at 6:28 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

You need only claim the events of your life to make yourself yours. When you truly possess all that you have been and done, which may take some time, you are fierce with reality.

- Florida Scott Maxwell

Posted by Coturnix at 3:57 AM • • 0 TrackBacks

New and Exciting in PLoS this week

Category: Science News

Sorry for missing in action. Lots of new articles in various PLoS journals yesterday and today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

A Sinister Bias for Calling Fouls in Soccer:

Distinguishing between a fair and unfair tackle in soccer can be difficult. For referees, choosing to call a foul often requires a decision despite some level of ambiguity. We were interested in whether a well documented perceptual-motor bias associated with reading direction influenced foul judgments. Prior studies have shown that readers of left-to-right languages tend to think of prototypical events as unfolding concordantly, from left-to-right in space. It follows that events moving from right-to-left should be perceived as atypical and relatively debased. In an experiment using a go/no-go task and photographs taken from real games, participants made more foul calls for pictures depicting left-moving events compared to pictures depicting right-moving events. These data suggest that two referees watching the same play from distinct vantage points may be differentially predisposed to call a foul.

Read on »

Posted by Coturnix at 10:22 PM • 1 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

The only time to eat diet food is while you're waiting for the steak to cook.

- Julia Child

Posted by Coturnix at 3:59 AM • 3 Comments • 0 TrackBacks

New and Exciting in PLoS this week

Category: Science News

There are new articles in four PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Read on »

Posted by Coturnix at 11:29 PM • • 0 TrackBacks

Future: News From The Year 2137 Trailer (video)

Category: Fun • Humor • Media

Future: News From The Year 2137 Trailer

For explanation, read this.

Posted by Coturnix at 8:25 PM • 1 Comments • 0 TrackBacks

Books: 'The Poisoner's Handbook' by Deborah Blum

Category: Books • History • History of Science • Medicine • Physiology • Technology

If you picked up The Poisoner's Handbook (amazon.com) looking for a fool-proof recipe, I hope you have read the book through and realized at the end that such a thing does not exist: you'll get busted. If they could figure it all out back in 1930s, can you imagine how much easier they can figure out a case of poisoning today, with modern sensitive techniques? And if you have read the book through, I hope you found it as fascinating as I did. Perhaps you should use your fascination with poisons to do good instead, perhaps become a forensic toxicologist?

My SciBling Deborah Blum (blog, Twitter) has done it again - written a fast-paced page-turner, full of action and intrigue, and with TONS of science in it. It reads like a detective novel. Oh, wait, it is a detective novel. Who said that an author has to invent a fictional detective, an Arsene Lupin or Hercule Poirot or Sherlock Holmes or the Three Investigators? There existed in history real people just like them, including Charles Norris and Alexander Gettler, the heroes of The Poisoner's Handbook.

Charles Norris was the first Chief Medical Examiner of the City of New York, or at least the first one who was actually qualified for that position which, before him, was a political appointment not requiring any expertise. Norris served in this role from 1918. to 1935. and revolutionized both the position and the science of forensic medicine. Alexander Gettler was one of his first appointees, who served as New York City's chief toxicologist until 1959.

The two of them used their prominent position to set the new high standards for the profession of a public medical examiner, and also set the new high standards for the scientific research in forensic pathology, including forensic toxicology - the study of the way poisons kill and how to detect it. They affected rules and legislation with their work, they sent clever murderers to the electric chair, and exonerated the innocents who were headed that way due to mistakes of the non-science-based courtroom battles. And in order to do that, they needed to do a lot of their own research during many years of long days and nights in the lab performing meticulous and often gruesome studies of the effects of various substances on animals, people, living and dead tissues and coming up with ever more sensitive and clever methods for detecting as small quantities of the poison as was technically possible at the time.

In the author's note at the end of the book, Deborah Blum notes that there were many other forensic scientists before, during and after the Norris-Gettner era, and many of them got mentioned in the book or are cited in the EndNotes (which I discovered only once I finished the book - I hate the way publishers do this these days!). But it is also true that Norris and Gettner were the leaders - they used their prominent position and political clout, and their meticulous research defined the high standards for the nascent discipline. In a way, the central importance and prominence of these two men worked well for the book - here we have two interesting characters to like and follow instead of a whole plethora of unfleshed names. And as each chapter focuses on one poisonous substance and one or two notorious cases of its use, it is just like following Holmes and Watson through a series of Sir Arthur Conan Doyle's stories - the two characters are the connecting thread, and they evolve throughout their lives and throughout the book, case by case.

Apart from being a history of forensic toxicology, the book has several other themes that keep recurring in each chapter, as they chronologically unfold. The book is also a history of 1920/30s New York City, and a history of technology and engineering. Carbon monoxide poisoning? That was the beginning of the car craze. Gas? Everyone cooked and heated with it at the time. Some other poisons were easily found in many over-the-counter products in stores and pharmacies.

Having just read On The Grid, I was also attuned to the discussions of infrastructure of NYC in the early 20th century. How did people transport themselves? Air pollution? Gas? Clean water? Wastewater? All sources of potentially toxic chemicals. How efficient was garbage collection? Not much....thus there were many rats. And rats needed to be controlled. And for that, there was plenty of rat poison to be bought. And rat poison can kill a human as well - inadvertently, as a method for suicide, or as a murder weapon. It is kinda fun to see some of the same infrastructure issues, like garbage disposal and pest extermination in N.Y.City, addressed from different angles in different books - this one, On The Grid, as well as Rats, another fascinating science book that covers New York City engineering, infrastructure and politics of the time. All the threads tie in together....

Another topic addressed in each chapter was Prohibition. One can certainly die of a huge overdose of ethyl alcohol normally found in drinks, but at the time when producing and selling drinks was illegal, people still drank, perhaps even more. And what did they drink? Whatever they could find on the black market - home-made concoctions brewed by unsavory types more interested in profit than the safety of their product. Instead of ethyl, those drinks were mostly made of methyl (wood) alcohol which is much more dangerous in much smaller doses. Prohibition saw a large increase in drinking-related deaths, a fact often loudly pronounced by Norris, leading to the eventual end of Prohibition. Can we apply that thinking to the War On Drugs now?

And the story of Prohibition has another element to it - the importance of regulation. An unregulated substance is potentially dangerous. By solving a number of poisoning cases, and by doing their research on the toxicity of then easily available substances, Norris and Gettner have managed to initiate regulation of a number of toxins, or even their removal from the market altogether. Some substances that were found in everything, even touted as health potions (even radioactive substances!!!) were discovered by forensic toxicologists to be deadly, and were subsequently banned or rigorously controlled. Today we have entire federal agencies dealing with regulation of dangerous chemicals, but in the early 20th century, it was the time of laissez-faire murder, suicide, suffering and death.

Finally, after I finished this fascinating book, I realized it gave me something more: an anchor, or a scaffolding, or a context, for every story about poisons I see now. Now every blog post on Deborah's blog makes more sense - I can fit it into a body of knowledge and understanding I would not have if I have not read the book. This really goes hand in hand with the recent discussions of #futureofcontext in journalism - see The Future Of Context for starters. The idea is that news stories do not provide enough context for readers who tune into a new topic for the first time. A story that is an update on an ongoing story is not comprehensible without some context, which the news story cannot provide. So now various media organizations are experimenting with ways to provide context for people who are just tuning in. The perfect source of context for a topic is a book, especially now that every book appears to have its own website with links and news and a blog and a Twitter feed and a Facebook page. The book provides context, and all these other things provide updates.

For example, reading Bonobo Handshake may not provide much more context for me about animal behavior and cognition since I already have that context, but it certainly now makes it easier for me to understand the news stories regarding conservation of great apes. And without that book I would never have sufficient background in the recent history of Congo to understand and appreciate this comment thread. 'On The Grid' gives me context for all news regarding infrastructure. Explaining Research is a great recent example of a book that is a great start on the topic, but which constantly reminds the reader that this field is in flux and that the book's website contains frequent updates and additional resources. The Immortal Life of Henrietta Lacks provides fantastic context for the discussions of medical ethics and its evolution in the USA in the past several decades, which I riffed off a little bit in my latest interview.

What reading The Poisoner's Handbook did for me is to give me enough knowledge and understanding on the topic that I can really appreciate it. I now get excited about news stories regarding poisons because I feel I understand them better. While reading Deborah Blum's blog was interesting before, now it is more than interesting - it is exciting and I can't wait for a new post to show up. I did not know how much I did not know. Now that I do, I want to know more. I am hungry for more knowledge, and more news, and more stories about toxins and poisons and how various strange and not so strange substances affect our bodies - where they come from, how they get in, how they hijack or disrupt our normal biochemical processes, how they kill us, and how do we figure that all out in the laboratory or in the basement of the mortuary. I hope you will feel the same once you finish reading this book. You will do that now, OK?

Posted by Coturnix at 9:19 AM • 1 Comments • 0 TrackBacks

3D Google Earth Tour of NC Maps (video)

Category: Earth • North Carolina

Posted by Coturnix at 8:11 AM • • 0 TrackBacks

Science Café Raleigh - A Nuclear Renaissance

Category: North Carolina • Science Education

Our July Science Café (description below) will be held on Tuesday 7/20 at Tir Na Nog on S. Blount Street. With the disastrous BP Gulf oil spill now continuing into its third month, every day we are reminded of the challenges our country faces with regards to our energy production and consumption. Can nuclear energy be a viable answer for some of our energy needs? Our café speaker for the evening will be Dr. David McNelis, the Director of the Center for Sustainable Energy, Environment, and Economic Development at UNC's Institute for the Environment. It should be an interesting evening for all of us to learn more about the pros and cons of nuclear power, and about how our choices about energy will impact our present and future world.

A Nuclear Renaissance

Tuesday, July 20, 2010

6:30-8:30 p.m. with discussion beginning at 7:00 followed by Q&A;

Tir Na Nog 218 South Blount Street, Raleigh, 833-7795

From its development in the 1950s and '60s to the protests against its use in the 1970s and '80s, commercial nuclear energy in the United States has always been surrounded by debate. Opponents of its use have presented possible risks to the environment and human health. Meanwhile, proponents cite it as a sustainable energy source that reduces carbon emissions and eases dependence on foreign oil. In February 2010, the federal government approved a loan guarantee for the construction of two nuclear reactors in Georgia, which would be the first plants to start construction in the U.S. since the 1970s. What does this renewed commitment to nuclear power mean to our energy future? What will it mean for our environment and our health? Come to our café and join in on a discussion of a Nuclear Renaissance.

About the Speaker:

Professor David N. McNelis has more than 45 years of environmental sciences and engineering experience in federal government, university and industry settings. He served in research and research management positions with the U.S. Army, the U.S. Public Health Service and the Environmental Protection Agency; with the Department of Energy's prime contractor for the Nevada Test Site; and with the University of Nevada, Las Vegas. He now serves as the Director of the Center for Sustainable Energy, Environment and Economic Development in the University of North Carolina at Chapel Hill's Institute for the Environment and as President of Nuclear Fuel Cycle Technologies, LLC. In addition to being a Research Professor in the Department of Environmental Sciences and Engineering at UNC, he is also an Adjunct Professor in the Department of Nuclear Engineering at NCSU. Currently Dr. McNelis specializes in conventional, alternative and nuclear energy systems and technologies and the nuclear fuel cycle (including partitioning, transmutation, repository capacity and nuclear non proliferation).

This café is sponsored by Progress Energy.

Posted by Coturnix at 7:01 AM • 2 Comments • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

Matisse makes a drawing, then he makes a copy of it. He recopies it five times, ten times, always clarifying the line. He's convinced that the last, the most stripped down, is the best, the purest, the definitive one; and in fact, most of the time, it was the first. In drawing, nothing is better than the first attempt.

- Pablo Picasso

Posted by Coturnix at 4:17 AM • • 0 TrackBacks

Virtual 'Frog Dissection' iPad app (video)

Category: Fun • Science Education • Technology

I can see this as instructional material while dissecting a real frog, getting a feel for its texture, smell, seeing the individual differences between the way multiple frogs look on the inside, but not as a replacement of the real thing. What do you think?

Posted by Coturnix at 2:25 PM • 6 Comments • 0 TrackBacks

Books: 'On The Grid' by Scott Huler

Category: Books • North Carolina • Society • Technology • Workplace

About a month ago, I told you about the book-reading event where Scott Huler (blog, Twitter, SIT interview) read from his latest book On The Grid (amazon.com). I read the book immediately after, but never wrote a review of my own. My event review already contained some of my thoughts about the topic, but I feel I need to say more, if nothing else in order to use this blog to alert more people about it and to tell everyone "Read This Book".

What I wrote last month,

"I think of myself as a reasonably curious and informed person, and I have visited at least a couple of infrastructure plants, but almost every anecdote and every little tidbit of information were new to me. Scott's point - that we don't know almost anything about infrastructure - was thus proven to me."

...was reinforced when I read the book itself: I don't know anything about infrastructure. But after reading the book I can say I know a little bit, understand how much I don't know, and realize how much more I'd like to know. I bet it was fun watching me as I was reading it, exclaiming on average five times per page "This is so cool", and "Hey, this is neat" and "Wow, I had no idea!" and (rarely) "w00t! Here's a tidbit I actually heard of before" and "Hey, I know where this is!" (as I lived in Raleigh for eleven years, I know the area well).

A few years ago, Scott was just as ignorant about infrastructure as most of us are. But then his curiosity got better of him and he started researching. He would start at his house in Raleigh and trace all the wires and cables and pipes going in and out of the house to see where they led. Sometimes there would be a crew on his street digging into the asphalt and fixing something and he would approach them and ask questions. At other times he would figure out where the headquarters are and who to ask to talk to:

"What Scott realized during the two years of research for the book is that people in charge of infrastructure know what they are doing. When something doesn't work well, or the system is not as up-to-date as it could be, it is not due to incompetence or ignorance, but because there is a lack of two essential ingredients: money and political will. These two factors, in turn, become available to the engineers to build and upgrade the systems, only if people are persuaded to act. And people are persuaded to act in two ways: if it becomes too costly, or if it becomes too painful to continue with the old way of doing things. It is also easier to build brand new systems for new services than it is to replace old systems that work 'well enough' with more more modern ways of providing the same service."

In a sense, this book is a memoir of curiosity as Scott describes his own adventures with a hard-hat, a modern Jean Valjean sloshing his way through the Raleigh sewers, test-driving the public transportation, and passing multiple security checks in order to enter the nearby nuclear plant.

But it is more than just a story of personal awe at modern engineering. Scott weaves in the explanations of the engineering and the underlying science, explains the history and the politics of the Raleigh infrastructure, the historical evolution of technologies underlying modern infrastructure, and illustrates it by comparisons to other infrastructures: how does New York City does that, how did Philadelphia did it 50 years ago, how did London 500 years ago, how about Rome 2000 years ago?

"What is really astonishing is how well the systems work, even in USA which has fallen way behind the rest of the developed world. We are taking it for granted that the systems always work, that water and electricity and phone and sewers and garbage collection and public transportation always work. We get angry on those rare occasions when a system temporarily fails. We are, for the most part, unprepared and untrained to provide some of the services ourselves in times of outages, or to continue with normal life and work when a service fails. And we are certainly not teaching our kids the necessary skills - I can chop up wood and start a wood stove, I can use an oil heater, I know how to slaughter and render a pig, how to get water out of a well, dig a ditch, and many other skills I learned as a child (and working around horses) - yet I am not teaching any of that to my own kids. They see it as irrelevant to the modern world and they have a point - chance they will ever need to employ such skills is negligible."

And this brings me to the point where I start musing about stuff that the book leaves out. As I was reading, I was constantly hungry for more. I wanted more comparisons with other cities and countries and how they solved particular problems. I wanted more history. I wanted more science. I wanted more about political angles. But then, when I finished, I realized that a book I was hungry for would be a 10-tome encyclopedic monograph and a complete flop. It is good that Scott has self-control and self-discipline as a writer to know exactly what to include and what to leave out. He provides an excellent Bibliography at the end for everyone who is interested in pursuing a particular interest further. His book's homepage is a repository for some really cool links - just click on the infrastructure you are interested in (note that "Communications" is under construction, as it is in the real world - it is undergoing a revolution as we speak so it is hard to collect a list of 'definitive' resources - those are yet to be written):

What many readers will likely notice as they go through the book is that there is very little about the environmental impacts of various technologies used to ensure that cities function and citizens have all their needs met. And I think this was a good strategy. If Scott included this information, many readers and critics would focus entirely on the environmental bits (already available in so many other books, articles and blogs) and completely miss what the book is all about - the ingenuity needed to keep billions of people living in some kind of semblance of normal life and the interconnectedness that infrastructure imposes on the society, even on those who would want not to be interconnected:

"There are people who advocate for moving "off the grid" and living a self-sufficient existence. But, as Scott discovered, they are fooling themselves. Both the process of moving off the grid and the subsequent life off the grid are still heavily dependent on the grid, on various infrastructure systems that make such a move and such a life possible, at least in the developed world."

My guess is, if there's anyone out there who could possibly not like this book, it will be die-hard libertarians who fantasize about being self-sufficient in this over-populated, inter-connected world.

At several places in the book, Scott tries to define what infrastructure is. It is a network that provides a service to everyone. It has some kind of control center, a collection center or distribution center. It has a number of peripheral stations and nodes. And there are some kinds of channels that connect the central place to the outside stations and those stations to the final users - every household in town. There is also a lot of redundancy built into the system, e.g., if a water main breaks somewhere, you will still get your water but it will come to you via other pipes in surrounding streets, with zero interruption to your service.

Scott covers surveying of land, stormwater, freshwater, wastewater, roads, power, solid waste, communications (phone, broadcast media, internet) and transportation (e.g., public transportation, trains, airplanes). These are the kinds of things that are traditionally thought of as 'infrastructure'. But aren't there other such systems? I'd think security has the same center-spokes model of organization as well: police stations and sub-stations (distribution centers) that can send cops out wherever needed (distribution channels), with potential criminals brought to court (processing centers) and if found guilty placed in prison (collection center). Similarly with fire-departments. Ambulances are just the most peripheral tentacles of the health-care infrastructure. The local-county-state-federal political system is also a kind of infrastructure. So is the military. So is the postal system. So is the food industry and distribution.

Thinking about all of these other potential examples of infrastructure made me realize how many services that require complex infrastructure undergo cycles of centralization and decentralization. For transportation, everyone needed to have a horse. Later, it was centralized into ship, railroad, bus and airline infrastructures. But that was counteracted by the popularity of individually owned cars. And of course taxis were there all along. And as each decade and each country has its own slight moves towards or away from centralization, in the end a balance is struck in which both modes operate.

You raised your own chickens. Then you bought them from mega-farms. Now many, but not most citizens, are raising their own chickens again. It is not feasible - not enough square miles on the planet - for everyone to raise chickens any more. But having everyone fed factory chicken is not palatable to many, either. Thus, a new, uneasy balance.

Nowhere is this seen more obviously today as in Communications infrastructure. We are in the middle of a big decentralization movement, away from broadcast (radio, TV and yes, newspaper industry infrastructure with its printing presses, distribution centers and trucks) infrastructure that marked about half of 20th century, and forward into something more resembling the media ecosystem of the most of human history - everyone is both a sender and a receiver, except that instead of writing letters or assembling at a pub every evening, we can do this online. But internet is itself an infrastructure - a series of tubes network of cables and it is essential not to allow any centralized corporation to have any power over what passes through those cables and who gets to send and receive stuff this way.

Finally, as I was reading the book I was often wishing to see photographs of places or drawings of the engineering systems he describes. As good as Scott is at putting it in words, there were times when I really wanted to actually see how something looks like. And there were times when what I really wanted was something even more interactive, perhaps an online visualization of an infrastructure system that allows me to change parameters (e.g., amount of rainfall per minute) and see how that effects some output (e.g., rate of clearing water off the streets, or speed at which it is rushing through the pipes, or how it affects the water level of the receiving river). That kind of stuff would make this really come to life to me.

Perhaps "On The Grid" will have an iPad edition in the future in which the text of the book is just a beginning of the journey - links to other sources (e,g., solutions around the globe, historical sources), to images, videos, interactive visualizations and, why not, real games. After all, it is right here in Raleigh that IBM is designing a game that allows one to plan and build modern infrastructure - CityOne. These two should talk to each other and make something magnificent like that.

Cross-posted from Science In The Triangle.

The small images are thumbnails - click on each to see the whole picture, full-size.

Posted by Coturnix at 11:20 AM • 1 Comments • 0 TrackBacks

Open Laboratory 2010 - submissions so far

Category: OpenLab10

The list is growing fast - check the submissions to date and get inspired to submit something of your own - an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

Read on »

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Clock Quotes

Category: Clock Quotes

A signature always reveals a man's character - and sometimes even his name.

- Evan Esar

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Clock Quotes

Category: Clock Quotes

To pierce the curtain of the future, to give shape and visage to mysteries still in the womb of time, is the gift of the imagination. It requires poetic sensibilities with which judges are rarely endowed and which their education does not normally develop.

- Felix Frankfurter

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Clock Quotes

Category: Clock Quotes

"Cats aren't clean, they're just covered with cat spit."

- John S. Nichols

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I'm a Social Media Guru (video)

Category: Blogging • Fun • Technology

On the other hand....read: Lesson From Social Media Day: I'm An Expert, Too.

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New and Exciting in PLoS ONE

Category: Science News

There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Radiographs Reveal Exceptional Forelimb Strength in the Sabertooth Cat, Smilodon fatalis:

The sabertooth cat, Smilodon fatalis, was an enigmatic predator without a true living analog. Their elongate canine teeth were more vulnerable to fracture than those of modern felids, making it imperative for them to immobilize prey with their forelimbs when making a kill. As a result, their need for heavily muscled forelimbs likely exceeded that of modern felids and thus should be reflected in their skeletons. Previous studies on forelimb bones of S. fatalis found them to be relatively robust but did not quantify their ability to withstand loading. Using radiographs of the sabertooth cat, Smilodon fatalis, 28 extant felid species, and the larger, extinct American lion Panthera atrox, we measured cross-sectional properties of the humerus and femur to provide the first estimates of limb bone strength in bending and torsion. We found that the humeri of Smilodon were reinforced by cortical thickening to a greater degree than those observed in any living felid, or the much larger P. atrox. The femur of Smilodon also was thickened but not beyond the normal variation found in any other felid measured. Based on the cross-sectional properties of its humerus, we interpret that Smilodon was a powerful predator that differed from extant felids in its greater ability to subdue prey using the forelimbs. This enhanced forelimb strength was part of an adaptive complex driven by the need to minimize the struggles of prey in order to protect the elongate canines from fracture and position the bite for a quick kill.

Is Thermosensing Property of RNA Thermometers Unique?:

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at various temperatures using the RNA folding software Vienna. In this study, we compared the thermosensing property of 100 randomly selected mRNAs and three well known thermometers - rpoH, ibpA and agsA sequences from E. coli. We also compared the rpoH sequences from 81 mesophilic proteobacteria. Although both rpoH and ibpA show a higher rate of melting at their RBS compared with the mean of non-thermometers, contrary to our expectations these higher rates are not significant. Surprisingly, we also do not find any significant differences between rpoH thermometers from other -proteobacteria and E. coli non-thermometers.

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Who are you, again?

Category: Blogging • Housekeeping

I see - DrugMonkey, Janet, Pal and Jason are reviving the annual tradition of asking readers to say in the comments who they are. I did this in 2008 bit can't find if I did it in 2009. The original questions and instructions are:

1) Tell me about you. Who are you? Do you have a background in science? If so, what draws you here as opposed to meatier, more academic fare? And if not, what brought you here and why have you stayed? Let loose with those comments.

2) Tell someone else about this blog and in particular, try and choose someone who's not a scientist but who you think might be interested in the type of stuff found in this blog. Ever had family members or groups of friends who've been giving you strange, pitying looks when you try to wax scientific on them? Send 'em here and let's see what they say.

But my blog is different - many different topics and only a handful of posts per year really dissecting a scientific study. There is much more about media, science journalism, blogging, social networking, communications, science publishing, Open Access and that kind of stuff. And videos. And I am always surprised how many people (including veteran serious bloggers) really like Clock Quotes! They get comments here and on FriendFeed and Facebook.

So, tell me also what kinds of posts you like here? What makes you keep coming back for more? What would you like me to do more? And also, what do you skip and ignore?

Posted by Coturnix at 5:34 PM • 8 Comments • 0 TrackBacks

Today's carnivals

Category: Carnivals

49th edition of the Festival of the Trees is up on The Organic Writer

Friday Ark #302 is up on Modulator.

Posted by Coturnix at 4:47 PM • • 0 TrackBacks

Clock Quotes

Category: Clock Quotes

If there were no schools to take the children away from home part of the time, the insane asylum would be filled with mothers.

- Edgar Watson Howe

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