Monthly Archives: July 2010

Is this something that NYTimes editors proudly allowed to get published?

A certain Virginia Heffernan (not known for being a zealot about great accuracy) published a piece in the New York Times Magazine section that is probably the very worst ever written about Scienceblogs.com, about science blogging, about blogging in general, about science, and about journalism – Unnatural Science.

Not much to say there – fisking line-by-line would be a useless pursuit and would take too much time.

Brief summary: society is suffering because science is taking over and fuzzy thinking is in retreat; Scienceblogs.com = science blogs, but she wouldn’t know since she doesn’t read them (but can write about them nonetheless); bloggers are mean, especially to the poor innocent religious types; peak oil is not a serious problem; a few misquotes; an open admission that she does not care about journalistic ethics very much; suggested readings: Derrida and the biggest climate change denialist blog. ‘Nuff said.

But if you want to read more, check out excellent responses by Zen Faulkes, Jason Goldman, Scott Rosenberg, P.Z. Myers and David Dobbs. Update: Also see commentary by Chad Orzel, Tim Lambert, ERV, Daniel Lende, T. Ryan Gregory, John Wilkins, Dave Wescott, Mike the Mad Biologist, Paul Raeburn, Dave Winer, Steve Mount, Joe Romm, Kathy Gill, Cheryl Rofer, Sharon Astyk and David Orr. Update 2: Also Andrew Sullivan, Jamie Vernon, David Wescott, Zen Faulkes, Chad Orzel, Jason Rosenhouse, gfish and Brian Switek.

On the Shoulders of Giants

…but skipping a few generations of ever smaller and smaller Giants in-between.

There will be more….but this pairing so far is awesome 😉

Bloggers, Evolving

Four stories today, each about bloggers and writers evolving and reminiscing about their trajectories as persons and as writers.

First out, my friend Anton Zuiker is celebrating his Tenth Blogiversary! Now that is a long blogging career! Happy blogiversary, Anton! On this occasion, Anton traces back his blogging history in a wonderful piece, and also links to a report about blogging he wrote all the way back in 2002 – Blog Together (the title of which later became the name of our local bloggers organization). Anton certainly bootstrapped the local blogging community!

I have used ecological metaphors to describe what just happened in the science blogosphere, but it takes an ecologist to really get that metaphor right. Delene certainly did, and added more thoughts about her own niche in that new ecosystem – Science blogs and ecosystem disturbance (Delene is also celebrating her blogiversary today – her first).

Over on HASTAC blogs, Cathy Davidson is wondering about her own blogging personality – Who Am I? The Multiple Personalities of a Blogger.

Finally, Ed Yong asked a bunch of science writers and bloggers to give their own stories how they became involved in science communication, and many of the most prominent ones have already responded (and you can, too) at On the Origin of Science Writers.

Sciencey Blog carnivals

I am just trying to put together a list of extant blog carnivals with science, nature and medical topics here. I am particularly interested in RSS feeds that track new editions as they go live. Please let me know in the comments if I missed some, or if there is a better homepage (or a good feed) to use to track these carnivals.

Scientia Pro Publica

Scientiae

The Giant’s Shoulders

Berry Go Round

Festival of the Trees

Grand Rounds

Change of Shift

Circus of the Spineless

Carnival of the Blue

The Carnal Carnival

Carnival of the Green

I and the Bird

Carnival of Evolution

The Accretionary Wedge

Carnival of Space

An Inordinate Fondness

House of Herps

The Moth and Me

The Fourth Stone Hearth

Cancer Research Blog Carnival

SurgeXperiences

Health Wonk Review

The MolBio Carnival

Friday Ark (does not seem to have up-to-date archives)

Science Blogging Networks: What, Why and How

Continuing with the theme from my ‘farewell to scienceblogs‘ post, I want to do some more thinking, out in public, about the current changes in the science blogging ecosystem. This post is probably going to end up being just a set of meandering thoughts and I hope people continue the discussion in the comments.

So, let’s start with history and then see how it may illuminate the present.

Inception of the Scienceblogs.com model

In 2006, Scienceblogs.com grew from initial 14 to about 45 blogs. At the time, there were only a couple of hundred science blogs written in English. Thus, the proportion of science blogs that were on Sb was huge, perhaps as many as 10% of them all were hosted on the network.

In 2006, one could argue that blogs on Scienceblogs.com included some or most of the “best” blogs, as well as a representative sample. Seed certainly targeted blogs that were well written and reliable. And Seed definitely tried to collect a diversity of topics, formats, styles and voices.

But Seed also biased their sample in two important ways:

First, they, initially at least, invited bloggers who already, for the 2006 standards, had large traffic. This was definitely a good strategy – the one that made them an instant success in comparison to other (some even older) networks who tried to get non-bloggers to become bloggers (and popular at that) over night. By joining the Seed’s network, these already popular bloggers brought their readers with them, immediately increasing the visibility of the network and immediately increasing the readership of the other blogs on the network. In 2006, some (though not all) science bloggers with the largest traffic, got to be popular by regularly tackling controversial topics (medical woo, pseudoscience, creationism, politics, religion, global warming, etc.) or by giving voice to groups that were up till then invisible in the society and mainstream media (e.g., female scientists, graduate students and postdocs revealing how the world looks like from their perspective, atheists, etc.). Those topics are very important, but are not representative of the broader science blogosphere any more.

Second, Seed initially invited the bloggers who posted frequently. It is not a bad idea, when starting a new network, to make sure there will be plenty of new content appearing all the time. But that kind of frequent blogging style is more of an exception than the norm. Very few bloggers naturally post with the frequency of PZ Myers, Ed Brayton, Grrrlscientist, Greg Laden or myself. And especially in science blogging, writing a detailed, high-quality post about science takes some time, research and effort which most of us cannot summon every day, let alone multiple times a day.

The popularity and visibility of Sb led many people to think “Hey, I can do this” and today there are thousands of science blogs out there. This means that even with 80+ blogs on the network (as of couple of weeks ago, now around 60), the SciBlings represented only a tiny sliver of the science blogosphere, perhaps around 0.1% (totally inventing the numbers here, but these things – what is an active science blog, for example – are very difficult to define, track and calculate).

Over the four years, the science blogging ecosystem changed. Many of us blogging at Scienceblogs.com also changed. Some noticeably reduced their posting frequency (perhaps moving some of the formerly bloggy material over to Twitter or Facebook). Others changed their interests and topics – this is normal as people change and their blogs evolve. These days I blog about scientific papers quite rarely, but blog often about the ways the Web is changing the world of scientific publishing, science journalism, science communication and science education. I completely understand that people who were reading my blog four years ago may not find my current blogging interesting any more (and vice versa).

Thus, in 2010, the Scienceblogs.com stable is even less representative than in 2006. And with thousands of science blogs out there, many of them excellent, nobody can claim that the blogs on Sb are “the best” any more. Some are among the best, but there are many more “best blogs” in the world not on Sb. But as the Scienceblogs.com network was huge, and hugely visible, and hugely respected, and hugely watched by MSM, all those wonderful science blogs outside the network were essentially invisible, living in the shadow of Sb and hoping we’d link to them sometimes (which we tried to do often, but that is not enough). It is like in the Mesozoic – all those tiny little shrew-like mammals hiding in underground burrows and foraging for seeds at night, being unable to spread into any other niches because the big, dangerous dinosaurs are roaming around the land.


[Image source]

But as the ecosystem was changing, the dinosaurs started feeling a little ill (at least for the past year or so). And then at one point, a giant asteroid (with a Pepsi logo on it) hit the Earth and the giant dinosaurs went extinct.

Now, looking at what is happening at Sb today, I feel that the network will survive, at least for a while. But it will be a smaller, more nimble network in which bloggers have a much bigger voice. The series of defections, followed by the blogger strike, and the management’s response to it suggest that from now on bloggers will be very much calling the shots, as they are the only viable part of the enterprise. Bloggers on the network are all experts in (self)promotion or they would never have ended on Sb in the first place. They can come up with fascinating ideas how to promote the network – and themselves as a part of it – that no traditionally trained PR person can even imagine. So, if the new model for Scienceblogs.com will be more along the lines of Workers’ self-management (also see), then we may see a continued evolution and continued high relevance of this network in the future – after all, dinosaurs are still around us, and they are very beautiful and nimble, though small: we now call them ‘Birds’.

But in the meantime, while Sb is rethinking itself, it is obvious that its size and reputation is smaller. This suddenly opened up the space for many other players to come in. An adaptive radiation of mammals after the K-T boundary, if you will….


[Image source]

The Present

So, there is an awful lot of evolutionary experimentation going on right now. Existing networks are expanding and changing their technological architecture to accommodate the growth. Individual blogs are turning into group blogs. Group blogs are turning into blogging networks. Brand new networks are being built. There will be successes and there will be failures, but when everything settles down, we will probably see a very different environment. Instead of one large island, there will be an entire archipelago of smaller islands. And the new ecosystem requires a new behavior in it, and a new way of thinking about it.

Take a look at my Blogroll on the right – most of that list are various science blogging networks. Some are run by big newspapers (The Guardian), several by popular magazines (National Geographic, Wired, Scientific American, Psychology Today, as well as Burda in Germany), some by university programs for science journalism (Scienceline, Elements), some by scientific publishers (Nature), some by scientific societies (American Chemical Society) and several are self-governing blogger cooperatives (interestingly, often aggregated around a single topic). Each of these networks thus has a somewhat different goal, and a different ‘business model’.

What worries me is that so many of these networks are trying to copy what Seed did in 2006. Now, don’t get me wrong – as I stated in my farewell post, Seed did many things right. Christopher Mims who conceptualized, started and then ran the network for the first six months was a visionary – some of the things he did with scienceblogs.com are now so “normal” that nobody can think how it could possibly be done any differently. It is certainly a good idea for all the other networks to analyze what Seed did right and what Seed did wrong, then to apply those lessons to their own goals and concepts. But they should also realize it is not 2006 any more. Four years are a millennium in Internet Time. The world has changed.

What is the overall goal?

My assumption is that most science blogs are tools for communication, popularization and education of science. The goal is to turn the world (including the individual nations in it) into a “scientific” world, aka, into a reality-based world.

If you think of science communication as a series of concentric circles, at the center are data. The only readers capable of understanding raw data are computers. Once computers analyze and visualize data, those can be understood by experts. But just like dumping reams of data online by WikiLeaks does not make an impact, raw data in science also do not make an impact on their own. Just like WikiLeaks outsources story-telling to the Media, so data need someone to turn them into a story. Those stories, the next bigger concentric circles, are scientific papers, readable (as of now, but this may change) mainly by other people in the same scientific field. The discussions going on in the comments on the papers (and this will, over time, become more common-place as more journals adopt the practice and people get used to seeing it everywhere) are the next circle.

The next big step is to translate those papers and discussions into something that can be understood by people outside of the narrow discipline – the lay audience. That lay audience is also stratified. A scientist in one field is lay audience for another field, but is highly educated and tends to think like a scientist. Then there are generally well educated people who are interested in science. And then there are people who don’t even know if they would be interested in science. Thus, there need to be several different levels of presenting science to the lay audience. And there need to be both “pull” (for interested audience) and “push” (for not yet interested audience) strategies for disseminating scientific information.

The “pull” outlets are science-specific, e.g., dedicated science pages in newspapers, science channels on cable TV, science programs on radio, popular science magazines, popular science books, and science blogs. They are seen by people with interest in science, and easily avoided by those who don’t care. Such outlets span a range of levels, from kids to scientists in other fields. Communication in this outlets is generally pretty good, with bloggers doing a great job at pitching to somewhat higher levels – the educated audience that is very interested in science (including scientists in other fields). This is also the level that is not at all covered by any of the legacy media, and has been missing until recently.

The “push” outlets are general media that may throw a science story into the mix. Such stories can be in papers, magazines, radio, TV, movies, eclectic websites, etc. Such stories tend to be written by general reporters, not specialist science journalists, and thus tend to be awful. But it is the bloggers who do a great job correcting such stories and ‘schooling’ journalist who make mistakes (who may, if their egos allows them, listen and learn and get better).

Both the push and pull versions of the traditional media have a large audience. But bloggers still don’t. Congregating into networks is what turns bloggers into Media, makes them highly visible to the legacy media that will spread stories (or correct their own) and make their spread and reach much wider. Building blogging networks is an application of the use of the ‘network effect’ to make this effort more efficient, by giving the bloggers greater visibility both to casual Web surfers and to the traditional media. Just like WikiLeaks is a global, non-national, crowd-sourced media organization that needs legacy media to make an impact with their stories, so blogging networks are also global, non-national (usually), crowd-sourced media organizations that need to be visible by legacy media in order to have their stories spread widely enough to make an impact.

The mindset that the world is a competitive place, where one company or organization will win and the others will go bankrupt (think of VHS beating Betamax and V2000), is a 20th century mindset. Yes, Google is the best and most popular search engine, but there are others and those others still are used by millions of people who have their own, often good, reasons for making that choice. Today, an ecosystem in which multiple, perhaps many, producers of the same thing, coexist, collaborate, co-depend, is becoming more and more of a reality in more and more areas of life, from globalization of the world (One Remaining Superpower model is gone, if you have not noticed), to industry, to publishing, to the Web. And so it is with science communication, which includes, among else, science blogging networks – many, not just one.

Instead of one huge network, there will be a couple of dozen smaller ones. Sharing similar goals, the networks should be collaborative, not competitive. Each network should display widgets showcasing the most recent posts from all the other networks. There should be a central place that sends people to all the networks. There should be common offline events. There should be actions that all networks participate in. Any network that decides to stay out of these things would self-isolate. And just like the world itself is now interconnected and being isolated does not work for you very well (think: North Korea), so blogging networks are interconnected and being isolated will not work for you either – nobody pays attention to you, and when they do they do not say nice things about you, you cannot control your own message and cannot respond to other people’s messages.

What does it mean to be a blogger these days?

Four years ago, one’s blog was the main and probably only way to communicate online. Blogging networks being blogging networks made perfect sense.

But today, there are many other ways to communicate online. One may exchange information on Twitter, discuss it on FriendFeed, keep social connections alive with friends (and blog fans) on Facebook, post shorter ideas on Posterous, cartoons and videos and quotes on Tumblr, upload videos on YouTube, podcasts on Imeem, slideshows on Slideshare, travel photos on Flickr or Picassa, art on DeviantArt, sell art on Etsy or swag on Zazzle (or CafePress), publish books on Lulu.com, submit scientific manuscripts to PLoS journals, edit Wikipedia, review books on Amazon or Shelfari, and use the blog only for longer, original, well-researched or more thoughtful pieces.

Different people will use their blogs in different ways, for different purposes, but in most cases the blog is not the only means of communication. If you go to an independent blog, you will often see not just the content of the blog but also a whole host of buttons and widgets showing that person’s online (and offline, including professional) activities elsewhere. I just started playing with WordPress, but you can already see on the right sidebar my latest tweets, the FriendFeed widget, links to ScienceOnline and to the Open Laboratory books, and to the homepage where you can find all sorts of buttons leading you to other places I can be found online.

For some people, their blog is their central place and all the other activity is satellite. For others, the focus may be on their MSM work, or their books, or activity on Twitter, and blog is just one of many “other places” where they sometimes do something interesting.

I think new blogging networks have to take this reality into consideration. Be networks of interesting people, whatever they do, not just networks of blogs. Help them showcase everything they do, not just blogging. And if, for technological or managerial reasons, an individual blogger is not capable of showing exactly where the blog sits in their own online work, they will not like it, and they will leave. No way to put all those widgets on the sidebar? The blog then feels isolated from the rest of that person’s work instead of as an integral part of it. The person will feel as giving up too much of their own personal ecosystem for the good of the network’s ecosystem.

Accommodate people who are infrequent bloggers, but do other interesting stuff (i.e., no frequency requirements at all). Promote their videos, podcasts, photography, art, books… Have an easy-to-find list of all of your bloggers’ Twitter feeds.

But serious content, the kind people put on blogs, still needs to be central to the project. Otherwise, it is just another social network (one of several dozen failed “facebooks for scientists”). While networking is important, good content is more than important: it is essential. I am watching Science 3.0 these days – less than a month old, thus no established blogs there as yet, but an interesting concept of putting together everything the members do.

Also, consider a way to preserve some of the content longer than the fleeting moment of a blog post. Collect “Basics” posts in one place, or have the bloggers collaborate on building so-called “explainers” on various topics. Such explainers would contain material at different levels – from kids to expert and everything in-between, including raw data and scientific papers, all clearly marked as to who the intended audience is. Such explainers would be updated (perhaps by editing, wiki-style, with preserved history of editing) as new information comes in. Such pages would also contain links to all the blog posts that the network has produced on that topic, and bloggers would likely send their readers to the Explainer page whenever they blog about that topic again. Build something more lasting out of the bloggers’ work.

Mobility and Exclusivity

This is a unique moment in the history of science blogging networks. This is the only time when people leaving a network are regarded as “hot property” and are actively courted by other networks. Being a SciBling has a certain element of reputation that other networks are now trying to capitalize on. At least six or seven networks have talked to me so far and I have yet to give a strong Yes or a strong No to any one of them. May even go solo for a little while longer.

Also, until now, it was difficult to leave the network – you leave Sb to go where? Into the dark abyss of anonymity and invisibility. Thus many people hung on….

But once there is an archipelago of networks, each roughly equally visible and respected, it will be easy to move from one to another. You join one, try it out for a month or two and, if you don’t like it, move on to another one. Networks should anticipate this, and implement a mechanism for easy move of bloggers in and out.

While networks will provide visibility and traffic, they will not automatically turn a blogger into a hot-shot any more. It is like good peer-review (or good editorial decisions in the media) – a blogger on a network has a seal of approval that s/he is OK, not spouting non-scientific nonsense, but there is no guarantee that the person is one of the elite best. For actual reputation, being a member of a network will not be sufficient any more – that, you will have to build for yourself, as an individual.

The exclusivity of the networks (“you can blog with us and nobody else”) has been eroding for quite a while now. At the beginnings of Scienceblogs.com we were expected to close our old blogs and move them to the network. Razib had quite a problem for continuing to run Gene Expression Classic. It is much more common now for bloggers to contribute to multiple personal, individual, corporate or group blogs, and even to have blogs on two or more networks. This will become even more common in the new ecosystem and any network that asks for exclusivity will not find many bloggers willing to join.

Building and Maintaining Community

With the ease of movement from one network to another, and with the ease of having a blog on multiple networks, how does any individual network get to keep anyone on board? How does one build loyalty? After all, each network is now just one node in the network, and many bloggers will feel a loyalty to the broader community but much less loyalty to the particular network they are on. It is also much easier to be a solo blogger today, as RSS is everywhere (no need to use Google Reader for it – RSS imports are on every social networking platform and more), social networking sites are busy, and multituded of networks will have to pay more attention to them now, if nothing else scouting for new talent.

One obvious way is money. If the business model allows it, and if finances allow it, pay more than the other networks, and this will persuade at least some people to come and to stay for quite a while. Bloggers on networks are media, thus they should be paid for their work, just as if they were journalists in a more traditional outlet.

Don’t pay by page-view. This creates internal hierarchies. This also creates pressures (even if there is no formal frequency minimum requirement in the contract) to post often and to post controversial stuff and to post silly stuff, diluting the science content on the network. Every month when you calculate the earnings and deduct the costs, share the rest equally among all members of the community, regardless of how much they contributed either by frequency of posting or by traffic.

Another obvious way is the opposite – promise never to have ads, never to have corporate interests involved, and never to pay anyone for anything. This is definitely appealing to some bloggers who draw salaries elsewhere and for whom complete editorial freedom and complete perception of ethical purity are essential.

Another way is to have kick-ass technical support. This is a big reason some bloggers like to be on the networks. They may have too large a traffic to be able to deal with it on their own. Or they may be too busy to deal with it. Or they may be great writers but with essentially zero technical skills. Reliable technology is a big plus. And rumors and gossip about the quality of tech support on various networks spread fast and wide.

Also, use platforms that are easy for bloggers to use and customize. These days, multi-blog WordPress seems to be in the lead. Drupal is great for developers and for making parts of the site that bloggers will not touch, but is non-intuitive and cumbersome for the non-techie users. MoveableType4 got clunky over time and requires tech support with high level of expertise and seems to be hard to be flexible with – you are building a site not just for 2010 but also a site that can nimbly change as the Web changes. One day Scripting2 will be available for everyone, and it is perfect for bloggers like me who write long posts – the asides, explanations of the basics, references, link-lists, things I inject into my posts as full paragraphs now can be hidden at first read and revealed by those who want to see them by a single click.

If you combine clunky tech-support, and no access to traffic data, with limits to editorial freedom, you get a revolt on your hands and people start leaving. If business ideas trump everything else, you’ll run afoul of the bloggers’ ethics and they willl leave really fast.

Make sure that blogs on your network have a good mobile version. Design good apps for iPhone and Ipad. Make sure your bloggers get them for free.

Provide cool swag. I have collected four Sb mugs over the past four years, one for each member of the family, and they are our favorites – I am actually drinking coffee from one of them right now. I have a t-shirt that says “Coturnix” on the back, with an Sb logo. Seed has provided, in the early years, swag for us to give to readers in contests. That is cool stuff.

Provide backchannel forums. Any platform will do, though I personally prefer Groupsite.com (formerly known as Collective X) as there is a possibility for exchanging large files, having rich profiles, having easy-to-find documents (e.g., How-To manuals for tech questions), having forums for organizing synchronized action, etc. Count on some members not participating there – there are some SciBlings who never logged into the back forums and thus never really felt like members of the community (and were also wildly uninformed about what is going on). Thus, if a network is too small (e.g., 10 or less), you’ll end up with three people chatting in the forums – that is not a community. Be a part of that forum yourself, regularly. Continuous conversation between bloggers and overlords is essential for developing trust, and thus loyalty.

Organize common actions. DonorsChoose drive every October was a great community-building activity on Scienceblogs.com, for an example.

See how your company/organization can help your bloggers’ careers. For example, if yours is a media company, you can help bloggers write for and get published in your magazine. If they publish a book, promote it. Promote the network and the individual bloggers in your promotional materials, in your magazine, on your website, etc. Also, ask bloggers to promote the network wherever they may be – especially if they go to conferences. Give them swag and let them spread the word about you.

Bloggers who come from a journalistic background want to learn how to use all these newfangled online tools. Bloggers who came from other (mainly scientific/academic) backgrounds want to widen their toolbox to include some of the traditional media. Help both groups as much as you can.

Organize offline events. Blogs are a means to finding people to do rhythmic things with. The two SciBlings meetups in 2007 and 2008 in NYC were amazing events! We gelled so well together as a group. We shared several meals, drank a lot, sang karaoke, met with our readers, met Adam Bly and others in the management, visited Seed offices, took group pictures, got tons of swag. It was a blast. It did wonders for our sense of identity as a group. Likewise, the 1.000,000th Comment parties were awesome – the NC event was at the Asheville Zoo with several SciBlings and several readers, followed by dinner.

And for the building of a broader community that includes all the networks, just come to ScienceOnline every January (the 2011 version is likely to be heavily invested in the building of the new ecosystem, so don’t miss it!), send your Overlords and a bunch of your bloggers, send swag, put up posters, moderate sessions, do a Demo of your network, promote Open Laboratory (and your own bloggers’ posts that made it into the latest edition) on your site, be a generous part of the new ecosystem and your own bloggers will love you for it.

Diversity

Make your network attractive to bloggers, feeling welcome there. If The Usual Suspects invite other Usual Suspects, A-listers invite other A-listers, a bunch of buddies who are all white men invite each other, you will have a problem. The first thing the blogosphere will notice, within the first millisecond of unveiling your network, is that there is no diversity on your network, just an Old Boys Club and an Old Clique. Instead of enjoying the attention, you will have to immediately switch into the PR disaster management mode.

Thus, make sure that at least 50% of your starting line-up are women. And hopefully not everyone’s white and middle-aged either. This will also change the internal dynamics of the community – male-dominated groups are much more competitive, and you want to foster a cooperative activity.

If you spent last few years mainly schmoozing with your buddies in science, or tech, or your neighbors in Silicon Valley, and you have no idea what women, minorities, seniors and youngsters to invite, you are a few years too late for this. If you decide to invite some of them to your network, they will probably be very polite in saying No, but to themselves they will be saying something like “Who the hell are you? What planet did you just fall from? I have never heard of you, you never read my blog, you never commented on my blog, so why this sudden interest in it, eh? You don’t follow me on Twitter, we are not Facebook friends, I am not on your blogroll, so why do you want me now? As a token to put on your pretty new network so you can add another notch on your “diversity” belt? Well, no, sirree!” And they will be perfectly correct in thinking that way.

But if you have started years ago, when science blogosphere was young, always looking around for new voices, reading the new blogs because they are fun, commenting not because it’s good for business but because you are personally motivated to say something, ask something, say Hello, than you are OK. Just by chance, half of these blogs will be written by women, some by older people, some by younger people, some by non-white people.

You would be reading them because their writing is great. You would be commenting, and blogrolling them, and linking to them, and promoting them because you love what they do, not for political motives. You would try to meet them in person when you travel, and you would invite them to conferences you organize. You would make fast friendships this way, without any ideas that this would potentially turn into anything like a business deal.

And then, if such an opportunity arises and you can start a new network, you will have a pool of hundreds or even thousands of cool bloggers to pick from, people with whom you already have a genuine friendship and mutual trust. And you would be VERY familiar with their work as you have followed it for years. Thus you will have plenty of choices who to invite in order to have a diversity of topics, formats, styles and voices – and pure statistics will ensure that about half of them will be female and a few of them non-white and non-middle-aged. No need to do anything artificial, or to do something out of the ordinary in order to get “proper balance” – it will just happen.

Later, once the network is live and kicking, you can do more stuff to promote diversity and especially to promote new and young bloggers. For example, you can make an “incubator” blog to which you invite a very new and young but talented blogger (or even a group, e.g., friends from a science journalism school) to guest-blog on for one month (Seed did that with a photoblog for a while). There is no guarantee, or even expectation that any of those guest-bloggers would ever be invited to join the network as individual bloggers, but that one month would be great training, great experience and great exposure to them, so once their month is over they can take their audience with them wherever they go, feeling confident in their blogging skills. You may specifically ask the readers to be “nice to the n00b” and ask your senior bloggers to keep an eye – be there to teach, to advise, and to defend against nasty commenters. And if an individual blogger really kicks butt, drawing a lot of traffic and comments with brilliant content, then you can certainly consider invitation for a more permanent slot on the network. In other words, be a factor in growing the community of science bloggers, not just defending your own turf.

Coda

There are many other ideas I have, and other people have. Each network will have to see what their goals are, what ambitions, what resources they have, etc.

I could have kept all of the above to myself, and charged a single network $100,000 to advise them and help them set up. But that would not work – it only works if most or all networks think about this the right way and do the right thing. A lone network doing it right cannot survive in the interconnectedness of the archipelago if all the other players adopt outdated ideas. It is a network or networks, and I hope that people who run or build networks right now read this, talk about it with each other, and come to ScienceOnline2011 to hatch a common strategy, because we have a common goal, and need to collaborate on reaching it.

Housekeeping, Banner, and stuff…

As you may see if you look around, I got to play with the blog a little bit. With help from Arikia I moved it from WordPress.com to WordPress.org. Thus the new URL is http://blog.coturnix.org and the new feed is https://blog.coturnix.org/feed/. But don’t worry – the previous wordpress URL and feed automatically redirect to the new URL. You can also always access the blog from my homepage if you click on the recognizable blog banner there.

Speaking of the banner, the beautiful piece of art that Carel Pieter Brest Van Kempen (you may also know his blog) made for my blog is now up on top. And this reminds me that nobody has yet seen it full-size. So if you click on this thumbnail, you can see it BIG:

In other news, there is a good article about Scienceblogs, Pepsi, etc, in Newsweek that goes into details about the other institutional blogs on the network and poses some good questions.

Open Laboratory 2010 – submissions so far

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.

Note: if you have recently moved your blog, please e-mail me the corrected URLs for your entries

Continue reading

Health and Medicine Poetry Contest

From Dr.Charles (sorry for copying and pasting the whole thing, but I thought all of the information is necessary):

Announcing the first annual 2010 Charles Prize for Poetry. Bold and pretentious name aside, the award will be given to the writer who submits for consideration the most outstanding poem within the context of health and medicine.

Open to everyone (patients, doctors, nurses, students, etc.). Limit 1 or 2 entries per person.

Poems should be related to experiencing, practicing, or reflecting upon a medical, scientific, or health-related matter.

The winner will be selected by a panel of three judges, including me. These other judges may or may not be Nobel Laureates, you never know, but all appreciate poetry. I may ask for your permission to post a copy of your poem on this blog as we go, with or without attribution as you wish.

Is such an eponymous contest grandiose? Yes. Does the limited poetry I’ve written carry the gravitas needed to make me an authority on the subject? No way.

But should your poem be selected as the winner, you shall receive a plaque, an award of $500, and a tasty cherry tomato from my garden. Seriously. At least one person has written that winning the cherry tomato is more important to her than all the gold in the world. I’m sorry that my budget is not higher, but I thought I could swing $500 without enlisting sponsorship. Who needs an iPhone anyway?

So have fun, find inspiration, and send your entry to:

drcharles.examining *at* gmail.com

Contest closes August 31st.

Blogging with substance

I was given a Blogging With Substance award and got tagged.

I need to answer two questions:

1. Sum up your blogging motivation, philosophy and experience in exactly 10 words.

Oh my! Is this the most difficult moment to answer this? Let’s say that I am now completely rethinking my blogging – my goals, my format, my style. The only thing I hope remains will be my voice. You just need to wait and watch this blog for a couple of more months, see it evolve.

2. Pass it on to 10 other blogs with substance.

All of the bloggers who recently left Scienceblogs.com got tagged at the same time as I was, so I cannot tag any of them. But there are many other great bloggers of substance, and it is hard to limit oneself to only ten. Here are ten that I have been reading very regularly (some for years, other starting more recently) and like very much (yes, I know, I cannot count, I stealthily added an eleventh one in):

Archy

EcoPhysioMichelle

Bjoern Brembs

Save Your Breath For Running Ponies

Sauropod Vertebra Picture of the Week

Byte Size Biology

Ben Young Landis

Wild Muse

The Language of Bad Physics

Culturing Science

Science with Moxie

Open Laboratory ’10 – announcement: new Editor

We are running a baton race this year, I think 😉

Anyway, Ben Young Landis got a great new job and is moving to California and will be busy getting started there, so he had to bow out of the Year’s Editor role (at least for this year!). Not a problem at all – there is already a new Editor in place.

Welcome Jason G. Goldman of The Thoughtful Animal blog. As he explains in his post he will be the one steering the ship this year. Thank you, Jason, so much for jumping in so fast in an emergency.

Ha! We got cartooned (again).

Remember this? A comic strip by Joseph Hewitt portraying SciBlings.

Well, he’s done it again:

Clever play on the words Diaspora and Panspermia. Just like Seedling Stars, the Sciblings are bursting out of their old sporangia and flying into the deep unknown, landing on faraway planets, adapting to them, geo- and bio- engineering them to fit them better. And of course, except during the Fail Whale moments, communicating across the lightyears via Twitter.

Or perhaps, to stay with the spores, better metaphor may be Pilobolus.

Thank you!

Wow! The last couple of days were quite an emotional roller-coaster. The comments on the old blog our now closed, but the farewell post on the old blog accumulated 89 comments and its copy here already has 40. And they have been so supportive. I am so humbled.

The outpouring of love and support on Twitter (and also some on FriendFeed and Facebook) was overwhelming. The link to my post was tweeted by hundreds of my friends, and also by such luminaries as Dan Gillmor, Dave Winer and Jay Rosen (twice). Unfortunately, Twitter Search works only for the tweets made over the past two weeks so all the replies, retweets and mentions (here or here) will disappear soon. But hashtags are easier to save – just check this out!!!. Wow! Just wow! I don’t know how to respond. #I Owe You All!

A number of people have left Scienceblogs recently, just before or just after me, but there is a common Sb Diaspora RSS feed so you can follow all of us. And a @SBExpats Twitter account.

I really need to thank all of the bloggers who wrote nice things about me or my post, and those who used it as a starting point to an important discussion about the future of the changing ecosystem of science blogging.

Please see the post by Abel Pharmboy, also his farewell post, his first post at the new blog and this amazingly generous post. Thank you so much, bro!

I am not sure if I managed to catch all the links to all the posts, but here is a good sampling. Check them all out: Danielle Lee, Henry Gee, SciCurious, Stephanie Zvan, DrugMonkey, Delene Beeland, Greg Laden, Pal MD, Allie Wilkinson, Grrrlscientist (also here and also her farewell post), Dr.Isis, Jason Thibeault, Ed Brayton, Orac, Carl Zimmer (who has more on the topic), Zuska (see her new digs), Mike Dunford, PZ Myers (who is mightily battling to keep the Sb ship afloat), Dave Dobbs (also in The Guardian), Dave Munger, Dave Bacon, Dave Wescott, Maryn McKenna (check her new blog), Deborah Blum (you can now find her here), EcoPhysioMichelle, John Hawks, mrswhatsit, Dana Hunter, John Dupuis, Sheril, Josh Rosenau, Sharon Astyk (and more), Misha Angrist, Pamela Ronald, Ian Brooks, Jason Goldman, John McKay, Ed Cone, Kristjan Wager, Greg Laden, Naon Tiotami, John Wilkins, John Lynch (more), Prof-like Substance, Grant Jacobs, Kent, Brian Krueger, gfish, Cameron Neylon, Richard Gayle (and two more intriguing posts on the aftermath here and here), Chad Orzel, Anna Tambour, Southern Fried Scientist, Mathew Lowry, Daniel Cressey at Nature News and Michael Whitney at Firedoglake. Edit: And now also Newsweek!

And Thank you to the Sb Overlord Evan Lerner for keeping this Buzz topic on the scienceblogs homepage for the third day in a row:

These are interesting times. For four years there was one huge volcanic island. Now it is erupting, lava is still hot, but it appears that once the lava stops and cools, there will be an entire archipelago of science blogging networks. It will be interesting to see if the original volcanic island sinks into the sea or remains and in what shape. It will be interesting to see how many new islands spring up, their shapes and sizes.

But what will be the most interesting to see is if the new island nations will war or trade with each other, or even join a loose confederation. What kinds of boats will be used to paddle between the islands? What kind of goods will be traded between them?

As for my own blog? No rush. I need to think. First, it will take me a few days (or weeks) to get this place in shape. I need to move from wordpress.com to wordpress.org (I own coturnix.org so I should make something like coturnix.org/blog and have it there). And make the place pretty.

The traffic at the old site went through the roof earlier this week, and the new site did fine during its first couple of days. I expect it to go lower, but that is OK:

As you may have already noticed, Clock Quotes are gone. “New and Exciting in PLoS” posts are now tweets (though I may figure out a way to do something similar on the everyONE blog, something like “Bora’s Bloggables”, making sure it is obviously my own choice, not that of the PLoS marketing department). Carnival announcements are also gone to Twitter. Announcements for events (e.g., local science cafes, Sigma Xi pizza lunches, World Science forums, etc,) I can bundle 2-3 in a single post instead of each separately. No pressure to have something always on the Last24H page as there is no such page for me now. I will continue doing updates on ScienceOnline2011 and Open Laboratory, posting Q&As with the past participants of ScienceOnline2010, and an occasional monstrously long post on one topic or another, perhaps even science! Whatever rocks my boat.

As for the future? I don’t know. We’ll see. I may stay solo for a while, perhaps end up on another network (or two, or three) further down the line. There is blogging to be done on ScienceInTheTriangle and everyONE blog, so who knows.  If I ever got the opportunity to try Scripting2, that seems to be a blogging platform one could love, not just be satisfied with. That can boost one’s blogging energies in itself.  But for now, blogging itself is not a priority for me right now.

The first priority is to find a way to support my family. If you want to help, check out this store – that is stuff we already have, boxed up and ready to go. If nothing there is interesting, there is always the Zazzle store but hold off on the CafePress as the items there need to have the URL changed first (I should get to it over the next few days). Or click here:

Then, also, Anton and I are now in fifth gear organizing ScienceOnline2011. In order to make the conference a little bit bigger (something like 130 people were left on the waitlist last year!) we need more new sponsors. If you know a potential sponsor, let us know, make contact.

Open Laboratory is also going to be a big project, as it is every year, so December and January will be busy around that as well.

You are all going to see my posts if you grab my feed (or the combined diaspora feed) or if you follow me on Twitter, FriendFeed or Facebook, so I’m fine.

Thank you all so much!

Update: I added more thoughts to the events and the future at Science Blogging Networks: What, Why and How

ScienceOnline2010 – interview with Stephanie Willen Brown

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 Stephanie Willen Brown to answer a few questions.

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?

I’m Stephanie Willen Brown, aka CogSciLibrarian living in the Triangle area in North Carolina. I’ve been a librarian since 1996, and I started calling myself the CogSciLibrarian in 2004, when I was the librarian for the School of Cognitive Science at Hampshire College in Amherst, MA. I started the blog as a way of sharing cool cognitive science stories and books that I thought my colleagues would enjoy.

My scientific background is limited to that of a librarian, supporting faculty and students working in cognitive science, communications, and psychology over the years. I’d grown up intimidated by math and science, but cognitive / brain / neuroscience is so interesting AND there is so much good, accessible writing about it that I have become a fan.

My current reading interests include the effect of mindfulness on the brain, the development and use of language, and concussions in NFL and other athletes.

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

I’m thrilled to be working at my dream job, as director of the Park Library at the School of Journalism and Mass Communication at the University of North Carolina, Chapel Hill. It incorporates many of my interests, such as library science, journalism, marketing, and advertising. I am a consumer of mass media, and I love to be around academics who are studying various aspects mass communication.

My first love is helping students and colleagues find resources that will enhance their research, and the work is double-plus good when it involves subject matter I find interesting as well as amazing library colleagues at the UNC Libraries.

I do miss supporting cognitive and communication science, as I don’t have much interaction with my all-time favorite database PsycINFO. It’s got great content and robust metadata (did you know you could limit your search to age group of subjects studied? Or that you can limit results to just empirical studies or literature reviews?), though it’s not the go-to database of choice for mass communication.

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

Science needs good public relations right now, and I agree with @ErinBiba’s essay in the May issue of Wired “Why Science Needs to Step Up Its PR Game.” I’d like to play a small part in the merger of science and PR by training public relations professionals to do good research and generally supporting their academic endeavors. Libraries and news* (newspapers, news outlets, etc.) need good public relations too, but that’s for another post.

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?

One of the great things about my job is that I feel empowered – even obligated! – to read about social networking and participate in various social networks professionally and personally. I promote the Park Library via Twitter (@JoMCParkLib and Facebook and have dabbled in FriendFeed.

I believe we in the School of Journalism and Mass Communication should be teaching our students to use social networks in their professional work, so I think of myself as modeling good professional use of social networks.

I tweet as @CogSciLibrarian as well, which is where I keep up with my science buddies and science news.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I discovered science blogs years ago as I began my own blog, though I read science librarian blogs such as John Dupuis’ Confessions of a Science Librarian more than practicing scientist blogs. I met science documentarian Kerstin Hoppenhaus at ScienceOnline2010 and really enjoy her More Than Honey blog.

I’ve since migrated to Twitter for most of my online / science interactions, and I follow some great science folks there, including @SteveSilberman , @tdelene (DeLene Beeland), @VaughanBell (contributor to Mind Hacks), and my favorite psychology radio show @allinthemind (Australia’s Natasha Mitchell).

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?

Gosh, I loved #scio10! It was great to be exposed to so much science in a casual, friendly environment, and I enjoyed spending time with like-minded librarians like Christina Pikas, John Dupuis, and Bonnie Swoger . I was also happy to meet Irtiqa’s Salman Hameed and Tom Linden’s Master’s students in UNC’s Program in Medical & Science Journalism. There were many more as well, but the most amazing aspect of ScienceOnline is the interaction with interesting and interested science, journalism, and library professionals. I have just put #scio11 on my calendar and look forward to meeting more interesting folks!

Thank you so much for the interview. I hope to see you soon, and of course at the next conference in January.

ScienceOnline2010 – interview with William Saleu

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 William Saleu to answer a few questions.

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?

My name is William Saleu and I blog at BomaiCruz. I am from Papua New Guinea (PNG), an independent island nation making up the eastern part of the island of New Guinea which lies immediately north of Australia. I am a research fellow at the Duke University Marine Lab (DUML) in Beaufort, North Carolina.

I am part of a team that studies population structure and species connectivity among invertebrates from hydrothermal vent systems from the western Pacific. Most of our samples were collected from PNG so as you can imagine I have naturally taken up a personal interest in this subject. My ultimate goal is to be able to use the results of this research and other similar work to help identify and design conservation strategies for these unique ecosystems in PNG.

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

So one might wonder how I ended up doing this. To answer that question I will have to take you back to my final days as an undergraduate at the University of Papua New Guinea (UPNG). I was a biophysics major and was almost at the end of my program when I realized that my options for employment after college were very slim and I decided to look at opportunities for post grad research at UPNG. I spoke to my physics advisor but he was not so enthusiastic about having me on his projects but told me to come up with my own project.

I was sitting in a microbiology class when I heard the professor say something about chemosynthetic bacteria and how they were the basis of life at hydrothermal vents but she went on to say that because of the extreme conditions they lived in, not much was known about them as it was very hard to culture them. I also found out then that we had hydrothermal vent systems in PNG that geologists were so interested in studying. This was it, this was the project I was looking for. I decided I was going to build an incubator that would house pressure sensors and thermometers and could go all the way down to the sea floor, collect these bacteria and bring them to the surface at similar conditions to that of their sea floor habitats, little did I know that people in the developed world have already invented deep sea submersibles and remotely operated vehicles that did the same thing. Anyway, my proposal never went through as no one in PNG ever took it seriously.

I ended up in the streets like so many other Papua New Guineas before me who had gone through college but could not find anything to do. Then, one day while reading a newspaper, I came across an advertisement for people with advanced degrees in science to submit applications for a semester long traineeship at Duke University Marine Lab (DUML). I did not have an advanced degree but one of the requirements was that applicants should have sound knowledge in molecular biology and lab work skills and I knew I could use this to my advantage as I had been an intern at the PNG Institute of Medical Research’s molecular and virology labs and this was the only lab in PNG doing molecular work.
Well, I submitted an application and got the opportunity and came over for the traineeship and went home but thanks to the network I have set up before, I am back now as a research fellow studying the same things that I wanted to work with when I was an undergrad.

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?

As far as my blogging family tree goes, I guess I will look up to Southern Fried Science as my blog parent and Deep Sea News as the granny. These guys have been awesome at helping me in everything from day one of BomaiCruz. The name ‘Bomai’ hails from the Simbu language of PNG and would translate for someone from the deep jungles, while ‘Cruz’ is from tok pisin, one of the three main languages of Papua New Guinea. ‘Cruz’ actually means to wonder around, hence, BomaiCruz, “someone from the deep jungles wondering around.”

I did not know about blogging, Twitter or Facebook before coming to the USA but am now on Twitter as BomaiBlat and on Facebook too. All this is very exciting for me but keeping up to speed with every one of them can be quite a hassle. I have found that networking can be quite addictive but is also so much fun and is a great way of sharing information and learning about what is going on in the world or just to take part in arguments and discussions. Personally, I have learnt so much more from networking and socializing with other members however, my only word of advice here is that networking and socializing can be so much fun as long as you know how to control its use.

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?

I know this is not going to go down well with other bloggers but I was lucky enough to attend the ScienceOnline conference just a few weeks after I posted the first blog post on my wall. Unfortunately I cannot make comparisons with past science online conferences but from what I saw in this year’s conference, I should say that it was one of the best conferences I have been to in terms of organization and set up. There are two sessions I will remember for a very long time, first was Rebecca Skloot where she was talking about her book and the second and I should say, the one I really liked was the Open Access talk. I think the importance of Open Access as outlined by the speakers is one thing I will take away with me and make sure to pass on to others that I might end up working with.

It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.

A Farewell to Scienceblogs: the Changing Science Blogging Ecosystem

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 loose.

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. There is also Lab Spaces. 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 non-selective 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 https://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.

Open Laboratory 2010 – submissions so far

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.

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A Blog Around The Clock: What does it mean that a nation is ‘Unscientific’?
A Blog Around The Clock: My latest scientific paper: Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird
A Blog Around The Clock: Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?

A Hot Cup of Joe: About Cognitive Archaeology
A Hot Cup of Joe: Application of Cognitive Archaeology

A Meandering Scholar: Back to basics: The Evolution of a Postdoc

A Wonderful Day for Anthropology: Sexual Dimorphism in Human Breasts: An Examination of Three Evolutionary Perspectives

Anna’s Bones: The Ape That Wouldn’t Grow Up

The Anthropology of Everyday Life: Step Right Up and Give Us Your DNA
The Anthropology of Everyday Life: The Angels are Flying
The Anthropology of Everyday Life: Dancing by the Nile, Ladies Loved His Style….
If The Shoe Fits

Anthropology in Practice: The Irish Diaspora: Why Even Trinidadians Are a Little Irish
Anthropology in Practice: RSVP–A Cultural Construct?
Anthropology in Practice: Death 2.0: Digital Mourning
Anthropology in Practice: Is Your Time My Time? Deconstructing “Social” Time (2)
Anthropology in Practice: Dealing With ‘Digital Distractions’ in the Classroom
Anthropology in Practice: Extra! Extra! (Some) Print Media Is Not Dead!
Anthropology in Practice: Bullying and Emotional Intelligence on the Web
Anthropology in Practice: Standardized Time and Power Relations

Archy: Mammoths, floods, and whatnot

Back Re(action): To whom it may concern (poem)
Back Re(action): What is a scientific prediction?

Bad Science: Is it okay to ignore results from people you don’t trust?

Bjoern Brembs Blog: In which potatoes in France are like high-ranking journals in science

The Black Hole: Say NO to the Second Post Doc!
The Black Hole: Devils of Details: Getting Scientists to Understand How Policy Making Works
The Black Hole: Two heads are better than one: Making a case for jointly run labs

Blag Hag: In the name of science, I offer my boobs and A quick clarification about Boobquake and Head of Iran’s Guardian Council supports Sedighi’s earthquake hypothesis and And the boobquake experiment has begun…, And the Boobquake results are in!, Why boobquake isn’t destroying feminism and The Iranian and Muslim response to Boobquake collected and edited as a single entry.

Built On Facts: The Theory of Theory

Byte Size Biology: Highly Evolved
Byte Size Biology: Well, color me surprised
Byte Size Biology: Obesity: the Role of the Immune System
Byte Size Biology: Comparative Functional Genomics: Penguin vs. Bacterium
Byte Size Biology: Protein function, promiscuity, moonlighting and philosophy

Canadian GirlPostdoc in America: Dissent gets a fat lip.
Canadian GirlPostdoc in America: Slow Science Gets the Shaft – Part Deux

Chronicles From Hurricane Country: Crispy on the Outside (poem)
Chronicles From Hurricane Country: Molecules of Song (poem)
Chronicles From Hurricane Country: Cryosat-2, Orbital Mosquito Hunter (poem)
Chronicles From Hurricane Country: Now You See It… (poem)
Chronicles From Hurricane Country: Military Objective (poem)
Chronicles From Hurricane Country: Avoiding the Sugar Buzz (poem)
Chronicles From Hurricane Country: 2010 GA6, Space Yacht (poem)
Chronicles From Hurricane Country: Gut Instinct (poem)
Chronicles From Hurricane Country: The Search For Night Life (poem)
Chronicles From Hurricane Country: Unruffled Tuxedos (poem)
Chronicles From Hurricane Country: Her Sense of Timing (poem)
Chronicles From Hurricane Country: Watching Their Backs (poem)
Chronicles From Hurricane Country: Disorienteering (poem)
Chronicles From Hurricane Country: Floral Rearrangement (poem)
Chronicles From Hurricane Country: In Development (poem)
Chronicles From Hurricane Country: Power Plant (poem)
Chronicles From Hurricane Country: Breathless Find (poem)
Chronicles From Hurricane Country: Eyjafjallajökull (poem)
Chronicles From Hurricane Country: A Grain of Exposure (poem)
Chronicles From Hurricane Country: A Project With Teeth (poem)
Chronicles From Hurricane Country: A Head For Fashion (poem)
Chronicles From Hurricane Country: Equatorial Engine (poem)
Chronicles From Hurricane Country: Inherited Hunger (poem)
Chronicles From Hurricane Country: Going the Distance (poem)
Chronicles From Hurricane Country: Manipulations (poem)
Chronicles From Hurricane Country: Current Events (poem)
Chronicles From Hurricane Country: Pattern Masters (poem)
Chronicles From Hurricane Country: Shutter Bug (poem)
Chronicles From Hurricane Country: Rules of Virtual Engagement (poem)
Chronicles From Hurricane Country: Reflections on 24-Themis (poem)

CMBR: Flu shots all around! But is it the best way?
CMBR: Attn: Science journalists. It’s time to break the mold.

Code For Life: Book sales, frumpy readers, and mental rotation of book titles

Computing Intelligence: Sloppy Language in Science on Human Uniqueness

Confessions of a (former) Lab Rat: On Peer Review

CultureLab: Celebrating the real Einstein

Culturing Science: Octopuses doing tricks on the internet and our search for non-human ‘intelligence’

Darryl Cunningham Investigates: The Facts In The Case Of Dr. Andrew Wakefield (comic strip)

Deep Thoughts and Silliness: Branch Lengths and Species

The Digital Cuttlefish: A Batty Problem (poem)

The Dispersal of Darwin: The Discovery Institute needs a dictionary

Dot Earth: My Second Half

Dot Physics: MythBusters’ energy explanation

Dr. Carin Bondar…biologist with a twist: Darwin’s ‘Survival of the Fittest’ meets the irresponsible Homo sapiens
Dr. Carin Bondar…biologist with a twist: Chemical Espionage, Anti-Aphrodisiacs and Hitchhiking…all in a Day’s Work for a Parasitoid Wasp!

Dr. Kaku’s Universe: The Bizarre and Wonderful World of Quantum Theory–And How Understanding It Has Ultimately Changed Our Lives

Endless Forms: Crown Jewel of Biodiversity on the Edge
Endless Forms: Saving face: Salamanders show why it’s important to know thy enemies
Endless Forms: Boozing Treeshrews: Heavyweight drinkers in small packages

Ever Wondered? (Scienceline): How Does a Venus Flytrap Work?

Freethinker’s Asylum: Alpha, Beta, and Power

Genetic Maize: GMOs Could Render Important Antibiotics Worthless

Greg Laden: Are you are real skeptic, or are you just faithing it?

hgg: Anthology of science writing: now almost 4 % with ovaries!

ICBS Everywhere: Fun Does Not Sell Smarts
ICBS Everywhere: BS for George Takei Fans and Consumers
ICBS Everywhere: There Must Be an Idiom
ICBS Everywhere: Narcissism + Incompetence = Ignorance and More Incompetence

Ionian Enchantment: Anecdotes as evidence
Ionian Enchantment: The Cost of Truth is Eternal Vigilance

Laelaps: Off the prehistoric coast of Panama, a mega-toothed shark nursery

The Language of Bad Physics: The Language of Science – it’s ‘just a theory’
The Language of Bad Physics: Experiments in Non-Relativistic Modified Newtonian Dynamics (MOND)

Living the Scientific Life (Scientist, Interrupted): Made for Each Other: Evolution of Monogamy in Poison Frogs
Living the Scientific Life (Scientist, Interrupted): UV, You See? Black Light Reveals Secrets in Fossils
Living the Scientific Life (Scientist, Interrupted): Fly Me to the Moon: The Incredible Migratory Journey of the Arctic Tern
Living the Scientific Life (Scientist, Interrupted): Darwin’s Finches Develop Immunity to Alien Parasites
Living the Scientific Life (Scientist, Interrupted): Is That A T. rex Up Your Nose? New Species of Nose-dwelling Leech Discovered
Living the Scientific Life (Scientist, Interrupted): (How) Are Birds Affected by Volcanic Ash?
Living the Scientific Life (Scientist, Interrupted): How Will You Celebrate International Migratory Bird Day?
Living the Scientific Life (Scientist, Interrupted): What do Great Tits Reveal about the Genetics of Personality?
Living the Scientific Life (Scientist, Interrupted): Racehorse Research Identifies Speed Gene
Living the Scientific Life (Scientist, Interrupted): Fossil Feather Colors Really ARE Written In Stone
Living the Scientific Life (Scientist, Interrupted): Fetid Fish Revise Understanding of Fossil Formation
Living the Scientific Life (Scientist, Interrupted): Oiled SeaBirds: To Kill Or Not To Kill? What Is The Ethical Thing To Do?
Living the Scientific Life (Scientist, Interrupted): Newly Described Bird-like Dinosaur Predates Archaeopteryx by 15-20 Million Years
Living the Scientific Life (Scientist, Interrupted): Gulf Oil Spill Disaster: Spawn of the Living Dead for Atlantic Bluefin Tuna?
Living the Scientific Life (Scientist, Interrupted): Ancient DNA from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds
Living the Scientific Life (Scientist, Interrupted): Orange Stripey Dinosaurs? Fossil Feathers Reveal Their Secret Colors
Living the Scientific Life (Scientist, Interrupted): Migratory Monarch Butterflies ‘See’ Earth’s GeoMagnetic Field
Living the Scientific Life (Scientist, Interrupted): Colorful Tits Produce Speedier Sperm
Living the Scientific Life (Scientist, Interrupted): Doing It For the Kids: The Evolution of Migration
Living the Scientific Life (Scientist, Interrupted): Distressed Ravens Show That Empathy Is For The Birds, Too

The Loom: Skull Caps and Genomes

Maniraptora: Tastes Like Chicken: Size Matters — Bigger is Better, Even for Male Pipefish
Maniraptora: Tastes Like Chicken: Gender-Bending Chickens: Mixed, Not Scrambled

The Martian Chronicles: How to cure the Avatar Blues

Mauka to Makai: Barnacle Sex

Maxwell’s Demon: Spirographs and the third dimension
Maxwell’s Demon: The Laws of Gelada (How to be a grad student)

Medical & Bio-Inspired Innovations: Blood Pressure, Medication, Diet, And Dementia: What The Recent Research Tells Us

Mental indigestion: Your microbiome and you (part I): Gut
Mental indigestion: The grass isn’t always greener…

Mind the Gap: In which I dream of revolution

Mr Science Show: For a healthy relationship, men should be ugly and rich, women pretty and mixed-race
Mr Science Show: Correlation of the Week: Liberals and Atheists Are More Intelligent
Mr Science Show: How do you spell goal?

Neurotopia: Attractiveness, anger, and warrior princess blondes
Neurotopia: A Letter to a Grad Student
Neurotopia: Friday Weird Science: Why does asparagus make your pee smell?
Neurotopia: On Animal Research

Nutrition Wonderland: The Truth About Organic Farming
Nutrition Wonderland: Understanding Our Bodies: Insulin

Observations of a Nerd: Evolution: The Curious Case of Dogs
Observations of a Nerd: Psych FAIL
Observations of a Nerd: Evolution: Watching Speciation Occur
Observations of a Nerd: Ancient Sex Scandals: Did We Get It On With Neandertals?
Observations of a Nerd: Reflections on the Gulf Oil Spill – Conversations With My Grandpa
Observations of a Nerd: Tuna

Opinionator (Olivia Judson): Laboratory Life
Opinionator (Olivia Judson): Evolving Sexual Tensions
Opinionator (Olivia Judson): Divide and Diminish
Opinionator (Olivia Judson): Enter the Chronotherapists

Oscillator: Knowledge is Power and Biology is Power, perhaps fused into a single essay.

Pharyngula: How to make a snake

PodBlack Cat: Presenting, Minorities And The Token Skeptic At #AtheistCon

Poseidon Sciences: The Agony and the Ecstasy: Why science writing is like learning tango and Chinese brush painting

Prof-Like Substance: Can I get a Land’s End catalog, STAT?

Promega Connections: How do I Describe Thee? Let Me Count the Ways
Promega Connections: Mate Selection at Frog Cocktail Parties: Keep it Short, Low, Loud, and Stand Out from the Crowd (Oh, and have a colorful vocal sac, too)

Reciprocal Space: I have discovered Jupiter
Reciprocal Space: Judgement Days

The Renaissance Mathematicus: Extracting the stopper.

Rennie’s Last Nerve: Blood Simple: Mammoths, mice, malaria and hemoglobin
Rennie’s Last Nerve: Energetically Batty

Respectful Insolence: When what an acupuncture study shows is much more interesting than what acupuncture believers think it shows

Sandwalk: On the Origin of the Double Membrane in Mitochondria and Chloroplasts

Saturday Morning Breakfast Cereal: Epistemological Anarchists (comic/cartoon)

Sauropod Vertebra Picture of the Week: Lies, damned lies, and Clash of the Dinosaurs

Save Your Breath For Running Ponies: Your Friends Aren’t Just Going To Forget You Envenomated Them, Sinornithosaurus.
Save Your Breath For Running Ponies: You Should Probably Just Move Oceans, Male Gulf Pipefish

Sciencebase: Whatever happened to the audiophile

Science in Seconds: Africa’s Next Top Hominid

Science In The Triangle (DeLene Beeland): Hibernation devastation: White-nose syndrome and our bats

Science Progress: Ecosystems In the Age of Cassandra

The Science Talent Project: Happy song scientists and sad song scientists

The Scientist: On Public Relations

Skeptic Wonder: Social onycophorans!

Skulls in the Stars: Perpetual motion — nonsense for over 100 years
Skulls in the Stars: Rolling out the (optical) carpet: the Talbot effect
Skulls in the Stars: Mythbusters were scooped — by 130 years! (Archimedes death ray)
Skulls in the Stars: Singular Optics: Light chasing its own tail
Skulls in the Stars: Shocking: Michael Faraday does biology! (1839)
Skulls in the Stars: Invisibility physics: Kerker’s ‘invisible bodies’

Southern Fried Scientist: The Data Speak
Southern Fried Scientist: Tournament marlins get bigger?
Southern Fried Scientist: Oil Spill vs. Hypoxic Zone
Southern Fried Scientist: Louis Agassiz and a brief history of early United States marine biology

Terra Sigillatta: Marking the magnificient memory of Henrietta Lacks

Testimony of the spade: Surveys on my mind
Testimony of the spade: Door to Door

Tetrapod Zoology: Testing the flotation dynamics and swimming abilities of giraffes by way of computational analysis

There and (hopefully) back again…: Everyday (lab) living

The Thoughtful Animal: Snakes on a Muppethugging Plane! (Monday Pets)

Through the Sandglass: Life and art, sand and glass: the wonders of Difflugia

UCAR Magazine: Brrr: The AO is way low

Uncertain Principles: Science Is More Like Sumo Than Soccer

Water Numbers: Peter Gleick at SFGate.com: The best argument against global warming

wet: Save the Whale Poop

Wild Muse: Social networks, and social animals
Wild Muse: Wolf recovery vs. ecosystem health
Wild Muse: Givin’ props to hybrids

WooFighters: My Inspiration for Woo Fighters

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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

Clock Quotes

Love makes the time pass. Time makes love pass.

– French proverb

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)

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

New and Exciting in PLoS this week

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:

Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking?:

Existing principles used to explain how locomotion is controlled predict average, long-term behavior. However, neuromuscular noise continuously disrupts these movements, presenting a significant challenge for the nervous system. One possibility is that the nervous system must overcome all neuromuscular variability as a constraint limiting performance. Conversely, we show that humans walking on a treadmill exploit redundancy to adjust stepping movements at each stride and maintain performance. This strategy is not required by the task itself, but is predicted by appropriate stochastic control models. Thus, the nervous system simplifies control by strongly regulating goal-relevant fluctuations, while largely ignoring non-essential variations. Properly determining how stochasticity affects control is critical to developing biological models, since neuro-motor fluctuations are intrinsic to these systems. Our work unifies the perspectives of time series analysis researchers, motor coordination researchers, and motor control theorists by providing a single dynamical framework for studying variability in the context of goal-directedness.

Morphometric Relationship, Phylogenetic Correlation, and Character Evolution in the Species-Rich Genus Aphis (Hemiptera: Aphididae):

The species-rich genus Aphis consists of more than 500 species, many of them host-specific on a wide range of plants, yet very similar in general appearance due to convergence toward particular morphological types. Most species have been historically clustered into four main phenotypic groups (gossypii, craccivora, fabae, and spiraecola groups). To confirm the morphological hypotheses between these groups and to examine the characteristics that determine them, multivariate morphometric analyses were performed using 28 characters measured/counted from 40 species. To infer whether the morphological relationships are correlated with the genetic relationships, we compared the morphometric dataset with a phylogeny reconstructed from the combined dataset of three mtDNA and one nuclear DNA regions. Based on a comparison of morphological and molecular datasets, we confirmed morphological reduction or regression in the gossypii group unlike in related groups. Most morphological characteristics of the gossypii group were less variable than for the other groups. Due to these, the gossypii group could be morphologically well separated from the craccivora, fabae, and spiraecola groups. In addition, the correlation of the rates of evolution between morphological and DNA datasets was highly significant in their diversification. The morphological separation between the gossypii group and the other species-groups are congruent with their phylogenetic relationships. Analysis of trait evolution revealed that the morphological traits found to be significant based on the morphometric analyses were confidently correlated with the phylogeny. The dominant patterns of trait evolution resulting in increased rates of short branches and temporally later evolution are likely suitable for the modality of Aphis speciation because they have adapted species-specifically, rapidly, and more recently on many different host plants.

Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function:

While sexual reproduction is widespread among animals, it remains enigmatic to what extent sexual reproduction is conserved and when sex-specific gametogenesis (spermatogenesis and oogenesis) originated in animals. Here we demonstrate the presence of the reproductive-specific protein Boule throughout bilaterally-symmetric animals (Bilateria) and the conservation of its male reproductive function in mice. Examination of Boule evolution in insect and mammalian lineages, representing the Protostome and Deuterostome clades of bilateral animals, failed to detect any evidence for accelerated evolution. Instead, purifying selection is the major force behind Boule evolution. Further investigation of Boule homologs among Deuterostome species revealed reproduction-specific expression, with a strong prevalence of testis-biased expression. We further determined the function of a deuterostomian Boule homolog by inactivating Boule in mice (a representative mammal, a class of Deuterostomes). Like its counterpart in Drosophila (a representative of the opposing Protostome clade), mouse Boule is also required only for male reproduction. Loss of mouse Boule prevents sperm production, resulting in a global arrest of spermatogenesis in remarkable similarity to that of Drosophila boule mutants. Our findings are consistent with a common origin for male gametogenesis among metazoans and reveal the high conservation of a reproduction-specific protein among bilaterian animals.

Dynamics of Person-to-Person Interactions from Distributed RFID Sensor Networks:

Digital networks, mobile devices, and the possibility of mining the ever-increasing amount of digital traces that we leave behind in our daily activities are changing the way we can approach the study of human and social interactions. Large-scale datasets, however, are mostly available for collective and statistical behaviors, at coarse granularities, while high-resolution data on person-to-person interactions are generally limited to relatively small groups of individuals. Here we present a scalable experimental framework for gathering real-time data resolving face-to-face social interactions with tunable spatial and temporal granularities. We use active Radio Frequency Identification (RFID) devices that assess mutual proximity in a distributed fashion by exchanging low-power radio packets. We analyze the dynamics of person-to-person interaction networks obtained in three high-resolution experiments carried out at different orders of magnitude in community size. The data sets exhibit common statistical properties and lack of a characteristic time scale from 20 seconds to several hours. The association between the number of connections and their duration shows an interesting super-linear behavior, which indicates the possibility of defining super-connectors both in the number and intensity of connections. Taking advantage of scalability and resolution, this experimental framework allows the monitoring of social interactions, uncovering similarities in the way individuals interact in different contexts, and identifying patterns of super-connector behavior in the community. These results could impact our understanding of all phenomena driven by face-to-face interactions, such as the spreading of transmissible infectious diseases and information.

Phylogenomic Analysis of Marine Roseobacters:

Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution. In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML) and neighbor joining (NJ). Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA), approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT) is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes. Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP) degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.

Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty:

In economic decision-making it is well-known that when decision-makers have several options, each associated with uncertain outcomes, their decision is not purely determined by the average payoff, but also takes into account the risk (that is, variability of the payoff) associated with each option. Some actions have a highly variable payoff, such as betting money on a horse, whereas others are much less variable, such as the return from a savings account. Whether an individual favors one action over the other depends on their risk-attitude. In contrast to economic decision-making, models of human motor control have exclusively focussed on models that maximize average rewards (minimize average cost). Here, we consider a computational model (an optimal feedback controller) that takes the variance of the cost into account when calculating the best movement strategy. We compare the model with the performance of human subjects in a sensorimotor task and find that the subjects’ behavior is consistent with the predictions of a risk-sensitive optimal feedback controller with most subjects being risk-averse.

ScienceOnline2010 – interview with Anne Frances Johnson

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?

Anne Johnson pic2.jpgWhen 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?

Anne Johnson pic1.jpgMy 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.

Clock Quotes

Time is a dressmaker specializing in alterations.

– Faith Baldwin

New World-Science Forum – The Origins of Kindness

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.

New and Exciting in PLoS ONE

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:

Chimpanzees Extract Social Information from Agonistic Screams:

Chimpanzee (Pan troglodytes) agonistic screams are graded vocal signals that are produced in a context-specific manner. Screams given by aggressors and victims can be discriminated based on their acoustic structure but the mechanisms of listener comprehension of these calls are currently unknown. In this study, we show that chimpanzees extract social information from these vocal signals that, combined with their more general social knowledge, enables them to understand the nature of out-of-sight social interactions. In playback experiments, we broadcast congruent and incongruent sequences of agonistic calls and monitored the response of bystanders. Congruent sequences were in accordance with existing social dominance relations; incongruent ones violated them. Subjects looked significantly longer at incongruent sequences, despite them being acoustically less salient (fewer call types from fewer individuals) than congruent ones. We concluded that chimpanzees categorised an apparently simple acoustic signal into victim and aggressor screams and used pragmatics to form inferences about third-party interactions they could not see.

Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity:

Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R2 = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5-95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust alternative to species-level predictions.

The Influence of Perceptual Training on Working Memory in Older Adults:

Normal aging is associated with a degradation of perceptual abilities and a decline in higher-level cognitive functions, notably working memory. To remediate age-related deficits, cognitive training programs are increasingly being developed. However, it is not yet definitively established if, and by what mechanisms, training ameliorates effects of cognitive aging. Furthermore, a major factor impeding the success of training programs is a frequent failure of training to transfer benefits to untrained abilities. Here, we offer the first evidence of direct transfer-of-benefits from perceptual discrimination training to working memory performance in older adults. Moreover, using electroencephalography to evaluate participants before and after training, we reveal neural evidence of functional plasticity in older adult brains, such that training-induced modifications in early visual processing during stimulus encoding predict working memory accuracy improvements. These findings demonstrate the strength of the perceptual discrimination training approach by offering clear psychophysical evidence of transfer-of-benefit and a neural mechanism underlying cognitive improvement.

Very Bright Green Fluorescent Proteins from the Pontellid Copepod Pontella mimocerami:

Fluorescent proteins (FP) homologous to the green fluorescent protein (GFP) from the jellyfish Aequorea victoria have revolutionized biomedical research due to their usefulness as genetically encoded fluorescent labels. Fluorescent proteins from copepods are particularly promising due to their high brightness and rapid fluorescence development. Here we report two novel FPs from Pontella mimocerami (Copepoda, Calanoida, Pontellidae), which were identified via fluorescence screening of a bacterial cDNA expression library prepared from the whole-body total RNA of the animal. The proteins are very similar in sequence and spectroscopic properties. They possess high molar extinction coefficients (79,000 M−1 cm−) and quantum yields (0.92), which make them more than two-fold brighter than the most common FP marker, EGFP. Both proteins form oligomers, which we were able to counteract to some extent by mutagenesis of the N-terminal region; however, this particular modification resulted in substantial drop in brightness. The spectroscopic characteristics of the two P. mimocerami proteins place them among the brightest green FPs ever described. These proteins may therefore become valuable additions to the in vivo imaging toolkit.

Effectiveness of Biodiversity Surrogates for Conservation Planning: Different Measures of Effectiveness Generate a Kaleidoscope of Variation:

Conservation planners represent many aspects of biodiversity by using surrogates with spatial distributions readily observed or quantified, but tests of their effectiveness have produced varied and conflicting results. We identified four factors likely to have a strong influence on the apparent effectiveness of surrogates: (1) the choice of surrogate; (2) differences among study regions, which might be large and unquantified (3) the test method, that is, how effectiveness is quantified, and (4) the test features that the surrogates are intended to represent. Analysis of an unusually rich dataset enabled us, for the first time, to disentangle these factors and to compare their individual and interacting influences. Using two data-rich regions, we estimated effectiveness using five alternative methods: two forms of incidental representation, two forms of species accumulation index and irreplaceability correlation, to assess the performance of ‘forest ecosystems’ and ‘environmental units’ as surrogates for six groups of threatened species–the test features–mammals, birds, reptiles, frogs, plants and all of these combined. Four methods tested the effectiveness of the surrogates by selecting areas for conservation of the surrogates then estimating how effective those areas were at representing test features. One method measured the spatial match between conservation priorities for surrogates and test features. For methods that selected conservation areas, we measured effectiveness using two analytical approaches: (1) when representation targets for the surrogates were achieved (incidental representation), or (2) progressively as areas were selected (species accumulation index). We estimated the spatial correlation of conservation priorities using an index known as summed irreplaceability. In general, the effectiveness of surrogates for our taxa (mostly threatened species) was low, although environmental units tended to be more effective than forest ecosystems. The surrogates were most effective for plants and mammals and least effective for frogs and reptiles. The five testing methods differed in their rankings of effectiveness of the two surrogates in relation to different groups of test features. There were differences between study areas in terms of the effectiveness of surrogates for different test feature groups. Overall, the effectiveness of the surrogates was sensitive to all four factors. This indicates the need for caution in generalizing surrogacy tests.

A Model for Transgenerational Imprinting Variation in Complex Traits:

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.

The Genetic, Morphological, and Physiological Characterization of a Dark Larval Cuticle Mutation in the Butterfly, Bicyclus anynana:

Studies on insect melanism have greatly contributed to our understanding of natural selection and the ultimate factors influencing the evolution of darkly pigmented phenotypes. Research on several species of melanic lepidopteran larvae have found that low levels of circulating juvenile hormone (JH) titers are associated with a melanic phenotype, suggesting that genetic changes in the JH biosynthetic pathway give rise to increased deposition of melanin granules in the cuticle in this group. But does melanism arise through different molecular mechanisms in different species? The present study reports on a Bicyclus anynana (Lepidoptera: Nymphalidae) dark larvae single locus mutation, in which larvae exhibit a darker cuticle relative to wild type. Unlike other lepidopteran melanic larvae mutations, this one is autosomal recessive and does not appear to involve a deficiency in JH titers. Unlike JH deficiency mutants, dark larvae mutants display similar growth rates and sexual behaviors as wild type, and topical application of a JH analogue failed to rescue the wild type cuticular coloration. Finally, transmission electron microscopy showed that sclerotization or deposition of diffuse melanin, rather than deposition of melanin granules, produces the dark coloration found in the cuticle of this species. We conclude that different molecular mechanisms underlie larval melanism in different species of Lepidoptera.

Seasonal Changes in Colour: A Comparison of Structural, Melanin- and Carotenoid-Based Plumage Colours:

Plumage coloration is important for bird communication, most notably in sexual signalling. Colour is often considered a good quality indicator, and the expression of exaggerated colours may depend on individual condition during moult. After moult, plumage coloration has been deemed fixed due to the fact that feathers are dead structures. Still, many plumage colours change after moult, although whether this affects signalling has not been sufficiently assessed. We studied changes in coloration after moult in four passerine birds (robin, Erithacus rubecula; blackbird, Turdus merula; blue tit, Cyanistes caeruleus; and great tit, Parus major) displaying various coloration types (melanin-, carotenoid-based and structural). Birds were caught regularly during three years to measure plumage reflectance. We used models of avian colour vision to derive two variables, one describing chromatic and the other achromatic variation over the year that can be compared in magnitude among different colour types. All studied plumage patches but one (yellow breast of the blue tit) showed significant chromatic changes over the year, although these were smaller than for a typical dynamic trait (bill colour). Overall, structural colours showed a reduction in relative reflectance at shorter wavelengths, carotenoid-based colours the opposite pattern, while no general pattern was found for melanin-based colours. Achromatic changes were also common, but there were no consistent patterns of change for the different types of colours. Changes of plumage coloration independent of moult are probably widespread; they should be perceivable by birds and have the potential to affect colour signalling.

A Quantitative Analysis of Flight Feather Replacement in the Moustached Tree Swift Hemiprocne mystacea, a Tropical Aerial Forager:

The functional life span of feathers is always much less than the potential life span of birds, so feathers must be renewed regularly. But feather renewal entails important energetic, time and performance costs that must be integrated into the annual cycle. Across species the time required to replace flight feather increases disproportionately with body size, resulting in complex, multiple waves of feather replacement in the primaries of many large birds. We describe the rules of flight feather replacement for Hemiprocne mystacea, a small, 60g tree swift from the New Guinea region. This species breeds and molts in all months of the year, and flight feather molt occurs during breeding in some individuals. H. mystacea is one to be the smallest species for which stepwise replacement of the primaries and secondaries has been documented; yet, primary replacement is extremely slow in this aerial forager, requiring more than 300 days if molt is not interrupted. We used growth bands to show that primaries grow at an average rate of 2.86 mm/d. The 10 primaries are a single molt series, while the 11 secondaries and five rectrices are each broken into two molt series. In large birds stepwise replacement of the primaries serves to increase the rate of primary replacement while minimizing gaps in the wing. But stepwise replacement of the wing quills in H. mystacea proceeds so slowly that it may be a consequence of the ontogeny of stepwise molting, rather than an adaptation, because the average number of growing primaries is probably lower than 1.14 feathers per wing.

Sexual Experience Promotes Adult Neurogenesis in the Hippocampus Despite an Initial Elevation in Stress Hormones:

Aversive stressful experiences are typically associated with increased anxiety and a predisposition to develop mood disorders. Negative stress also suppresses adult neurogenesis and restricts dendritic architecture in the hippocampus, a brain region associated with anxiety regulation. The effects of aversive stress on hippocampal structure and function have been linked to stress-induced elevations in glucocorticoids. Normalizing corticosterone levels prevents some of the deleterious consequences of stress, including increased anxiety and suppressed structural plasticity in the hippocampus. Here we examined whether a rewarding stressor, namely sexual experience, also adversely affects hippocampal structure and function in adult rats. Adult male rats were exposed to a sexually-receptive female once (acute) or once daily for 14 consecutive days (chronic) and levels of circulating glucocorticoids were measured. Separate cohorts of sexually experienced rats were injected with the thymidine analog bromodeoxyuridine in order to measure cell proliferation and neurogenesis in the hippocampus. In addition, brains were processed using Golgi impregnation to assess the effects of sexual experience on dendritic spines and dendritic complexity in the hippocampus. Finally, to evaluate whether sexual experience alters hippocampal function, rats were tested on two tests of anxiety-like behavior: novelty suppressed feeding and the elevated plus maze. We found that acute sexual experience increased circulating corticosterone levels and the number of new neurons in the hippocampus. Chronic sexual experience no longer produced an increase in corticosterone levels but continued to promote adult neurogenesis and stimulate the growth of dendritic spines and dendritic architecture. Chronic sexual experience also reduced anxiety-like behavior. These findings suggest that a rewarding experience not only buffers against the deleterious actions of early elevated glucocorticoids but actually promotes neuronal growth and reduces anxiety.

Dietary Determinants of Changes in Waist Circumference Adjusted for Body Mass Index – a Proxy Measure of Visceral Adiposity:

Given the recognized health effects of visceral fat, the understanding of how diet can modulate changes in the phenotype “waist circumference for a given body mass index (WCBMI)”, a proxy measure of visceral adiposity, is deemed necessary. Hence, the objective of the present study was to assess the association between dietary factors and prospective changes in visceral adiposity as measured by changes in the phenotype WCBMI. We analyzed data from 48,631 men and women from 5 countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Anthropometric measurements were obtained at baseline and after a median follow-up time of 5.5 years. WCBMI was defined as the residuals of waist circumference regressed on body mass index, and annual change in WCBMI (ΔWCBMI, cm/y) was defined as the difference between residuals at follow-up and baseline, divided by follow-up time. The association between energy, energy density (ED), macronutrients, alcohol, glycemic index (GI), glycemic load (GL), fibre and ΔWCBMI was modelled using centre-specific adjusted linear regression, and random-effects meta-analyses to obtain pooled estimates. Men and women with higher ED and GI diets showed significant increases in their WCBMI, compared to those with lower ED and GI [1 kcal/g greater ED predicted a ΔWCBMI of 0.09 cm (95% CI 0.05 to 0.13) in men and 0.15 cm (95% CI 0.09 to 0.21) in women; 10 units greater GI predicted a ΔWCBMI of 0.07 cm (95% CI 0.03 to 0.12) in men and 0.06 cm (95% CI 0.03 to 0.10) in women]. Among women, lower fibre intake, higher GL, and higher alcohol consumption also predicted a higher ΔWCBMI. Results of this study suggest that a diet with low GI and ED may prevent visceral adiposity, defined as the prospective changes in WCBMI. Additional effects may be obtained among women of low alcohol, low GL, and high fibre intake.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

RSA Animate – Smile or Die (video)

Clock Quotes

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

– Edith Wharton

Oxygen (video)

New and Exciting in PLoS this week

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 http://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.

The Vaccine Song (video)

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

New and Exciting in PLoS ONE

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.

Suggest sessions for ScienceOnline2011

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.

Open Laboratory 2010 – submissions so far

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.

============================

A Blog Around The Clock: What does it mean that a nation is ‘Unscientific’?
A Blog Around The Clock: My latest scientific paper: Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird
A Blog Around The Clock: Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?

A Hot Cup of Joe: About Cognitive Archaeology
A Hot Cup of Joe: Application of Cognitive Archaeology

A Meandering Scholar: Back to basics: The Evolution of a Postdoc

A Wonderful Day for Anthropology: Sexual Dimorphism in Human Breasts: An Examination of Three Evolutionary Perspectives

Anna’s Bones: The Ape That Wouldn’t Grow Up

The Anthropology of Everyday Life: Step Right Up and Give Us Your DNA
The Anthropology of Everyday Life: The Angels are Flying
The Anthropology of Everyday Life: Dancing by the Nile, Ladies Loved His Style….

Anthropology in Practice: The Irish Diaspora: Why Even Trinidadians Are a Little Irish
Anthropology in Practice: RSVP–A Cultural Construct?
Anthropology in Practice: Death 2.0: Digital Mourning
Anthropology in Practice: Is Your Time My Time? Deconstructing “Social” Time (2)
Anthropology in Practice: Dealing With ‘Digital Distractions’ in the Classroom
Anthropology in Practice: Extra! Extra! (Some) Print Media Is Not Dead!
Anthropology in Practice: Bullying and Emotional Intelligence on the Web
Anthropology in Practice: Standardized Time and Power Relations

Archy: Mammoths, floods, and whatnot

Back Re(action): To whom it may concern (poem)
Back Re(action): What is a scientific prediction?

Bad Science: Is it okay to ignore results from people you don’t trust?

Bjoern Brembs Blog: In which potatoes in France are like high-ranking journals in science

The Black Hole: Say NO to the Second Post Doc!
The Black Hole: Devils of Details: Getting Scientists to Understand How Policy Making Works
The Black Hole: Two heads are better than one: Making a case for jointly run labs

Blag Hag: In the name of science, I offer my boobs and A quick clarification about Boobquake and Head of Iran’s Guardian Council supports Sedighi’s earthquake hypothesis and And the boobquake experiment has begun…, And the Boobquake results are in!, Why boobquake isn’t destroying feminism and The Iranian and Muslim response to Boobquake collected and edited as a single entry.

Built On Facts: The Theory of Theory

Byte Size Biology: Highly Evolved
Byte Size Biology: Well, color me surprised
Byte Size Biology: Obesity: the Role of the Immune System
Byte Size Biology: Comparative Functional Genomics: Penguin vs. Bacterium
Byte Size Biology: Protein function, promiscuity, moonlighting and philosophy

Canadian GirlPostdoc in America: Dissent gets a fat lip.
Canadian GirlPostdoc in America: Slow Science Gets the Shaft – Part Deux

Chronicles From Hurricane Country: Crispy on the Outside (poem)
Chronicles From Hurricane Country: Molecules of Song (poem)
Chronicles From Hurricane Country: Cryosat-2, Orbital Mosquito Hunter (poem)
Chronicles From Hurricane Country: Now You See It… (poem)
Chronicles From Hurricane Country: Military Objective (poem)
Chronicles From Hurricane Country: Avoiding the Sugar Buzz (poem)
Chronicles From Hurricane Country: 2010 GA6, Space Yacht (poem)
Chronicles From Hurricane Country: Gut Instinct (poem)
Chronicles From Hurricane Country: The Search For Night Life (poem)
Chronicles From Hurricane Country: Unruffled Tuxedos (poem)
Chronicles From Hurricane Country: Her Sense of Timing (poem)
Chronicles From Hurricane Country: Watching Their Backs (poem)
Chronicles From Hurricane Country: Disorienteering (poem)
Chronicles From Hurricane Country: Floral Rearrangement (poem)
Chronicles From Hurricane Country: In Development (poem)
Chronicles From Hurricane Country: Power Plant (poem)
Chronicles From Hurricane Country: Breathless Find (poem)
Chronicles From Hurricane Country: Eyjafjallajökull (poem)
Chronicles From Hurricane Country: A Grain of Exposure (poem)
Chronicles From Hurricane Country: A Project With Teeth (poem)
Chronicles From Hurricane Country: A Head For Fashion (poem)
Chronicles From Hurricane Country: Equatorial Engine (poem)
Chronicles From Hurricane Country: Inherited Hunger (poem)
Chronicles From Hurricane Country: Going the Distance (poem)
Chronicles From Hurricane Country: Manipulations (poem)
Chronicles From Hurricane Country: Current Events (poem)
Chronicles From Hurricane Country: Pattern Masters (poem)
Chronicles From Hurricane Country: Shutter Bug (poem)
Chronicles From Hurricane Country: Rules of Virtual Engagement (poem)
Chronicles From Hurricane Country: Reflections on 24-Themis (poem)

CMBR: Flu shots all around! But is it the best way?
CMBR: Attn: Science journalists. It’s time to break the mold.

Code For Life: Book sales, frumpy readers, and mental rotation of book titles

Computing Intelligence: Sloppy Language in Science on Human Uniqueness

Confessions of a (former) Lab Rat: On Peer Review

CultureLab: Celebrating the real Einstein

Culturing Science: Octopuses doing tricks on the internet and our search for non-human ‘intelligence’

Darryl Cunningham Investigates: The Facts In The Case Of Dr. Andrew Wakefield (comic strip)

Deep Thoughts and Silliness: Branch Lengths and Species

The Digital Cuttlefish: A Batty Problem (poem)

The Dispersal of Darwin: The Discovery Institute needs a dictionary

Dot Earth: My Second Half

Dot Physics: MythBusters’ energy explanation

Dr. Carin Bondar…biologist with a twist: Darwin’s ‘Survival of the Fittest’ meets the irresponsible Homo sapiens
Dr. Carin Bondar…biologist with a twist: Chemical Espionage, Anti-Aphrodisiacs and Hitchhiking…all in a Day’s Work for a Parasitoid Wasp!

Dr. Kaku’s Universe: The Bizarre and Wonderful World of Quantum Theory–And How Understanding It Has Ultimately Changed Our Lives

Endless Forms: Crown Jewel of Biodiversity on the Edge
Endless Forms: Saving face: Salamanders show why it’s important to know thy enemies
Endless Forms: Boozing Treeshrews: Heavyweight drinkers in small packages

Ever Wondered? (Scienceline): How Does a Venus Flytrap Work?

Freethinker’s Asylum: Alpha, Beta, and Power

Genetic Maize: GMOs Could Render Important Antibiotics Worthless

Greg Laden: Are you are real skeptic, or are you just faithing it?

hgg: Anthology of science writing: now almost 4 % with ovaries!

ICBS Everywhere: Fun Does Not Sell Smarts
ICBS Everywhere: BS for George Takei Fans and Consumers
ICBS Everywhere: There Must Be an Idiom
ICBS Everywhere: Narcissism + Incompetence = Ignorance and More Incompetence

Ionian Enchantment: Anecdotes as evidence

Laelaps: Off the prehistoric coast of Panama, a mega-toothed shark nursery

The Language of Bad Physics: The Language of Science – it’s ‘just a theory’
The Language of Bad Physics: Experiments in Non-Relativistic Modified Newtonian Dynamics (MOND)

Living the Scientific Life (Scientist, Interrupted): Made for Each Other: Evolution of Monogamy in Poison Frogs
Living the Scientific Life (Scientist, Interrupted): UV, You See? Black Light Reveals Secrets in Fossils
Living the Scientific Life (Scientist, Interrupted): Fly Me to the Moon: The Incredible Migratory Journey of the Arctic Tern
Living the Scientific Life (Scientist, Interrupted): Darwin’s Finches Develop Immunity to Alien Parasites
Living the Scientific Life (Scientist, Interrupted): Is That A T. rex Up Your Nose? New Species of Nose-dwelling Leech Discovered
Living the Scientific Life (Scientist, Interrupted): (How) Are Birds Affected by Volcanic Ash?
Living the Scientific Life (Scientist, Interrupted): How Will You Celebrate International Migratory Bird Day?
Living the Scientific Life (Scientist, Interrupted): What do Great Tits Reveal about the Genetics of Personality?
Living the Scientific Life (Scientist, Interrupted): Racehorse Research Identifies Speed Gene
Living the Scientific Life (Scientist, Interrupted): Fossil Feather Colors Really ARE Written In Stone
Living the Scientific Life (Scientist, Interrupted): Fetid Fish Revise Understanding of Fossil Formation
Living the Scientific Life (Scientist, Interrupted): Oiled SeaBirds: To Kill Or Not To Kill? What Is The Ethical Thing To Do?
Living the Scientific Life (Scientist, Interrupted): Newly Described Bird-like Dinosaur Predates Archaeopteryx by 15-20 Million Years
Living the Scientific Life (Scientist, Interrupted): Gulf Oil Spill Disaster: Spawn of the Living Dead for Atlantic Bluefin Tuna?
Living the Scientific Life (Scientist, Interrupted): Ancient DNA from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds
Living the Scientific Life (Scientist, Interrupted): Orange Stripey Dinosaurs? Fossil Feathers Reveal Their Secret Colors
Living the Scientific Life (Scientist, Interrupted): Migratory Monarch Butterflies ‘See’ Earth’s GeoMagnetic Field
Living the Scientific Life (Scientist, Interrupted): Colorful Tits Produce Speedier Sperm
Living the Scientific Life (Scientist, Interrupted): Doing It For the Kids: The Evolution of Migration
Living the Scientific Life (Scientist, Interrupted): Distressed Ravens Show That Empathy Is For The Birds, Too

The Loom: Skull Caps and Genomes

Maniraptora: Tastes Like Chicken: Size Matters — Bigger is Better, Even for Male Pipefish
Maniraptora: Tastes Like Chicken: Gender-Bending Chickens: Mixed, Not Scrambled

Mauka to Makai: Barnacle Sex

Maxwell’s Demon: Spirographs and the third dimension
Maxwell’s Demon: The Laws of Gelada (How to be a grad student)

Medical & Bio-Inspired Innovations: Blood Pressure, Medication, Diet, And Dementia: What The Recent Research Tells Us

Mental indigestion: Your microbiome and you (part I): Gut
Mental indigestion: The grass isn’t always greener…

Mind the Gap: In which I dream of revolution

Mr Science Show: For a healthy relationship, men should be ugly and rich, women pretty and mixed-race
Mr Science Show: Correlation of the Week: Liberals and Atheists Are More Intelligent
Mr Science Show: How do you spell goal?

Neurotopia: Attractiveness, anger, and warrior princess blondes
Neurotopia: A Letter to a Grad Student
Neurotopia: Friday Weird Science: Why does asparagus make your pee smell?
Neurotopia: On Animal Research

Nutrition Wonderland: The Truth About Organic Farming
Nutrition Wonderland: Understanding Our Bodies: Insulin

Observations of a Nerd: Evolution: The Curious Case of Dogs
Observations of a Nerd: Psych FAIL
Observations of a Nerd: Evolution: Watching Speciation Occur
Observations of a Nerd: Ancient Sex Scandals: Did We Get It On With Neandertals?
Observations of a Nerd: Reflections on the Gulf Oil Spill – Conversations With My Grandpa
Observations of a Nerd: Tuna

Opinionator (Olivia Judson): Laboratory Life
Opinionator (Olivia Judson): Evolving Sexual Tensions
Opinionator (Olivia Judson): Divide and Diminish
Opinionator (Olivia Judson): Enter the Chronotherapists

Oscillator: Knowledge is Power and Biology is Power, perhaps fused into a single essay.

Pharyngula: How to make a snake

PodBlack Cat: Presenting, Minorities And The Token Skeptic At #AtheistCon

Poseidon Sciences: The Agony and the Ecstasy: Why science writing is like learning tango and Chinese brush painting

Prof-Like Substance: Can I get a Land’s End catalog, STAT?

Promega Connections: How do I Describe Thee? Let Me Count the Ways
Promega Connections: Mate Selection at Frog Cocktail Parties: Keep it Short, Low, Loud, and Stand Out from the Crowd (Oh, and have a colorful vocal sac, too)

Reciprocal Space: I have discovered Jupiter
Reciprocal Space: Judgement Days

The Renaissance Mathematicus: Extracting the stopper.

Rennie’s Last Nerve: Blood Simple: Mammoths, mice, malaria and hemoglobin
Rennie’s Last Nerve: Energetically Batty

Respectful Insolence: When what an acupuncture study shows is much more interesting than what acupuncture believers think it shows

Sandwalk: On the Origin of the Double Membrane in Mitochondria and Chloroplasts

Saturday Morning Breakfast Cereal: Epistemological Anarchists (comic/cartoon)

Sauropod Vertebra Picture of the Week: Lies, damned lies, and Clash of the Dinosaurs

Save Your Breath For Running Ponies: Your Friends Aren’t Just Going To Forget You Envenomated Them, Sinornithosaurus.
Save Your Breath For Running Ponies: You Should Probably Just Move Oceans, Male Gulf Pipefish

Sciencebase: Whatever happened to the audiophile

Science in Seconds: Africa’s Next Top Hominid

Science In The Triangle (DeLene Beeland): Hibernation devastation: White-nose syndrome and our bats

Science Progress: Ecosystems In the Age of Cassandra

The Science Talent Project: Happy song scientists and sad song scientists

The Scientist: On Public Relations

Skeptic Wonder: Social onycophorans!

Skulls in the Stars: Perpetual motion — nonsense for over 100 years
Skulls in the Stars: Rolling out the (optical) carpet: the Talbot effect
Skulls in the Stars: Mythbusters were scooped — by 130 years! (Archimedes death ray)
Skulls in the Stars: Singular Optics: Light chasing its own tail
Skulls in the Stars: Shocking: Michael Faraday does biology! (1839)
Skulls in the Stars: Invisibility physics: Kerker’s ‘invisible bodies’

Southern Fried Scientist: The Data Speak
Southern Fried Scientist: Tournament marlins get bigger?
Southern Fried Scientist: Oil Spill vs. Hypoxic Zone
Southern Fried Scientist: Louis Agassiz and a brief history of early United States marine biology

Terra Sigillatta: Marking the magnificient memory of Henrietta Lacks

Tetrapod Zoology: Testing the flotation dynamics and swimming abilities of giraffes by way of computational analysis

There and (hopefully) back again…: Everyday (lab) living

The Thoughtful Animal: Snakes on a Muppethugging Plane! (Monday Pets)

Through the Sandglass: Life and art, sand and glass: the wonders of Difflugia

UCAR Magazine: Brrr: The AO is way low

Uncertain Principles: Science Is More Like Sumo Than Soccer

Water Numbers: Peter Gleick at SFGate.com: The best argument against global warming

wet: Save the Whale Poop

Wild Muse: Social networks, and social animals
Wild Muse: Wolf recovery vs. ecosystem health
Wild Muse: Givin’ props to hybrids

WooFighters: My Inspiration for Woo Fighters

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Clock Quotes

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

– Francis Bacon

Clock Quotes

“Cats are smarter than dogs. You can’t get eight cats to pull a sled through snow.”

– Jeff Valdez

Another interesting graph….

Click on image to check stats, play around…

The PepsiGate linkfest

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

Update: You can find follow-ups by me (and by others, linked within) at:

A Farewell to Scienceblogs: the Changing Science Blogging Ecosystem
Thank you!
Science Blogging Networks: What, Why and How
Is this something that NYTimes editors proudly allowed to get published?
Welcome Scientopia, a new science blogging network

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

An interesting chart….

From here

MSM Orientation (video)

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

New and Exciting in PLoS this week

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.

Intergenomic Arms Races: Detection of a Nuclear Rescue Gene of Male-Killing in a Ladybird:

Normally, in sexually reproducing organisms, the sex ratio (ratio of males to females) is 1:1. However, examples are known where this is not the case and there are more females than males in a population. Extreme bias in sex ratio can lead to females failing to find a mate. We studied Cheilomenes sexmaculata, a ladybird species that has females that produce more female than male offspring. In aphid-eating ladybirds, this phenomenon has been widely reported and is known to be due to the presence of bacteria that live inside the mother and are passed via her eggs to her offspring. In eggs destined to become male, the bacteria kill the embryo by some unknown mechanism. This is known as male-killing. Female offspring develop normally. Evolutionary theory predicts that in such systems, the genome of the host can fight back if a variant arises that stops the bacteria killing male offspring. In C. sexmaculata we found females that carried the male-killer but the sex ratio of their offspring depended on the male that they mated with. We carried out breeding tests to show that some ladybirds had a version of a gene that rescued the male offspring from the pathological effects of the male-killer.

Herbivory on Temperate Rainforest Seedlings in Sun and Shade: Resistance, Tolerance and Habitat Distribution:

Differential herbivory and/or differential plant resistance or tolerance in sun and shade environments may influence plant distribution along the light gradient. Embothrium coccineum is one of the few light-demanding tree species in the temperate rainforest of southern South America, and seedlings are frequently attacked by insects and snails. Herbivory may contribute to the exclusion of E. coccineum from the shade if 1) herbivory pressure is greater in the shade, which in turn can result from shade plants being less resistant or from habitat preferences of herbivores, and/or 2) consequences of damage are more detrimental in the shade, i.e., shade plants are less tolerant. We tested this in a field study with naturally established seedlings in treefall gaps (sun) and forest understory (shade) in a temperate rainforest of southern Chile. Seedlings growing in the sun sustained nearly 40% more herbivore damage and displayed half of the specific leaf area than those growing in the shade. A palatability test showed that a generalist snail consumed ten times more leaf area when fed on shade leaves compared to sun leaves, i.e., plant resistance was greater in sun-grown seedlings. Herbivore abundance (total biomass) was two-fold greater in treefall gaps compared to the forest understory. Undamaged seedlings survived better and showed a slightly higher growth rate in the sun. Whereas simulated herbivory in the shade decreased seedling survival and growth by 34% and 19%, respectively, damaged and undamaged seedlings showed similar survival and growth in the sun. Leaf tissue lost to herbivores in the shade appears to be too expensive to replace under the limiting light conditions of forest understory. Following evaluations of herbivore abundance and plant resistance and tolerance in contrasting light environments, we have shown how herbivory on a light-demanding tree species may contribute to its exclusion from shade sites. Thus, in the shaded forest understory, where the seedlings of some tree species are close to their physiological tolerance limit, herbivory could play an important role in plant establishment.

Can Bacteria Evolve Resistance to Quorum Sensing Disruption?:

Traditional treatment of bacterial infections relies heavily on the use of antibacterial compounds that either kill bacteria (bactericidal) or inhibit their growth (bacteriostatic). Typically, the targets for the main conventional antibiotics are essential cellular processes such as bacterial cell wall biosynthesis, bacterial protein synthesis, and bacterial DNA replication and repair. However, resistance to these drugs arises and spreads very rapidly, even to such an extent that bacteria have been identified that are simultaneously resistant to all available antibiotics [1]. The increasing occurrence of resistant bacteria gradually renders antibiotics ineffective in treating infections and has enormous human and economic consequences worldwide. As a result, the identification of novel drug targets and the development of novel therapeutics constitute an important area of current scientific research. An alternative to killing or inhibiting growth of pathogenic bacteria is the specific attenuation of bacterial virulence, which can be attained by targeting key regulatory systems that mediate the expression of virulence factors. One of the target regulatory systems is quorum sensing (QS), or bacterial cell-to-cell communication. QS is a mechanism of gene regulation in which bacteria coordinate the expression of certain genes in response to the presence or absence of small signal molecules (Figure 1).

Making the Invisible Visible: Verbal but Not Visual Cues Enhance Visual Detection:

Can hearing a word change what one sees? Although visual sensitivity is known to be enhanced by attending to the location of the target, perceptual enhancements of following cues to the identity of an object have been difficult to find. Here, we show that perceptual sensitivity is enhanced by verbal, but not visual cues. Participants completed an object detection task in which they made an object-presence or -absence decision to briefly-presented letters. Hearing the letter name prior to the detection task increased perceptual sensitivity (d′). A visual cue in the form of a preview of the to-be-detected letter did not. Follow-up experiments found that the auditory cuing effect was specific to validly cued stimuli. The magnitude of the cuing effect positively correlated with an individual measure of vividness of mental imagery; introducing uncertainty into the position of the stimulus did not reduce the magnitude of the cuing effect, but eliminated the correlation with mental imagery. Hearing a word made otherwise invisible objects visible. Interestingly, seeing a preview of the target stimulus did not similarly enhance detection of the target. These results are compatible with an account in which auditory verbal labels modulate lower-level visual processing. The findings show that a verbal cue in the form of hearing a word can influence even the most elementary visual processing and inform our understanding of how language affects perception.

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species:

Adaptation of sessile animals, such as molluscs, to stress is achieved by a number of molecular mechanisms, few of which are clearly understood. Insights from this research can provide clues about stress tolerance both for sessile and mobile organisms. The Mediterranean mussel, of the genus Mytilus, is a model organism for the study of stress at the molecular level, with sufficient gene structure and function data available. We have thus investigated a key stress response gene, Hsp90, and in particular its upstream region, using a combination of sequence and expression analysis approaches. We demonstrate that this region, responsible for the regulation of heat shock-associated gene expression, exhibits an unparalleled structural and functional complexity compared to other model organisms, as well as subtle gene expression patterns across multiple tissues. These results form the basis upon which the heat shock response can be used as a molecular biosensor for environmental monitoring in the future.

Vitamin C: Intravenous Use by Complementary and Alternative Medicine Practitioners and Adverse Effects:

Anecdotal information and case reports suggest that intravenously administered vitamin C is used by Complementary and Alternate Medicine (CAM) practitioners. The scale of such use in the U.S. and associated side effects are unknown. We surveyed attendees at annual CAM Conferences in 2006 and 2008, and determined sales of intravenous vitamin C by major U.S. manufacturers/distributors. We also queried practitioners for side effects, compiled published cases, and analyzed FDA’s Adverse Events Database. Of 199 survey respondents (out of 550), 172 practitioners administered IV vitamin C to 11,233 patients in 2006 and 8876 patients in 2008. Average dose was 28 grams every 4 days, with 22 total treatments per patient. Estimated yearly doses used (as 25g/50ml vials) were 318,539 in 2006 and 354,647 in 2008. Manufacturers’ yearly sales were 750,000 and 855,000 vials, respectively. Common reasons for treatment included infection, cancer, and fatigue. Of 9,328 patients for whom data is available, 101 had side effects, mostly minor, including lethargy/fatigue in 59 patients, change in mental status in 21 patients and vein irritation/phlebitis in 6 patients. Publications documented serious adverse events, including 2 deaths in patients known to be at risk for IV vitamin C. Due to confounding causes, the FDA Adverse Events Database was uninformative. Total numbers of patients treated in the US with high dose vitamin C cannot be accurately estimated from this study. High dose IV vitamin C is in unexpectedly wide use by CAM practitioners. Other than the known complications of IV vitamin C in those with renal impairment or glucose 6 phosphate dehydrogenase deficiency, high dose intravenous vitamin C appears to be remarkably safe. Physicians should inquire about IV vitamin C use in patients with cancer, chronic, untreatable, or intractable conditions and be observant of unexpected harm, drug interactions, or benefit.

A Threshold Equation for Action Potential Initiation:

Neurons communicate primarily with stereotypical electrical impulses, action potentials, which are fired when a threshold level of excitation is reached. This threshold varies between cells and over time as a function of previous stimulations, which has major functional implications on the integrative properties of neurons. Ionic channels are thought to play a central role in this modulation but the precise relationship between their properties and the threshold is unclear. We examined this relationship in biophysical models and derived a formula which quantifies the contribution of various mechanisms. The originality of our approach is that it provides an instantaneous time-varying value for the threshold, which applies to the highly fluctuating regimes characterizing neurons in vivo. In particular, two known ionic mechanisms were found to make the threshold adapt to the membrane potential, thus providing the cell with a form of gain control.

Uncertainty Compensation in Human Attention: Evidence from Response Times and Fixation Durations:

Uncertainty and predictability have remained at the center of the study of human attention. Yet, studies have only examined whether response times (RT) or fixations were longer or shorter under levels of stimulus uncertainty. To date, no study has examined patterns of stimuli and responses through a unifying framework of uncertainty. We asked 29 college students to generate repeated responses to a continuous series of visual stimuli presented on a computer monitor. Subjects produced these responses by pressing on a keypad as soon a target was detected (regardless of position) while the durations of their visual fixations were recorded. We manipulated the level of stimulus uncertainty in space and time by changing the number of potential stimulus locations and time intervals between stimulus presentations. To allow the analyses to be conducted using uncertainty as common description of stimulus and response we calculated the entropy of the RT and fixation durations. We tested the hypothesis of uncertainty compensation across space and time by fitting the RT and fixation duration entropy values to a quadratic surface. The quadratic surface accounted for 80% of the variance in the entropy values of both RT and fixation durations. RT entropy increased as a function of spatial and temporal uncertainty of the stimulus, alongside a symmetric, compensatory decrease in the entropy of fixation durations as the level of spatial and temporal uncertainty of the stimuli was increased. Our results demonstrate that greater uncertainty in the stimulus leads to greater uncertainty in the response, and that the effects of spatial and temporal uncertainties are compensatory. We also observed compensatory relationship across the entropies of fixation duration and RT, suggesting that a more predictable visual search strategy leads to more uncertain response patterns and vice versa.

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data:

Classical morphological taxonomy places the approximately 1400 recognized species of Scleractinia (hard corals) into 27 families, but many aspects of coral evolution remain unclear despite the application of molecular phylogenetic methods. In part, this may be a consequence of such studies focusing on the reef-building (shallow water and zooxanthellate) Scleractinia, and largely ignoring the large number of deep-sea species. To better understand broad patterns of coral evolution, we generated molecular data for a broad and representative range of deep sea scleractinians collected off New Caledonia and Australia during the last decade, and conducted the most comprehensive molecular phylogenetic analysis to date of the order Scleractinia. Partial (595 bp) sequences of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene were determined for 65 deep-sea (azooxanthellate) scleractinians and 11 shallow-water species. These new data were aligned with 158 published sequences, generating a 234 taxon dataset representing 25 of the 27 currently recognized scleractinian families. There was a striking discrepancy between the taxonomic validity of coral families consisting predominantly of deep-sea or shallow-water species. Most families composed predominantly of deep-sea azooxanthellate species were monophyletic in both maximum likelihood and Bayesian analyses but, by contrast (and consistent with previous studies), most families composed predominantly of shallow-water zooxanthellate taxa were polyphyletic, although Acroporidae, Poritidae, Pocilloporidae, and Fungiidae were exceptions to this general pattern. One factor contributing to this inconsistency may be the greater environmental stability of deep-sea environments, effectively removing taxonomic “noise” contributed by phenotypic plasticity. Our phylogenetic analyses imply that the most basal extant scleractinians are azooxanthellate solitary corals from deep-water, their divergence predating that of the robust and complex corals. Deep-sea corals are likely to be critical to understanding anthozoan evolution and the origins of the Scleractinia.

Clock Quotes

The only time to eat diet food is while you’re waiting for the steak to cook.
– Julia Child

New and Exciting in PLoS this week

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:

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Future: News From The Year 2137 Trailer (video)

Future: News From The Year 2137 Trailer
For explanation, read this.

Books: ‘The Poisoner’s Handbook’ by Deborah Blum

Poisoner's Handbook cover.jpgIf 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?

3D Google Earth Tour of NC Maps (video)

Science Café Raleigh – A Nuclear Renaissance

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.