A Blog Around The Clock

Texting for Anglers at ScienceOnline2010 (video) - Part 1

Sat, 13 Mar 2010 13:16:46 -0500

North Carolina Sea Grant fisheries specialist Scott Baker talks about "RECTEXT" -- a system that lets tournament anglers report catch data via cell phone text messaging.
Fisheries managers often meet hurdles in collecting recreational fishing data, but RECTEXT has the potential to provide valuable information for gamefish population research. Learn more at www.rectext.org.

Baker demonstrated RECTEXT at the ScienceOnline2010 conference on Jan. 15, 2010. Filmed at Sigma Xi in Research Triangle Park, NC. Flipcam donated by a ScienceOnline sponsor.

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Clock Quotes

Sat, 13 Mar 2010 03:55:50 -0500

"Why do you sit there looking like an envelope without any address on it?"

- Mark Twain

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We got cartooned!!!

Fri, 12 Mar 2010 09:24:24 -0500

ROFL! Can you recognize your favourite sciencebloggers in this comic strip by Joseph Hewitt? To see larger (and read the associated text) go to Ataraxia Theatre

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ScienceOnline2010 - Trust and Critical Thinking (video), Part 6

Fri, 12 Mar 2010 09:15:54 -0500

Saturday, January 16 at 4:40 - 5:45pm
C. Trust and Critical Thinking - Stephanie Zvan, PZ Myers, Desiree Schell, Greg Laden, Kirsten Sanford

Description: Lay audiences often lack the resources (access to studies, background knowledge of fields and methods) to evaluate the trustworthiness of scientific information as another scientist or a journalist might. Are there ways to usefully promote critical thinking about sources and presentation as we provide information? Can we teach them to navigate competing claims? And can we do it without promoting a distrust of science itself?

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New and Exciting in PLoS ONE

Fri, 12 Mar 2010 07:46:24 -0500

There are 19 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:

Plant Species and Functional Group Combinations Affect Green Roof Ecosystem Functions:

Green roofs perform ecosystem services such as summer roof temperature reduction and stormwater capture that directly contribute to lower building energy use and potential economic savings. These services are in turn related to ecosystem functions performed by the vegetation layer such as radiation reflection and transpiration, but little work has examined the role of plant species composition and diversity in improving these functions. We used a replicated modular extensive (shallow growing- medium) green roof system planted with monocultures or mixtures containing one, three or five life-forms, to quantify two ecosystem services: summer roof cooling and water capture. We also measured the related ecosystem properties/processes of albedo, evapotranspiration, and the mean and temporal variability of aboveground biomass over four months. Mixtures containing three or five life-form groups, simultaneously optimized several green roof ecosystem functions, outperforming monocultures and single life-form groups, but there was much variation in performance depending on which life-forms were present in the three life-form mixtures. Some mixtures outperformed the best monocultures for water capture, evapotranspiration, and an index combining both water capture and temperature reductions. Combinations of tall forbs, grasses and succulents simultaneously optimized a range of ecosystem performance measures, thus the main benefit of including all three groups was not to maximize any single process but to perform a variety of functions well. Ecosystem services from green roofs can be improved by planting certain life-form groups in combination, directly contributing to climate change mitigation and adaptation strategies. The strong performance by certain mixtures of life-forms, especially tall forbs, grasses and succulents, warrants further investigation into niche complementarity or facilitation as mechanisms governing biodiversity-ecosystem functioning relationships in green roof ecosystems.

Cerebral Asymmetries: Complementary and Independent Processes:

Most people are right-handed and left-cerebrally dominant for speech, leading historically to the general notion of left-hemispheric dominance, and more recently to genetic models proposing a single lateralizing gene. This hypothetical gene can account for higher incidence of right-handers in those with left cerebral dominance for speech. It remains unclear how this dominance relates to the right-cerebral dominance for some nonverbal functions such as spatial or emotional processing. Here we use functional magnetic resonance imaging with a sample of 155 subjects to measure asymmetrical activation induced by speech production in the frontal lobes, by face processing in the temporal lobes, and by spatial processing in the parietal lobes. Left-frontal, right-temporal, and right-parietal dominance were all intercorrelated, suggesting that right-cerebral biases may be at least in part complementary to the left-hemispheric dominance for language. However, handedness and parietal asymmetry for spatial processing were uncorrelated, implying independent lateralizing processes, one producing a leftward bias most closely associated with handedness, and the other a rightward bias most closely associated with spatial attention.

Purification and Functional Characterisation of Rhinocerase, a Novel Serine Protease from the Venom of Bitis gabonica rhinoceros:

Serine proteases are a major component of viper venoms and are thought to disrupt several distinct elements of the blood coagulation system of envenomed victims. A detailed understanding of the functions of these enzymes is important both for acquiring a fuller understanding of the pathology of envenoming and because these venom proteins have shown potential in treating blood coagulation disorders. In this study a novel, highly abundant serine protease, which we have named rhinocerase, has been isolated and characterised from the venom of Bitis gabonica rhinoceros using liquid phase isoelectric focusing and gel filtration. Like many viper venom serine proteases, this enzyme is glycosylated; the estimated molecular mass of the native enzyme is approximately 36kDa, which reduces to 31kDa after deglycosylation. The partial amino acid sequence shows similarity to other viper venom serine proteases, but is clearly distinct from the sequence of the only other sequenced serine protease from Bitis gabonica. Other viper venom serine proteases have been shown to exert distinct biological effects, and our preliminary functional characterization of rhinocerase suggest it to be multifunctional. It is capable of degrading α and β chains of fibrinogen, dissolving plasma clots and of hydrolysing a kallikrein substrate. A novel multifunctional viper venom serine protease has been isolated and characterised. The activities of the enzyme are consistent with the known in vivo effects of Bitis gabonica envenoming, including bleeding disorders, clotting disorders and hypotension. This study will form the basis for future research to understand the mechanisms of serine protease action, and examine the potential for rhinocerase to be used clinically to reduce the risk of human haemostatic disorders such as heart attacks and strokes.

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Clock Quotes

Fri, 12 Mar 2010 03:54:50 -0500

Man must sit in chair with mouth open for very long time before roast duck fly in.

- Chinese proverb

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ScienceOnline2010 - interview with Russ Williams

Thu, 11 Mar 2010 11:51:37 -0500

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 Russ Williams from North Carolina Zoological Society and the Russlings blog 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 an English major from Northeastern Pennsylvania who works at the North Carolina Zoo (24 years executive director, N.C. Zoological Society). I try to stay somewhat current, despite my age (north of 60). For example, I am listening these days to music by Death Cab for Cutie, Arcade Fire, Flaming Lips, Radiohead and Pole Cat Creek, along with the oldies (Nirvana, Pearl Jam, Springsteen, Bob Dylan, Tom Waits, Hank [and Lucinda] Williams, Coltrane and Bach).

Started personally blogging about zoo animals and issues about five years ago. (Took an intro course in blogging at UNC-Greensboro by G'boro blogfather Ed Cone (Word Up). Found I was learning much from Google searches, and then by following the blogs and tweets of certain science journalists and bloggers, conservation researchers, etc. (The blogs and tweets of Wild Muse/@tdelene and you, BoraZ, are favorite sources.) Flickr and YouTube have provided much for my blogs and tweets too.

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

Had no idea I'd work for a Zoo. (Even named a son Noah; would never do that to someone by plan!) Growing up, I knew I would have a career in advertising, like my father. Did do some retail advertising (broadcast and newspaper) after graduation - early 1970's. Didn't like it. Backpacked in Europe for two months. Returned to work with weekly newspapers. This led to public relations/communications for non-profits. This led to fund raising. This led to North Carolina (United Way in Winston-Salem, 1980-85). This led to the NC Zoo Society - 1985-now.

Result: accidental zoology tinkerer.

What does it mean to be the Director of the NC Zoological Society? What does the job entail?

Always remember that I have about 100,000 bosses, in about 27,000 NC Zoo Society member households. Our staff tries to provide excellent customer service to our members and to be their "champions" when it comes to getting a good return on their investments in the Zoo in general or a very specific program, like Field Trip Earth (recognized as a Landmark website by the American Association of School Librarians - one of 21, including Google Earth, Library of Congress, NASA and Smithsonian Education).

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

Proud of my small role in how the NC Zoo and Zoo Society have grown and the creation of both Field Trip Earth (our educational website featuring journals and other media offered by conservation researchers around the world) and Sylvan Heights Waterfowl Park (the largest such gathering, offering and breeding of rare and endangered ducks, geese and swans in the world).

Really enjoy helping folks accomplish what they want to accomplish for the future of the NC Zoo through "The Lions Pride", a grouping of people who have made planned arrangements for their Zoo, mainly through wills.

Capital campaigns, like Project: Pachyderms (African elephants and southern white rhinos) and Project: Polar Bears also meet my need to attain goals requiring some considerable preparation and effort. (I've also plodded through a few full, running marathons and to the top of Mt. Kilimanjaro, at 55).

NC Zoo has something else unique about it - the Zoo School! Can you tell us more about it?

A "magnet" Asheboro City high school, the Zoo School is right on site here. It uses the Zoo as a teaching tool not just to study biology and geography, but for all learning, making use of the Zoo for English composition and communications, mathematics, business and many other studies.

What was the best aspect of ScienceOnline2010 for you?

Appreciate your prodding, Bora, to demonstrate Field Trip Earth at ScienceOnline2010. The Charlotte Observer science editor attended our demonstration and the result was an 85-column-inch article in both the Observer and Raleigh News & Observer by T. DeLene Beeland, whose Wild Muse blog and tweets were already favorites of mine, introduced by your RTs, Bora. I want to take in more of the sessions the next time. Only got to one session (other than our own series of demos) and it was exceptional.

It was so nice to see you again and thank you for the interview. I'll see you at the Zoo soon....and at ScienceOnline2011, of course!

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ScienceOnline2010 - Trust and Critical Thinking (video), Part 5

Thu, 11 Mar 2010 09:14:43 -0500

Saturday, January 16 at 4:40 - 5:45pm
C. Trust and Critical Thinking - Stephanie Zvan, PZ Myers, Desiree Schell, Greg Laden, Kirsten Sanford

Description: Lay audiences often lack the resources (access to studies, background knowledge of fields and methods) to evaluate the trustworthiness of scientific information as another scientist or a journalist might. Are there ways to usefully promote critical thinking about sources and presentation as we provide information? Can we teach them to navigate competing claims? And can we do it without promoting a distrust of science itself?

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New and Exciting in PLoS ONE

Thu, 11 Mar 2010 07:59:31 -0500

There are 15 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:

Extreme Female Promiscuity in a Non-Social Invertebrate Species:

While males usually benefit from as many matings as possible, females often evolve various methods of resistance to matings. The prevalent explanation for this is that the cost of additional matings exceeds the benefits of receiving sperm from a large number of males. Here we demonstrate, however, a strongly deviating pattern of polyandry. We analysed paternity in the marine snail Littorina saxatilis by genotyping large clutches (53-79) of offspring from four females sampled in their natural habitats. We found evidence of extreme promiscuity with 15-23 males having sired the offspring of each female within the same mating period. Such a high level of promiscuity has previously only been observed in a few species of social insects. We argue that genetic bet-hedging (as has been suggested earlier) is unlikely to explain such extreme polyandry. Instead we propose that these high levels are examples of convenience polyandry: females accept high numbers of matings if costs of refusing males are higher than costs of accepting superfluous matings.

Record Dynamics in Ants:

The success of social animals (including ourselves) can be attributed to efficiencies that arise from a division of labour. Many animal societies have a communal nest which certain individuals must leave to perform external tasks, for example foraging or patrolling. Staying at home to care for young or leaving to find food is one of the most fundamental divisions of labour. It is also often a choice between safety and danger. Here we explore the regulation of departures from ant nests. We consider the extreme situation in which no one returns and show experimentally that exiting decisions seem to be governed by fluctuating record signals and ant-ant interactions. A record signal is a new 'high water mark' in the history of a system. An ant exiting the nest only when the record signal reaches a level it has never perceived before could be a very effective mechanism to postpone, until the last possible moment, a potentially fatal decision. We also show that record dynamics may be involved in first exits by individually tagged ants even when their nest mates are allowed to re-enter the nest. So record dynamics may play a role in allocating individuals to tasks, both in emergencies and in everyday life. The dynamics of several complex but purely physical systems are also based on record signals but this is the first time they have been experimentally shown in a biological system.

Are Maternal Antibodies Really That Important? Patterns in the Immunologic Development of Altricial Passerine House Sparrows (Passer domesticus):

Maternal antibodies are believed to play an integral role in protecting immunologically immature wild-passerines from environmental antigens. This study comprehensively examines the early development of the adaptive immune system in an altricial-developing wild passerine species, the house sparrow (Passer domestics), by characterizing the half-life of maternal antibodies in nestling plasma, the onset of de novo synthesis of endogenous antibodies by nestlings, and the timing of immunological independence, where nestlings rely entirely on their own antibodies for immunologic protection. In an aviary study we vaccinated females against a novel antigen that these birds would not otherwise encounter in their natural environment, and measured both antigen-specific and total antibody concentration in the plasma of females, yolks, and nestlings. We traced the transfer of maternal antibodies from females to nestlings through the yolk and measured catabolisation of maternal antigen-specific antibodies in nestlings during early development. By utilizing measurements of non-specific and specific antibody levels in nestling plasma we were able to calculate the half-life of maternal antibodies in nestling plasma and the time point at which nestling were capable of synthesizing antibodies themselves. Based on the short half-life of maternal antibodies, the rapid production of endogenous antibodies by nestlings and the relatively low transfer of maternal antibodies to nestlings, our findings suggest that altricial-developing sparrows achieve immunologic independence much earlier than precocial birds. To our knowledge, this is the first in depth analyses performed on the adaptive immune system of a wild-passerine species. Our results suggest that maternal antibodies may not confer the immunologic protection or immune priming previously proposed in other passerine studies. Further research needs to be conducted on other altricial passerines to determine if the results of our study are a species-specific phenomenon or if they apply to all altricial-developing birds.

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Clock Quotes

Thu, 11 Mar 2010 03:25:07 -0500

"He loves nature in spite of what it did to him."

- Forrest Tucker

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ScienceOnline2010 - interview with DeLene Beeland

Wed, 10 Mar 2010 11:59:34 -0500

Today, I asked T. DeLene Beeland to answer a few questions.

Geography: I live in North Carolina, but my heart is still in Florida, where I spent my whole life prior to 2009. Perspective: I love nature and learning about the natural world. I am a freelance writer with graduate training in ecology, natural resources management and journalism.

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

It's been more of a higgledy-piggledy switch-back path than a trajectory. Let's see...I'm 33 and have been freelancing for a little more than one year. This is actually my second career - my first was as a commercial interior designer (not a decorator, an interior architectural space planner - very different). While working in design, I was bored down to my bones. I'd also had a health crisis that forced the soul-searching question: if I can do anything in the world, what would it be? My inner voice kept answering, "Be a writer, study ecology." So I did.

While in grad school (Univ. of Florida) I worked for two years as a staff science writer at the Florida Museum of Natural History. The science divisions in this museum are vast, there are 20-plus scientific departments. I wrote about goings-on in ichthyology, herpetology, four different archaeology departments, a Lepidoptera center and of course, vertebrate and invertebrate paleontology - oh, and ornithology, palynology and paleobotany too! It was a cool gig, except for the money. Shortly after graduating I took a similar position with the Emerging Pathogens Institute at UF, except they were a start-up so I built their science communications from scratch.

Today, I'm building a freelance writing business and working on a natural history book. I feel like I'm at a point where I've struggled to the bottom-rung of the freelancing career and I've got a toehold but still have a marathon climbing trek ahead of me.

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

Trying to afford health insurance. (Kidding! Sort of.) Seriously, trying to carve time to research and write my book; stay afloat with freelance work and expanding my professional network. Yep, that pretty much consumes most of my time. And watching the birds at my seed feeder - that soaks up a lot of time too. I like watching them over time and learning their seasonal behaviors.

What aspect of science communication interests you the most?

Finding an interesting story, pitching, finding the lede to a story... Figuring out how to break complex things down into interesting reads; making science relatable to everyday people who may not be into it - these are communication elements I'm interested in. I see my science writing as in its infancy. I'm still really focused on explanatory approaches (here is what they found, this is what the results mean, etc.) Which is fine for being a science evangelist and getting people interested, but in the future I hope to be doing more critical pieces and analysis; especially concerning conservation biology and species conservation and extinction, topics that I always feel drawn to. I am interested in learning to do profile pieces better too - getting at the personalities who do science. I've also been sinking time into reading about narrative writing craft and how to bring story-telling elements into science writing: using dialogue (well), orchestrating plot and conflict, stuff like that.

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?

It is a small part of my professional life. I write blogs for one client (Science in the Triangle), and I write a personal blog, Wild Muse. But blogging is not my primary writing outlet and is a small fraction of my income; and because of that, the majority of my time and effort goes into other types of print communication work. I started blogging as an experiment, mostly because all the freelance business articles I was reading said "You Must Blog. Period."

I use my personal blog to explore things I'm interested in: wolf studies, birds, ecology the environment... It's really more of an online journaling exercise. I'm a highly kinetic reader. I have to underline and scrawl copious notes in the margins in order to process ideas... and blogging, for me, is kind of the online analog to that learning process. The happy accidental side effect of it is that I've met many people through the process of blogging - like you - and now have a wider and richer online social network because of it.

Facebook I reserve for my personal life. Twitter, I treat a little more professionally. I've made a point to use it more tied to my online presence as a science and nature writer.

When and how did you first discover science blogs? What are some of your favourites?

Ah, British spelling?

Shortly after moving to N.C., and hooking up with the SCONC group. As for favorite blogs... I graze a lot. Since I'm new to the blogosphere - Wild Muse is only seven or eight months old - I flit around a lot and skim many people's blogs just to see what is out there. Some faves in my Google Reader are: CreatureCast, Round Robin, Wolves of the High Arctic and Ralph Maughan's Wildlife News... but if you notice, these are not blogs you go to for interesting writing or science news, my preferences are more clustered around content I find intriguing. Deep Sea News is great too because it has a unique tone. Scads of people have great blogs, but I can't say I'm a very loyal daily reader of any single person's blog. I get impatient, bored and turned off by blogs that are self-promotional or bloggers who take themselves too seriously, and usually won't go back if I get that vibe from someone's site. But if they have good content and package it well, I'll flit back to it.

Is there anything that happened at ScienceOnline2010 - 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?

Hands-down, the fact-checking session won my interest. There are cases where you can't just take your source's word for it. Just because someone says something, does not make it true. Writers are not transcriptionists. You have to check with a second or third source to verify what the first said if something does not feel right or sounds off or contradicts what you know. This happened to me recently on an assignment... a project manager told me they had discovered one species trend, then a person collecting data on the project told me the exact opposite. So I had to run it by others to find out the reality. Sometimes people think they are telling you the "truth" but really they are only telling you their perspective of what they experienced - and it's your job as the writer to sift through and drill down to the un-colored reality. So yeah, I'd say that was the best lesson and what I took home with me. You really get into the danger zone when you think you know something, but don't check it to verify that what you think you know is in fact true.

It was so nice to see you again and thank you for the interview. I'll see you around.

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New science journalism ecosystem: new inter-species interactions, new niches

Wed, 10 Mar 2010 11:20:00 -0500

Almost a year ago, Nature published a set of opinion articles, including Science journalism: Toppling the priesthood by Toby Murcott. I did not react at the time, but JR Minkel and Jessica Palmer did and got some interesting responses in the comments. The article was brought to my attention by Gozde Zorlu who is ruminating on the same ideas and will have a blog post about it shortly (and I will let you know when it's up).

The article covers a lot of ground and has many layers. I finally read it and these are just some really quick thoughts, just to provoke discussion.....

First, Murcott is complaining about being essentially a lay-person outside of his own domain in biochemistry. That is true. Science reporters who don't have any scientific background are in an even worse shape - they definitely have a handicap, but not something they cannot overcome with years of study. But for this, they need to have the freedom to focus on only one area of science, e.g., Andy Revkin focusing on climate, Carl Zimmer on evolution, etc. I wrote a little bit about this before.

If you have spent some time in science before moving into journalism, you understand that years of total immersion in the field are necessary to fully understand it - I mean a narrow field! And not just the purely scientific information, but also historical, philosophical and social context, who-is-who in the field, relative strengths of various hypotheses, etc. You understand that it is impossible for a single person to gain a full understanding of every area of science.

- Can you play violin?
- Sure, of course
- Have you ever played?
- No. But it looks easy, I'm sure I can do it.

This is how non-scientists often think about science. This includes some journalists, until they get started on science reporting and realize that it's not as easy as it looks. But their editors do not grok it. Editors think of 'science' as a single thing - there is a sports-guy and a fashion-guy and a science-guy in the newsroom and they get assignments accordingly. Which means that the poor science reporter has to report on everything from cosmology to math to medicine to ecology with no time to actually study these areas sufficiently to understand them. Of course they get nervous and exhausted and touchy... ;-)

But in the era where newsrooms are firing in-house journalists and relying more and more on freelancers, this is an opportunity for freelance journalists to put a stake into a particular territory: specialize in one field and refuse to write stories outside it. That way, a journalist who has become, over years of study and reporting, an expert in field A, will only report on A, will be on rolodexes (I guess not virtual but real physical ones) of every editor in the country/world for stories on A and will be asked all the time by everyone to cover A. And will do it really well. Each editor will have a list of experts on A, B, C and every other area of science. With specialization, biochemists will not have to risk showing off their ignorance of astronomy, media organizations will know they have all topics covered by the best of the best, and the general quality of reporting science will increase.

In the next segment of the article, Murcott seems to want more investigative science journalism. But, compare this to this. Connie St.Louis and I have the opposite ideas what science journalism is. I am not specifically targeting Connie, it just happens that I am aware of her post that puts into words, very clearly, what many other journalists say or at least hint at.

Everything that I think is science journalism, she dismisses as not being 'real' science journalism: science reportage and explaining. And one aspect of it that she thinks is the real science journalism is the only one I think is really not - "investigative science journalism" is, in my book, just the regular investigative journalism in which the people under scrutiny just happen accidentally to be scientists. The former (science reporting and explaining) requires that the journalist understands science, the latter (investigating potential misconduct by people who happen to be scientists) does not. As I said before, if the investigation involves analysis of data, it is done by scientists and reported in specialized media: scientific journals (these can be then translated into lay language by journalists and reported to the general audience). If the investigation involves potential misconduct of humans who happen to be scientists, it is done by journalists, but it is not science journalism any more - it is more something like political journalism (as misconduct usually involves money and prestige).

Steve Mirsky (editor at Scientific American: here on Twitter ) once said, and I agree with him, that all of science journalism should be activist: evangelizing for truth (not capitalized). There is no mealy-mouthed HeSaidSheSaid, False-Balance, View-From-Nowhere tabulation of opinions held by people. Science journalism is straightforward: this is how the world works and this is how we learned it.

Which brings me to another important question: why professional journalists dismiss Press Information Officers. If journalists think that journalism that investigates scientists is what should be called 'science journalism', and see that what PIOs are doing is not that, they will not think of PIOs as journalists. On the other hand, if you agree with me that investigation of scientists is not science journalism, but reporting and explaining science is, than PIOs, many of whom have science degrees, are actually doing the brunt of science journalism these days. Sure, not all of them are perfect, and not all press releases are good, but they are getting better (as science majors are replacing j-school majors as PIOs at many institutions), they are, seeing how media is crumbling, starting to see themselves as serious journalists filling the void left by the massive layoffs of science reporters in the MSM, and are writing better and better copy, usually much better than what remaining newsroom reporters write under horrendous deadlines and pressure.

In other words, as we realize that scientists, PIOs, journalists and audience are in it together, collaborating on science reporting, we need to eliminate this antagonism between newsroom journalists and institutional journalists (formerly known as PIOs). For that antagonism to be eliminated, the two need to agree on what the definition of science journalism is. And I don't think defining it as 'investigating potential misconduct of scientists' is a good and healthy definition. It is much more productive to leave that kind of stuff to political reporters (who will be tipped off by scientists themselves, as was always the case: all data-fudging was first discovered by other scientists, the only people with expertise to notice it in the first place) and have everyone focus on real science journalism - reporting and explaining science.

Next, Murcott wants to move science journalism from a) presenting facts (including results of latest studies), to b) presenting how scientists work and their method. He, and many others, forget that the key element is the third level: c) trust. Read this carefully to understand why. So, all three things need to be reported. Eyeing every paper and every press release as suspect, and treating scientists as dishonest until proven otherwise, is one of the journalistic techniques that undermines the trust in science. Whose side are you on, guys? Creationists, GW-denialists, HIV-denialists and anti-vaccers? Job of a journalist is to explain the world as it is. Science is the best method to figure out how the world works. Use this method as a journalistic method.

Scientific method has several (actually many) elements in phases, but one can oversimplify here: get an idea, test it, communicate it. Yes, communicating science is a part of scientific method. Which is why both scientists and journalists have to do it, hopefully together as allies, not as opponents eyeing each other with suspicion. See also many of the reports from scio10 - almost all of them focus on the need for collaboration between scientists, press officers and journalists, not antagonism. It's a new ecosystem today. And the new niche for science journalists is NOT the top predator any more - the mindset has to shift from the competitive to a collaborative view of media ecology.

More and more people studying the evolution of media are coming around to the idea that the job of a journalist these days is a person who collects, aggregates and interprets information. Even data.

The story is important, as humans are storytellers by nature, but the story is a hook that takes people to the wealth of underlying information, the background, and the data. Each news-report needs to be embedded in a broader structure that also contains an "explainer". Which is why it is essential for the story, the "hook", to link to all the relevant background information and data.

Finally, we get to Murcott's wish to see reviews....the reviews that scientists have written during the process of peer-review of manuscripts. Murcott, pressed for time, thinks that being able, as a journalist, to see the reviews, would help him understand the story better and glean some of the context that he is missing because is writing a story outside of his area of expertise and has not time to study it first. In essence, he is asking for a shortcut that helps him do his job. But he is not considering how this would affect the review process.

First, it is important to remind everyone that peer-review is a very new thing. Only one minor paper by Einstein went through peer-review. Nature only started experimenting with it in the late 1960s. Yet lots and lots of great science was published before this was instituted. There is no data supporting the view that peer-review actually does much good.

We at PLoS ONE are trying to improve the process. What we have noticed (and most of our academic editors and authors agree) is that by eliminating the need for reviewers to evaluate if a manuscript is novel, exciting, revolutionary, paradigm-shifting, mind-boggling and Earth-shaking, and only asking them to evaluate the technical aspects of the work, the review becomes MUCH better:

As the scientific paper itself evolves, more and more of the peer-review will happen after publication, on the paper or connected to it and journalists need to be a part of it.

You can search the Web for many discussions of "open review" and you will see that there are many more cons than pros. The reviewers will find it difficult to be frank. Fewer people will agree to review (and there is already too many manuscripts for the available number of reviewers). Showing reviews to journalists would have exactly the same effect, for good or ill. Having a journalist see reviews is ...a crutch for a journo who does not have the time, or expertise, or inclination to do the heavy lifting of personal education and everybody would object to this, rightly so.

Specialization of journalists - each grabbing one's own area of expertise - and the collaborative journalism done by scientists, PIOs, journalists and audience, would make a 'peek' at reviewers' comments unnecessary and irrelevant. The collective WILL have all the necessary expertise and historical/philosophical/sociological/theoretical/methodological context to get the story (and attached data/information) right.

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ScienceOnline2010 - Trust and Critical Thinking (video), Part 4

Wed, 10 Mar 2010 09:14:05 -0500

Saturday, January 16 at 4:40 - 5:45pm
C. Trust and Critical Thinking - Stephanie Zvan, PZ Myers, Desiree Schell, Greg Laden, Kirsten Sanford

Description: Lay audiences often lack the resources (access to studies, background knowledge of fields and methods) to evaluate the trustworthiness of scientific information as another scientist or a journalist might. Are there ways to usefully promote critical thinking about sources and presentation as we provide information? Can we teach them to navigate competing claims? And can we do it without promoting a distrust of science itself?

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New and Exciting in PLoS ONE

Wed, 10 Mar 2010 06:31:39 -0500

There are 35 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:

Does Tropical Forest Fragmentation Increase Long-Term Variability of Butterfly Communities?:

Habitat fragmentation is a major driver of biodiversity loss. Yet, the overall effects of fragmentation on biodiversity may be obscured by differences in responses among species. These opposing responses to fragmentation may be manifest in higher variability in species richness and abundance (termed hyperdynamism), and in predictable changes in community composition. We tested whether forest fragmentation causes long-term hyperdynamism in butterfly communities, a taxon that naturally displays large variations in species richness and community composition. Using a dataset from an experimentally fragmented landscape in the central Amazon that spanned 11 years, we evaluated the effect of fragmentation on changes in species richness and community composition through time. Overall, adjusted species richness (adjusted for survey duration) did not differ between fragmented forest and intact forest. However, spatial and temporal variation of adjusted species richness was significantly higher in fragmented forests relative to intact forest. This variation was associated with changes in butterfly community composition, specifically lower proportions of understory shade species and higher proportions of edge species in fragmented forest. Analysis of rarefied species richness, estimated using indices of butterfly abundance, showed no differences between fragmented and intact forest plots in spatial or temporal variation. These results do not contradict the results from adjusted species richness, but rather suggest that higher variability in butterfly adjusted species richness may be explained by changes in butterfly abundance. Combined, these results indicate that butterfly communities in fragmented tropical forests are more variable than in intact forest, and that the natural variability of butterflies was not a buffer against the effects of fragmentation on community dynamics.

Large-Scale Movement and Reef Fidelity of Grey Reef Sharks:

Despite an Indo-Pacific wide distribution, the movement patterns of grey reef sharks (Carcharhinus amblyrhynchos) and fidelity to individual reef platforms has gone largely unstudied. Their wide distribution implies that some individuals have dispersed throughout tropical waters of the Indo-Pacific, but data on large-scale movements do not exist. We present data from nine C. amblyrhynchos monitored within the Great Barrier Reef and Coral Sea off the coast of Australia. Shark presence and movements were monitored via an array of acoustic receivers for a period of six months in 2008. During the course of this monitoring few individuals showed fidelity to an individual reef suggesting that current protective areas have limited utility for this species. One individual undertook a large-scale movement (134 km) between the Coral Sea and Great Barrier Reef, providing the first evidence of direct linkage of C. amblyrhynchos populations between these two regions. Results indicate limited reef fidelity and evidence of large-scale movements within northern Australian waters.

Evolutionary Divergence in Brain Size between Migratory and Resident Birds:

Despite important recent progress in our understanding of brain evolution, controversy remains regarding the evolutionary forces that have driven its enormous diversification in size. Here, we report that in passerine birds, migratory species tend to have brains that are substantially smaller (relative to body size) than those of resident species, confirming and generalizing previous studies. Phylogenetic reconstructions based on Bayesian Markov chain methods suggest an evolutionary scenario in which some large brained tropical passerines that invaded more seasonal regions evolved migratory behavior and migration itself selected for smaller brain size. Selection for smaller brains in migratory birds may arise from the energetic and developmental costs associated with a highly mobile life cycle, a possibility that is supported by a path analysis. Nevertheless, an important fraction (over 68%) of the correlation between brain mass and migratory distance comes from a direct effect of migration on brain size, perhaps reflecting costs associated with cognitive functions that have become less necessary in migratory species. Overall, our results highlight the importance of retrospective analyses in identifying selective pressures that have shaped brain evolution, and indicate that when it comes to the brain, larger is not always better.

How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?:

We recently used computational phylogenetic methods on lexical data to test between two scenarios for the peopling of the Pacific. Our analyses of lexical data supported a pulse-pause scenario of Pacific settlement in which the Austronesian speakers originated in Taiwan around 5,200 years ago and rapidly spread through the Pacific in a series of expansion pulses and settlement pauses. We claimed that there was high congruence between traditional language subgroups and those observed in the language phylogenies, and that the estimated age of the Austronesian expansion at 5,200 years ago was consistent with the archaeological evidence. However, the congruence between the language phylogenies and the evidence from historical linguistics was not quantitatively assessed using tree comparison metrics. The robustness of the divergence time estimates to different calibration points was also not investigated exhaustively. Here we address these limitations by using a systematic tree comparison metric to calculate the similarity between the Bayesian phylogenetic trees and the subgroups proposed by historical linguistics, and by re-estimating the age of the Austronesian expansion using only the most robust calibrations. The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations.

The Association between Proximity to Animal Feeding Operations and Community Health: A Systematic Review:

Background
A systematic review was conducted for the association between animal feeding operations (AFOs) and the health of individuals living near AFOs. The review was restricted to studies reporting respiratory, gastrointestinal and mental health outcomes in individuals living near AFOs in North America, European Union, United Kingdom, and Scandinavia. From June to September 2008 searches were conducted in PUBMED, CAB, Web-of-Science, and Agricola with no restrictions. Hand searching of narrative reviews was also used. Two reviewers independently evaluated the role of chance, confounding, information, selection and analytic bias on the study outcome. Nine relevant studies were identified. The studies were heterogeneous with respect to outcomes and exposures assessed. Few studies reported an association between surrogate clinical outcomes and AFO proximity. A negative association was reported when odor was the measure of exposure to AFOs and self-reported disease, the measure of outcome. There was evidence of an association between self-reported disease and proximity to AFO in individuals annoyed by AFO odor. There was inconsistent evidence of a weak association between self-reported disease in people with allergies or familial history of allergies. No consistent dose response relationship between exposure and disease was observable.

Human Mammary Epithelial Cells Exhibit a Bimodal Correlated Random Walk Pattern:

Organisms, at scales ranging from unicellular to mammals, have been known to exhibit foraging behavior described by random walks whose segments confirm to Lévy or exponential distributions. For the first time, we present evidence that single cells (mammary epithelial cells) that exist in multi-cellular organisms (humans) follow a bimodal correlated random walk (BCRW). Cellular tracks of MCF-10A pBabe, neuN and neuT random migration on 2-D plastic substrates, analyzed using bimodal analysis, were found to reveal the BCRW pattern. We find two types of exponentially distributed correlated flights (corresponding to what we refer to as the directional and re-orientation phases) each having its own correlation between move step-lengths within flights. The exponential distribution of flight lengths was confirmed using different analysis methods (logarithmic binning with normalization, survival frequency plots and maximum likelihood estimation). Because of the presence of non-uniform turn angle distribution of move step-lengths within a flight and two different types of flights, we propose that the epithelial random walk is a BCRW comprising of two alternating modes with varying degree of correlations, rather than a simple persistent random walk. A BCRW model rather than a simple persistent random walk correctly matches the super-diffusivity in the cell migration paths as indicated by simulations based on the BCRW model.

Localization of Canine Brachycephaly Using an Across Breed Mapping Approach:

The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10-30) and control (20-60) samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.

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Clock Quotes

Wed, 10 Mar 2010 03:46:55 -0500

Time is the coin of your life. It is the only coin you have, and only you can determine how it will be spent. Be careful lest you let other people spend it for you.

- Carl Sandburg

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