Blog Post Of The Month at PLoS ONE

The winner has just been announced – you will need to click to see who it is!

My picks from ScienceDaily

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Clock Quotes

Tobacco, coffee, alcohol, hashish, prussic acid, strychnine, are weak dilutions; the surest poison is time.
– Ralph Waldo Emerson

New and Exciting in PLoS ONE

You really need to go to a PLoS ONE paper and take a look – we have done some nifty home remodeling 😉
What is really new and important is that there are all sorts of article-level metrics on each paper. The same goes for all the other TOPAZ-based PLoS journals (i.e., all but PLoS Biology – you may have noticed that PLoS Medicine has migrated onto TOPAZ as well).
Mark Patterson explains what and why. Pete Binfield gives you a new house tour. And Richard Cave gives the information for those interested in the technical side of the changes.
Please take a look and give us feedback at any of those three links above, or here and here.
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. Due to the upgrade, trackbacks are temporarily invisible. But send them anyway – the system is saving them and will make them visible soon.
You can now also easily place articles on various social services (CiteULike, 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:
Ants Can Learn to Forage on One-Way Trails:

The trails formed by many ant species between nest and food source are two-way roads on which outgoing and returning workers meet and touch each other all along. The way to get back home, after grasping a food load, is to take the same route on which they have arrived from the nest. In many species such trails are chemically marked by pheromones providing orientation cues for the ants to find their way. Other species rely on their vision and use landmarks as cues. We have developed a method to stop foraging ants from shuttling on two-way trails. The only way to forage is to take two separate roads, as they cannot go back on their steps after arriving at the food or at the nest. The condition qualifies as a problem because all their orientation cues – chemical, visual or any other – are disrupted, as all of them cannot but lead the ants back to the route on which they arrived. We have found that workers of the leaf-cutting ant Atta sexdens rubropilosa can solve the problem. They could not only find the alternative way, but also used the unidirectional traffic system to forage effectively. We suggest that their ability is an evolutionary consequence of the need to deal with environmental irregularities that cannot be negotiated by means of excessively stereotyped behavior, and that it is but an example of a widespread phenomenon. We also suggest that our method can be adapted to other species, invertebrate and vertebrate, in the study of orientation, memory, perception, learning and communication.

Local Individual Preferences for Nest Materials in a Passerine Bird:

Variation in the behavioural repertoire of animals is acquired by learning in a range of animal species. In nest-building birds, the assemblage of nest materials in an appropriate structure is often typical of a bird genus or species. Yet plasticity in the selection of nest materials may be beneficial because the nature and abundance of nest materials vary across habitats. Such plasticity can be learned, either individually or socially. In Corsican populations of blue tits Cyanistes caeruleus, females regularly add in their nests fragments of several species of aromatic plants during the whole breeding period. The selected plants represent a small fraction of the species present in the environment and have positive effects on nestlings. We investigated spatiotemporal variations of this behaviour to test whether the aromatic plant species composition in nests depends on 1) plant availability in territories, 2) female experience or 3) female identity. Our results indicate that territory plays a very marginal role in the aromatic plant species composition of nests. Female experience is not related to a change in nest plant composition. Actually, this composition clearly depends on female identity, i.e. results from individual preferences which, furthermore, are repeatable both within and across years. A puzzling fact is the strong difference in plant species composition of nests across distinct study plots. This study demonstrates that plant species composition of nests results from individual preferences that are homogeneous within study plots. We propose several hypotheses to interpret this pattern of spatial variation before discussing them in the light of preliminary results. As a conclusion, we cannot exclude the possibility of social transmission of individual preferences for aromatic plants. This is an exciting perspective for further work in birds, where nest construction behaviour has classically been considered as a stereotypic behaviour.

Cellular Communication through Light:

Information transfer is a fundamental of life. A few studies have reported that cells use photons (from an endogenous source) as information carriers. This study finds that cells can have an influence on other cells even when separated with a glass barrier, thereby disabling molecule diffusion through the cell-containing medium. As there is still very little known about the potential of photons for intercellular communication this study is designed to test for non-molecule-based triggering of two fundamental properties of life: cell division and energy uptake. The study was performed with a cellular organism, the ciliate Paramecium caudatum. Mutual exposure of cell populations occurred under conditions of darkness and separation with cuvettes (vials) allowing photon but not molecule transfer. The cell populations were separated either with glass allowing photon transmission from 340 nm to longer waves, or quartz being transmittable from 150 nm, i.e. from UV-light to longer waves. Even through glass, the cells affected cell division and energy uptake in neighboring cell populations. Depending on the cuvette material and the number of cells involved, these effects were positive or negative. Also, while paired populations with lower growth rates grew uncorrelated, growth of the better growing populations was correlated. As there were significant differences when separating the populations with glass or quartz, it is suggested that the cell populations use two (or more) frequencies for cellular information transfer, which influences at least energy uptake, cell division rate and growth correlation. Altogether the study strongly supports a cellular communication system, which is different from a molecule-receptor-based system and hints that photon-triggering is a fine tuning principle in cell chemistry.

Skin Blood Perfusion and Oxygenation Colour Affect Perceived Human Health:

Skin blood perfusion and oxygenation depends upon cardiovascular, hormonal and circulatory health in humans and provides socio-sexual signals of underlying physiology, dominance and reproductive status in some primates. We allowed participants to manipulate colour calibrated facial photographs along empirically-measured oxygenated and deoxygenated blood colour axes both separately and simultaneously, to optimise healthy appearance. Participants increased skin blood colour, particularly oxygenated, above basal levels to optimise healthy appearance. We show, therefore, that skin blood perfusion and oxygenation influence perceived health in a way that may be important to mate choice.

Non-Destructive Sampling of Ancient Insect DNA:

A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago – an alternative approach that also does not involve destruction of valuable material. The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers. The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

Spatio-Temporal Transmission Patterns of Black-Band Disease in a Coral Community:

Transmission mechanisms of black-band disease (BBD) in coral reefs are poorly understood, although this disease is considered to be one of the most widespread and destructive coral infectious diseases. The major objective of this study was to assess transmission mechanisms of BBD in the field based on the spatio-temporal patterns of the disease. 3,175 susceptible and infected corals were mapped over an area of 10×10 m in Eilat (northern Gulf of Aqaba, Red Sea) and the distribution of the disease was examined monthly throughout almost two full disease cycles (June 2006-December 2007). Spatial and spatio-temporal analyses were applied to infer the transmission pattern of the disease and to calculate key epidemiological parameters such as (basic reproduction number). We show that the prevalence of the disease is strongly associated with high water temperature. When water temperatures rise and disease prevalence increases, infected corals exhibit aggregated distributions on small spatial scales of up to 1.9 m. Additionally, newly-infected corals clearly appear in proximity to existing infected corals and in a few cases in direct contact with them. We also present and test a model of water-borne infection, indicating that the likelihood of a susceptible coral becoming infected is defined by its spatial location and by the relative spatial distribution of nearby infected corals found in the site. Our results provide evidence that local transmission, but not necessarily by direct contact, is likely to be an important factor in the spread of the disease over the tested spatial scale. In the absence of potential disease vectors with limited mobility (e.g., snails, fireworms) in the studied site, water-borne infection is likely to be a significant transmission mechanism of BBD. Our suggested model of water-borne transmission supports this hypothesis. The spatio-temporal analysis also points out that infected corals surviving a disease season appear to play a major role in the re-introduction of the disease to the coral community in the following season.

Today’s carnivals

Encephalon #67 is up on Neuroskeptic
Podcast Of The Blue #1 is up on Malaria, Bedbugs, Sea Lice, and Sunsets
Grand Rounds Vol. 5 No. 28 are up on Running a hospital
Carnival of the Green #173 is up on Eco Joe’s
Friday Ark #236 is up on Modulator

My picks from ScienceDaily

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Clock Quotes

When half the world is still plagued by terror and distress, you stop guiltily sometimes in the midst of your house-laughter and wonder if you’ve a right to it. Ought any of us to laugh, until all of us can again, you ask yourself, sometimes.
– Margaret Lee Runbeck

New and Exciting in PLoS Biology and PLoS ONE

Truth or Consequences? Engaging the ‘Truth’ of Evolution:

John is the only one of the four evangelists who recounts Jesus’ (possibly apocryphal) statement to Pilate that he was in fact a king whose role was “to bear witness to the truth; and all who are on the side of truth listen to my voice.” Pilate is said to have replied to this, “What is truth?”
This is a question that Jerry Coyne never really engages in his excellent new book [1], which purports to explain why evolution is “true.” This raises the question of who his intended audience is. But we’ll get there in a minute. First, make no mistake: this is a wonderful book, as far as the explanation of many of the interesting lines of evidence and case histories for evolution go. Coyne is a professor at the University of Chicago who specializes in the genetics of speciation (his previous book on the subject, with H. Allen Orr, is widely recognized [2]). He explains the evidence for evolution not just in terms of speciation, however. He revisits many of Darwin’s arguments, such as the progression of fossils, the importance of vestigial organs, how evolution explains biogeographic patterns, and sexual selection. But he is also able to go far beyond the evidence available to Darwin, with topics such as genetic and molecular support for species divergence, and the record of human evolution.

Hydrodynamics-Based Functional Forms of Activity Metabolism: A Case for the Power-Law Polynomial Function in Animal Swimming Energetics:

The first-degree power-law polynomial function is frequently used to describe activity metabolism for steady swimming animals. This function has been used in hydrodynamics-based metabolic studies to evaluate important parameters of energetic costs, such as the standard metabolic rate and the drag power indices. In theory, however, the power-law polynomial function of any degree greater than one can be used to describe activity metabolism for steady swimming animals. In fact, activity metabolism has been described by the conventional exponential function and the cubic polynomial function, although only the power-law polynomial function models drag power since it conforms to hydrodynamic laws. Consequently, the first-degree power-law polynomial function yields incorrect parameter values of energetic costs if activity metabolism is governed by the power-law polynomial function of any degree greater than one. This issue is important in bioenergetics because correct comparisons of energetic costs among different steady swimming animals cannot be made unless the degree of the power-law polynomial function derives from activity metabolism. In other words, a hydrodynamics-based functional form of activity metabolism is a power-law polynomial function of any degree greater than or equal to one. Therefore, the degree of the power-law polynomial function should be treated as a parameter, not as a constant. This new treatment not only conforms to hydrodynamic laws, but also ensures correct comparisons of energetic costs among different steady swimming animals. Furthermore, the exponential power-law function, which is a new hydrodynamics-based functional form of activity metabolism, is a special case of the power-law polynomial function. Hence, the link between the hydrodynamics of steady swimming and the exponential-based metabolic model is defined.

Getting the Measure of Positional Information:

Understanding the mechanisms that underlie pattern formation is one of the major challenges of developmental biology. The complexity and beauty of the patterns on butterfly wings, fish scales, or bird feathers are not only remarkable products of developmental processes but puzzles that tease our intellects. If we are to understand these beautiful products of cellular activity, we need to first investigate simpler patterns, which are more tractable experimentally. A good example is the subdivision of an embryo along its main axis, which can be represented as a polarized subdivision of a cellular field. Over 40 years ago, Lewis Wolpert offered a conceptual solution to this problem in the form of the French Flag model [1]. The central element of the proposal is that spatial gradients of substances called morphogens are the cause of such subdivision (Figure 1, left panel). The idea is simple: specific concentration thresholds in the gradient are detected by cells in the target tissue and lead to the expression of distinct sets of target genes. The crucial ingredient of the argument was a precise and direct correlation between the input (the gradient) and the output (the response of the tissue)–each threshold corresponds precisely to a border of an expression territory.

A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms:

Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer functionally relevant DDIs from PPI data. We created a comprehensive, non-redundant dataset of 209,165 experimentally-derived PPIs by combining datasets from five major interaction databases. We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting domains, which can map the interacting propensity of two domains in many dimensions. This method outperforms similar existing methods both in the accuracy of prediction and in the coverage of domain interaction space. We predicted a set of 52,492 high-confidence DDIs to carry out cross-species comparison of DDI conservation in eight model species including human, mouse, Drosophila, C. elegans, yeast, Plasmodium, E. coli and Arabidopsis. Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species. Pair-wise analysis of DDI conservation revealed a ‘sliding conservation’ pattern between the evolutionarily neighboring species. Our methodology and the high-confidence DDI predictions generated in this study can help to better understand the functional significance of PPIs at the modular level, thus can significantly impact further experimental investigations in systems biology research.

A Computational Framework for Ultrastructural Mapping of Neural Circuitry:

Building an accurate neural network diagram of the vertebrate nervous system is a major challenge in neuroscience. Diverse groups of neurons that function together form complex patterns of connections often spanning large regions of brain tissue, with uncertain borders. Although serial-section transmission electron microscopy remains the optimal tool for fine anatomical analyses, the time and cost of the undertaking has been prohibitive. We have assembled a complete framework for ultrastructural mapping using conventional transmission electron microscopy that tremendously accelerates image analysis. This framework combines small-molecule profiling to classify cells, automated image acquisition, automated mosaic formation, automated slice-to-slice image registration, and large-scale image browsing for volume annotation. Terabyte-scale image volumes requiring decades or more to assemble manually can now be automatically built in a few months. This makes serial-section transmission electron microscopy practical for high-resolution exploration of all complex tissue systems (neural or nonneural) as well as for ultrastructural screening of genetic models.

The Brightness of Colour:

The perception of brightness depends on spatial context: the same stimulus can appear light or dark depending on what surrounds it. A less well-known but equally important contextual phenomenon is that the colour of a stimulus can also alter its brightness. Specifically, stimuli that are more saturated (i.e. purer in colour) appear brighter than stimuli that are less saturated at the same luminance. Similarly, stimuli that are red or blue appear brighter than equiluminant yellow and green stimuli. This non-linear relationship between stimulus intensity and brightness, called the Helmholtz-Kohlrausch (HK) effect, was first described in the nineteenth century but has never been explained. Here, we take advantage of the relative simplicity of this ‘illusion’ to explain it and contextual effects more generally, by using a simple Bayesian ideal observer model of the human visual ecology. We also use fMRI brain scans to identify the neural correlates of brightness without changing the spatial context of the stimulus, which has complicated the interpretation of related fMRI studies. Rather than modelling human vision directly, we use a Bayesian ideal observer to model human visual ecology. We show that the HK effect is a result of encoding the non-linear statistical relationship between retinal images and natural scenes that would have been experienced by the human visual system in the past. We further show that the complexity of this relationship is due to the response functions of the cone photoreceptors, which themselves are thought to represent an efficient solution to encoding the statistics of images. Finally, we show that the locus of the response to the relationship between images and scenes lies in the primary visual cortex (V1), if not earlier in the visual system, since the brightness of colours (as opposed to their luminance) accords with activity in V1 as measured with fMRI. The data suggest that perceptions of brightness represent a robust visual response to the likely sources of stimuli, as determined, in this instance, by the known statistical relationship between scenes and their retinal responses. While the responses of the early visual system (receptors in this case) may represent specifically the statistics of images, post receptor responses are more likely represent the statistical relationship between images and scenes. A corollary of this suggestion is that the visual cortex is adapted to relate the retinal image to behaviour given the statistics of its past interactions with the sources of retinal images: the visual cortex is adapted to the signals it receives from the eyes, and not directly to the world beyond.

Defining the Journalism vs. Blogging Debate, with a Science Reporting angle

You know I have been following the “death of newspapers” debate, as well as “bloggers vs. journalists” debate, and “do we need science reporters” debate for a long time now. What I have found – and it is frustrating to watch – is that different people use different definitions for the same set of words and phrases. “News”, “reporting”, “media”, “press”, “journalism”, “Web”, “Internet”, “blog”, “citizen journalist”, “newspapers”, “communication”, etc. are defined differently by different people. Usually they do not explicitly define the terms, but it is possible to grasp their definition from context. Sometimes, people use one definition in their initial article, but once the debate heats up, they switch the definitions. Some define terms too broadly, others too narrowly, depending on their own background, biases or agendas. Some make the error of using several of those terms interchangeably, where a clear distinction exists. Thus, in many of the debates, it is a conversation of the deaf – the opponents do not understand that they actually agree (or allies don’t see that they actually disagree) because they do not use the terms the same way.
This post is my attempt to clear up a lot of that mess, at least for myself, by coming up with my own definitions: the way I think of these terms. Please use the comments thread to point out where I am wrong, or offer better definitions.
This post is also a response to a whole slew of online discussions in the wake of this Clay Shirky post – Newspapers and Thinking the Unthinkable, including some responses by Dave Winer.
And finally, this post is also a response to the big discussion we recently had in the aftermath of the Nature article about science journalism and science blogging.
What I will try to do is define some terms and try to find (and link to if possible – though checking through the links on this post, as well checking what I “Like” on FriendFeed, following Jay Rosen on Twitter, or digging through my Media category) examples of people using the term in the same way as well as in alternative ways. I will also try to explain my thinking; provide a historical context (and again, correct me when I am wrong as I am not a media historian); explain what is happening today and what a possible future may be (feel free to disagree); and finally see how science reporting is similar or different from the rest of reporting. Let’s start….
Breaking News
journalist.gifSomething (Event A) happens at Time X. Nobody could have expected or predicted that A would happen at all, or at least that it would happen at the particular time X. It is a new data point. Not ‘information’ yet, just data. It may be interesting or important enough to notify the world that A happened.
The key to breaking news is speed. It needs to be relayed as close to Real Time as possible.
“A plane just landed on Hudson”
“A plane landed on Hudson, took pic with cellphone, see it here:”
“A plane landed on Hudson, on ferry going to save people”
“A plane landed on Hudson, I am on it, everyone alive”
“I am a pilot. I just landed a plane on Hudson. Bird strike – both engines”
What do the above statements do? They answer just one of the canonical journalistic questions: What? Inevitably, such breaking news reports will contain answers to some other questions, e.g., Where? (Hudson), When? (look at time-stamps of the reports), perhaps Who? (pilot and passengers). It is too early to add answers to the questions How and Why. The premium is on speed, accuracy and fact-checking will have to come later.
Notice something? Each of the statements above is shorter than 140 characters. Perfectly possible to post on Twitter (or a twitter-like platform). From a mobile device. By eye-witnesses, not professional journalists (Note: some of them are paraphrases of actual twitter messages, others are hypotheticals I invented).
About 12 minutes later, the online media sources (AP, Reuters, CNN, etc.) will break the news as well. What info are they going with? What they read on Twitter, or perhaps they got some phone calls. It will take them some time to dispatch professional reporters to the scene.
Once the crews are on the scene, they will have text, audio and video done pretty quickly, so the breaking news can show up on radio and TV. Newspapers? You will read those stale news the next morning. Probably incomplete because it will miss all the new incoming information that happens between the dispatch is filed in the evening and the time you get to read your paper with your morning coffee.
How about accuracy? As the premium is on speed, accuracy check has to come later. How many times have you noticed breaking news on CNN saying there are 6 dead, then 30 minutes later changing that to 9 dead, then another hour later changing that to 15 dead, etc. The mainstream media also have to make corrections if their initial reports were inaccurate. There is nothing new about that.
Is there a potential for abuse, e.g., hoaxes? Yes. The mainstream media has been taken in by hoaxes before, and will be again, and the subsequent accuracy check reveals this and the media retracts and apologizes. Nothing new there, either.
What about the questions of How and Why? That comes later and is not a part of “Breaking News”, it is a part of “News Analysis”. Who will provide those answers? Professional journalists will interview the officials (e.g., from the airline), read the official reports, interview participants (e.g., the pilot, passengers), and the eye-witnesses and will try to put together a more-or-less complete story about the Event A. Some will do this better than others. Some events are easier to report on than others due to, for instance, political sensitivity.
Can Citizen Journalists do the same? Yes and No. The professional reporters will be able to enter a press briefing and interview the officials. This is more difficult for bloggers to do, but that is changing fast – bloggers are getting press passes more and more these days. On the other hand, an eye-witness will be more relaxed and open to a neighbor with a cell phone than with a reporter shoving his/her microphone in your face and shouting questions. When approached by the press, most people recoil, get all their red flags up, get very cautious what they are saying, and generally do not blurt out everything they really know or think. It is much harder for pros to get the information out of regular citizens, even if it is, for now, easier for them to get information out of officials.
Remember when the bridge fell down in Minnesota about a year ago? Who did the best reporting? The guy who lives in the first house next to the bridge. He was there at the moment of the event. He ran down and took pictures. He talked to the passers-by and neighbors. Many knew him and trusted him. He got involved in the rescue and interviewed the people he rescued. And he posted all of that on his blog in as close to Real Time as was humanely possible.
How did the local media do in comparison? Quite poorly. It took them time to get there, it took them time to gather the facts, they could not get honest, personal accounts from eye-witnesses and victims who viewed them with suspicion. It took them even more time to find more information and put together their stories. And then they abandoned the story, while the rescue was still going on.
So, is that blogger a journalist? Yes and No. He was, for a time, an Accidental Journalist. He just happened to be there at the right time and right place and he did his civic duty to find information and report it. He never asked for money for doing it (although, if I remember correctly, readers asked him to put up a PayPal button so they could financially reward him for his service) – he felt it was his obligation as he could do a more thorough job than the pros at this particular story. Did it make him want to become a journalist? I don’t know, but I guess not [oops – I guess he does!]. I think he went back afterwards to his own life, blogging whatever he wanted to blog about, probably satisfied that he did his citizen’s job well and was widely recognized for doing so.
The same goes for many other news events. For instance, a guy tweeted from the Boulder airplane accident (12 minutes before any other news source had anything out) a couple of months ago.
How about news in other countries? How about, for instance, the Mumbai terrorist attack? Lots of eye-witnesses posted on Twitter frantically for a couple of weeks. They were all Accidental Journalists. Do you “trust” each and every individual and each and every tweet? No, but when you look at the entire collection, yes, a pattern emerges, and you can trust them as a group, quite obviously. So, why many journos and readers did not trust them? And waited patiently for US/UK media to send their pros to the scene?
It is a mix of ethnocentrism, racism and anti-democratic sentiments that many still, unfortunately, harbor. There is no reason to trust NYT and WaPo reporters better than the Indian twitterers. But, hey, they are not trained in the NYT newsroom, and they are Indian – ergo, not to be trusted. Excuse: they are biased.
Bias? What bias – all they did was input the data: what, where, when. They did not write 1000-word essays, just information. Also, unlike the Western journalists that later arrived on the scene, the locals were much more familiar with the context: the map of the city, the history, the players, the politics of it all, which made them much more efficient news gatherers as they knew where to go, who to talk to, what to ask and what to do. They were far better informed than the foreign reporters, and thus I trusted them much more than the foreign reporters. In subsequent News Analysis, both the locals and foreign experts could write longer pieces and that is where, perhaps, bias of both sources could show up. But not at the Breaking News stage yet.
So, my definition of Breaking News:
Informing the world about novel, unpredicted data about the world in as close to Real Time as possible.
Professional journalists are almost never going to personally witness the events as they happen (they can’t be everywhere at all times – not enough of them for this to be so). Eye-witnesses are those who will break the news (and pros can work with those data later, for more in-depth coverage). Are we there yet? No, but getting close.
Imagine the Hudson airplane event again, but let’s say it happens five or ten years from now in the future. Let’s say there are 100 people on board. All 100, in that future, will have cell-phones with online access and will be familiar, comfortable and fluent in the use of microblogging services, just like most people today are fluent with using a phone. The plane crashes. 10 are too hurt to do anything. 20 are too scared to think straight. 55 pull out their cellphones and tweet “holy cow – I was just in a plane accident”. Not too informative, but the sheer numbers help spread the news virally faster. The remaining 15 have enough presence of mind and enough understanding of what they are supposed to do, they will tweet much more information. “Crashed on Hudson, nobody dead, 10 hurt”, “Heard explosion, both engines on fire before the crash”, “Saw flock of ducks around the wings just before the accident”, etc. When you take the total output of all of them – that is Breaking News. Sufficient information to put pieces together in real time. Accidental Journalists, who will afterwards go back to their normal lives. Unpaid.
How about science? What would be the equivalent for science journalism?
A famous scientist dies (that is kind-a meta-science, not science itself). An ‘Eureka’ moment from someone’s lab or from the field. Creationists just introduced another stealth legislation to wedge religion into science classes. The last individual of a species dies in a zoo. An observatory detects an asteroid hurling towards Earth. Mars Rover detects water. A revolutionary discovery announced at a hastily-arranged press conference. That’s about it. Again, it is just a data-point, in Real Time, something that every citizen involved or eye-witnessing can competently report: What, Where, When.
Reporting News
journalist2.gifWhat is the difference between Breaking News and Reporting News? I think an important difference is in predictability. If we know that something newsworthy will happen at a particular time and place, we can have whatever infrastructure and equipment is needed in place to capture and broadcast that information in real time. We can send camera crews and reporters to a football game or horse races, or to a meeting of the City Council, or to Congress when it is in session, or to New Orleans as Katrina is approaching, or to an event which started as ‘breaking news’ but is now ‘ongoing news’ (think of the Tsunami in Indonesia a couple of years ago). We can even automate some of that stuff, e.g,. weather, stock market ticker-tape, Racing Form, just off the top of my head. Do we need the Turing test? Who cares, as long as the data are made readily available.
What we’ll get from there is a video or audio of the event. And a quick summary report. Traditional media of all kinds: newspapers, radio, TV have an advantage here, at this point in history, over any kind of non-traditional journalists due to infrastructure – they have the equipment, they have the channels, they have enormous audiences.
Where Internet kills the traditional media is in the lack of limits. Radio or TV will have a 2-minute summary, a newspaper will have a predetermined amount of space for it. This will tell you briefly What, Who, Where, When, How and perhaps even a little bit of Why, but cannot, by definition tell the whole story. If you are not interested, this is enough for you. If you are interested, or if you are suspicious of the source, you are left hanging and unsatisfied. But online, that short summary will provide a link to something that no other medium can afford to have: the entire transcript of the session, the entire video of the whole football game, full uncut interviews instead of brief quotes, further links to additional relevant information.
While traditional media are good and fast at quickly relaying the summaries of the news, the Web can provide a full record of the event far beyond the summary and keep it there, as a record, forever, when all the tapes and paper are already rotten and gone. Smart traditional media are already starting to do exactly that – the radio or TV program or the newspaper are just the vehicles that deliver the audience to the website where the full information can be found.
A good example of this is the Election here in the USA. On November 4th, you can watch the pundits blabber on CNN, but what CNN provided that was really useful was their website where every result of every race in every state, county and precinct was reported as soon as the data became available. There were several such websites on that day, and they were much more useful than any broadcast. Newspapers? Well, a lot of people bought the papers next morning because they wanted to have a cover with a big Obama picture on it as a souvenir. Nobody actually learned the result from the papers.
Again, as bloggers (those who are interested and ambitious about it) are more and more treated as journalists, given press passes and given journalistic privileges, some of them will be able to report news just as well as the traditional media, and since they do not have the space and time limits of radio, TV and papers, they can make both their summaries and their complete reports as short or as long as they want, with as much supporting documentation as they can find, and the audience will pick and choose what to read according to their own levels of interest.
Finally, as many newspapers go belly up, there will be a vaccuum on local reporting. How will that vaccuum get filled, who will report from the City Council meetings? Well, every community will solve that problem differently: some will find a way to pay a blogger or two to do it. Others will require all sessions to be taped and full videos, full transcripts and full texts of documents be placed online immediately after the session is over.
So, my definition of Reporting News:
Informing the world about novel, yet predictable data about the world in as close to Real Time as possible, using either personal or automated reporting systems.
How about science?
These days a predictable event is a publication of a paper. It may come with a press release. It can be covered as news. Science reporters know exactly which journal publishes on which day of the week, subscribe to e-mail announcements, get PDFs in advance, and write short reports that are released at the time embargo is lifted. Fine. Very traditional. It is similar with conferences, where talks can be reported on. Announcing the Nobel Prize winners is another example.
But the new trends in science, as well as new online technologies, allow for something different: data become available for broadcast as soon as they are produced. Folks in the Open Notebook Science movement are posting all of their data online as soon as the data are generated. The information is not just What, but also How (materials and methods), the time-stamps tells us When, the owner of the site is the Who, and the lab where the data originated is the Where. No need to do any Why yet (apart from the initial motivation to do the experiment to begin with – the stated hypothesis).
Moreover, those same folks are now working on ways to automate the process. Instead of typing the new data into the wiki in the evening, they are coaxing their laboratory equipment to automatically post the data on the Web. Likewise, the Mars Rover was tweeting from Mars. That is scientists broadcasting data to the world.
But “citizen scientists” do the same. Christmas bird watch? Species location and identification? Plant phenology data? The Galaxy Zoo project? Live-blogging data from the field research? All the data go online in real time. The NC fishermen will tweet their catch in real time. Just ‘data’. Not ‘information’ yet. Certainly not analysis yet. That’s News Reporting. Straight from the horse’s mouth.
News Analysis
journalist3.jpgNow we are getting to a place where being in the right place at the right time is not enough. Knowledge, expertise, and ability to find and parse through sources, becomes important. News are data. News analysis is information – ‘data made meaningful’. Breaking News and Reporting News just provide the raw data – News Analysis connects the dots, places the new data-set into the context of other related data-sets, and provides historical, philosophical, theoretical, methodological, economic, political, sociological, etc, contexts. It also tries to answer the hardest of the canonical questions of journalism: Why?
This is also a place where access to additional sources of information is important. The sources of information are: a) documents, and b) people.
Documents, which formerly had to be dug up in libraries or various repositories, necessitating travel (which costs) or permission (which journalists could get using their employers’ brand names), are now for the most part freely available online. Full transcripts of interviews, full videos of events, full texts of pieces of legislation – all of this is now easily found on the Web and will be even more so in the near future. Thus, anyone who has the time and passion and expertise to dig out all the information and put it all together, can do so. Who do you trust on economics more: an economist or a journalist? Who has the proper training, knowledge, experience and expertise and is less likely to fall for the sweet-talking, nonsense-speaking PR shills for the special interests?
People are tougher. Pro journalists nurture special relationships with the people in power. They have access to them that you and I don’t (yet). Thus, people in power are more likely to give interviews to pros than to amateurs. There are pros and cons to this, of course. The intimate relationship biases the reporter – just look at The Village in D.C., totally corrupted by the PR that politicos push on them at all those cocktail parties, and thus oblivious to any other views, including the views of most regular people. And as the transparency is the new motto in D.C. and more and more people in power are themselves present online, it is gradually becoming easier for all of us to gain access even to the most reclusive and the most powerful people. Just give it a few more years – the non-responsive will not get re-elected so easily any more (it’s already happening at the local level – if you want to get elected here in Orange County, you better show up at Orange Politics blog, answer questions, and moreover answer the question in a satisfactory way).
On the other hand, as I noted above, an amateur journalist will get a much more honest response from a regular person who is suspicious of the corporate media.
But the greatest advantage of the Web, no matter if the article is written by a professional journalist or an amateur with expertise in the topic as opposed as in journalism, is space. Radio will give you at most an hour for such a big story, if you are very lucky to be picked by editors to say it. Television is even more competitive and hour-long stories are very rare. If you look at New York Times (or any other big daily paper), such an in-depth story of the requiered length happens mainly once a week in the Sunday Magazine – rarely outside of it.
So, the News Analysis stories get cut in length and parade as news reporting. Instead of complete interviews, you get brief quotes. Now, think about it for a minute. You talk to a reporter for an hour. It is because what you have to say requires an hour to explain. You see yourself quoted the next day in the newspapers. Even if the quote is verbatim, it is nonetheless a misquote, or a ‘quote out of context’ because it lacks all of the other stuff you said before and after that sentence – all the context and background and caveats and examples are gone. Even if your quote is verbatim, it may lead the reader to assume that you meant opposite of what you really meant. Or at least, something tangential and certainly not the main point you really wanted to hammer home (for instance, even if those quotes are verbatim and I really said that, this was not what my Main Take Home Message for this article was, not even close).
Online, there are no limits to length. Your story will be as short or as long as it needs to be. When you quote someone, you, right there and then, link to the complete transcript of the interview so the people can go and find the context for themselves and check if you quoted them correctly. You link to all the relevant documents so people can check if you cited them correctly. The ethic of the hyperlink that you use in your online article will always trump the articles by the best and most ethical professional journalists just because of space limitations – their analysis has to be incomplete and they cannot know what pieces of information can be omitted.
Doing News Analysis takes time and effort. Not everyone has the time required and not everyone has the motivation to do this. But if you look around the blogosphere, it becomes obvious that many people find time and have the motivation to do this on a regular basis. If paid, even more of them would do it even more regularly (I know I would). Plus, unlike the journalists, they have the required expertise in the topic, which makes them more reliable and trustworthy than the journalists (or at least most journalists – some got good by covering the topic for decades, an unusual and unofficial way to get an informal ‘social equivalent’ of a PhD on the topic).
As traditional media goes bankrupt and journalists are laid off, some will start doing this online as freelancers. Some bloggers will continue doing this. The line between journalism and blogging will become even more fuzzy. And some traditional media will figure out how to do journalism online and allow their paid journalists to adopt the online form and use the unlimited space, time and hyperlinking that makes online journalism better than the one done on paper.
So, my definition of News Analysis:
Turning a data-set into Information by connecting it to other related data-sets and providing meaningful context and explanation.
How about science?
The ur-example of this is the scientific paper itself: Who, Where and When (authors, affiliations, publication date), Why (Introduction), How (Materials and Methods), What (title, abstract, Results, statistics, graphs, complete data-sets and supplementary data), Context and Analysis (Discussion) and relationship to related data-sets (List of References).
Of course, the data and the context and the analysis are presented by the authors of the data-set themselves, which raises concerns about objectivity. Which is why we insist on having the manuscript pass peer-review and editorial decision to publish in a reputable scientific journal. But as more people move to real-time Open Notebook Science, as talks and posters presented at (formerly assumed to be closed to a small circle) conferences become liveblogged, and as the process of publication become both more dynamic and more collaborative, the peer-review itself will have to become more dynamic and collaborative. Instead of 2-3 people doing it at one point before the publication, now many people will keep doing it throughout the process of publication and afterwards, leaving their commentary/review attached to the paper itself forever. Additional review will happen outside of the paper itself, in an outer circle of the ecosystem: in the media, almost all of it in the online media, aka blogs, and trackbacked to the paper itself for easy discovery.
At this level of communication, speaking good English is nice, but real expertise in that area of science is far more important. Thus, very rarely will this kind of analysis be done by people who are primarily journalists (unless they, over the decades of reporting on that one area of science, have become as expert as working scientists are on that topic – a very rare occasion). This will be done almost entirely by scientists (in the broader sense of the term – not just currently active researchers, but all who are trained in science irrespective of their current job description).
Science bloggers may not cover every new paper, or even every new hot paper, and may not care about timeliness of writing in time for the embargo-lift (I know how hard it is to get them to do it immediately!), but when they write about a study, they will write kick-ass stuff that almost all journalists can only dream of doing. And more importantly, they will rarely focus only on that one paper – they are much more likely to provide a deeper context for it as they already know the relevant literature: they don’t need to dig for it for the first time today. And if they get a fact wrong, the commenters, themselves mainly scientists, will be quick to point that out in the comments.
So, today we have a situation in which authors write papers which get published months or years after the data have been gathered. Their institutions write press releases. Science reporters, those who still have jobs in this economy, are so pressed for time covering so many stories simultaneously, they just regurgitate the press releases. Then bloggers jump on them for sensationalism and for the lack of accuracy, and for missing out the context.
Tomorrow, with jobs in science being so scarce, many people with science degrees, including many with PhDs will want to change their career paths. Instead of doing research, or teaching high-school, they may want to do science journalism. But there are no jobs in traditional media for this – science journalists are getting fired left and right! Well, they can get hired by universities and write press releases, which will thus become better than what we are used to seeing now. Or they can freelance. Or start science blogs.
It’s a new world – it used to be you apply to jobs and once you are hired you start to work. Today, you start working for free and hope that it is good. You accumulate a portfolio that you can show when you apply for jobs. You develop a good reputation that brings you job offers out of the blue. It is nerve-wrecking, but if you are good, something good will happen to you as people will not allow good stuff to remain unrewarded for too long.
With Open Access (and importantly, Historical Open Access), with Open Notebook Science, with scientists writing press releases, with scientists writing blogs, and with all those getting connected by hyperlinks, the audience will get everything: science reporting from authors directly, both in formal (journal papers) and informal (blogs) settings AND via intermediaries who are also trained in science. That kind of information combo can be trusted. A quick hyping report in a newspaper, radio or TV cannot.
Investigative Reporting
DANGERexpectations.jpgThis is what the curmudgeons like to say – bloggers can’t do investigative reporting. Really? But what is it? Going to a press conference and asking Obama a gotcha question is not reporting – it is manufacturing news. You are not trying to find out what Obama is planning or doing or saying, but what he says in response to your question. That’s news? No, without your question, he would not have said anything – you made the news by asking, and reporting his answer is not reporting the news, and certainly not investigative reporting. You inserted yourself into the world and caused news (“what he said”) to happen.
Investigative reporting is uncovering data and information that does not want to be uncovered. Hmm, sounds like a definition, so here it is italicized:
Investigative reporting is uncovering data and information that does not want to be uncovered.
It is hidden, often because someone is purposefully hiding it, i.e., suppresing it and does not want the world to know. That’s tough to do. Go out and ask someone where one can buy a physical newspaper in your town. Then go and buy one. Look at every page. How many pieces of investigative reporting did you find – information that someone tried to suppress but the brave reporter uncovered? If you find one on any given day, your local newspaper is really, really good!
Yes, it happens. Pulitzers are given for a reason to worthy investigative reporters.
But how about blogs? Firedoglake crew did the investigative reporting on the entire Valerie Plame outing and Skooter Libby trial. They dug up documents. They interviewed people. They sat in court every second of the proceedings. They posted bried summaries for people who had just a passing, superficial interest in the story. They posted detailed analyses. They posted lengthy interviews. They posted entire documents. They posted legal analysis (as some of them are lawyers). The entire traditional media on the planet, when put together, did not cover the case as much and as well as that one little blog. And they would have covered even less if they were not pushed and shamed by Firedoglake to do so.
Do I need to remind you of Talking Points Memo? Mudflats digging up the backstory on Sarah Palin? The Durham bloggers and the Lacrosse case? And many, many more. Police beat is tough to do for non-professionals, yet bloggers have been known to uncover and bring to life issues like corruption in their police departments, or cases of anwarranted use of force and abuse by officers.
How about science?
Whose investigative reporting led to resignation of Deutch, the Bush’s NASA censor? Nick Anthis, a (then) small blogger (who also later reported on the Animal Rights demonstrations and counter-demonstrations in Oxford in great detail as well).
Who blew up the case of plagiarism in dinosaur palaenthology, the so-calles Aetogate? A bunch of bloggers.
Who blew up, skewered and castrated the PRISM, the astroturf organization designed to lobby the Senate against the NIH Open Access bill? A bunch of bloggers. The bill passed.
Remember the Tripoli 6?
Who pounced on George Will and WaPo when he trotted out the long-debunked lie about global warming? And forced them to squirm, and respond, and publish two counter-editorials? A bunch of bloggers.
Who dug up all the information, including the most incriminating key evidence against Creationists that was used at the Dover trial? A bunch of bloggers.
And so on, and so on, this was just scratching the surface with the most famous stories.
When a person is slighted, or detects some unfairness of foul play, that person is highly motivated to dig deeper and uncover the truth. In earlier times, this required finding and persuading a reporter to do it for you. Today, you can do it yourself and, by recruiting hundreds of other bloggers to your cause, raise enough of a stink that the corporate media cannot ignore the story any more and is forced to report it. Even if that means they have to report on something outside of their ‘sphere‘ of “what is considered normal”, and thus helping, against their best instincts, to move the Overton Window in the direction of reality.
Opinion, Entertainment, Storytelling, etc.
The four aspects of journalism above – Breaking News, Reporting News, News Analysis and Investigative Reporting – are often considered to be ‘journalism proper’. As we saw above, the Web is the best medium for all four due to speed, hyperlinks and limitless space. All four can be and have been done by non-professionals. For some, such non-professionals are already demonstrating they are better. For others, the traditional media still has the upper hand to some extent, though this is changing.
Nobody says that everybody can do it or wants to do it or will do it, but it shows that professional journalistic training is not a necessary pre-requisite for doing it right. It only says something about the medium, not the people or training. Amateurs, by and large, do not have access to the newspapers, radio and television. But both professionals and amateurs have access to the Web, and both can potentially do all four types of journalism online and do it correctly. Amateurs and professionals are on equal footing here and their work and work alone will determine who will gather a following by building trust with the audience, and who will have to find a different day job.
But the above four are not the only parts of journalism, if one thinks of it a little broader. In many minds, journalism is “everything that shows up in newspapers, on the radio, on TV, and online”. Not just news. Also ads, obituaries, sports, nice pictures, drawings and cartoons and comic strips, stories, poems, opinion-pieces, crossword puzzles, quiz shows, commercials, travelogues, diaries, funny videos and so on, and so on….
With paper, radio and TV, editors decide what goes in. With the Internet, everything gets published and the audience fliters the content, buries the bad and promotes the good, so, at least in theory, the best stuff, after a while, rises to the top and becomes very, very “famous”. The technology-based and people-based filters that do this are still imperfect but are in the process of constant tweaking and improvement. Google search is the best known of the technological filters. There are others. For people-based filters, check out Blog Carnivals. For science, there are Google Scholar, CiteULike and Mendeley. We are all Editor now.
And, as Digby and Glenn Greenwald and Amanda Marcotte and Melissa and Hilzoy write better op-eds – in every sense of the term: better use of English, better thinking, more accurate facts – than David Brooks or Maureen Dowd or George Will, soon there will be no reason to pay Brooks or Dowd or Will to produce stuff that most people don’t read and others read for laughs. It is a big cost for the NYT, with nothing to show for it but embarrassment.
The same goes for other stuff: stories, comic strips, art….
It already killed the music industry, it is now killing the newspaper as well.
Journalism is EVERYTHING that appears in the media.
And in this sense, we are all journalists. Even if we never break news or do investigative reporting, if we write poetry on our blogs, we are journalists. And the world is our editor.
How about science?
Thus, in this sense, science bloggers are all science journalists as well. We disseminate cool educational videos, announcements of interesting lectures and meetings, we write opinion pieces, we write educational pieces (e.g., the Basics), we dispel the myths of anti-social dorky stereotypes of scientists by writing personal stories, we connect science to art, literature, politics and culture, and we do something uniquely useful by discussing the trials and tribulations of career paths in science. And we are fun. So people keep coming back for more. Thank you 😉
Newspapers
Newspaper is a bunch of loose pieces of paper with stuff printed on them. It is one of many ways to deliver various kinds of content, including news. It is not the one and only, or even the best ‘defender of Democracy.
Newspapers does not equal news.
Breaking news, reporting news, news analysis, investigative reporting, opinion, storytelling, entertainment, art, sports results, scientific data, advertising – none of that inherently HAS to be printed on paper. All of that can be done and is done daily on the radio, on TV and online.
Paper, ink, printing presses, trucks….all of that is extremely expensive. And that technology is far too slow for the 21st century. And the limited real-estate on the paper forces a system in which content to be printed has to be chosen in advance – by editors – and chopped down to size – by editors – before it sees the light of day, several hours after it ceased to be news.
The newspaper has a very limited scope to deliver content in comparison to technologies that arrived later. Radio and TV are likewise constrained by time. Internet has no space or time constraints, thus there is no need for any editors to make choices as to what goes and what doesn’t, and there is no need for longer pieces to get cut shorter by editors either (heck, I’d love to have an editor to fix my typos, bad grammar, wrong punctuation, and suggest improvements in style, as long as my content remains unbutchered and I have a final say what goes online in the end).
In traditional media, all the filtering is done by editors before the transmission. In online media, all the filtering is done by a collective editorial choice of the readership, after the transmission. In online media, there are no length limits, thus a journalist is at freedom to include all the relevant information. Additional information is linked to. Feedback is instant, in the comments. The best pieces rise to the top, eventually.
Before I go on, I need to be fair. Just like there are many different kinds of blogs, so there are many different kinds of newpapers. If you are in Manhattan right now, go outside and look at the newspaper stand down the street. What do you see? Just New York Times? No, there will be that other rightwingnutospheric rag, the New York Post, there as well. There will be also many other newspapers, with narrower niches, covering art, or underground music scene, or Real Estate listings. And then there are magazines – weekly or monthly or quarterly.
Remember that NYTimes also once published their first ever copy, at the time when nobody suspected they would become the “newspaper of record”. Many New York City newspapers have come and gone over the decades, and who could have guessed that out of all of them it would be the New York Times to survive this long?! And it’s not even that good!
If you are not in Manhattan, go out and buy USA Today and your local metro. Take a good look at both. Which one do you like better? Which one of the two do you think will survive? Which one of the two you wish will survive? I bet that, almost everywhere in the USA you may be (and I guess there are equivalent examples in other countries), the answer to all those questions is: USA Today. Why?
USA Today will have LOTS of news – something for everyone every day. It has excellent reporters and journalists and op-ed writers. There is, in each day’s issue, quality content that you cannot find anywhere else. And furthermore, if the brevity of an article frustrates you, the paper tells you to go to their website. There, you will not just find the copy+paste of the printed article. You will also find more information, and often links to additional information. They are not perfect, but they are slowly getting there.
In contrast, your local metro will consist mostly of advertising, AP stories, syndicated columnists and comic strips, horoscope, a local mouthbreathing op-ed writer spouting rushlimbaughisms and, if you are lucky, a reprint of a two-days-old Krugman editorial. How many locally produced news? Very little. Reports from the meetings of the City Council or School Board? Nope. Investigative reporting? Zero. I hope you have a birdcage that needs lining or own a fish store that needs cheap wrapping paper.
But what if you live in a place like Carrboro, NC? You will go out and pick, of course, Carrboro Citizen. Two years old. Free to pick up anywhere. Increasing their print volume every week. Their problem? So many people outside Carrboro – in Chapel Hill, greater Orange County and northern Chatham County want not just to read it but also for the Citizen to cover their areas. Why are they so successful?
First: it is web-to-print. Pieces written by locals, or by UNC students, are posted online, get comments, and then are edited for printing.
Second: it is hyperlocal, containing advertising for local businesses and covering stories of local interest, including those pesky City Council and School Board meetings – stuff that cannot be found anywhere else in print or on the Web.
Third: it does not pretend to be “objective” or “fair and balanced” – it cares about truth and reality, not the he-said-she-said Broderian journalism. They write it as they see it, and they see it as they uncover the facts. So, if reality has a liberal bias, so be it. After all, Carrboro was one of the few places in which Kucinich won the primaries in 2004, so nobody here complains about liberal bias. A similar paper in a conservative town would probably have a conservative bias, and that is fine (let them live in delusions, I guess). You can disagree, but you cannot complain about dishonesty, or bias or hidden agendas, because nothing is hidden. And that is so refreshing after years of rage-inspiring so-called journalism of the other local papers, e.g., Raleigh News & Observer.
Such newspapers – hyperlocal, community (or even family, club, team, organization) newspapers – will survive. The big, international, good papers like USA Today will survive by becoming “table of contents” for what they offer on their websites. The chain-owned metros will die. And good riddance because they have quit doing quality journalism a long time ago. Not because the reporters were bad, or even because their editors were biased, but because the owners made every wrong move in the book business-wise: cutting away what was unique and locally relevant, while keeping copy+paste syndicated stuff that everyone can find online in a thousand copies. Why would anyone ever pay for that?
How about science?
Both the scientific journals and the popular science magazines are facing a business crisis. The scientific journals are saving themselves by going fully online (and will probably, more and more, completely abandon the print editions) and by going Open Access (as libraries cannot afford their subscription rates any more). Those who are digging in their heels will go extinct. Just like the most heard-headed newspapers.
Popular science magazines are in a different kind of trouble. More and more, people can go directly to the primary sources for information as they become freely available online. More and more, their audience gets captured by science blogs which are both more fun and elicit greater respect, as they are written by scientists.
Those who turn to sensationalism, like The New Scientist, will lose their last customers quickly and will go under. Those that are trying to improve the quality of their magazine, like the American Scientist, hiring the PhDs in science who want to switch to journalism, producing fascinating, scientifically accurate stories that require much more time and effort than your average science blogger is willing to put into a post, getting top class artists to illustrate their stories, providing uniquely good book reviews or news that cannot be found elsewhere, and release all of their articles online soon after the print edition goes out, will persist for a while longer. Those who do science with a twist, like Seed Magazine connects science to culture, art and politics, will also persist.
Science reporting in newspapers? Dead. Because the newspapers are dead. The few mega-big papers that survive
will have good science coverage by a stable of excellent freelance journalists, each covering a different area of science and bringing in decades of expertise on the topic. The hyperlocals, if they have a scientific community locally (as the Triangle does), will have good locally-relevant science coverage. Otherwise, they will have none. Most science beat reporters will, like their colleagues covering other beats, have to find new jobs. It hurts, but it is a fact of life. There is no going back now.
Blogs, bloggers and blogging
As I have said many times before:
Blog is software.
Bloggers are people who use blogging software. Blogging is using the blogging software. Period.
Bloggers are not alien invaders from outer space. Bloggers are humans, citizens, silent majority that never had a voice until now. Bloggers are former and usually current consumers of the media. And re-producers of the media (yup, those guys that drive the traffic to your sites). And commenters on the media (guys who keep you honest and make you better if you are open-minded enough to listen). As well as producers of the media.
When journalistic curmudgeons want to denigrate bloggers, they point to the blogs containing LOLcats and teenage angst. They conveniently forget Talking Point Memo, Huffington Post, Firedoglake, Scienceblogs.com, or for that matter Slate, Salon and Atlantic 😉
It is not what you use, but how you use it. 90% of everything on blogs is crap. 90% of everything in newspapers is also crap. So goes for the radio and TV. If you complain that we should not point out the worst of the newspapers and focus on the best instead, then please reciprocate: point to the best of blogs, not the worst. Then perhaps we can have a discussion.
Same goes for microblogging services like Twitter and FriendFeed, or social networking sites like Facebook. If all you see is boring stuff, you are following the wrong people. If you do not like Livecasting (“what I had for breakfast”) which is actually an important aspect of human communication, then start following people who do Mindcasting instead and you will get more than you bargained for in terms of intellectual nourishment and uncomfortable thought-provocation.
And how do you find quality blogs? Well, how did you find quality newspapers? Someone told you, perhaps your parents when you were a child (or you just saw which newspaper came to your home every morning). Then you checked it out. Then you read it for a while and made up your own mind. You can do the same with blogs. Why do you need instant gratification – do your work and you will find excellent blogs that trounce traditional media in every way. Don’t just sit around and complain how many blogs there are and how all of them must be bad, but you will not waste your time finding out if you are correct about it or not. That’s lazy and dishonest.
Some of the best blogs out there are now becoming true New Media establishments, paying their bloggers to do “real journalism”, including investigative reporting, getting their bloggers press badges for important events (e.g., party conventions in election years). TPM is hiring. Huffington Post just got a nice sum of money to do exactly that – I hope they will ditch their Chopras and Kennedys and other nutcases and do the same for the quality of their science/health reporting which is atrocious.
As newspapers are dying, they leave a vacuum. Most places either have an existing blog, or immediately start a new one, to replace the vanished newspaper. The medium is different, more conducive to quality journalism than any of the previous communication channels, but also requires much fewer people to get the job done. It will be different than the newspaper it replaces. It will try to fulfill the needs of the community that the newspaper did, but also fulfill the needs of the community that the newspaper never could do.
We’ll all be watching those valiant new efforts. Something will come out of them. A single business model? No, of course not – as many business models as there are communities. Some will work better than others, and some will work better in some places than in other places. No need to have an expectation that a single business model will win and be adopted by all. After all, the newspapers never had a single universal business model themselves, so why expect anything else from the New Media?
When a newspaper folds, many people lose their jobs. And it hurts. And in this economy, it is hard for them to find other jobs. Typesetters, printers, packers, truck drivers will have to find new lines of work. Editors, technical editors, copy editors, accountants, lawyers, artists, and yes, reporters, will have to find new jobs. What took thousands of people to produce – a newspaper – now takes a dozen people, and they can do the job better.
There is a lot of pain going around. But it is not the fault of bloggers, or of Blogspot, WordPress and MoveableType. It is these that will do the journalism in the future, and some of the former newspaper journalists will find jobs in the online media if they are open minded and willing to learn how to adopt to the new medium. Quality journalism will survive, in this medium or another, but will require fewer paid professionals to do so. A core professional stuff, plus crowdsourcing, will produce news and entertainment and everything in-between.
But the old journos will suffer in the meantime. And I feel for them. Most of them are good people, and good at what they do. They get flack from readers when some editor slaps a silly headline on top of their work, or when some editor cuts the key paragraph out of the article, or some editor rewrites the article beyond recognition. Many have learned to suffer in silence about such indignities in order to save their jobs. They have learned to play the game. Many of them will feel relieved – oh such a sense of freedom, finally! – when they move online and adapt to its practices. And they will produce great journalism, many of them for the first time in their lives. It is unfortunate that so few of them can get paid to do it. Just an economic reality.
So, the whole “bloggers will replace journalists” trope is silly and wrong. No, journalists will replace journalists. It’s just that there will be fewer of them paid, and more of us unpaid. Some will be ex-newspapermen, others ex-bloggers, but both will be journalists. Instead of on paper, journalism will happen online. Instead of massaging your article to fit into two inches of the paper column, you will make your article’s focus be on information, accuracy and truth. Instead of cringing at the readers’ comments, you will learn how to moderate them and appreciate them and learn from them.
Many sources will speak directly to the audience, instead of via middle-men. From Obama to scientists. But some sources will not speak unless forced to by a journalist. And some sources are not humans, but animals, or machines, or natural phenomena, or old documents, and cannot talk to the audience without a middle-man.
Many of us will be both consumers and producers of media in our spare time. We may become journalists if news fall into our laps – we become Accidental Journalists for a day or a week, and provide information that others cannot but we, due to circumstances, can. That will not eliminate a journalist’s job, but provide a journalist with a source and a story.
Many of us will occasionally commit acts of journalism, or provide information needed for a story, or provide opinion needed for an op-ed, but very few of us will care to do that for a living, every day. We don’t want to take the journalists’ jobs away, we want them to thrive, but it is a reality that there are too many of them, and that many of the aspects of their job descriptions are now better done by machines, or by crowds of people, than by individuals. Let the best of them remain journalists, adapted to the new, better ways of doing things. Let’s hope the others find decent jobs elsewhere so they can feed their families.
A 100 years ago, many horse trainers, saddle-makers and blacksmiths became car repairmen. A much better career decision than just sitting there and complaining how cars will never replace the horses. My father owned a printing press, and worked in the printing business his entire life. I went with him there several times as a kid. I loved the typesetting machines, and the printing presses, and the smells and sounds. I loved printing stuff at home with my letter stamps. I love the feel and smell of a fresh print. Both my brother and I were in some way involved with school newspapers and such when we were young. But that era is now gone.
I also spent most of my life working with horses. I love the feeling of riding a horse, the smell of fresh hay, the sounds of horses munching their oats. But I do not saddle up my horse to go to the grocery store. I don’t even own a horse any more. It is just not a viable method of transportation any more.
But that does not mean that horses are extinct. There are thousands being bred every year for sport and show and leisure. They are pampered and loved much better than when they were just means of transport, when both people who loved them and who hated them had to use them. Horses (or mules or oxen or llamas or camels) are also still a key method of transportation in those places in the world where there is no infrastructure for the cars: roads, gas stations, garages.
Likewise, newspapers will become extinct as a major means of news-delivery. But they will persist in the hands of hobbyists and local communities who love them. And they will persist in places in the world where there is no infrastructure for the Internet: electricity, computers, wifi. Perhaps those who so strongly agitate for saving the newspapers should go there – their services will be useful in such places for a while longer. There, they can be analog bloggers.
Let us get on with the business of building a new journalism, fit for the new century and Millennium. The rest is nostalgia. Counterproductive.
How about science?
Oh, we had many, many discussions about science blogging, and why do we blog, and how we find time to blog, and why scientists and academics should blog, there have been articles and editorials published on this topic and even peer-reviewed articles, not to mention various conferences.
Then, an article came out in Nature a couple of weeks ago after which we all piled up. Read the article itself, the adjoining editorial and the responses by:
Jessica Palmer, Michael Tobis, PZ Myers and commenters, Larry Moran, Janet Raloff, LouScientist , John Timmer, Anthony, Francis Sedgemore, Curtis Brainard, John Wilkins, Derek Lowe, Ed Silverman, WFSJ, Sean Carroll, Kristi Vogel, Philip Davis, David Crotty, Eric Berger, John Hawks, Jennifer Gardy, Bee, Text Technologies, Chris Mooney, Carl Zimmer, Henry Gee, Mr. Gunn, Mark Liberman, Ben Goldacre, Chris Patiland Vivian Siegel, Chris Mooney again, Joseph Romm, Bex Walton, Abel Pharmboy, Mike the Mad Biologist, Phil Plait, Simon Baron-Cohen, Larry Moran again and again and Jessica Palmer again.
One of the major questions that crops up repeatedly in these discussions is the matter of reach. Science blogs, similarly to popular science magazines, are in the “pull” more – attracting readers who are a priori interested in science. But how do we do “push”, i.e., throw science at unsuspected citizens, in hope they will find it interesting or useful?
Sure, having science taught well in schools is the best ‘push’ strategy because it is mandated by the state. When I graduated from high school I had 8 years of physics, 8 years of chemistry and 8 years of biology behind me, instead of one of each as US students get.
But besides that, ‘push’ is very difficult. Back when there were only a couple of TV channels, if there is an hour-long science documentary, everyone watched it because that was on the program. And people liked it. But today, there is none on major TV channels and one has to seek science, nature or medicine on specialized channels. Likewise for radio – there is Ira Flatow every Friday on NPR and that is about it – easy to flip the station or put in a CD instead.
If at any time in the past, newspapers had a lot of (and good) science coverage, that would have been somewhat of a ‘push’ strategy. At that time, people were not inundated with information and were more likely to read the paper cover-to-cover. They could still skip the science section, but on some days a headline might have piqued their curiosity and made them read. Today, newspapers have little to no science, and there is less and less paper anyway.
But, as soon as the newspaper dies in any given market, the people are forced to go online for information. If the local newspaper is replaced by a news website or blog, this is where people will go (and sooner the papers die, sooner their monopoly on information will go away, so online upstarts can move into the void).
Once people are online, they will be there in as great numbers as newspapers ever had. Now, if that local news-site does not hide its science section a click or two away (“pull”), but showcases the science headlines right there on the front page, this will be better push than newspapers could ever do. No need to turn the leaf, or click – the headlines are staring at you.
If a site like Huffington Post, which just got funds to pay reporters, publicly eliminates their pseudoscience, HIV denialist, New Age woo-mongers and hires some real science/nature/medicine reporters instead, it is in a position to do the ‘push strategy’ on science. I bet some of the science bloggers would like to get that gig. And then link to us who are doing the ‘pull’ strategy here on Scienceblogs.com (or Nature Network or Discover).
Update: I have collected the responses to this post here and written, so far, two follow-up posts: New Journalistic Workflow and ‘Journalists vs. Blogs’ is bad framing

UNC Nobel Laureate on the importance of information access to scientific research

This is today:

A Conversation with Dr. Oliver Smithies
Excellence Professor of Pathology and Laboratory Medicine
2007 Nobel Laureate
Moderated by Dr. Tony Waldrop, Vice Chancellor for Research and Economic Development
Monday, March 30, 2009
4:00 pm – 5:30 pm
Room 527
Health Sciences Library
Light refreshments to follow
Join us for a chat with Dr. Oliver Smithies about the importance of information access to scientific research, especially his own. Audience participation will be encouraged. Don’t miss this opportunity to have your questions answered by Dr. Smithies. You may also submit questions for Dr. Smithies when you register to attend.
Space is limited and registration is required. To ensure your seat, register today!
HSL will also make a video of this discussion with Dr. Smithies available online at a later date.

If you cannot make it, you can follow the liveblogging by Paul Jones on Twitter. You can tweet questions to Paul to ask there in real time as well.

My picks from ScienceDaily

Optimal Running Speed Associated With Evolution Of Early Human Hunting Strategies:

Runners, listen up: If your body is telling you that your pace feels a little too fast or a little too slow, it may be right. A new study, published online March 18 in the Journal of Human Evolution, shows that the efficiency of human running varies with speed and that each individual has an optimal pace at which he or she can cover the greatest distance with the least effort.

Early Agriculture Left Traces In Animal Bones:

Unraveling the origins of agriculture in different regions around the globe has been a challenge for archeologists. Now researchers writing in the Proceedings of the National Academy of Sciences report finding evidence of early human experiments with grain cultivation in East Asia. They gathered this information from an unlikely source―dog and pig bones.

Video Games, Cell Phones And Academic Performance: Some Good News:

Using cell phones and playing video games may not be as harmful to children’s academic performance as previously believed, according to new research by a team of Michigan State University scholars. In fact, cell phones had no effect on academic performance among a group of 12-year-olds, the researchers found in a three-year study published by the Conference Proceedings of the International Association for Development of the Information Society, or IADIS, in Barcelona, Spain.

Clock Quotes

Nothing destroys authority so much as the unequal and untimely interchange of power, pressed too far and relaxed too much.
– Francis Bacon

The Open Laboratory 2009 – the submissions so far

OpenLab logo.jpg
Here are the submissions to date. Please use the submission form to add more of your and other people’s posts:
A Blog Around The Clock: Circadian Rhythm of Aggression in Crayfish
A Blog Around The Clock: Co-Researching spaces for Freelance Scientists?
A Blog Around The Clock: The Shock Value of Science Blogs
a k8, a cat, a mission: Moms asking for help
a k8, a cat, a mission: What does good mentorship look like?
a k8, a cat, a mission: Praise and Appreciation
a k8, a cat, a mission: Proximate mechanisms
a k8, a cat, a mission: The lives of women in science
Biochemical Soul: Darwin and the Heart of Evolution
Birds and Science: Caged budgerigars and invasive parakeets
Birds and Science: How do huge bird colonies synchronize?
Brontossauros em meu Jardim: Navigation is required*: the incredible case of the desert ant
Coyote Crossing: Spermophilus
Expression Patterns: A Squishy Topic
Expression Patterns: Mr. Darwin, you make me blush
Highly Allochthonous: Is the Earth’s magnetic field about to flip?
The Intersection: Singled Out
Island of Doubt: Sea level rise a red herring?
Living the Scientific Life: Genetic Compatibility Drives Choice of Mates and Sex of Chicks in Gouldian Finches, Erythrura gouldiae
Made With Molecules: Hey Baby, what’s your AVPR1A like?
Malaria, Bedbugs, Sea Lice, and Sunsets: An Interesting Patch of Quicksand
Masks of Eris: Mathematics instruction as a fish
Mind the Gap: In which I ponder economies of scale
Mind the Gap: In which I tend a strange garden
Mind the Gap: In which I ramp up
Mind the Gap: In which I muster a hypothesis
Mind the Gap: In which I continue to suspend disbelief
Mind the Gap: In which the data back up our habitual suspicions
Mind the Gap: In which I wade through the fringes of textbook fact
Mind the Gap: In which I dally with both sides
Mind the Gap: In which I am given weird treasures
Neurophilosophy: Amnesia in the movies
Neurophilosophy: Brain & behaviour of dinosaurs
Neurophilosophy: Voluntary amputation and extra phantom limbs
Neurotopia: The Value of Stupidity: are we doing it right?
Observations of a Nerd: How big things relate to sex, stress and testosterone
Observations of a Nerd: Why I am not a Darwinist, but we should celebrate Darwin Day
Observations of a Nerd: Darwin’s Degenerates – Evolution’s Finest
Pharyngula: A brief moment in the magnificent history of mankind
Prerogative of Harlots: He Blinded Me With Science
The Primate Diaries: The Nature of Partisan Politics
Reciprocal Space: This is not good enough
The Scientist: On the nature of faith: Part 1
The Scientist: On the last days
The Scientist: On the passing of reprints
The Scientist: On saying goodbye
The Scientist: Ontology
The Scientist: Ontology #2
The Scientist: On winding down
The Scientist: On the weekend
The Scientist: On small victories
The Scientist: On the nature of networking: reprise
The Scientist: Grey Council
The Scientist: On interfaces
The Scientist: Coincidental Chemistry
The Scientist: On the Future
The Scientist: The year of living dangerously–Part 1
The Scientist: The year of living dangerously–Part 2
The Scientist: The year of living dangerously–Finale
The Scientist: What I want to do when I grow up
The Scientist: Inspiration
The Scientist: In which I watch the Watchmen, and land a new job
The Scientist: Ongoing
Skulls in the Stars: Michael Faraday, grand unified theorist? (1851)
Song for jasmine: Charles Darwin’s first theory of evolution
Stripped Science: The right pairing (comic strip)
Suppertime Sonnets: In Which I Celebrate A Certain Member of the Lycaenidae Family (poem)
Ways.org: The journal scope in focus — putting scholarly communication in context
White Coat Underground: Journeys
Why Science: Beautiful and essential
xkcd: Correlation (cartoon)

My picks from ScienceDaily

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Clock Quotes

The right word may be effective, but no word was ever as effective as a rightly timed pause.
– Mark Twain

20 Things To Do With Matzah (video)


[from Mom, via Bride Of Coturnix on Facebook]

My picks from ScienceDaily

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Clock Quotes

The Unexpected always comes at the most awkward times.
– Larry Niven

Medbloggers at BlogWorld/New Media Expo ’09

Kim is excited:

It’s official!
The Medbloggers are now a part of BlogWorld/New Media Expo 09!
Thanks to sponsorship from Johnson & Johnson and MedPage Today, the “Medlblogger Meet-Up” is now a reality.
But it is so much more than “just” a meet-up.
A full day of topics, voted on by the medical bloggers themselves, will be presented, with plenty of time to mix and mingle with our blogging colleagues.
Blog World/New Media Expo 09 will take place at the Las Vegas Convention Center the weekend of October 15-17.
New blogger, established blogger, podcaster or internet broadcaster, there is a place for you in Las Vegas!
Interested in just the Medblogger topics?
You’ll want to join us on October 15th, when the Medbloggers will take their place in the premier blogging conference by holding a full day of sessions and meetings devoted specifically to medblogging.
Want to get deep into the heart of blogging as a lifestyle? Ready to take your blog to the next level?
Then you’ll want to attend the entire BlogWorld/New Media Expo conference where you will learn from the very best of the blogosphere. If you’ve heard of them, they will be at the BlogWorld/New Media Expo 09.
The option is yours.
The pleasure is ours.
Please join us!
Registration opens at www.blogworldexpo.com soon!

Blog Pick Of The Month at PLoS ONE

If you write blog posts about PLoS ONE papers, you are eligible for a prize every month! I explain in some detail here, but this is the main point:

…every month, I will read all the blog coverage aggregated on ResearchBlogging.org and pick a blog post that, in my opinion, showcases the best coverage of a PLoS ONE article. I know, there is no way to quantify the “quality” of writing, so my picks will be personal. I will be looking for the posts that do the best job at connecting the center of the [science publishing] ecosystem – the paper – to the outside world. I will announce the winner here on the 1st of the following month and we’ll send the blogger a small prize as a sign of our appreciation.

You still have four days to write for the March prize, then keep writing with the April prize in sight…

Last Extinction on PBS

Check out the show’s web page:

Fifteen thousand years ago North America was like the Serengeti on steroids, with mega-creatures roaming a continent teeming with incredible wildlife. But then, in a blip of geologic time, somewhere between 15 and 35 magnificent large types of animals went extinct. In a television exclusive, NOVA joins forces with prominent scientists to test a startling theory that may finally explain the Last Extinction, on Tuesday, March 31 at 8pm ET/PT on PBS (check local listings). The program features scientists representing all sides of this debate.

What is dopamine? (video)

My picks from ScienceDaily

Continue reading

Clock Quotes

Early in life I had noticed that no event is ever correctly reported in a newspaper
– George Orwell

New and Exciting in PLoS this week

Let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Association of Tinnitus and Electromagnetic Hypersensitivity: Hints for a Shared Pathophysiology?:

Tinnitus is a frequent condition with high morbidity and impairment in quality of life. The pathophysiology is still incompletely understood. Electromagnetic fields are discussed to be involved in the multi-factorial pathogenesis of tinnitus, but data proofing this relationship are very limited. Potential health hazards of electromagnetic fields (EMF) have been under discussion for long. Especially, individuals claiming themselves to be electromagnetic hypersensitive suffer from a variety of unspecific symptoms, which they attribute to EMF-exposure. The aim of the study was to elucidate the relationship between EMF-exposure, electromagnetic hypersensitivity and tinnitus using a case-control design. Tinnitus occurrence and tinnitus severity were assessed by questionnaires in 89 electromagnetic hypersensitive patients and 107 controls matched for age-, gender, living surroundings and workplace. Using a logistic regression approach, potential risk factors for the development of tinnitus were evaluated. Tinnitus was significantly more frequent in the electromagnetic hypersensitive group (50.72% vs. 17.5%) whereas tinnitus duration and severity did not differ between groups. Electromagnetic hypersensitivity and tinnitus were independent risk factors for sleep disturbances. However, measures of individual EMF-exposure like e.g. cell phone use did not show any association with tinnitus.

Burst of Young Retrogenes and Independent Retrogene Formation in Mammals:

Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes using 4 non-mammalian genomes as a contrast. There has been a burst of young retrogenes not only in primate lineages as suggested in a recent study, but also in other mammalian lineages. In mammals, most of the retrofamilies (the gene families that have retrogenes) are shared between species. In these shared retrofamilies, 14%-18% of functional retrogenes may have originated independently in multiple mammalian species. Notably, in the independently originated retrogenes, there is an enrichment of ribosome related gene function. In sharp contrast, none of these patterns hold in non-mammals. Our results suggest that the recruitment of the specific L1 retrotransposons in mammals might have been an important evolutionary event for the split of mammals and non-mammals and retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals.

‘I Look in Your Eyes, Honey’: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing:

Imagine a photograph showing your friend’s face. Although you might think that every single detail in his face matters for recognizing him, numerous experiments have shown that the brain prefers a rather coarse resolution instead. This means that a small rectangular photograph of about 30 to 40 pixels in width (showing only the face from left ear to right ear) is optimal. But why? To answer this question, I analyzed a large number of male and female face images. (The analysis was designed to mimic the way that the brain presumably processes them.) The analysis was carried out separately for each of the internal face features (left eye, right eye, mouth, and nose), which permits us to identify the responsible feature(s) for setting the resolution level, and it turns out that the eyes and the mouth are responsible for setting it. Thus, looking at eyes and mouth at the mentioned coarse resolution gives the most reliable signals for face recognition, and the brain has built-in knowledge about that. Although a preferred resolution level for face recognition has been observed for a long time in numerous experiments, this study offers, for the first time, a plausible explanation.

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale:

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti:

D. deserti belongs to the Deinococcaceae, a family of bacteria characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents, including ionizing radiation, UV light, and desiccation. It was isolated from Sahara surface sands, an extreme and nutrient-poor environment, regularly exposed to intense UV radiation, cycles of extreme temperatures, and desiccation. The evolution of organisms that are able to survive acute irradiation doses of 15,000 Gy is difficult to explain given the apparent absence of highly radioactive habitats on Earth over geologic time. Thus, it seems more likely that the natural selection pressure for the evolution of radiation-resistant bacteria was chronic exposure to nonradioactive forms of DNA damage, in particular those promoted by desiccation. Here, we report the first complete genome sequence of a bacterium, D. deserti VCD115, isolated from hot, arid desert surface sand. Accurate genome annotation of its 3,455 genes was guided by extensive proteome analysis in which 1,348 proteins were uncovered after growth in standard conditions. Supplementary genes involved in manganese import, in nutrient import, and in DNA repair were identified and are likely important for survival and adaptation of D. deserti to its hostile environment.

Today’s carnivals

Diversity in Science Carnival #2: Women Achievers in STEM – Past and Present, is up on Thus Spake Zuska
The 108th Skeptic’s Circle is up on PodBlack Cat
Grand Rounds Vol. 5 No. 27 are up on Code blog
Carnival of the Green #172 is up on The Evangelical Ecologist

Human circadian rhythms and sleep

BBC 4 had a fascinating half-hour show yesterday, interviewing Till Roenneberg and Helen Emsellem on all sorts of fascinating new findings in the field of human chronobiology. Well worth a listen. But hurry up as the podcast is available only for another six days! (what do they do afterwards? why such a limited time? archives should be freely available forever).

Evolution and education with Texas State Board of Education chair Don McLeroy

How should students learn about evolution?
On Thursday morning’s Takeaway (at about 6:30 a.m. or 8:30 a.m.
Eastern), we’re talking with Don McLeroy, chair of the Texas State
Board of Education. He’s believes that students should have the
opportunity to question evolution (and that God created the Earth a
few thousand years ago). Texas is expected to vote this week on new
science standards that could influence textbooks and how more states
treat this controversial issue.
Evolution and education with Texas State Board of Education chair Don McLeroy
The Texas Board of Education is in the midst of a major fight this
week over a new science curriculum that’s designed to challenge the
principle of evolution. The Board will vote tomorrow on standards that
will govern science teaching on evolution in Texas for the next 10
years.
Here’s a direct link to the audio.
It’s also in the podcast.
The Takeaway’s homepage

Clock Quotes

People of mediocre ability sometimes achieve outstanding success because they don’t know when to quit. Most men succeed because they are determined to.
– George Herbert Allen (1922-90)

My picks from ScienceDaily

Wild Bees Can Be Effective Pollinators:

Over the past few years, honey bee keepers have experienced problems due to Colony Collapse Disorder (CCD), which has hurt honey bee populations, causing some growers of fruits, nuts and vegetables to wonder how their crops will be pollinated in the future.

Bees Prefer Shortest Distance Between Two Flowers:

Insects such as honeybees and bumble bees are predictable in the way they move among flowers, typically moving directly from one flower to an adjacent cluster of flowers in the same row of plants. The bees’ flight paths have a direct affect on their ability to hunt for pollen and generate “gene flow”, fertilization and seed production that results when pollen moves from one plant to another.

Climate Change Found To Have Paradoxical Effects In Coastal Wetlands:

Rising atmospheric carbon dioxide is largely responsible for recent global warming and the rise in sea levels. However, a team of scientists, including two Smithsonian ecologists, have found that this same increase in CO2 may ironically counterbalance some of its negative effects on one of the planet’s most valuable ecosystems–wetlands.

New and Exciting in PLoS ONE

There are 8 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, 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 Dance to the Music of Time: Aesthetically-Relevant Changes in Body Posture in Performing Art:

In performing arts, body postures are both means for expressing an artist’s intentions, and also artistic objects, appealing to the audience. The postures of classical ballet obey the body’s biomechanical limits, but also follow strict rules established by tradition. This combination offers a perfect milieu for assessing scientifically how the execution of this particular artistic activity has changed over time, and evaluating what factors may induce such changes. We quantified angles between body segments in archive material showing dancers from a leading company over a 60-year period. The data showed that body positions supposedly fixed by codified choreography were in fact implemented by very different elevation angles, according to the year of ballet production. Progressive changes lead to increasingly vertical positions of the dancer’s body over the period studied. Experimental data showed that these change reflected aesthetic choices of naïve modern observers. Even when reduced to stick figures and unrecognisable shapes, the more vertical postures drawn from later productions were systematically preferred to less vertical postures from earlier productions. This gradual change within a conservative art form provides scientific evidence that aesthetic change may arise from continuous interaction between artistic tradition, individual artists’ creativity, and a wider environmental context. This context may include social aesthetic pressure from audiences.

Early Fasting Is Long Lasting: Differences in Early Nutritional Conditions Reappear under Stressful Conditions in Adult Female Zebra Finches:

Conditions experienced during early life can have profound effects on individual development and condition in adulthood. Differences in nutritional provisioning in birds during the first month of life can lead to differences in growth, reproductive success and survival. Yet, under natural conditions shorter periods of nutritional stress will be more prevalent. Individuals may respond differently, depending on the period of development during which nutritional stress was experienced. Such differences may surface specifically when poor environmental conditions challenge individuals again as adults. Here, we investigated long term consequences of differences in nutritional conditions experienced during different periods of early development by female zebra finches (Taeniopygia guttata) on measures of management and acquisition of body reserves. As nestlings or fledglings, subjects were raised under different nutritional conditions, a low or high quality diet. After subjects reached sexual maturity, we measured their sensitivity to periods of food restriction, their exploration and foraging behaviour as well as adult resting metabolic rate (RMR). During a short period of food restriction, subjects from the poor nutritional conditions had a higher body mass loss than those raised under qualitatively superior nutritional conditions. Moreover, subjects that were raised under poor nutritional conditions were faster to engage in exploratory and foraging behaviour. But RMR did not differ among treatments. These results reveal that early nutritional conditions affect adult exploratory behaviour, a representative personality trait, foraging and adult’s physiological condition. As early nutritional conditions are reflected in adult phenotypic plasticity specifically when stressful situations reappear, the results suggest that costs for poor developmental conditions are paid when environmental conditions deteriorate.

The Growth of Easements as a Conservation Tool:

The numerous studies examining where efforts to conserve biodiversity should be targeted are not matched by comparable research efforts addressing how conservation investments should be structured and what balance of conservation approaches works best in what contexts. An obvious starting point is to examine the past allocation of effort among conservation approaches and how this has evolved. We examine the past allocation of conservation investment between conservation easements and fee simple acquisitions using the largest land trust in operation, The Nature Conservancy (TNC), as a case study. We analyse the balance of investments across the whole of the US and in individual states when measured in terms of the area protected and upfront cost of protecting land. Across the US as a whole, the proportion of conservation investment allocated to easements is growing exponentially. Already 70% of the area of land protected in a given year, and half of all the financial investment in land conservation, is allocated to easements. The growth rate of conservation easements varies by a factor of two across states when measured in terms of the area protected and by a factor of three in terms of financial expenditure. Yet, we were unable to find consistent predictors that explained this variation. Our results underscore the urgency of implementing best practice guidelines for designing easements and of initiating a wider discussion of what balance of conservation approaches is desirable.

Smoke Signals, Blogs, and the Future of Politics

Smoke Signals, Blogs, and the Future of PoliticsI first posted this on June 24, 2004 on the http://www.jregrassroots.org forums, then republished on August 23, 2004 on Science And Politics, then a couple of times on this blog.
Why did I decide to re-post it today?
Because I have been thinking and reading about the current state and potential future of journalism, including science journalism, and writing (still in my head) a post about it. So, I am forcing myself to go through my evolution of thinking about the topic, digging through my categories on the Media, Science Reporting, Blogging, Open Science, onlin Technology, etc. and this essay was the first time I ever wrote on anything related to this topic.
It is interesting to me, first, how my writing got better over the years. Then, it is interesting to see where I was prophetic, where I was over-optimistic, and where I was just plain wrong. Then I can start thinking about the way my ideas have evolved over time and what precipitated that evolution. I hope you also find it thought-provoking (especially the new readers) – under the fold:

Continue reading

My picks from ScienceDaily

In Horse Play, Adult-to-young Ratio Is Key:

Adults of many animal species play a crucial role in the social development of youngsters. A new study reveals that the ratio of adults to young plays a much more important role in social development than the mere presence of adults.

Triceratops Was A Social Animal, Group Of Dinosaur Fossils Suggests:

Until now, Triceratops was thought to be unusual among its ceratopsid relatives. While many ceratopsids–a common group of herbivorous dinosaurs that lived toward the end of the Cretaceous–have been found in enormous bonebed deposits of multiple individuals, all known Triceratops (over 50 in total) fossils have been solitary individuals.

More….

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Clock Quotes

Few men during their lifetime come anywhere near exhausting the resources dwelling within them. There are deep wells of strength that are never used.
– Richard Evelyn Byrd

The Open Laboratory 2009 – the submissions so far

OpenLab logo.jpg
Here are the submissions to date – 64 entries. Please use the submission form to add more of your and other people’s posts:
A Blog Around The Clock: Circadian Rhythm of Aggression in Crayfish
A Blog Around The Clock: Co-Researching spaces for Freelance Scientists?
A Blog Around The Clock: The Shock Value of Science Blogs
a k8, a cat, a mission: Moms asking for help
a k8, a cat, a mission: What does good mentorship look like?
a k8, a cat, a mission: Praise and Appreciation
a k8, a cat, a mission: Proximate mechanisms
a k8, a cat, a mission: The lives of women in science
Biochemical Soul: Darwin and the Heart of Evolution
Birds and Science: Caged budgerigars and invasive parakeets
Birds and Science: How do huge bird colonies synchronize?
Brontossauros em meu Jardim: Navigation is required*: the incredible case of the desert ant
Coyote Crossing: Spermophilus
Expression Patterns: A Squishy Topic
Expression Patterns: Mr. Darwin, you make me blush
Highly Allochthonous: Is the Earth’s magnetic field about to flip?
Island of Doubt: Sea level rise a red herring?
Living the Scientific Life: Genetic Compatibility Drives Choice of Mates and Sex of Chicks in Gouldian Finches, Erythrura gouldiae
Made With Molecules: Hey Baby, what’s your AVPR1A like?
Masks of Eris: Mathematics instruction as a fish
Mind the Gap: In which I ponder economies of scale
Mind the Gap: In which I tend a strange garden
Mind the Gap: In which I ramp up
Mind the Gap: In which I muster a hypothesis
Mind the Gap: In which I continue to suspend disbelief
Mind the Gap: In which the data back up our habitual suspicions
Mind the Gap: In which I wade through the fringes of textbook fact
Mind the Gap: In which I dally with both sides
Mind the Gap: In which I am given weird treasures
Neurophilosophy: Amnesia in the movies
Neurophilosophy: Brain & behaviour of dinosaurs
Neurotopia: The Value of Stupidity: are we doing it right?
Observations of a Nerd: Why I am not a Darwinist, but we should celebrate Darwin Day
Observations of a Nerd: Darwin’s Degenerates – Evolution’s Finest
Prerogative of Harlots: He Blinded Me With Science
The Primate Diaries: The Nature of Partisan Politics
Reciprocal Space: This is not good enough
The Scientist: On the nature of faith: Part 1
The Scientist: On the last days
The Scientist: On the passing of reprints
The Scientist: On saying goodbye
The Scientist: Ontology
The Scientist: Ontology #2
The Scientist: On winding down
The Scientist: On the weekend
The Scientist: On small victories
The Scientist: On the nature of networking: reprise
The Scientist: Grey Council
The Scientist: On interfaces
The Scientist: Coincidental Chemistry
The Scientist: On the Future
The Scientist: The year of living dangerously–Part 1
The Scientist: The year of living dangerously–Part 2
The Scientist: The year of living dangerously–Finale
The Scientist: What I want to do when I grow up
The Scientist: Inspiration
The Scientist: In which I watch the Watchmen, and land a new job
The Scientist: Ongoing
Song for jasmine: Charles Darwin’s first theory of evolution
Stripped Science: The right pairing (comic strip)
Suppertime Sonnets: In Which I Celebrate A Certain Member of the Lycaenidae Family (poem)
Ways.org: The journal scope in focus — putting scholarly communication in context
Why Science: Beautiful and essential
xkcd: Correlation (cartoon)

New and Exciting in PLoS ONE

There are 14 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, 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:
Light-Induced Fos Expression in Intrinsically Photosensitive Retinal Ganglion Cells in Melanopsin Knockout (Opn4−/−) Mice:

Retinal ganglion cells that express the photopigment melanopsin are intrinsically photosensitive (ipRGCs) and exhibit robust synaptically driven ON-responses to light, yet they will continue to depolarize in response to light when all synaptic input from rod and cone photoreceptors is removed. The light-evoked increase in firing of classical ganglion cells is determined by synaptic input from ON-bipolar cells in the proximal sublamina of the inner plexiform layer. OFF-bipolar cells synapse with ganglion cell dendrites in the distal sublamina of the inner plexiform layer. Of the several types of ipRGC that have been described, M1 ipRGCs send dendrites exclusively into the OFF region of the inner plexiform layer where they stratify near the border of the inner nuclear layer. We tested whether M1 ipRGCs with dendrites restricted to the OFF sublamina of the inner plexiform layer receive synaptic ON-bipolar input by examining light-induced gene expression in vivo using melanopsin knockout mice. Mice in which both copies of the melanopsin gene (opn4) have been replaced with the tau-lacZ gene (homozygous tau-lacZ+/+ knockin mice) are melanopsin knockouts (opn4−/−) but M1 ipRGCs are specifically identified by their expression of β-galactosidase. Approximately 60% of M1 ipRGCs in Opn4−/− mice exposed to 3 hrs of light expressed c-Fos; no β-galactosidase-positive RGCs expressed c-Fos in the dark. Intraocular application of L-AP4, a compound which blocks transmission of visual signals between photoreceptors and ON-bipolar cells significantly reduced light-evoked c-Fos expression in M1 ipRGCs compared to saline injected eyes (66% saline vs 27% L-AP4). The results are the first description of a light-evoked response in an ipRGC lacking melanopsin and provide in vivo confirmation of previous in vitro observations illustrating an unusual circuit in the retina in which ganglion cells sending dendrites to the OFF sublamina of the inner plexiform layer receive excitatory synaptic input from ON-bipolar cells.

A Chromosomal Inversion Unique to the Northern White-Cheeked Gibbon:

The gibbon family belongs to the superfamily Hominoidea and includes 15 species divided into four genera. Each genus possesses a distinct karyotype with chromosome numbers varying from 38 to 52. This diversity is the result of numerous chromosomal changes that have accumulated during the evolution of the gibbon lineage, a quite unique feature in comparison with other hominoids and most of the other primates. Some gibbon species and subspecies rank among the most endangered primates in the world. Breeding programs can be extremely challenging and hybridization plays an important role within the factors responsible for the decline of captive gibbons. With less than 500 individuals left in the wild, the northern white-cheeked gibbon (Nomascus leucogenys leucogenys, NLE) is the most endangered primate in a successful captive breeding program. We present here the analysis of an inversion that we show being specific for the northern white-cheeked gibbon and can be used as one of the criteria to distinguish this subspecies from other gibbon taxa. The availability of the sequence spanning for one of the breakpoints of the inversion allows detecting it by a simple PCR test also on low quality DNA. Our results demonstrate the important role of genomics in providing tools for conservation efforts.

Physiological Stress Mediates the Honesty of Social Signals:

Extravagant ornaments used as social signals evolved to advertise their bearers’ quality. The Immunocompetence Handicap Hypothesis proposes that testosterone-dependent ornaments reliably signal health and parasite resistance; however, empirical studies have shown mixed support. Alternatively, immune function and parasite resistance may be indirectly or directly related to glucocorticoid stress hormones. We propose that an understanding of the interplay between the individual and its environment, particularly how they cope with stressors, is crucial for understanding the honesty of social signals. We analyzed corticosterone deposited in growing feathers as an integrated measure of hypothalamic-pituitary-adrenal activity in a wild territorial bird, the red grouse Lagopus lagopus scoticus. We manipulated two key, interrelated components, parasites and testosterone, which influence both ornamentation and fitness. Birds were initially purged of parasites, and later challenged with parasites or not, while at the same time being given testosterone or control implants, using a factorial experimental design. At the treatment level, testosterone enhanced ornamentation, while parasites reduced it, but only in males not implanted with testosterone. Among individuals, the degree to which both parasites and testosterone had an effect was strongly dependent on the amount of corticosterone in the feather grown during the experiment. The more stressors birds had experienced (i.e., higher corticosterone), the more parasites developed, and the less testosterone enhanced ornamentation. With this unique focus on the individual, and a novel, integrative, measure of response to stressors, we show that ornamentation is ultimately a product of the cumulative physiological response to environmental challenges. These findings lead toward a more realistic concept of honesty in signaling as well as a broader discussion of the concept of stress.

Welcome to EveryONE

EveryONE? What’s that? It is the new PLoS ONE community blog:

Why a blog and why now? As of March 2009, PLoS ONE, the peer-reviewed open-access journal for all scientific and medical research, has published over 5,000 articles, representing the work of over 30,000 authors and co-authors, and receives over 160,000 unique visitors per month. That’s a good sized online community and we thought it was about time that you had a blog to call your own. This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.

Just launched, this blog will have posts about all aspects of PLoS ONE, from technical to editorial, about Open Access, etc. I will give you more information soon. Join the community and contribute. Chris Patil and Neil Saunders already did.

My picks from ScienceDaily

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Clock Quotes

Well, it’s amazing how time can so softly change your ways and make you look at things that can’t be seen. And how the years that roll by can start you listening not just to what they say, but what they mean.
– Michael Nesmith

Carrboro Citizen – the hyperlocal newspapers are here to stay

This week, Carrboro Citizen celebrated its second anniversary. I explained in detail before their model and why I think this is the future of journalism. Now, the Editor, Kirk Ross, gives us the inside story:

You can’t be in this business without wondering how much wilder the ride can get. I’ve written about this before, so I’ll spare you the wind up. The talking points are that not every newspaper is in trouble and that most that are hurting are chain-owned metro dailies burdened by debt brought on by a mergers-and-acquisition craze reminiscent of the Dutch tulip bubble.
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To be honest, when we started that was a pretty lonely place. Some of the better business minds in the area were quick to point out that we were daft since print is a dying part of the information industry. Our contention was then, and is now, that print may be shrinking, but it is hardly dying. Having the opportunity to start from scratch, post Internet, provided us with the chance to incorporate a lot of hard-learned lessons.
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But all that and the print product too would be worthless without the one thing that gives purpose to our endeavor: journalism. It is quality work, solid reporting and good storytelling that empties the racks each week. Technological advances can enhance that, but not replace it.
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If there is anything that underlines the insanity of the current situation in newspapers, it’s seeing another round of layoffs at a paper that is still turning a profit. I’ve had a lot of very sobering discussions of late with young people interested in taking up journalism. They are genuinely worried, and rightly so. They know that for the near term their chosen profession is on shifting sands.
You hold in your hand the first issue of the third volume of The Carrboro Citizen. Each week, more than 5,000 people like you prove to those students and to us that there is a future for journalism.

Emphases mine. Yes, this is the only newspaper I read in hardcopy. And the only newspaper I truly enjoy reading instead of cussing and cursing at the idiotic coverage of news or silly editorials which other papers serve. May they publish on paper forever!

Latest journal ranking in the biological sciences

Take a look at this picture:
PLoSONEonMendeley.jpg
It shows the top five journals ordered by the numbers of papers that Mendeley users decided are worth keeping for future reference. The discussion of the meaning of these numbers is here. I sure like that #5 there….

An Innovative Use of Twitter: monitoring fish catch!

From NC Sea Grant:

….At nearly every fisheries management meeting he attends, Baker hears the same complaint: North Carolina’s recreational fishermen don’t have to account for their catch. Two years ago, during a regional meeting about snapper and grouper, Baker looked down at his hands and finally saw a possible answer: his mobile phone.
“I wondered if you could send a text message to a computer database somewhere instead of just texting from phone to phone,” he says. “And if you could do that, maybe that was something recreational fishermen could do to track their catches and fishing effort.”
Commercial fishermen and seafood dealers must submit extensive paperwork tracking what they bring in on a daily basis. But there is no such requirement in the recreational industry.
———-snip————-
Baker first shared his text messaging idea with friend Ian Oeschger, a software developer. A self-described “nerdy person,” Oeschger was intrigued. He agreed to build a system to accept text messages from anglers and translate that information into data.
“When I think of an idea that seems juicy like that, I just can’t help myself,” Oeschger says.
With funding from a North Carolina Sea Grant minigrant, Baker and Oeschger designed a pilot project to test their idea. The pair asked six Wilmington-area charter boat captains to use pre-paid mobile phones to text their fishing reports to an online text messaging service called “Twitter” (www.twitter.com).
A free service, Twitter allows people to connect with each other through “micro-blogging,” or posting messages that are no more than 140 characters. Once used primarily by teenagers and Blackberry addicts, “tweeting” is entering the mainstream — NASA even has a Twitter account posting status updates for high profile projects like the Mars I-Rover.
For Baker and Oeschger, Twitter provided an ideal online “collection bin” for the anglers’ experimental texts. Oeschger then built a separate database to continually query Twitter for new updates and put data into useable form.
“Most of the work was figuring out, ‘What does the data need to do?’ and ‘What is the most concise way for fishermen to communicate?'” Oeschger explains.
To answer these questions, he and Baker designed a compact syntax for fishermen to text in their reports, thereby minimizing reporting time and allowing for more content to be submitted in a single text message. For example, N2 E4 FA8R BL3 WEx20 translates to: Two anglers fished (N2), They fished for four hours (E4), They released eight false albacore (FA8R), they kept three Bluefish (BL3), and they kept one 20-inch weakfish (WEx20).
During an 18-week period, the charter captains submitted 128 trip reports describing 1957 finfish catches – 1123 were kept, 834 released. The captains describe the system as convenient, cost efficient and timely.
———-snip—————
In addition to more accurate data, the immediacy of text-message based reporting systems may help all fishermen feel a greater sense of ownership when it comes to management decisions, Baker points out. Extensive paperwork for commercial fishermen and third person reports from the recreational industry’s MRIP can take several weeks or months to process. During that time, fisheries may be opened and closed based on old data, something that affects livelihoods on both sides.
“By having fishermen report data in a fast and efficient manner, you make them a greater part of the management process.”

Wow! Read the entire text for more details. This strikes me as a really innovative and useful application of Twitter. Hopefully it will spawn other copy-cats by people who can put microblogging platforms to a good use in scientific, medical or environmental fields.

So long, and thanks for all the fish

Another tectonic shift just occurred today in the science blogging ecosystem – Chris and Sheril have announced today that they have moved The Intersection from scienceblogs.com to the new digs on Discover (joining the likes of Bad Astronomy, The Loom and Cosmic Variance) at http://blogs.discovermagazine.com/intersection.
Adjust your bookmarks/blogrolls/feeds accordingly.

New and Exciting in PLoS Biology and PLoS Medicine

Open Revolution:

In 2001, Charles Vest, then President of the Massachusetts Institute of Technology, announced that MIT would make most of its course material freely available online. Browsing the Web site of MIT’s Open Courseware (OCW) project (http://ocw.mit.edu), you feel the stirring of a “my God, it’s full of stars” transformation: you can borrow material for your courses, study other teachers’ teaching methods, maybe even retake college courses you regret having slept through! Remarkably, OCW is just one highly visible part of an “open education movement.” The essays collected in Opening Up Education, edited by Toru Iiyoshi and M.S. Vijay Kumar, describe ways in which individuals and institutions intend to exploit digital communications technology, develop innovative and freely redistributable educational methods and resources, and improve education at all levels throughout the world.
But what does “open education” really mean? What is “closed” about education? Should education be free as in no cost, or is there something about education that needs to be freed as in freedom? This sort of ground is already well-trampled by debates about two better-known “open” predecessors, open-source software and open-access publication, and it is instructive to make the comparison.

Going With the Glow: How Bacteria Integrate Molecular Signals to Synchronize Bioluminescence:

After a long day in the microbiology lab, Vibrio harveyi may just want to relax, but if enough of its neighbors are game for a group project, it just can’t say no. V. harveyi is a bioluminescent marine bacterium that uses a chemical peer-pressure process called quorum sensing to determine whether to emit light and carry out other collective activities. Quorum sensing, which occurs in other bacteria as well, is both fascinating in itself and instructive for an array of disciplines from entomology to robotics. It goes like this: Quorum-sensing bacteria release small molecules called autoinducers. These molecules convey the presence of the cells to neighboring bacteria. When enough autoinducer molecules float around in the extracellular medium, the bacteria, sensing a critical mass, produce a synchronized response–in V. harveyi’s case, this response is a group glow.
Quorum sensing in bacteria that respond to a single autoinducer is understood fairly well to cause changes in gene expression that are induced by the accumulated autoinducer. V. harveyi, however, uses three autoinducers to get its herd mentality message across. The three autoinducers, called AI-1, CAI-1, and AI-2, are detected by the transmembrane receptors LuxN, CqsS, and LuxPQ, respectively, which then inhibit the transcription of genes whose products, in turn, block the production of another protein, LuxR. When the autoinducer concentration “tipping point” is reached, gene transcription is inhibited sufficiently and thus LuxR is produced, causing the bacteria to glow.

A World Malaria Map: Plasmodium falciparum Endemicity in 2007:

Malaria is one of the most common infectious diseases in the world and one of the greatest global public health problems. The Plasmodium falciparum parasite causes approximately 500 million cases each year and over one million deaths in sub-Saharan Africa. More than 40% of the world’s population is at risk of malaria. The parasite is transmitted to people through the bites of infected mosquitoes. These insects inject a life stage of the parasite called sporozoites, which invade human liver cells where they reproduce briefly. The liver cells then release merozoites (another life stage of the parasite), which invade red blood cells. Here, they multiply again before bursting out and infecting more red blood cells, causing fever and damaging vital organs. The infected red blood cells also release gametocytes, which infect mosquitoes when they take a blood meal. In the mosquito, the gametocytes multiply and develop into sporozoites, thus completing the parasite’s life cycle. Malaria can be prevented by controlling the mosquitoes that spread the parasite and by avoiding mosquito bites by sleeping under insecticide-treated bed nets. Effective treatment with antimalarial drugs also helps to decrease malaria transmission.

The Alcohol Flushing Response: An Unrecognized Risk Factor for Esophageal Cancer from Alcohol Consumption:

Approximately 36% of East Asians (Japanese, Chinese, and Koreans) show a characteristic physiological response to drinking alcohol that includes facial flushing (see Figure 1), nausea, and tachycardia [1] . This so-called alcohol flushing response (also known as “Asian flush” or “Asian glow”) is predominantly due to an inherited deficiency in the enzyme aldehyde dehydrogenase 2 (ALDH2) [2]. Although clinicians and the East Asian public generally know about the alcohol flushing response (e.g., http://www.echeng.com/asianblush/), few are aware of the accumulating evidence that ALDH2-deficient individuals are at much higher risk of esophageal cancer (specifically squamous cell carcinoma) from alcohol consumption than individuals with fully active ALDH2. This is particularly unfortunate as esophageal cancer is one of the deadliest cancers worldwide [3], with five-year survival rates of 15.6% in the United States, 12.3% in Europe, and 31.6% in Japan [4].

Guidelines for Field Surveys of the Quality of Medicines: A Proposal:

There has been relatively little apparent interest in the quality of medicines used to treat common life-threatening diseases despite the logical implication that poor-quality medicines will reduce the effectiveness of therapy and encourage drug resistance. Evidence suggests that a significant proportion of drugs consumed in the developing world are of poor quality [1-25]. Translating evidence on drug treatment outcomes into treatment policy is futile if the medicines actually used have substantially inferior efficacy compared with the medicines originally evaluated [7]. Poor-quality medicines are conventionally classified into three main categories: counterfeit, substandard, and degraded (Box 1).

New and Exciting in PLoS ONE

There are 13 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, 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:
Expert Financial Advice Neurobiologically ‘Offloads’ Financial Decision-Making under Risk:

Financial advice from experts is commonly sought during times of uncertainty. While the field of neuroeconomics has made considerable progress in understanding the neurobiological basis of risky decision-making, the neural mechanisms through which external information, such as advice, is integrated during decision-making are poorly understood. In the current experiment, we investigated the neurobiological basis of the influence of expert advice on financial decisions under risk. While undergoing fMRI scanning, participants made a series of financial choices between a certain payment and a lottery. Choices were made in two conditions: 1) advice from a financial expert about which choice to make was displayed (MES condition); and 2) no advice was displayed (NOM condition). Behavioral results showed a significant effect of expert advice. Specifically, probability weighting functions changed in the direction of the expert’s advice. This was paralleled by neural activation patterns. Brain activations showing significant correlations with valuation (parametric modulation by value of lottery/sure win) were obtained in the absence of the expert’s advice (NOM) in intraparietal sulcus, posterior cingulate cortex, cuneus, precuneus, inferior frontal gyrus and middle temporal gyrus. Notably, no significant correlations with value were obtained in the presence of advice (MES). These findings were corroborated by region of interest analyses. Neural equivalents of probability weighting functions showed significant flattening in the MES compared to the NOM condition in regions associated with probability weighting, including anterior cingulate cortex, dorsolateral PFC, thalamus, medial occipital gyrus and anterior insula. Finally, during the MES condition, significant activations in temporoparietal junction and medial PFC were obtained. These results support the hypothesis that one effect of expert advice is to “offload” the calculation of value of decision options from the individual’s brain.

Detecting Linkage between a Trait and a Marker in a Random Mating Population without Pedigree Record:

Modern linkage-based approaches employing extended pedigrees are becoming powerful tools for localizing complex quantitative trait loci. For these linkage mapping methods, it is necessary to reconstruct extended pedigrees which include living individuals, using extensive pedigree records. Unfortunately, such records are not always easy to obtain and application of the linkage-based approaches has been restricted. Within a finite population under random mating, latent inbreeding rather than non-random inbreeding by consanguineous marriages is expected to occur and is attributable to coalescence in a finite population. Interestingly, it has been revealed that significant random inbreeding exists even in general human populations. Random inbreeding should be used to detect the hidden coancestry between individuals for a particular chromosomal position and it could also have application in linkage mapping methods. Here we present a novel method, named finite population based linkage mapping (FPL) method, to detect linkage between a quantitative trait and a marker via random inbreeding in a finite population without pedigree records. We show how to estimate coancestry for a chromosomal position between individuals by using multipoint Bayesian estimation. Subsequently, we describe the FPL method for detecting linkage via interval mapping method using a nonparametric test. We show that the FPL method does work via simulated data. For a random sample from a finite population, the FPL method is more powerful than a standard pedigree-based linkage mapping method with using genotypes of all parents of the sample. In addition, the FPL method was demonstrated by actual microsatellite genotype data of 750 Japanese individuals that are unrelated according to pedigree records to map a known Psoriasis susceptible locus. For samples without pedigree records, it was suggested that the FPL method require limited number of individuals, therefore would be better than other methods using thousands of individuals.

The Good, The Bad and The Ugly: Exploring the ecology of insects (video)

My picks from ScienceDaily

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Today’s carnivals

World Water Day synchroblogging is up on Crikey Creek
Gene Genie #44 is up on Mary Meets Dolly
Friday Ark #235 is up on Modulator

Clock Quotes

All the world’s a stage and most of us are desperately unrehearsed.
– Sean O’Casey, Irish dramatist (1880 – 1964)

Paul Sereno: What can fossils teach us? (video)