The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Kevin Emamy from CiteULike to answer a few questions. Hi, Welcome to A Blog Around The Clock. Tell us more about CiteULike – what is it, how does it work, where did you get the idea to develop it? CiteULike is a quick and simple way to save references where one finds them (online), a highly effective social filter of academic literature, and (relative to the alternatives) a pure triumph of function and performance over form. It’s also unashamedly a pure web application, for all the right reasons.
What’s interesting about it is the social discovery you can generate by the simple act of keeping your references public on a web page.
If you find another user’s library that interests you, you can browse it like a good independent bookshop. The point is to help you discover research. The papers saved by people who share your interests are remarkable. It’s wonderful to peek through the pipes and spy on other peoples’ bookshelves like this.
Today we took the first step towards automating this process somewhat by launching article recommendations. Your library is compared to all the other libraries on CiteULike and a list of recommended articles is produced. It’s a type of collaborative filter. We have worked with Toine Bogers on this. I believe this is the first time this has been done live in production for journal papers.
What is pretty unique about the CiteULike dataset is that we now have about 5 years worth of data created by users posting papers, one by one, as they find them. That’s one of the things that makes the recommendations so effective (we hope).
[Watch this brief video for a demo of Recommendations on CiteULike – BZ] What aspect of science communication and/or particular use of the Web in science interests you the most?
Helping people find the good stuff in the garbage dump. A social filter says that as everyone is building up their own map of the the dump, why not share those maps?
It is exciting for us that PLoS are using social bookmarking data as part of their article level metrics project. You can go from the number of bookmarks on a PLoS article page straight through to the users whose bookmarks are being counted. It’s all open for anyone to see. How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook?
I am an active lurker. I don’t neccessarily want to jump in with my own agenda, but my colleagues answer direct questions about CiteULike anywhere they find them, FriendFeed and Twitter being the most active outside of our own forums.
For me they all boil down to social discovery. Search is the best answer for finding something specific. If you want to find something interesting to read, it’s blogs, Twitter, delicious and CiteULike all the way. Many of these often point back to articles in journals etc., but the filter of other people finding stuff worth posting helps me find interesting stuff everyday, in places I’d never look. That’s another advantage of having everything online, You can share what you find elsewhere. When and how did you discover science blogs?
From ScienceOnline09. What are some of your favourites?
A blog Around the Clock, of course. What do you want to do/be when (and if ever) you grow up?
That’s kind of you, but it’s too late for me. It was so nice to meet you and thank you for the interview. I hope to see you again next January.
==========================
See the 2008 interview series and 2009 series for more.
Just a few updates on the progress in the organization of ScienceOnline2010 to those of you who do not follow me (or scio10) on Twitter.
The main event – the actual sessions of the conference – will be held, like last two years, in the beuatiful building of Sigma Xi, the Scientific Research Society (and publisher of American Scientist). The main conference program will occur on Saturday, January 16th and half of Sunday, January 17th, 2010. Breakfast, lunch, tea and coffee will be catered there on both days.
As we did every year, we will have an Early Bird Dinner on Thursday night. This is usually a smaller affair – the Early Birds are usually people who fly in from distant parts of the globe (and this year we expect many of those, including people from Poland, Italy, Serbia and New Zealand). Some of the locals also join in for an evening of good food and fun. We are thinking of making this even more fun with a special event – we’ll keep you posted about that later (it’s a secret for now).
Friday will be a busy day. Guests will be arriving throughout the day, but those who come early enough will be able to sign up for a variety of activities.
There will be Food Tours at breakfast and lunch times. Remember Coffee Cupping last year? We’ll do more things like that.
There will be Lab Tours in the afternoon (with probably more choices this year as well).
Hands-on workshops and tutorials that may require you to bring in your laptops will be offered on Friday late morning at the PRC center of RTP – if you are interested in either teaching or attending one of these, let me know (or add your name to the bottom of the Program page). Which topics? Start a blog, learn to make podcasts, learn how to make good videos, build your own social network or use the existing ones, paint your own images, then use your new skills during the conference and post the results online for other participants to see.
Friday night and Saturday night events are still in the early planning stages, but at least one of these will happen at the gorgeous new Headquarters of the Research Triangle Park, our new partner and sponsor of the conference. There is likely to be a talk by a prominent speaker on one of these two nights, while on the other night we’ll probably have an Ignite session (do you want to do one?) and perhaps even a local band! And on both nights there will be good food, wine and/or beer, and opportunity to meet local scientists, science journalists and bloggers and get to know more about RTP and all the cool science and tech happening in the area.
Registration will be capped at 250 participants. Even this number will make Sigma Xi start bursting at the seams but if everyone’s in a good mood, we’ll be fine. So far, about double that number has showed interest in coming to the conference so there will be feisty competition for those 250 slots, we expect.
Thus, we will make sure that speakers/moderators/panelists/presenters get registered first. We will open for registration later than last year (late October) when people have a better idea if they can truly come or not. We will have the Program pretty much set up and public by then so you can see exactly what you can expect. And we will ask for a small registration fee (graded according to employment status or something) to ensure that only dedicated travelers and local participants actually register (i.e., nobody registers and then does not show up, leaving serious contenders on the waiting list).
We are also working hard on making sure that there is plenty of bandwidth for all the participants to be able to go online at the same time, to have some or all sessions (moderators permitting – some are pseudonymous) live-streamed and recorded, and to have a portion of the conference also paralleled in SecondLife. Thus, even those who cannot be present in person will be able to participate virtually in parts of the conference.
If you or your organization are interested in sponsoring an aspect of the conference (a meal, an event, a tour, travel-grants for students, etc.) please let us know.
Sign up here to receive advance notice about registration and other conference updates.
Add ideas for the program at this page.
Follow us on Twitter, FriendFeed and Facebook for RealTime news and updates.
Most of us, swimming against the tides of trouble the world knows nothing about, need only a bit of praise or encouragement and we will make the goal.
– Jerome P. Fleishman
A) If you click on any individual post on any Scienceblogs.com blog, you will see new sharing buttons on the bottom which make it very easy for you to, with a single click, send the link to that post to Twitter, Facebook and other social networking services (or e-mail to friends).
B) There is a new page on Scienceblogs.com – this one – where you can see all the comments made recently on all of our blogs. And, lo and behold, they are not all on Pharyngula posts! Once you scroll down and read them all, just refresh the page to see the new ones. Click and add your own comments. Get to know the bloggers (and their regular commenters) you are not familiar with yet. You can get to that page from any blog by looking at the right-hand margin and clicking on the “More Scienceblogs” menu, then choose “The Latest Comments”.
Photosynthetic eukaryotes with a secondary plastid of red algal origin (cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans) are hypothesized to share a single origin of plastid acquisition according to Chromalveolate hypothesis. Recent phylogenomic analyses suggest that photosynthetic “chromalveolates” form a large clade with inclusion of several non-photosynthetic protist lineages. Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated. Here, we report a newly discovered flagellate, Roombia truncata gen. et sp. nov., that is related to katablepharids, but is morphologically distinct from othermembers of the group in the following ways: (1) two flagella emerge from a papilla-like subapical protrusion, (2) conspicuous ejectisomes are aligned in multiple (5-11) rows, (3) each ejectisome increases in size towards the posterior end of the rows, and (4) upon feeding, a part of cytoplasm elastically stretch to engulf whole prey cell. Molecular phylogenies inferred from Hsp90, SSU rDNA, and LSU rDNA sequences consistently and strongly show R. truncata as the sister lineage to all other katablepharids, including lineages known only from environmental sequence surveys. A close association between katablepharids and cryptophytes was also recovered in most analyses. Katablepharids and cryptophytes are together part of a larger, more inclusive, group that also contains haptophytes, telonemids, centrohelids and perhaps biliphytes. The monophyly of this group is supported by several different molecular phylogenetic datasets and one shared lateral gene transfer; therefore, we formally establish this diverse clade as the “Hacrobia.” Our discovery of R. truncata not only expands our knowledge in the less studied flagellate group, but provide a better understanding of phylogenetic relationship and evolutionary view of plastid acquisition/losses of Hacrobia. Being an ancestral to all katablepharids, and readily cultivable, R. truncata is a good candidate for multiple gene analyses that will contribute to future phylogenetic studies of Hacrobia.
Preliminary evidence indicates that dopamine given by mouth facilitates the learning of motor skills and improves the recovery of movement after stroke. The mechanism of these phenomena is unknown. Here, we describe a mechanism by demonstrating in rat that dopaminergic terminals and receptors in primary motor cortex (M1) enable motor skill learning and enhance M1 synaptic plasticity. Elimination of dopaminergic terminals in M1 specifically impaired motor skill acquisition, which was restored upon DA substitution. Execution of a previously acquired skill was unaffected. Reversible blockade of M1 D1 and D2 receptors temporarily impaired skill acquisition but not execution, and reduced long-term potentiation (LTP) within M1, a form of synaptic plasticity critically involved in skill learning. These findings identify a behavioral and functional role of dopaminergic signaling in M1. DA in M1 optimizes the learning of a novel motor skill.
Background
The early evolution of sauropod dinosaurs is poorly understood because of a highly incomplete fossil record. New discoveries of Early and Middle Jurassic sauropods have a great potential to lead to a better understanding of early sauropod evolution and to reevaluate the patterns of sauropod diversification. Principal Findings
A new sauropod from the Middle Jurassic of Niger, Spinophorosaurus nigerensis n. gen. et sp., is the most complete basal sauropod currently known. The taxon shares many anatomical characters with Middle Jurassic East Asian sauropods, while it is strongly dissimilar to Lower and Middle Jurassic South American and Indian forms. A possible explanation for this pattern is a separation of Laurasian and South Gondwanan Middle Jurassic sauropod faunas by geographic barriers. Integration of phylogenetic analyses and paleogeographic data reveals congruence between early sauropod evolution and hypotheses about Jurassic paleoclimate and phytogeography. Conclusions
Spinophorosaurus demonstrates that many putatively derived characters of Middle Jurassic East Asian sauropods are plesiomorphic for eusauropods, while South Gondwanan eusauropods may represent a specialized line. The anatomy of Spinophorosaurus indicates that key innovations in Jurassic sauropod evolution might have taken place in North Africa, an area close to the equator with summer-wet climate at that time. Jurassic climatic zones and phytogeography possibly controlled early sauropod diversification.
To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts were regulated by at least 1.5 fold, 30 minutes after exposure to 30 µM H2O2. Parallel proteomic analyses using two-dimensional differential gel electrophoresis (2D-DIGE), monitored more than 800 proteins 30 and 105 minutes after exposure and found that 18 had significant changes in abundance. A recently characterized ferritin-like antioxidant protein, DPSL, was the most highly regulated species of mRNA and protein, in addition to being post-translationally modified. As expected, a number of antioxidant related mRNAs and proteins were differentially regulated. Three of these, DPSL, superoxide dismutase, and peroxiredoxin were shown to interact and likely form a novel supramolecular complex for mitigating oxidative damage. A scheme for the ability of this complex to perform multi-step reactions is presented. Despite the central role played by DPSL, cells maintained a lower level of protection after disruption of the dpsl gene, indicating a level of redundancy in the oxidative stress pathways of S. solfataricus. This work provides the first “omics” scale assessment of the oxidative stress response for an archeal organism and together with a network analysis using data from previous studies on bacteria and eukaryotes reveals evolutionarily conserved pathways where complex and overlapping defense mechanisms protect against oxygen toxicity.
Marine snow (small amorphous aggregates with colloidal properties) is present in all oceans of the world. Surface water warming and the consequent increase of water column stability can favour the coalescence of marine snow into marine mucilage, large marine aggregates representing an ephemeral and extreme habitat. Marine mucilage characterize aquatic systems with altered environmental conditions. We investigated, by means of molecular techniques, viruses and prokaryotes within the mucilage and in surrounding seawater to examine the potential of mucilage to host new microbial diversity and/or spread marine diseases. We found that marine mucilage contained a large and unexpectedly exclusive microbial biodiversity and hosted pathogenic species that were absent in surrounding seawater. We also investigated the relationship between climate change and the frequency of mucilage in the Mediterranean Sea over the last 200 years and found that the number of mucilage outbreaks increased almost exponentially in the last 20 years. The increasing frequency of mucilage outbreaks is closely associated with the temperature anomalies. We conclude that the spreading of mucilage in the Mediterranean Sea is linked to climate-driven sea surface warming. The mucilage can act as a controlling factor of microbial diversity across wide oceanic regions and could have the potential to act as a carrier of specific microorganisms, thereby increasing the spread of pathogenic bacteria.
Gray wolves (Canis lupus) were reintroduced into Yellowstone National Park (YNP) after a >70 year absence, and as part of recovery efforts, the population has been closely monitored. In 1999 and 2005, pup survival was significantly reduced, suggestive of disease outbreaks. We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991-2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5-0.9 yr]: 91%, adults [≥1 yr]: 96%; coyote juveniles [0.5-1.5 yrs]: 18%, adults [≥1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6-4.9 yrs]: 51%, old adults [≥5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes. An average of 50% of wolves exhibited exposure to the protozoan parasite, Neospora caninum, although individuals’ odds of exposure tended to increase with age and was temporally variable. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. The years of high wolf-pup mortality in 1999 and 2005 in the northern region of the park were correlated with peaks in CDV seroprevalence, suggesting that CDV contributed to the observed mortality. Of the pathogens we examined, none appear to jeopardize the long-term population of canids in YNP. However, CDV appears capable of causing short-term population declines. Additional information on how and where CDV is maintained and the frequency with which future epizootics might be expected might be useful for future management of the Northern Rocky Mountain wolf population.
Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases. Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within http://www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period. Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting ‘citizen scientists’ to contribute data easily to central databases through their mobile phone.
Infants’ sensitivity to social or behavioral contingency has been examined in the field of developmental psychology and behavioral sciences, mainly using a double video paradigm or a still face paradigm. These studies have shown that infants distinguish other individuals’ contingent behaviors from non-contingent ones. The present experiment systematically examined if this ability extends to the detection of non-humanoids’ contingent actions in a communicative context. We examined two- to three-year-olds’ understanding of contingent actions produced by a non-humanoid robot. The robot either responded contingently to the actions of the participants (contingent condition) or programmatically reproduced the same sequence of actions to another participant (non-contingent condition). The results revealed that the participants exhibited different patterns of response depending on whether or not the robot responded contingently. It was also found that the participants did not respond positively to the contingent actions of the robot in the earlier periods of the experimental sessions. This might reflect the conflict between the non-humanlike appearance of the robot and its humanlike contingent actions, which presumably led the children to experience the uncanny valley effect.
17 years ago, there were no broods of periodic cicadas emerging (and also none this year). But that year something much more momentous happened, on this day exactly – Catharine changed her name….into something translatable as ‘The Bride Of Coturnix’ 😉
Happy anniversary, medawlin’
How will the public learn about important breakthroughs at leading research universities as traditional news outlets continue to shrink?
The site is taking selected science stories from the participating Universities and putting them together in one place, sorted by topics and searchable by tags (by topic or by school). Let’s hope that more schools choose to join in, and also, that their feed gets incorporated on major news sites. The site is a “pull” strategy vehicle (it will be found and read by people who are interested in science and actively seaching for information) and inclusion on front pages of mainstream media sites would add a “push” strategy (making sure everybody sees the science news, even those who are not specifically looking, but may say “Wow – this is cool!”) which is necessary for more widespread popularisation of science.
Monday, Monday – let’s see what’s new. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites: Real Lives and White Lies in the Funding of Scientific Research:
It is a summer day in 2009 in Cambridge, England, and K. (39) looks out of his lab window, wondering why he chose the life of a scientist [1]. Yet it had all begun so well! His undergraduate studies in Prague had excited him about biomedical research, and he went on to a PhD at an international laboratory in Heidelberg. There, he had every advantage, technical and intellectual, and his work had gone swimmingly. He had moved to a Wellcome-funded research institute in England in 1999. And although his postdoc grant, as is typical, was for only two years, he won a rare career development award that gave him some independence for four more years. A six-year postdoc was an unusual opportunity, and it allowed him to define his own research field. By 2004, he had published six experimental papers in good journals, and on four of these, he was first author. It was the high point in his career, and when he applied for posts in Cambridge, London, Stanford, and Tubingen, he was short-listed for them all. He chose Cambridge University and a Royal Society Research Fellowship that offered him up to ten years’ salary. This should have brought the peace of mind to plan projects that would take five years, or even longer. So, what went wrong?
Amphibians became the most ancient class of land-dwelling vertebrates when, 360 million years ago, primitive amphibia such as Ichthyostega first hauled themselves out of their aquatic environment. Since that ancient event, the amphibia have ramified into over 6,300 species of breathtaking diversity: they inhabit all continents (excepting Antarctica), from deserts to altitudes of over 5,300 metres, manufacture an astoundingly complex arsenal of chemicals, and undergo complex metamorphic transitions that bridge aquatic and terrestrial ecosystems….
Evidence-based practice requires translating research findings into clinical and policy decision making. Clinical practice guidelines (CPGs) serve this purpose by evaluating evidence and making recommendations about therapeutic and diagnostic interventions and clinical management strategies. Systematic reviews are considered the best available evidence and are often used in the development of CPGs [1],[2]. Since guideline development involves an assessment of the overall quality of evidence and complex balancing of trade-offs between the important benefits and harms of any given intervention, arbitrariness, value judgements, and subjectivity ultimately come into play in the guideline development process and associated recommendations [3]. In order to minimize cognitive bias in interpreting evidence and make the inherently subjective process more transparent and consistent, CPGs have traditionally employed formal systems or frameworks to understand and grade the quality of the body of evidence and strength of recommendations [4],[5].
The unique metabolism of tumors was described many years ago by Otto Warburg, who identified tumor cells with increased glycolysis and decreased mitochondrial activity. However, “aerobic glycolysis” generates fewer ATP per glucose molecule than mitochondrial oxidative phosphorylation, so in terms of energy production, it is unclear how increasing a less efficient process provides tumors with a growth advantage. We carried out a screen for loss of genetic elements in pancreatic tumor cells that accelerated their growth as tumors, and identified mitochondrial ribosomal protein L28 (MRPL28). Knockdown of MRPL28 in these cells decreased mitochondrial activity, and increased glycolysis, but paradoxically, decreased cellular growth in vitro. Following Warburg’s observations, this mutation causes decreased mitochondrial function, compensatory increase in glycolysis and accelerated growth in vivo. Likewise, knockdown of either mitochondrial ribosomal protein L12 (MRPL12) or cytochrome oxidase had a similar effect. Conversely, expression of the mitochondrial uncoupling protein 1 (UCP1) increased oxygen consumption and decreased tumor growth. Finally, treatment of tumor bearing animals with dichloroacetate (DCA) increased pyruvate consumption in the mitochondria, increased total oxygen consumption, increased tumor hypoxia and slowed tumor growth. We interpret these findings to show that non-oncogenic genetic changes that alter mitochondrial metabolism can regulate tumor growth through modulation of the consumption of oxygen, which appears to be a rate limiting substrate for tumor proliferation.
Enantiomers differ only in the left or right handedness (chirality) of their orientations and exhibit identical chemical and physical properties. In chemical communication systems, enantiomers can be differentially active at the physiological and behavioral levels. Only recently were enantioselective odorant receptors demonstrated in mammals while their existence in insects has remained hypothetical. Using the two-microelectrode voltage clamp of Xenopus oocytes, we show that the yellow fever mosquito, Aedes aegypti, odorant receptor 8 (AaOR8) acts as a chiral selective receptor for the (R)-(–)-enantiomer of 1-octen-3-ol, which in the presence of other kairomones is an attractant used by blood-sucking insects to locate their hosts. In addition to steric constraints, chain length and degree of unsaturation play important roles in this recognition process. This is the first characterization of an enantioselective odorant receptor in insects and the results demonstrate that an OR alone, without helper proteins, can account for chiral specificity exhibited by olfactory sensory neurons (OSNs).
For many technology-driven visuomotor tasks such as tele-surgery, human operators face situations in which the frames of reference for vision and action are misaligned and need to be compensated in order to perform the tasks with the necessary precision. The cognitive mechanisms for the selection of appropriate frames of reference are still not fully understood. This study investigated the effect of changing visual and kinesthetic frames of reference during wrist pointing, simulating activities typical for tele-operations. Using a robotic manipulandum, subjects had to perform center-out pointing movements to visual targets presented on a computer screen, by coordinating wrist flexion/extension with abduction/adduction. We compared movements in which the frames of reference were aligned (unperturbed condition) with movements performed under different combinations of visual/kinesthetic dynamic perturbations. The visual frame of reference was centered to the computer screen, while the kinesthetic frame was centered around the wrist joint. Both frames changed their orientation dynamically (angular velocity = 36°/s) with respect to the head-centered frame of reference (the eyes). Perturbations were either unimodal (visual or kinesthetic), or bimodal (visual+kinesthetic). As expected, pointing performance was best in the unperturbed condition. The spatial pointing error dramatically worsened during both unimodal and most bimodal conditions. However, in the bimodal condition, in which both disturbances were in phase, adaptation was very fast and kinematic performance indicators approached the values of the unperturbed condition. This result suggests that subjects learned to exploit an “affordance” made available by the invariant phase relation between the visual and kinesthetic frames. It seems that after detecting such invariance, subjects used the kinesthetic input as an informative signal rather than a disturbance, in order to compensate the visual rotation without going through the lengthy process of building an internal adaptation model. Practical implications are discussed as regards the design of advanced, high-performance man-machine interfaces.
Introducing the Briefly series. Taking theory and presenting it in it’s most concise form.
We start with the Big Bang because the theory is important and amazing, but often misunderstood.
This video was produced without any funding from any outside sources. It was put together with donated creative time from a group with a desire to further public cognition of science.
Science has many amazing stories to tell, this is the first. The Big Bang Briefly.
Here are the submissions for OpenLab 2009 to date. As we have surpassed 360 entries, all of them, as well as the “submit” buttons and codes and the bookmarklet, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
I heard someone else in the blogosphere does this on Fridays, but I could not resist stomping into his territory as this video is Teh Awesome, from the Seaplex expedition – a dead Giant Squid, torn apart by hungry marine biologists:
Carbon cycling in Southern Ocean is a major issue in climate change, hence the need to understand the role of biota in the regulation of carbon fixation and cycling. Southern Ocean is a heterogeneous system, characterized by a strong seasonality, due to long dark winter. Yet, currently little is known about biogeochemical dynamics during this season, particularly in the deeper part of the ocean. We studied bacterial communities and processes in summer and winter cruises in the southern Drake Passage. Here we show that in winter, when the primary production is greatly reduced, Bacteria and Archaea become the major producers of biogenic particles, at the expense of dissolved organic carbon drawdown. Heterotrophic production and chemoautotrophic CO2 fixation rates were substantial, also in deep water, and bacterial populations were controlled by protists and viruses. A dynamic food web is also consistent with the observed temporal and spatial variations in archaeal and bacterial communities that might exploit various niches. Thus, Southern Ocean microbial loop may substantially maintain a wintertime food web and system respiration at the expense of summer produced DOC as well as regenerate nutrients and iron. Our findings have important implications for Southern Ocean ecosystem functioning and carbon cycle and its manipulation by iron enrichment to achieve net sequestration of atmospheric CO2.
Invasive species are recognized as a primary driver of native species endangerment and their removal is often a key component of a conservation strategy. Removing invasive species is not always a straightforward task, however, especially when they interact with other species in complex ways to negatively influence native species. Because unintended consequences may arise if all invasive species cannot be removed simultaneously, the order of their removal is of paramount importance to ecological restoration. In the mid-1990s, three subspecies of the island fox Urocyon littoralis were driven to near extinction on the northern California Channel Islands owing to heightened predation by golden eagles Aquila chrysaetos. Eagles were lured to the islands by an abundant supply of feral pigs Sus scrofa and through the process of apparent competition pigs indirectly facilitated the decline in foxes. As a consequence, both pigs and eagles had to be removed to recover the critically endangered fox. Complete removal of pigs was problematic: removing pigs first could force eagles to concentrate on the remaining foxes, increasing their probability of extinction. Removing eagles first was difficult: eagles are not easily captured and lethal removal was politically distasteful. Using prey remains collected from eagle nests both before and after the eradication of pigs, we show that one pair of eagles that eluded capture did indeed focus more on foxes. These results support the premise that if the threat of eagle predation had not been mitigated prior to pig removal, fox extinction would have been a more likely outcome. If complete eradication of all interacting invasive species is not possible, the order in which they are removed requires careful consideration. If overlooked, unexpected consequences may result that could impede restoration.
Only when an organization exists in stable circumstances, when its operations resemble clockwork, unvarying in their practices, can individuals be taken for granted or ignored without peril.
– Rosabeth Moss-Kanter
PLoS Medicine turns 5 years old on October 19th, 2009. To highlight the crucial importance of open access in medical publishing we’re holding a competition to find the best medical paper published under an open-access license anywhere (not just in PLoS) since our launch.
Vote for your choice from the 6 competing papers, detailed below — nominated and then shortlisted by our editorial board. Winners will be announced during Open-Access week (19-23rd October 2009). If you’re interested in how we came up with this shortlist of top-quality open-access medicine papers, please read on below the poll.
I have been remiss this week….so here’s a sampling from all seven PLoS journals over the course of this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
What’s Bugging You? Animals We Love to Hate
Wednesday, September 30, 2009
8:00 – 10:00 am with discussion beginning at 9:00 followed by Q&A
Location: The Acro Cafe – 4th Floor of the Museum of Natural Sciences
Fire ants. Mosquitoes. Flies. Ticks. Gnats. Bed Bugs. The list goes on and on.
They disturb our sleep, sting us, envenomate us, suck our blood, eat our food, crawl on us…yet at the same time, they pollinate our food and flowers, provide insect control, and increase biodiversity. So, what is a pest? Are some of these pests invasive species? What can or should be done about them?
About the Speaker:
Join Dr.Colin Brammer, Entomologist and Curator of the Museum’s Naturalist Center for a discussion on all things pest related in our next Breakfast with a Side of Science
Quiet minds can’t be perplexed or frightened, but go on in fortune or misfortune at their own private pace, like a clock during a thunderstorm.
– Robert Louis Stevenson
Here are the submissions for OpenLab 2009 to date. As we have surpassed 360 entries, all of them, as well as the “submit” buttons and codes and the bookmarklet, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
Professor Nicky Clayton researches the social behaviour, intelligence and dance credentials of birds! As an accomplished dancer in her own right she has fused her passions by collaborating with Rambert Dance Company to produce a Darwinian inspired ballet called The Comedy of Change.
Tuesday, September 22, 2009
6:30-8:30 pm with discussion beginning at 7:00 followed by Q&A
Location: The Irregardless Café, 901 W. Morgan Street, Raleigh 833-8898
Memory problems have become increasingly common as our population ages. The fear of developing dementia is one of the greatest fears of most Americans. There can be memory changes as one grows older, but what determines if these changes are benign versus the beginning of a dementia process like Alzheimer’s disease? We will discuss types of memory, the neurobiological basis of memory, and ways to tell normal aging from the beginnings of significant memory loss. We will also discuss symptoms and treatment for people who have been diagnosed with dementia.
About the speaker:
Sandeep Vaishnavi, M.D., PhD serves as Medical Director at North Carolina Neuropsychiatry Clinic in Raleigh. Dr. Vaishnavi specializes in memory and memory disorders. He has been a fellow at Johns Hopkins Hospital and as part of the Duke-GlaxoSmithKline Psychopharmacology program. He has also been nominated for and/or received both clinical and research awards from Duke Medical Center.
I know everyone in the sci-blogosphere is swooning over Carl Sagan. But as a kid I never cared much about him – I usually fell asleep halfway through each episode of ‘Cosmos’. But I would not miss for anything an episode of ‘The Underwater Odyssey of Commander Cousteau’ with Jacques-Yves Cousteau. That was breathtaking. And what he and the crew of Calypso did was truly ground-breaking, both in terms of scientific discoveries and in terms of under-water filming. And those discoveries and breakthroughs were shared with us, the audience, in an intimate and immediate manner.
That was a long time ago. The techniques of under-water filming pioneered by the crew are now probably considered to be ‘nothing special’. And I bet half the crew of Calypso were cameramen and sound engineers and lighting engineers and video mixers and other TV and movie professionals.
Can’t do that any more. Or rarely, with a huge cost, only on a very limited number of voyages on very large ships.
But what one can do, even on vessels much smaller than Calypso, is to have an embedded reporter. Not an old-timey one, but a modern reporter: someone who can search the Web for information, who can write, and blog, and tweet, and take and post photographs, and record and post audio podcasts, and record and post videos, all without help from any professional engineers, using small portable digital equipment and, most importantly, doing it in nearly Real Time, not after the ship docks after the voyage.
One of those new-style embedded reporters on a research ship is Lindsey Hoshaw. I was alerted to her by a tweet by Jay Rosen on Saturday. How did she get to do that?
She is a Stanford graduate in environmental journalism who was interested in the Pacific Garbage Patch and she put her proposal on Spot.us and asked people to help her raise the necessary funds:
I’ve been offered a space aboard the ship as the only journalist to chronicle this voyage. My enthusiasm for this project is only surpassed by the amazing opportunity I’ve been offered by The New York Times to publish an article and accompanying photos of my journey.
The Times has never written extensively about the Garbage Patch and my multimedia slideshow and article will be the first of its kind for the newspaper’s website.
As a recent graduate of Stanford University’s communications program, I have a background in environmental journalism. I have produced podcasts, audio slideshows and videos about environmental issues in the Bay Area and I have been studying the Garbage Patch for the past three years.
From their side the New York Times did not promise they’ll carry the story, but appear quite inclined to do so if the quality of her work is good:
LINDSEY HOSHAW, a freelance journalist in Palo Alto, Calif., hopes to sell a multimedia slide show and maybe an article to The Times about the Great Pacific Garbage Patch, a mass of floating plastic trash caught in swirling currents in a stretch of ocean twice the size of Texas.
But first, she has to get there. To help finance a $10,000 reporting trip aboard a research vessel, Hoshaw has turned to Spot.Us, a Web site where reporters appeal for donations to pay for their projects. If she can raise $6,000 before the September departure date — so far, only about $1,600 has come in — she will take out a loan for the rest, she said.
The Times has told Hoshaw that it might pay about $700 for the pictures, more if it also buys a story.
To some, this is exploitation — the mighty New York Times forcing a struggling journalist to beg with a virtual tin cup. But Hoshaw does not think so. To her, it is an opportunity she cannot pass up — a story she has long dreamed of, and a chance for a byline in The Times. To David Cohn, the founder of the nonprofit Spot.Us, it is a way for the public to commission journalism that it wants. For The Times, it is another step into a new world unthinkable even a few years ago.
She got on the ship today! You can follow Lindsey Hoshaw’s trip on Twitter (which she wisely separated from her personal account) and on her brand new blog.
You can follow her voyage on the Facebook page as well, where she also wrote:
What does this all mean both for Spot.Us and for the potential future of journalism? We would never claim to have answers, but we do have theories.
Every pitch on Spot.Us is defacto a collaboration. At the very least it is between the reporter and the community of supporters.
But often news organizations get involved. Sometimes we get TWO news organizations involved. In the future – I hope we can get THREE news organizations to collaborate around a single pitch.
We are producing a custom CMS that is based around the idea that “collaboration is queen.” It is the acknowledgment that no single news organization can do everything and that it is okay to “link to the rest.” It requires a new level of transparency and honesty in our reporting.
On Rebooting the News #24 this morning (I am assuming that all my readers listen to the show religiously every Monday), Jay and Dave talked about her as well:
On September 8, Lindsey Hoshaw set sail for The Great Pacific Garbage Patch, a huge pool of debris out in the middle of the Pacific that’s been known about for a while but rarely reported on or photographed. Her trip has been funded by users who think it’s an important venture. That happened at spot.us, the crowd-funding site for investigative journalism created by David Cohn, who used to work with Jay on NewAssignment.Net. (Background: See Lindsey’s original pitch in July 2009 and Jay’s original post for NewAssignment.Net back in 2006.) The New York Times has agreed to run her account and photos if they are up to Times standards. Meanwhile you can follow along on Twitter by adding thegarbagegirl.
That’s the re-booted system of news at work, already at work!
Dave: we’ve had reporters there before. Anyone who sailed by the Garbage Patch could have been our correspondent on the scene. We just have to teach them to do it.
Jay: it’s unlikely we’d be able to fund a reporter and a photographer and a videographer, which is why it’s important for journalists to be able to do multiple things.
Now you may say “Hmmm, that sounds familiar….didn’t I hear something about this before?” And yes, you did.
Another research vessel just returned from the Pacific Gyre where the crew studied the Garbage Patch. That was the Seaplex expedition, led by Miriam Goldstein, a well-known ocean blogger from the Oyster’s Garter blog. Miriam too, separated her personal Twitter account from the expedition account (I don’t actually know who from the crew tweeted from the official account). And she also blogged about it on the official Seaplex blog. So that crew also had an ’embedded reporter’ of sorts – Miriam herself.
But take another look at the crew. Notice something? Miriam was not the only experienced blogger there. Or even the most experienced as a reporter. There were three other people there whose main purpose was to record and report from the trip – the Project Kaisei people, who also used their own Twitter account. One of them is Annie Crawley, founder of DiveImagination who also tweeted from the voyage.
So it seems all these trips have young journalists embedded as reporters, or as parts of the scientific crew, using all the modern communication technologies to report from the voyages in real time as well as to prepare more robust reports afterwards.
Oh, did I say that’s all? No, Lindsey Hoshaw is not the only person with reporting and blogging experience on that ship. There is also Bonnie Monteleone on board. Bonnie is a blogger on The Plastic Ocean (associated with the organization of the same name (hat-tip to North Carolina Sierra Club Blog):
UNCW’s Bonnie Monteleone and Jennifer O’Keefe, Director of Keep America Beautiful- New Hanover County, will represent North Carolina’s passion for the ocean by going out into the Atlantic Gyre, followed by Monteleone joining Algalita Marine Research Foundation into the North Pacific Gyre. They will be taking samples to quantify pelagic plastics found on the oceans surface, collecting surface feeding fish to necropsy for ingested plastics and bringing national awareness to the issues of man made debris entering our oceans. Most of this research is personally funded and why they need your help.
So Bonnie, who is both a student at UNC-Wilmington and staff in the Department of Chemistry & Biochemistry there, will be able to do a direct comparison between the Atlantic and Pacific Garbage Patches. And write and post videos from both expeditions.
Ah, what a tangled web! And the distinctions are getting blurry – who is a scientist, who is crew, who is journalist? Everyone is a little bit of everything these days. The journalists are surrounded by scientists – a constant source of information – and scientists are surrounded by journalists – a constant source of questions. They both also help with the daily ship routines (there is no space on small ships for freeloaders – hoist the sails!). And they all report from the voyage, each in his or her own way, some focusing more on the science, others more on the human connection, both at least some on the personal experience.
Now, if you’ve ever been to one of the ScienceOnline conferences (e.g., last year, or the year before….), you know that Ocean Bloggers are a jolly bunch – they come to the conference and what do they do for three days non-stop? They sing Sea Shanties! But they also do the best, most creative and most informative sessions! They are totally at the cutting edge of the new online technologies and many of them are awesome writers. Karen, Craig, Kevin, Miriam, Mark, Jennifer, Rick, Allie, Christie, James, Jason, Sheril, Andrew and David and many others are all amazing bloggers! And very active on Twitter, FriendFeed, Facebook and elsewhere online (it is entirely possible that Karen tweets more times per day than I do!).
And I know that most of them are planning to come to ScienceOnline2010. I have learned that the best thing to do with the Ocean Bloggers is to give them an one-hour time slot and let them loose. They don’t need no guidance from me – they are much more creative than I am and ‘get’ the spirit of the Unconference better than most. They’ll plot something in secret and surprise us all right there and then.
Also, what I did as soon as I saw Jay’s original tweet was start following Lindsey Hoshaw on Twitter. She followed me back so we could exchange Direct Messages….and, she’ll also try to come to ScienceOnline2010. Now I just need to catch Bonnie (she is in Wilmington, an hour’s drive from here – perhaps she can carpool with Anne-Marie) and Annie Crawley and all the ’embedded reporters’ and bloggers from all of this summer’s Garbage Patch voyages will be there. So perhaps they can all get together and tell us all about it – compare notes. Each one of them came to this with a different background, with different skills and experiences, with different goals. What did they learn about modern journalism out at sea?
Or perhaps they can put all of their stuff together – all the tweets, blog posts, photographs, podcasts, videos and polished articles (or at least links to polished articles if they are published in corporate media, e.g., New York Times) can, perhaps, be placed in a single online spot which we can then all link to and boost the Google rank so people who search for the ‘Garbage Patch’ find it up high in their searches. Perhaps they can plot how to do it at their session. Or, knowing them, they can do it quicker and use the conference to unveil the site to the world.
Remember what Lindsey Hoshaw wrote (above):
What does this all mean both for Spot.Us and for the potential future of journalism? We would never claim to have answers, but we do have theories. Every pitch on Spot.Us is defacto a collaboration. At the very least it is between the reporter and the community of supporters. But often news organizations get involved. Sometimes we get TWO news organizations involved. In the future – I hope we can get THREE news organizations to collaborate around a single pitch. We are producing a custom CMS that is based around the idea that “collaboration is queen.” It is the acknowledgment that no single news organization can do everything and that it is okay to “link to the rest.” It requires a new level of transparency and honesty in our reporting.
Today, we are all Jacques-Yves Cousteau. And all of the filming crew.
Last year some of the ocean bloggers were involved in the session with the title “Hey! You Can’t Say That!”. Perhaps next year they can call the session “Oh, You Bet I Can Talk Trash!” or “Blogging Garbage” or, like this post, “Talking Trash”….
Whatever they decide to do, I am looking forward to the result, and to their session. And the Sea Shanties the evening after it.
Dinosaur fossils have been dug out for a couple of centuries now. They have been cleaned up and mounted in museums and described in papers and monographs. The way this is all done has evolved over time – the early techniques were pretty crude compared to what palaeontologists do today. One of the important techniques is actually quite simple: making measurements of bones. And yes, many such bones have been measured and the measurements reported in the literature. And that literature is scattered all over the place in many different formats in many different journals. Nobody has put all the measurements in one place where one could do statistics with the numbers and perhaps learn something from the exercise.
Now Andy Farke, Matt Wedel and Mike Taylor want to do just that:
We want to put together a paper on the multiple independent transitions from bipedality to quadrupedality in ornithischians, and we want to involve everyone who’s interested in helping out. We’ll get to the details later, but the basic idea is to amass a huge database of measurements of the limb bones of ornithischian dinosaurs, to which we can apply various statistical techniques. Hopefully we’ll figure out how these transitions happened — for example, whether ceratopsians, thyreophorans and ornithopods all made it in the same way or differently.
So, in order to accomplish this enormous project, they founded the Open Dinosaur Project – you can be a co-author of the resulting paper if you contribute! What is the idea? To crowdsource the effort. Published measurements need to be all copied into a single place for analysis. Bones not yet measured as well – if you are at a museum or university or in some other ways have access to the fossils, you can take your measuring tools and go down to the vaults and send in the numbers. They explain:
Constructing the Database
A huge, virtually untapped resource of skeletal measurements resides in the published scientific literature. In order to put these measurements to good use, it is necessary to place the data into a form that can be analyzed mathematically. Essentially, we aim to construct a giant spreadsheet with as many measurements for ornithischian dinosaur limb bones as possible. For simplicity, we will focus on bone lengths and maximum diameters along the shaft. From the forelimb, we will look at the scapula, coracoid, sternal plates, humerus, radius, ulna, and manus (“hand”). Within the hind limb, we will look at the femur, tibia, fibula, and pes (“foot”).
In the old days, this would require a lot of time in the library stacks. Some aspects of the project may still require this. But, a number of scientific papers are now freely available to the general public! So, anyone with an internet connection can help out. Who Can Participate?
Anyone! We do not care about your age, education, previous paleontological experience, or geographic location. You don’t have to be a professional paleontologist – just a person who is willing to act professionally in the accurate and ethical collection, analysis, and interpretation of real scientific data. What Can I Do?
It’s simple! Just locate the necessary scientific papers, and start entering data into our spreadsheet. If you have access to real specimens, you may enter these data. What Do I Get Out of This?
Two things – 1) the thrill of participating in real scientific research; and 2) an opportunity for authorship on a scientific paper. Yes, you read that correctly. All contributors to the database are given the option of joining us as authors for the final published paper. If you opt out of authorship, you will still be listed in the acknowledgments (unless you request otherwise). How Do I Sign Up?
Simply drop an email to project head Andy Farke – andrew.farke@gmail.com – with your name and preferred email address. If you have an institutional affiliation, please include that also. . .but remember that a formal academic affiliation is not required! In all aspects of the project, we ask that you use your real name rather than an on-line handle or other pseudonym. This is important both for personal accountability, as well as a professional standard. We may not all be professionals, but we will certainly conduct ourselves professionally! Help! I’m Lost!
Never fear. . .we’re going to publish a series of tutorials in the next few days outlining how to search for scientific literature, what measurements to look for, and other important introductory pieces for those new at the research game.
So if you can, participate. And if the analysis uncovers a new species – there’s a little paper right there as well. And if the project works well for ornithischians, then future projects may turn to theropods or whatever else strikes the paaleontologists’ fancy.
Also nice – the resulting paper(s) will be published in Open Access venues. I am salivating at the prospect of seeing these things published in PLoS ONE and joining the fast-growing Paleontology Collection….
And blog from there? For the Quark expedition!
The voting has been going on for quite a while now, but now we are in the final stretch. There are several hundred contestants, but only the top few vote-getters have a chance (they also need to pass an in-person interview).
The voting is well controlled – it requires a simple registration – so it is not possible to game the system (too much). It is also possible to change your vote, so if you have already voted for someone who now has no chance, you may want to switch to someone who has.
Several people at the top are good (including Danielle Lee!), but the first three are probably the only ones with a realistic chance.
In the first place is some Portuguese radio DJ. He must not be that popular with his listeners if even with a radio station broadcasting his pleas for his audience to vote, he only accumulated 5952 Votes so far.
In the second place is some guy whose claim to fame is family relationship with some celebrity – does his last name ring a bell? He’s got 1858 Votes to date via his celebrity network.
And in the third place is our own Grrrlscientist the top vote-getting real, true, nature/science blogger who can actually know what to look for and how to write about what she sees in Antarctica. Right now she has 1753 votes. No radio station, no celebrity fan-club, just some blog readers. But she can have more….if you vote now and tell all your friends to do the same.
That, if then I had waked after a long sleep,
will make me sleep again;
and then, in dreaming,
the clouds me thought would open and show riches ready to drop upon me;
that, when I waked I cried to dream again.
– William Shakespeare
I am superhappy with my brand new Homepage. So now I want to do all sorts of fixin’ around here.
The About page was horrendously out-dated so I did some quick fixes and edits to make it a little less embarrassing, though it probably needs a complete rethinking and rewriting from scratch one of these days.
But what should I do with the Blogroll?!?!
It is huge. And it is so out-of-date. And unmanageable. So many broken and dead links. Blogs that have quit months or years ago. And lacking so many blogs that I read now.
Option 1) delete the whole thing (nobody uses blogrolls any more)
Option 2) delete the whole thing and rebuild it, smaller, from scratch (people left out will be mad!)
Option 3) spend a few weeks fixing it: removing bad links, adding new blogs (will I ever find time and energy?)
Option 4) fix the existing or make a new blogroll and then make a widget on the sidebar that links to five random blogs from the blogroll (too scared to mess with templates on the new MT4 scienceblogs.com platform – likely to mess up the blog majorly).
Which option should I choose?
If you are a regular reader of this blog, you know Tatjana Jovanovic-Grove. Or you can remind yourself by checking this, this, this, this and this.
If you came to ScienceOnline09 (or followed virtually) you will remember that she co-moderated two sessions there: Open Access in the networked world: experience of developing and transition countries and How to paint your own blog images .
Well, today, Tatjana is in New York Times! I hear from those who get the papers in hardcopy, that the article starts on the front page, but the part with the interview with Tatjana and her husband Doug is on the third page of the online version of the article. I wish the theme of the piece was happier….but who knows, perhaps appearance in the Old Media (especially if the link is spread virally via New Media) may bring in a job!
What is really nice is that the online version of the article links to Tatjana’s Etsy store, so perhaps she’ll get some business that way!
All of us are watchers – of television, of time clocks, of traffic on the freeway – but few are observers. Everyone is looking, not many are seeing.
– Peter M. Leschak
Here are the submissions for OpenLab 2009 to date. As we have surpassed 340 entries, all of them, as well as the “submit” buttons and codes and the bookmarklet, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):
A Blog Around The Clock 