tags: bpr3.org/?p=52, birds, aves, ornithology, Zosterops somadikartai, Togian white-eye, Indonesia, Sulawesi

An undated artist's rendering of Zosterops somadikartai, or Togian white-eye.

This small greenish bird that has been playing hide-and-seek with ornithologists on a remote Indonesian island since 1996, but was declared a newly discovered species on March 14, 2008 and promptly recommended for endangered lists.

Image: Agus Prijono.

Sharp-eyed scientists have discovered a new species of bird on a remote Indonesian archipelago in the Southern Pacific Ocean. A formal description of this new species, the Togian white-eye, Zosterops somadikartai, was just published in the March issue of the ornithological journal, The Wilson Journal of Ornithology. Not only was this bird recognized as a new species, but its small population and home range were sufficient for recommendation to the international endangered species lists. Read the rest of this post... | Read the comments on this post...

What are you currently reading?

I'm reading Three Cups of Tea, which Misty sent me ('cuz she's awesome like that), and it is just so inspiring. Tres teaspoony!

The Fat Princess thread has proven enormously amusing, as the fat-hating, homophobic, misogynist dancing monkeys have boogied to the sound of my organ grinding [insert your own double entendre here] without a hint of irony or self-awareness all day, but my email has been providing me with lots of treats, too. This one was too good not to share:


Thanks, Sean. Not only was I enormously worried, but I totally give a shit what you think—so your email came just in time.

And I'll be sure to pass on the good word to my husband, too.

Here's some news from the old country. Okmok Volcano on Umnak Island in the eastern Aleutian Islands (the end near the mainland) started erupting on July 12 and continues to produce explosions and ash plumes through a newly created vent. The initial eruption sent a cloud to 35,000 feet. Most of ash and gas from that explosion blew southward over the North Pacific, but some of it spread eastward enough to reach the port of Dutch Harbor. Sulfur dioxide injected into the upper atmosphere stayed aloft long enough to drift south and get caught in the mid-latitude wins that blow eastward across the lower forty eight United States. It was detected as far inland as Eastern Montana on the 17th. Mount Cleveland on Chuginadak Island and ninety miles west of Okmok burst into action on Monday with a 20,000 foot plume. Two eruptions at once is a rare event and will keep the state geologists busy for the next few weeks.

Alaska has more big, active volcanoes than the the rest of the United States combined. They can affect the global climate and crops, but you hear much less about them because most of them only directly endanger a small number of people. That is a function of how large and sparsely populated Alaska is. Umnak Island, for example is larger than Oahu in Hawaii. But while Oahu has almost nine hundred thousand people, Umnak has only thirty nine--not thirty nine thousand, just thirty nine thousand people. Although these volcanoes are on the end of the Aleutians closest to the mainland, they are still almost a thousand miles away from Anchorage. The tourists on the cruise ships sailing into Southeastern Alaska and Anchorage will not be aware that two volcanoes are erupting in the state unless they buy a local newspaper.

Okmok is a shadow of its former self. The current erupting cone sits inside the crater rim of a collapsed caldera almost exactly the same size as Crater Lake in Oregon. Okmok has apparently undergone two caldera collapses in the last 10,000 years. The earlier was around 6200 BC, or five hundred years before Mazama became Crater Lake. The more recent collapse was in about 400 BC. Both of those occurred while people were living in the Aleutians, possibly on that island.

How Not to Help Barack Obama Get Elected
by Melissa McEwan

Don't use the phrase "tar baby."

The End.

* * *
Now, someone in the senate office of Senator John Kerry (D-MA) put my new book on his summer reading list, 'k?


I'll just repeat what I said when Rep. Tom Davis (R-Va.) used the term back in May:
Cue the usual excuses about how Davis Kerry "didn't know" and "didn't intend" and blahbity-blahbity-blah. Except that Davis Kerry really, really, really should have known, given that almost exactly two years ago to the day, Tony Snow made his grand entrance as White House Press Hack by using the term tar baby not once, but twice, to a resulting shitstorm. Snow was followed soon thereafter by Mitt Romney using the term and being forced to apologize. And, if that weren't enough, the GOP nominee, John McCain, found himself apologizing for using the phrase just over a year ago.

[And, of course, ADD HERE what Davis pulled in May.]

So, unless Davis Kerry is completely and utterly detached from what's going on with prominent members of his own the opposition party, he ought to have, at some point, gotten the memo that "tar baby" is not a turn of phrase that has any place in public discourse in modern America. (Or private discourse, quite frankly.)It's not enough that the current Democratic nominee is giving me reasons not to vote for him or his stinking party; now the former nominee is, too.

[H/T to Renee of Womanist Musings, whose post you should read as well. "Six-Word Novel" concept nicked from The Heretik.]

Don't get any ideas, boys—Johnny Mac is spoken for!
Republican presidential candidate U.S. Senator John McCain (R-AZ) (L) arrives for a news conference with former U.S. President George Bush on a golf cart at former President Bush's residence on Walker's Point in Kennebunkport, Maine July 21, 2008. REUTERS/Brian Snyder (UNITED STATES)

With some now questioning whether The Dark Knight is the best movie of all time, I can't stand it anymore. Yes, it's one of those rare films that gets both popular and critical acclaim. It’s set new box office records. People talk about a posthumous Oscar for Heath Ledger. I went to see it last night with my son (who loves it and was seeing it for the third time).

I’ve got to say, I don’t see what all the fuss is about. I think it was a load of batcrap.

One of the few critics who panned the movie said it was a visually incoherent film. I didn’t quite know what that meant until I saw it and began thinking about why I thought it was so bad. Film is primarily a visual medium, and a good director should tell his story primarily through visuals. That’s even more imperative in a comic book movie, where the stories were originally told in images; no one buys a comic book (excuse me, graphic novel) because it has great dialogue. So the chief problem with this movie is that significant plot points are conveyed in quickly-spoken dialogue rather than in pictures.

Two major characters are kidnapped, but we don’t see the kidnapping or even see the aftermath of their abductions (i.e., no anguished spouses or coworkers realizing that so-and-so has disappeared).  Hostages are taken, but who are they?  I'm told that there was one quick line of dialogue that explained it, and I’m sure he’s right, but I missed it, and once again, there were no pictures to tell the story either of the hostage-taking or to explain who these people are.  In one scene, the Joker is in an interrogation room of a police station, and in the next he’s in a different room holding a knife to a cop’s throat.  How did that happen?  We don’t know.  Another character is apparently shot and killed, but not really—and we never find out if he planned to fake his own death, if it was a spur-of-the-moment improvisation, or if he was really even shot.

The script is a mess.  One major monologue appears to have been written without any reference to the film in which they are encased.  How else to explain the nice soliloquy by The Joker about how Batman and the police commissioner are all full of plans and schemes while he, The Joker, is not about plans but about chaos?  Didn’t the screen writers remember The Joker’s elaborate bank robbery plan which opens the film?  Or The Joker’s use of multiple vehicles and weapons during an attempt to kill one of the main characters?  Or his elaborate double-ferryboat explosion scheme?  Or his plan to force Batman to rescue one character or the other but not both?

The script introduces interesting ideas and characters and then drops them.  The inclusion of a subplot about a Chinese financier appears to have been inserted just to give the director the excuse to film Batman swooping around Hong Kong’s skyscrapers.  The idea of having costumed Batman wannabes trying to fight crime was a nice dig at fanboy enthusiasm, but it's dropped after the first third of the film.  The climactic final battle between Batman and The Joker ends, well, anticlimactically.  I couldn’t even remember what happened to The Joker at the end of the movie, until my son reminded me he was left hanging upside down off a building while Batman dashed off to fight evil elsewhere.  Instead of a dramatic arc, the filmmakers have given us a series of zigzags and squiggles.

What I liked about Batman Begins was its exploration of how Bruce Wayne came to be Batman.  That movie was all about characterization.  In this one, however, there is no characterization of anyone except The Joker—and his motivations are deliberately left unexplained.  He’s sort of an existential villain; he just is evil.  This isn’t a bad narrative choice; indeed, it makes The Joker all the more frightening because we don’t know what really motivates him or how he got to be the way he is.  The problem comes in when you drop him into a movie where no one else’s motivations are explained either, except in the most cartoonish two-dimensional terms.  At no time did I feel emotionally moved, because the filmmakers didn’t allow the audience any real points of emotional access to their characters.

Christian Bale has the unenviable job, for an actor, of trying to communicate from behind a mask.  While Hugo Weaving did that well in V for Vendetta by using his voice, whenever Bale dons the batcowl, he talks like he is incredibly constipated.  Without an expressive face or voice, what’s an actor to do?  Bale is much better as Bruce Wayne, when he talks normally and we can see his face and the many subtle and arch expressions that flit across it.

Was there ever an actress so ill-served by makeup, costuming and cinematography than Maggie Gyllenhaal in this movie?  You know those two lines that everyone has running vertically from their noses to their upper lips in the mustache area?  Gyllenthal’s are so prominently visible here as to make her look alien.  While she’s not a knockout under any circumstances, this film made her look almost dumpy, which was surely not its intention.  And she has absolutely zero romantic chemistry either of the two men her character is supposedly attracted to.

As to Heath Ledger, it’s clear that dying was an excellent career move for him.  He turns in a fine performance as The Joker, but it’s not amazing, it’s not extraordinary, it’s not astonishing.  He did a very good job with a mediocre script, and I think that had he not died everyone would recognize it as such.  Instead, he’s being praised to the high heavens.  Apparently death bumps you up one letter grade.

The chase and fight scenes are ho-hum and did not convey to me any sense of excitement or peril.  A lot of them are filmed in murky lighting, with the director using a lot of rapid-fire jump cuts to give the impression of much action and excitement rather than to actually tell what is happening in the action.  I couldn’t help but compare the action shots in this movie unfavorably to those of Vantage Point, another summer popcorn flick that for me succeeded in many areas where Batman failed.

I wanted to like this film.  I like Batman.  I was really in the mood for a summer movie.  Oh well.

Yes, the sad little cracker has met its undignified end, so stop pestering me. The cracker, the koran, and another surprise entry have been violated and are gone. You'll have to wait until tomorrow for the details, what little of them there are. I must quickly apologize to all you good Catholics who were hoping to attend Mass, since you can't anymore — I have been told many hundreds of times now that cracker abuse violates your right to practice your religion. I guess you'll have to adapt. Secular humanism is a good alternative, if you aren't already flocking to join the Mormons.

Anyway, I've got important things to do today. It's my oldest son's birthday, and I told him that as a gift to me him, I'd take myself him to see The Dark Knight. I sure hope the world doesn't end before the movie does.

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tags: Piping Plover, Charadrius melodus, birds, nature, Image of the Day

Piping Plover, Charadrius melodus, at Bolivar Flats, Texas.

Image: Joseph Kennedy, 15 July 2008 [larger view].

Nikon D200, Kowa 883 telescope with TSN-PZ camera eyepiece 1/640s f/8.0 at 1000.0mm iso400.

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Olivia Judson has, so far, posted four parts of her Darwin series. We ("we" meaning "bloggers' including myself) have already commented on some of these, but here is the entire series (so far, I hope there will be more) for ease of use:

Darwinmania!

An Original Confession

Let's Get Rid of Darwinism

A Natural Selection

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There are 51 new papers in PLoS ONE this week - check them out for stuff you are interested in (and post comments, notes and ratings and send trackbacks), but here are my personal picks:

Sample Size and Precision in NIH Peer Review:

The Working Group on Peer Review of the Advisory Committee to the Director of NIH has recommended that at least 4 reviewers should be used to assess each grant application. A sample size analysis of the number of reviewers needed to evaluate grant applications reveals that a substantially larger number of evaluators are required to provide the level of precision that is currently mandated. NIH should adjust their peer review system to account for the number of reviewers needed to provide adequate precision in their evaluations.

Measuring Co-Authorship and Networking-Adjusted Scientific Impact:

Appraisal of the scientific impact of researchers, teams and institutions with productivity and citation metrics has major repercussions. Funding and promotion of individuals and survival of teams and institutions depend on publications and citations. In this competitive environment, the number of authors per paper is increasing and apparently some co-authors don't satisfy authorship criteria. Listing of individual contributions is still sporadic and also open to manipulation. Metrics are needed to measure the networking intensity for a single scientist or group of scientists accounting for patterns of co-authorship. Here, I define I1 for a single scientist as the number of authors who appear in at least I1 papers of the specific scientist. For a group of scientists or institution, In is defined as the number of authors who appear in at least In papers that bear the affiliation of the group or institution. I1 depends on the number of papers authored Np. The power exponent R of the relationship between I1 and Np categorizes scientists as solitary (R>2.5), nuclear (R = 2.25-2.5), networked (R = 2-2.25), extensively networked (R = 1.75-2) or collaborators (R<1.75). R may be used to adjust for co-authorship networking the citation impact of a scientist. In similarly provides a simple measure of the effective networking size to adjust the citation impact of groups or institutions. Empirical data are provided for single scientists and institutions for the proposed metrics. Cautious adoption of adjustments for co-authorship and networking in scientific appraisals may offer incentives for more accountable co-authorship behaviour in published articles.

Circadian Genes Are Expressed during Early Development in Xenopus laevis:

Circadian oscillators are endogenous time-keeping mechanisms that drive twenty four hour rhythmic changes in gene expression, metabolism, hormone levels, and physical activity. We have examined the developmental expression of genes known to regulate circadian rhythms in order to better understand the ontogeny of the circadian clock in a vertebrate. In this study, genes known to function together in part of the core circadian oscillator mechanism (xPeriod1, xPeriod2, and xBmal1) as well as a rhythmic, clock-controlled gene (xNocturnin) were analyzed using in situ hybridization in embryos from neurula to late tailbud stages. Each transcript was present in the developing nervous system in the brain, eye, olfactory pit, otic vesicle and at lower levels in the spinal cord. These genes were also expressed in the developing somites and heart, but at different developmental times in peripheral tissues (pronephros, cement gland, and posterior mesoderm). No difference was observed in transcript levels or localization when similarly staged embryos maintained in cyclic light were compared at two times of day (dawn and dusk) by in situ hybridization. Quantitation of xBmal1 expression in embryonic eyes was also performed using qRT-PCR. Eyes were isolated at dawn, midday, dusk, and midnight (cylic light). No difference in expression level between time-points was found in stage 31 eyes (p = 0.176) but stage 40 eyes showed significantly increased levels of xBmal1 expression at midnight (RQ = 1.98+/−0.094) when compared to dawn (RQ = 1+/−0.133; p = 0.0004). We hypothesize that when circadian genes are not co-expressed in the same tissue during development that it may indicate pleiotropic functions of these genes that are separate from the timing of circadian rhythm. Our results show that all circadian genes analyzed thus far are present during early brain and eye development, but rhythmic gene expression in the eye is not observed until after stage 31 of development.

Disturbed Clockwork Resetting in Sharp-1 and Sharp-2 Single and Double Mutant Mice:

The circadian system provides the basis to anticipate and cope with daily recurrent challenges to maintain the organisms' homeostasis. De-synchronization of circadian feedback oscillators in humans causes 'jet lag', likely contributes to sleep - , psychiatric - , metabolic disorders and even cancer. However, the molecular mechanisms leading to the disintegration of tissue-specific clocks are complex and not well understood. Based on their circadian expression and cell culture experiments, the basic Helix-Loop-Helix (bHLH) transcription factors SHARP-1(Dec2) and SHARP-2(Stra13/Dec1) were proposed as novel negative regulators of the molecular clock. To address their function in vivo, we generated Sharp-1 and Sharp-2 single and double mutant mice. Our experiments reveal critical roles for both factors in regulating period length, tissue-specific control of clock gene expression and entrainment to external cues. Light-pulse experiments and rapid delays of the light-dark cycle (experimental jet lag) unravel complementary functions for SHARP-1 and SHARP-2 in controlling activity phase resetting kinetics. Moreover, we show that SHARP-1 and 2 can serve dual functions as repressors and co-activators of mammalian clock gene expression in a context-specific manner. This correlates with increased amplitudes of Per2 expression in the cortex and liver and a decrease in the suprachiasmatic nucleus (SCN) of double mutant mice. The existence of separate mechanisms regulating phase of entrainment, rhythm amplitude and period length has been postulated before. The differential effects of Sharp-deficiency on rhythmicity and behavioral re-entrainment, coupled to tissue-dependent regulatory functions, provide a new mechanistic basis to further understand the complex process of clock synchronizations.

Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity:

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene--or both--have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area.

Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense:

Many plants and animals are defended from predation or herbivory by inhibitory secondary metabolites, which in the marine environment are very common among sessile organisms. Among bacteria, where there is the greatest metabolic potential, little is known about chemical defenses against bacterivorous consumers. An emerging hypothesis is that sessile bacterial communities organized as biofilms serve as bacterial refuge from predation. By testing growth and survival of two common bacterivorous nanoflagellates, we find evidence that chemically mediated resistance against protozoan predators is common among biofilm populations in a diverse set of marine bacteria. Using bioassay-guided chemical and genetic analysis, we identified one of the most effective antiprotozoal compounds as violacein, an alkaloid that we demonstrate is produced predominately within biofilm cells. Nanomolar concentrations of violacein inhibit protozoan feeding by inducing a conserved eukaryotic cell death program. Such biofilm-specific chemical defenses could contribute to the successful persistence of biofilm bacteria in various environments and provide the ecological and evolutionary context for a number of eukaryote-targeting bacterial metabolites.

Changes in Gray Matter Induced by Learning--Revisited:

Recently, activation-dependant structural brain plasticity in humans has been demonstrated in adults after three months of training a visio-motor skill. Learning three-ball cascade juggling was associated with a transient and highly selective increase in brain gray matter in the occipito-temporal cortex comprising the motion sensitive area hMT/V5 bilaterally. However, the exact time-scale of usage-dependant structural changes occur is still unknown. A better understanding of the temporal parameters may help to elucidate to what extent this type of cortical plasticity contributes to fast adapting cortical processes that may be relevant to learning. Using a 3 Tesla scanner and monitoring whole brain structure we repeated and extended our original study in 20 healthy adult volunteers, focussing on the temporal aspects of the structural changes and investigated whether these changes are performance or exercise dependant. The data confirmed our earlier observation using a mean effects analysis and in addition showed that learning to juggle can alter gray matter in the occipito-temporal cortex as early as after 7 days of training. Neither performance nor exercise alone could explain these changes. We suggest that the qualitative change (i.e. learning of a new task) is more critical for the brain to change its structure than continued training of an already-learned task.

Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis:

Unisexual all-female lizards of the genus Darevskia that are well adapted to various habitats are known to reproduce normally by true parthenogenesis. Although they consist of unisexual lineages and lack effective genetic recombination, they are characterized by some level of genetic polymorphism. To reveal the mutational contribution to overall genetic variability, the most straightforward and conclusive way is the direct detection of mutation events in pedigree genotyping. Earlier we selected from genomic library of D. unisexualis two polymorphic microsatellite containg loci Du281 and Du215. In this study, these two loci were analyzed to detect possible de novo mutations in 168 parthenogenetic offspring of 49 D. unisexualis mothers and in 147 offspring of 50 D. armeniaca mothers . No mutant alleles were detected in D. armeniaca offspring at both loci, and in D. unisexualis offspring at the Du215 locus. There were a total of seven mutational events in the germ lines of four of the 49 D. unisexualis mothers at the Du281 locus, yielding the mutation rate of 0.1428 events per germ line tissue. Sequencing of the mutant alleles has shown that most mutations occur via deletion or insertion of single microsatellite repeat being identical in all offspring of the family. This indicates that such mutations emerge at the early stages of embryogenesis. In this study we characterized single highly unstable (GATA)n containing locus in parthenogenetic lizard species D. unisexualis. Besides, we characterized various types of mutant alleles of this locus found in the D. unisexualis offspring of the first generation. Our data has shown that microsatellite mutations at highly unstable loci can make a significant contribution to population variability of parthenogenetic lizards.

Universal Scaling in the Branching of the Tree of Life:

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

The Male Sex Pheromone of the Butterfly Bicyclus anynana: Towards an Evolutionary Analysis:

Female sex pheromones attracting mating partners over long distances are a major determinant of reproductive isolation and speciation in Lepidoptera. Males can also produce sex pheromones but their study, particularly in butterflies, has received little attention. A detailed comparison of sex pheromones in male butterflies with those of female moths would reveal patterns of conservation versus novelty in the associated behaviours, biosynthetic pathways, compounds, scent-releasing structures and receiving systems. Here we assess whether the African butterfly Bicyclus anynana, for which genetic, genomic, phylogenetic, ecological and ethological tools are available, represents a relevant model to contribute to such comparative studies. Using a multidisciplinary approach, we determined the chemical composition of the male sex pheromone (MSP) in the African butterfly B. anynana, and demonstrated its behavioural activity. First, we identified three compounds forming the presumptive MSP, namely (Z)-9-tetradecenol (Z9-14:OH), hexadecanal (16:Ald ) and 6,10,14-trimethylpentadecan-2-ol (6,10,14-trime-15-2-ol), and produced by the male secondary sexual structures, the androconia. Second, we described the male courtship sequence and found that males with artificially reduced amounts of MSP have a reduced mating success in semi-field conditions. Finally, we could restore the mating success of these males by perfuming them with the synthetic MSP. This study provides one of the first integrative analyses of a MSP in butterflies. The toolkit it has developed will enable the investigation of the type of information about male quality that is conveyed by the MSP in intraspecific communication. Interestingly, the chemical structure of B. anynana MSP is similar to some sex pheromones of female moths making a direct comparison of pheromone biosynthesis between male butterflies and female moths relevant to future research. Such a comparison will in turn contribute to understanding the evolution of sex pheromone production and reception in butterflies.

Neutrality and the Response of Rare Species to Environmental Variance:

Neutral models and differential responses of species to environmental heterogeneity offer complementary explanations of species abundance distribution and dynamics. Under what circumstances one model prevails over the other is still a matter of debate. We show that the decay of similarity over time in rocky seashore assemblages of algae and invertebrates sampled over a period of 16 years was consistent with the predictions of a stochastic model of ecological drift at time scales larger than 2 years, but not at time scales between 3 and 24 months when similarity was quantified with an index that reflected changes in abundance of rare species. A field experiment was performed to examine whether assemblages responded neutrally or non-neutrally to changes in temporal variance of disturbance. The experimental results did not reject neutrality, but identified a positive effect of intermediate levels of environmental heterogeneity on the abundance of rare species. This effect translated into a marked decrease in the characteristic time scale of species turnover, highlighting the role of rare species in driving assemblage dynamics in fluctuating environments.

Cheating on the Edge:

We present the results of an individual agent-based model of antibiotic resistance in bacteria. Our model examines antibiotic resistance when two strategies exist: "producers"-who secrete a substance that breaks down antibiotics-and nonproducers ("cheats") who do not secrete, or carry the machinery associated with secretion. The model allows for populations of up to 10,000, in which bacteria are affected by their nearest neighbors, and we assume cheaters die when there are no producers in their neighborhood. Each of 10,000 slots on our grid (a torus) could be occupied by a producer or a nonproducer, or could (temporarily) be unoccupied. The most surprising and dramatic result we uncovered is that when producers and nonproducers coexist at equilibrium, nonproducers are almost always found on the edges of clusters of producers.

Network Evolution of Body Plans:

One of the major goals in evolutionary developmental biology is to understand the relationship between gene regulatory networks and the diverse morphologies and their functionalities. Are the diversities solely triggered by random events, or are they inevitable outcomes of an interplay between evolving gene networks and natural selection? Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band development, respectively. Moreover, a combination of both is found in intermediate germ-band development. Regulatory genes relevant for stripe formation are evolutionarily conserved among arthropods, therefore the differences in the observed traits are thought to have originated from how the genes are wired. To reveal the basic differences in the network structure, we have numerically evolved hundreds of gene regulatory networks that produce striped patterns of gene expression. By analyzing the topologies of the generated networks, we show that the characteristics of stripe formation in long and short germ-band development are determined by Feed-Forward Loops (FFLs) and negative Feed-Back Loops (FBLs) respectively, and those of intermediate germ-band development are determined by the interconnections between FFL and negative FBL. Network architectures, gene expression patterns and knockout responses exhibited by the artificially evolved networks agree with those reported in the fly Drosophila melanogaster and the beetle Tribolium castaneum. For other arthropod species, principal network architectures that remain largely unknown are predicted. Our results suggest that the emergence of the three modes of body segmentation in arthropods is an inherent property of the evolving networks.

Does Pathogen Spillover from Commercially Reared Bumble Bees Threaten Wild Pollinators?:

The conservation of insect pollinators is drawing attention because of reported declines in bee species and the 'ecosystem services' they provide. This issue has been brought to a head by recent devastating losses of honey bees throughout North America (so called, 'Colony Collapse Disorder'); yet, we still have little understanding of the cause(s) of bee declines. Wild bumble bees (Bombus spp.) have also suffered serious declines and circumstantial evidence suggests that pathogen 'spillover' from commercially reared bumble bees, which are used extensively to pollinate greenhouse crops, is a possible cause. We constructed a spatially explicit model of pathogen spillover in bumble bees and, using laboratory experiments and the literature, estimated parameter values for the spillover of Crithidia bombi, a destructive pathogen commonly found in commercial Bombus. We also monitored wild bumble bee populations near greenhouses for evidence of pathogen spillover, and compared the fit of our model to patterns of C. bombi infection observed in the field. Our model predicts that, during the first three months of spillover, transmission from commercial hives would infect up to 20% of wild bumble bees within 2 km of the greenhouse. However, a travelling wave of disease is predicted to form suddenly, infecting up to 35-100% of wild Bombus, and spread away from the greenhouse at a rate of 2 km/wk. In the field, although we did not observe a large epizootic wave of infection, the prevalences of C. bombi near greenhouses were consistent with our model. Indeed, we found that spillover has allowed C. bombi to invade several wild bumble bee species near greenhouses. Given the available evidence, it is likely that pathogen spillover from commercial bees is contributing to the ongoing decline of wild Bombus in North America. Improved management of domestic bees, for example by reducing their parasite loads and their overlap with wild congeners, could diminish or even eliminate pathogen spillover. Read the comments on this post...

Commercial Bees Spreading Disease To Wild Pollinating Bees:

Bees provide crucial pollination service to numerous crops and up to a third of the human diet comes from plants pollinated by insects. However, pollinating bees are suffering widespread declines in North America and scientists warn that this could have serious implications for agriculture and food supply. While the cause of these declines has largely been a mystery, new research reveals an alarming spread of disease from commercial bees to wild pollinators.

Unique Fossil Discovery Shows Antarctic Was Once Much Warmer:

A new fossil discovery- the first of its kind from the whole of the Antarctic continent- provides scientists with new evidence to support the theory that the polar region was once much warmer.

New Population Of Highly Threatened Greater Bamboo Lemur Found In Madagascar:

Researchers in Madagascar have confirmed the existence of a population of greater bamboo lemurs more than 400 kilometers (240 miles) from the only other place where the Critically Endangered species is known to live, raising hopes for its survival.

Some Earthworms Make Septic Systems Work Better, Others Do The Opposite:

The right earthworms can make home septic systems work better. The wrong ones could do the opposite.

Hormone Oxytocin May Inhibit Social Phobia:

Swedish and British scientists have shown using functional magnetic resonance imaging (fMRI) that the hormone oxytocin can inhibit feelings of anxiety in specific individuals. Their discovery might lead to a better understanding and the improved treatment of psychiatric affections in which people feel distressed when meeting others, such as in cases of autism and social phobia.

Pollination Habits Of Endangered Texas Rice Revealed To Help Preservation:

A type of wild rice that only grows in a small stretch of the San Marcos River is likely so rare because it plays the sexual reproduction game poorly, a study led by the Lady Bird Johnson Wildflower Center at The University of Texas at Austin has revealed.

Genetics Of White Horses Unraveled: One Mutation Makes Ordinary Horses Turn Grey, Then White, Very Young:

The white horse is an icon for dignity which has had a huge impact on human culture across the world. An international team led by researchers at Uppsala University has now identified the mutation causing this spectacular trait and show that white horses carry an identical mutation that can be traced back to a common ancestor that lived thousands of years ago.

Environmental Factors Linked To Sex Ratio Of Plants Discovered:

Environmental factors can transform the ratio of females to males in plant populations according to new research out of the University of Toronto. Read the comments on this post...

I guess it takes one to know one.

The complexity of sharing scientific databases:

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it's protected until 70 years after your death. Facts, however, are another matter - they can't be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome - DNA sequences, for instance - aren't. But the containers they're stored in - the databases they're held in - can be copyrighted.

Breaking News: Open access to large-scale drug discovery data at EBI:

The Wellcome Trust has awarded £4.7 million to the European Bioinformatics Institute (EBI) to support the transfer of a large collection of information on the properties and activities of drugs and a large set of drug-like small molecules from BioFocus DPI, part of the publicly listed company Galapagos to the public domain.

What scientists are we talking about?:

This discussion seems to have focused on just a small fraction (but an important one) of the number of scientists who would benefit from these tools. These researchers are funded by grants and are in tenure-track positions at 4 year research universities.

More scientists work at non-profits. What sorts of pressures are brought to bear there to prevent open collaboration? How different are these pressures from a research university? Those in business might also benefit from these approaches but have another set of barriers. Can they be surmounted?

This discussion is really important but it also conflates a large number of scientists/engineers who have different needs and pressures. There are 12 million in business who will have different needs than the 1.6 million at research universities.

MedPedia Is Wikifying the Medical Search Space:

The medical industry is one that thrives on innovation and evolution. New procedures, medicines, diseases, and theories are released practically every day. In such an environment, the need for a website to reflect and allow for documentation is apparent.

Open Access to Health and Human Rights:

Here's another important step forward in the open access movement. Under its new editor Paul Farmer (who is often talked about as a future Nobel laureate), the international journal Health and Human Rights (HHR) has become fully open access.

The entire contents are freely available and are published under a progressive copyright license that allows readers to reuse the materials for any legal non-commercial purpose.

Indexing Institutional Repositories and Authors Self-Archived Collections:

The question then is whether or not ChemSpider can index institutional repositories or authors self-archived collections on their university research group websites. The authors self-archived collections will be very valuable but of course most likely to upset the publishers. We'd like to do both.

I envisage a time when articles are indexed and searchable even before they are published and indexed by others. Why not? If there are changes to the article between pre-and post-publication both can be indexed.

Another Wiki, WikiPathways:

I've already made known my "skeptical optimism" for wikis for biological data known in a previous post, reading this later paper, that would still apply here. But right now I'm not going to write beyond that, I'm just going to point you to this paper and wiki. Later (this week, next at the latest) I'll be critiquing this paper more fully and more generally look at this trend currently to use wikis for community curation and documentation of biological data and databases.

Tracking the openness of databases:

Shirley Fung has launched Molecular Biology Databases, a website to evaluate the openness of databases in molecular biology.

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Fung evaluates 34 databases to date, under six criteria: Downloadable, Offers Batch Processing, Offers a Query Interface, No Registration Required, Policy is Available, Public Domain. Her website supports the open-data research of Melanie Dulong de Rosnay, described last week by Ethan Zuckerman (and blogged here).

This is a very time-consuming but useful job. Everyone in molecular biology should be grateful, especially if the project leads to more consistent policies on open data across the field.

Fair game: a grad student's adventures in fair use and copyright:

For scholars who study media, the internet has broadened research horizons and expanded the reach of teaching and publications. But powerful gatekeepers remain. From academic journals seeking to control our intellectual property to lawyers crying foul when we quote from copyrighted material, we are bombarded with a myriad of confusing and dubious restrictions. In short, the implied threat of legal action creates a chilling effect that impacts us all. Some have pushed back, arguing that our educational activities are protected under the "fair use" statute. But this is a risky game to play. The rules aren't always clear. And when it comes to fair use, we either use it, or lose it.

Where should we spend our money?:

The lesson here seems to be that the digital environment is inevitably going to change the environment for textbooks as it has for most other kinds of intellectual property, for good or for ill. Georgia seems to feel that the publishers will eventually figure the market out and move to new profit models while supporting open access. But I think there is also an opportunity here for institutions to be more proactive and seek ways to invest in open access textbooks on a campus-wide level.

STM publishers imprisoned in their own walled gardens?:

Journals aggregate interesting science - many scientists still very much like a group of qualified editors and peer reviewers providing a filter on the deluge. Secondly, while knowledge discovery requires unfettered access for machines to content, I don't see why that necessarily implies unfettered access for humans. You can perfectly well have an API that lets machines mine full-text, while still putting up a paywall for humans. As well, I think the versions issue is very challenging, and we are a long way from reliable automatic disambiguation and identification of authoritative copies. Finally, many conference proceedings already are peer-reviewed, and we can certainly imagine peer review extending to other areas, such as data sets.

History of the Journal Nature:

Nature introduced their formal peer review system in... 1967!

Who comments on scientific papers - and why?:

The quality of comments at BMC is high and the vast majority add value to the paper, though the numbers involved are relatively low (would a larger audience reading higher impact papers be different?).

Perhaps unsurprisingly comments on papers are not like comments on blogs; they're far more formal (only 8% of comments were of the chatty, supportive variety) and it's not the same people coming back each time (with the exception of the crazy 2%).

Read the comments on this post...

Olivia Judson has a lovely article about ongoing examples of evolution.

Before the creationists start whining, I know — they're still birds and lizards and flies. Get over it. They've changed, as evolution predicts.

Read the comments on this post...

The recipe this week comes from Shaker datacine for all the sashimi lovers out there:
Hawaiian Ahi Poke (Hawaiian Sashimi)
1 lb. Sashimi Grade Tuna
1/2 Cup Soy Sauce
1/2 cup sliced Scallions
1 TBS Sesame Oil
1 1/2 TSP Toasted Sesame Seeds
Crushed Red Peppers to taste
1 TBS finely chopped Macadamia Nuts

Cut tuna to 1/2" to 3/4" cubes. This can be done more easily if you put the piece of tuna (this works or any meat you need to cut raw) into the freezer for about 20 to 30 minutes. The meat will get just frozen enough to be easily cut. In a medium size ceramic bowl, combine Ahi, soy sauce, onions, sesame oil, sesame seeds, chili pepper, and macadamia nuts, and mix well. Chill at least 2 hours before serving.
He notes: "You may play with the amounts of soy to oil. More oil less soy, whatever your taste requires. NO RULES!!!! Use Tamari or any other good soy sauce. Enjoy with a nice lager of your choice."

John and Linda Johnson, parents of PFC LaVena Lynn Johnson, were interviewed on Democracy Now! by host Amy Goodman. Activist and retired Army colonel Ann Wright was also part of the program.

Three years ago, on July 19, 2005, Army Private First Class LaVena Johnson was found dead in Balad, Iraq. Her body was found in a tent belonging to the private military contractor KBR. She had abrasions all over her body, a broken nose, a black eye, burned hands, loose teeth, acid burns on her genitals, and a bullet hole in her head. The Army labeled Johnson’s death a suicide. But her parents never believed that story. They think she was raped and murdered and are now demanding a full congressional investigation into their daughter’s death.The program is available at the Democracy Now! site for viewing or listening in a number of formats: Real Video stream, Real Audio stream, MP3 download, and others. A partial transcript is up as well; I expect a full version will be made available later.

What's the frequency, Shakers?

Recommended Reading:

Ginger: The 61st Carnival of Feminists

Mannion: That Voyeur Thing

Amanda T: What's Next for the Netroots?

PSoTD: The Presidential Debates

Cara: Bill O'Reilly Is Getting Desperate

The Rotund: Flying While Fat

Autumn: In Uniformed Employment, Should Government Enforce Societal Gender Norms?

Leave your links in comments...

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here's a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there's about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

(Click for larger image)
Vertebral formula and somitogenesis in the corn snake. a, Alizarin staining of a corn snake showing 296 vertebrae, including 3 cervical, 219 thoracic, 4 cloacal (distinguishable by their forked lymphapophyses) and 70 caudal. b, Time course of corn snake development after egg laying (118-somite embryo on the far left) until the end of somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

Read the rest of this post... | Read the comments on this post...