Yearly Archives: 2007

Marbles and Orange Julius

These were taken the day after the pseudo-move, as soon as the cats came back from a weekend at the vet. Biscuit was hiding, but the other two explored the new environs:
Marbles%20head.jpg
Julius.jpg

Check the NYTimes Election Guide on Climate Change

What all the candidates are saying.

New and Exciting in PLoS ONE

Steve Irwin’s last paper is not the only exciting article to appear on PLoS ONE today – there are 40 more, and here are a few I am excited about – a veritable embarassment of riches! When am I ever going to find time to read them all!
Oxytocin in the Circadian Timing of Birth (hey, it’s by Erik Herzog, so you know I’ll blog about this paper in a separate post later):

Very little is known about the molecular components that determine the timing for birth in mammals. This study compares the timing of births between mice with and without the chemical oxytocin (OT) when exposed to shifts in the light cycle. The results show that OT-deficient mice give birth at random times throughout the light cycle, while mice with OT maintain a normal clustered birth profile, thus suggesting that oxytocin is necessary in the timing of birth.

A Visual Pathway Links Brain Structures Active during Magnetic Compass Orientation in Migratory Birds:

The magnetic compass of migratory birds has been suggested to be light-dependent. Retinal cryptochrome-expressing neurons and a forebrain region, “Cluster N”, show high neuronal activity when night-migratory songbirds perform magnetic compass orientation. By combining neuronal tracing with behavioral experiments leading to sensory-driven gene expression of the neuronal activity marker ZENK during magnetic compass orientation, we demonstrate a functional neuronal connection between the retinal neurons and Cluster N via the visual thalamus. Thus, the two areas of the central nervous system being most active during magnetic compass orientation are part of an ascending visual processing stream, the thalamofugal pathway. Furthermore, Cluster N seems to be a specialized part of the visual wulst. These findings strongly support the hypothesis that migratory birds use their visual system to perceive the reference compass direction of the geomagnetic field and that migratory birds “see” the reference compass direction provided by the geomagnetic field.

Do Individual Females Differ Intrinsically in Their Propensity to Engage in Extra-Pair Copulations?:

While many studies have investigated the occurrence of extra-pair paternity in wild populations of birds, we still know surprisingly little about whether individual females differ intrinsically in their principal readiness to copulate, and to what extent this readiness is affected by male attractiveness.
To address this question I used captive zebra finches (Taeniopygia guttata) as a model system. I first measured female readiness to copulate when courted by a male for the first time in life. Second, I conducted choice-chamber experiments to assess the mating preferences of individual females prior to pair formation. I then paired females socially with a non-desired mate and once they had formed a stable pair bond, I observed the inclination of these females to engage in extra-pair copulations with various males. Females showing a high readiness to copulate when courted by a male for the first time in life were much more likely to engage in extra-pair copulations later in life than others. Male attractiveness, as measured in choice tests, was a useful predictor of whether females engaged in extra-pair copulations with these males, but, surprisingly, the attractiveness of a female’s social partner had no effect on her fidelity. However, it remained unclear what made some males more attractive than others. Contrary to a widespread but rarely tested hypothesis, females did not preferentially copulate with males having a redder beak or singing at a higher rate. Rather it seemed that song rate was a confounding factor in choice-chamber experiments: song attracted the female’s attention but did not increase the male’s attractiveness as a copulation partner.
Intrinsic variation in female readiness to copulate as well as variation in the attractiveness of the extra-pair male but not the social partner decided the outcome of extra-pair encounters.

Evolution of Female Preference for Younger Males:

Previous theoretical work has suggested that females should prefer to mate with older males, as older males should have higher fitness than the average fitness of the cohort into which they were born. However, studies in humans and model organisms have shown that as males age, they accumulate deleterious mutations in their germ-line at an ever-increasing rate, thereby reducing the quality of genes passed on to the next generation. Thus, older males may produce relatively poor-quality offspring. To better understand how male age influences female mate preference and offspring quality, we used a genetic algorithm model to study the effect of age-related increases in male genetic load on female mate preference. When we incorporate age-related increases in mutation load in males into our model, we find that females evolve a preference for younger males. Females in this model could determine a male’s age, but not his inherited genotype nor his mutation load. Nevertheless, females evolved age-preferences that led them to mate with males that had low mutation loads, but showed no preference for males with respect to their somatic quality. These results suggest that germ-line quality, rather than somatic quality, should be the focus of female preference in good genes models.

Causal Inference in Multisensory Perception:

Perceptual events derive their significance to an animal from their meaning about the world, that is from the information they carry about their causes. The brain should thus be able to efficiently infer the causes underlying our sensory events. Here we use multisensory cue combination to study causal inference in perception. We formulate an ideal-observer model that infers whether two sensory cues originate from the same location and that also estimates their location(s). This model accurately predicts the nonlinear integration of cues by human subjects in two auditory-visual localization tasks. The results show that indeed humans can efficiently infer the causal structure as well as the location of causes. By combining insights from the study of causal inference with the ideal-observer approach to sensory cue combination, we show that the capacity to infer causal structure is not limited to conscious, high-level cognition; it is also performed continually and effortlessly in perception.

Antagonistic Bacterial Interactions Help Shape Host-Symbiont Dynamics within the Fungus-Growing Ant-Microbe Mutualism:

Conflict within mutually beneficial associations is predicted to destabilize relationships, and theoretical and empirical work exploring this has provided significant insight into the dynamics of cooperative interactions. Within mutualistic associations, the expression and regulation of conflict is likely more complex than in intraspecific cooperative relationship, because of the potential presence of: i) multiple genotypes of microbial species associated with individual hosts, ii) multiple species of symbiotic lineages forming cooperative partner pairings, and iii) additional symbiont lineages. Here we explore complexity of conflict expression within the ancient and coevolved mutualistic association between attine ants, their fungal cultivar, and actinomycetous bacteria (Pseudonocardia). Specifically, we examine conflict between the ants and their Pseudonocardia symbionts maintained to derive antibiotics against parasitic microfungi (Escovopsis) infecting the ants’ fungus garden. Symbiont assays pairing isolates of Pseudonocardia spp. associated with fungus-growing ants spanning the phylogenetic diversity of the mutualism revealed that antagonism between strains is common. In contrast, antagonism was substantially less common between more closely related bacteria associated with Acromyrmex leaf-cutting ants. In both experiments, the observed variation in antagonism across pairings was primarily due to the inhibitory capabilities and susceptibility of individual strains, but also the phylogenetic relationships between the ant host of the symbionts, as well as the pair-wise genetic distances between strains. The presence of antagonism throughout the phylogenetic diversity of Pseudonocardia symbionts indicates that these reactions likely have shaped the symbiosis from its origin. Antagonism is expected to prevent novel strains from invading colonies, enforcing single-strain rearing within individual ant colonies. While this may align ant-actinomycete interests in the bipartite association, the presence of single strains of Pseudonocardia within colonies may not be in the best interest of the ants, because increasing the diversity of bacteria, and thereby antibiotic diversity, would help the ant-fungus mutualism deal with the specialized parasites.

Do Haematophagous Bugs Assess Skin Surface Temperature to Detect Blood Vessels?:

It is known that some blood-sucking insects have the ability to reach vessels under the host skin with their mouthparts to feed blood from inside them. However, the process by which they locate these vessels remains largely unknown. Less than 5% of the skin is occupied by blood vessels and thus, it is not likely that insects rely on a “random search strategy”, since it would increase the probability of being killed by their hosts. Indeed, heterogeneities along the skin surface might offer exploitable information for guiding insect’s bites.
We tested whether the bug Rhodnius prolixus can evaluate temperature discontinuities along the body surface in order to locate vessels before piercing the host skin. When placed over a rabbit ear, the bug’s first bites were mostly directed towards the main vessels. When insects were confronted to artificial linear heat sources presenting a temperature gradient against the background, most bites were directly addressed to the warmer linear source, notwithstanding the temperature of both, the source and the background. Finally, tests performed using uni- and bilaterally antennectomized insects revealed that the bilateral integration of thermal inputs from both antennae is necessary for precisely directing bites.
R. prolixus may be able to exploit the temperature differences observed over the skin surface to locate blood vessles. Bugs bite the warmest targets regardless of the target/background temperatures, suggesting that they do not bite choosing a preferred temperature, but select temperature discontinuities along the skin. This strategy seems to be an efficient one for finding blood vessels within a wide temperature range, allowing finding them on different hosts, as well as on different areas of the host body. Our study also adds new insight about the use of antennal thermal inputs by blood sucking bugs.

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks:

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

Also:
Lactate, Fructose and Glucose Oxidation Profiles in Sports Drinks and the Effect on Exercise Performance
Cultural Diversity, Economic Development and Societal Instability
Stochastic Species Turnover and Stable Coexistence in a Species-Rich, Fire-Prone Plant Community
Global Patterns of City Size Distributions and Their Fundamental Drivers
Children’s Health Status: Examining the Associations among Income Poverty, Material Hardship, and Parental Factors
As always: read, rate, comment, annotate, use and reuse and, if you blog about the PLoS ONE papers, try to use the correct form of the URL in order to generate a trackback.

Last paper by Steve Irwin!

Just published about an hour ago (if it was in hardcopy, it would still be hot off the presses). And it is a wonderful paper! Australian crocs can and will travel much longer distances than was previously thought and their homing instinct is strong and navigational capacity excellent, even in a case where a large obstacle (Cape York Peninsula) needed to be navigated around:
Satellite Tracking Reveals Long Distance Coastal Travel and Homing by Translocated Estuarine Crocodiles, Crocodylus porosus:

Crocodiles are widely distributed and can usually be found in remote areas, however very little is known about their movements on a larger scale. In this study, Read and colleagues (including the late Steve Irwin) use satellite tracking to report the movements of three large male crocodiles, which were relocated up to 411km from their capture sites in Northern Australia. The results show that each crocodile returned to its original capture site within days, indicating that homing abilities are present amongst crocodiles.

croc.jpg
Can you imagine anyone doing this work without Steve Irwin? Who else would be able to grab a big croc, attach a satellite tracker, load it and unload it some hundreds of miles away, then follow their movements on the computer screen? Would you dare ask your grad students to do that?

Computational Biology around the world

Johanna Dehlinger writes:

In September, PLoS Computational Biology begins a series entitled “Developing Computational Biology” about the pursuit of scientific endeavors in computational biology around the world. Each country has unique features in areas from educational programs, types of research being undertaken and the ways that research is funded. The series starts with a perspective on computational biology in Mexico, followed by contributions about Brazil, Cuba, Argentina, China, and South Africa.

This will be interesting to watch – tune in.

Come to ConvergeSouth

This is why you should attend ConvergeSouth. OK, Anton will lead a session, and so will I, but check out the entire program – it is just getting more and more amazing every year! And it is probably the most pleasant and enjoyable conference in any given year.

Brian Russell is now a Social Software and Multimedia Consultant for Hire

And it is hard to find anyone better than Brian:

I am now available for hire to consult on the creation, care, and feeding of online communities. Plus I can create audio and video for the web. To get an idea of my professional experience you can check out my resume here and my portfolio here.
————————-
I’m interested in working for non-profits, businesses, and progressive political campaigns. I can help you make your own media and demonstrate how it will strengthen your mission and benefit your organization financially. But most important is communicating with customers, members, and constituents. Please contact me and I’ll help you accomplish your goals.

Today’s Carnivals

What’s Up, Postdoc? September Carnival is up on … ponderings of a fool.
Grand Rounds is starting its 4th year of existence up on Kevin MD’s blog. Congratulations!
Carnival of the Green #96 is up on Karavans.

New and Exciting in PLoS Medicine and PLoS Biology

A bunch of new articles got published in PLoS Medicine and PLoS Biology yesterday. Here are my two picks, and you go and check the rest:
Brain Dynamics Underlying the Nonlinear Threshold for Access to Consciousness:

Understanding the neural mechanisms that distinguish between conscious and nonconscious processes is a crucial issue in cognitive neuroscience. In this study, we focused on the transition that causes a visual stimulus to cross the threshold to consciousness, i.e., visibility. We used a backward masking paradigm in which the visibility of a briefly presented stimulus (the “target”) is reduced by a second stimulus (the “mask”) presented shortly after this first stimulus. (Human participants report the visibility of the target.) When the delay between target and mask stimuli exceeds a threshold value, the masked stimulus becomes visible. Below this threshold, it remains nonvisible. During the task, we recorded electric brain activity from the scalp and reconstructed the cortical sources corresponding to this activity. Conscious perception of masked stimuli corresponded to activity in a broadly distributed fronto-parieto-temporal network, occurring from about 300 ms after stimulus presentation. We conclude that this late stage, which could be clearly separated from earlier neural events associated with subliminal processing and mask-target interactions, can be regarded as a marker of consciousness.

The Absolute Risk of Venous Thrombosis after Air Travel: A Cohort Study of 8,755 Employees of International Organisations:

Background.
Blood normally flows smoothly throughout the human body, supplying the brain and other vital organs with oxygen and nutrients. When an injury occurs, proteins called clotting factors make the blood gel or coagulate at the injury site. The resultant blood clot (thrombus) plugs the wound and prevents blood loss. Sometimes, however, a thrombus forms inside an uninjured blood vessel and partly or completely blocks the blood flow. A clot inside one of the veins (vessels that take blood to the heart) deep within the body is called a deep vein thrombosis (DVT). Symptoms of DVT (which usually occurs in the deep veins of the leg) include pain, swelling, and redness in one leg. DVT is usually treated with heparin and warfarin, two anticoagulant drugs that stop the blood clot growing. If left untreated, part of the clot (an embolus) can break off and travel to the lungs, where it can cause a life-threatening condition called pulmonary embolism (PE). Fortunately, DVT and PE are rare but having an inherited blood clotting disorder, taking an oral contraceptive, and some types of surgery are all risk factors for them. In addition, long-haul plane travel increases the risk of DVT and PE, known collectively as venous thrombosis (VT) 2- to 4-fold, in part because the enforced immobilization during flights slows down blood flow.
Why Was This Study Done?
Although the link between air travel and VT was first noticed in the 1950s, exactly how many people will develop DVT and PE (the absolute risk of developing VT) after a long flight remains unknown. This information is needed so that travelers can be given advice about their actual risk and can make informed decisions about trying to reduce that risk by, for example, taking small doses of anticoagulant medicine before a flight. In this study, the researchers have determined the absolute risk of VT during and after long-haul air travel in a large group of business travelers.
What Did the Researchers Do and Find?
The researchers enrolled almost 9,000 employees from several international companies and organizations and followed them for an average of 4.4 years. The details of flights taken by each employee were obtained from company records, and employees completed a Web-based questionnaire about whether they had developed VT and what risk factors they had for the condition. Out of 53 thrombi that occurred during the study, 22 occurred within eight weeks of a long-haul flight (a flight of more than four hours). From this and data on the total time employees spent on long-haul flights, the researchers calculated that these flights tripled the risk of developing VT, and that the absolute risk (the probability of something occurring in a certain time period) of a VT occurring shortly after such travel was one event per 4,656 flights. They also calculated that the risk of VT was increased by exposure to more flights during a short period and to longer flights and was greatest in the first two weeks after a flight. In addition, the risk of VT was particularly high in young employees, women taking oral contraceptives, and people who were short, tall or overweight.
What Do These Findings Mean?
The main finding of this study is that the absolute risk of VT after of a long-haul flight is low–only one passenger out of nearly 5,000 is likely to develop VT because of flying. However, the study included only healthy people without previous VT whose average age was 40 years, so the absolute risk of VT after long-haul flights might be higher in the general traveling population. Even so, this finding strongly suggests that prophylactic (preventative) use of anticoagulants by all long-haul travelers may not be justified because these drugs have potentially dangerous side effects (for example, they can cause uncontrolled bleeding). Subgroups of travelers with additional risk factors for VT might, however, benefit from the use of this and other prophylactic measures, but randomized trials are needed to find out who would benefit most from which prophylactic measure.

My picks from ScienceDaily

If You Want More Babies, Find A Man With A Deep Voice:

Men who have lower-pitched voices have more children than do men with high-pitched voices, researchers have found. And their study suggests that for reproductive-minded women, mate selection favours men with low-pitched voices.

Spaceflight Can Change Bacteria Into More Infectious Pathogens:

Space flight has been shown to have a profound impact on human physiology as the body adapts to zero gravity environments.

Making Bicycles That Balance Better:

For nearly 150 years, scientists have been puzzled by the bicycle. How on earth is it possible that a moving bicycle can, all by itself, be so stable? Researchers of the Delft University of Technology (TU Delft), working with colleagues from Cornell University and the University of Nottingham, UK, believe they have now found the ultimate model of the bicycle.

How Does The Brain Develop During Embryogenesis?:

One of the great questions of neurobiology, how the brain is built up during embryonic development, could be resolved by a young French scientist in an award winning project organised by the European Science Foundation (ESF) and the European Heads of Research Councils (EuroHORCS).

Controlling For Size May Also Prevent Cancer:

Scientists at Johns Hopkins recently discovered that a chemical chain reaction that controls organ size in animals ranging from insects to humans could mean the difference between normal growth and cancer.

New Dinosaur Species Found In Montana:

A dinosaur skeleton found 24 years ago near Choteau has finally been identified as a new species that links North American dinosaurs with Asian dinosaurs. The dinosaur would have weighed 30 to 40 pounds, walked on two feet and stood about three feet tall. The fossil came from sediment that’s about 80 million years old.

Hormone Therapy Boosts Sexual Interest But Not Memory, Study Suggests:

Hormone therapy in early post-menopause increases sexual interest, but does not improve memory, according to a new study. “Contrary to what we predicted, hormone therapy did not have a positive affect on memory performance in younger mid-life women,” said Pauline Maki, associate professor of psychiatry and psychology at the University of Illinois at Chicago, who led the study.

ClockQuotes

While reason is puzzling itself about mystery, faith is turning it to daily bread, and feeding on it thankfully in her heart of hearts.
– F. D. Huntington

Fungus eats radiation for breakfast at Chernobyl!

Sarah Wallace, Matt Ford, ScienceGoGo and Jason Stajich comment on the fungus that gets its energy from radiation. I’ve heard of Deinococcus radiodurans before, but this is a fungus! Well, if there is an energy source to tap into, even if it is in the middle of Chernobyl, some life form is likely to find a way to do it.

Today’s Carnivals

Encephalon #32 is up on Living the Scientific Life.
Gene Genie #16 is up on Neurophilosophy.

ClockQuotes

Come out of the circle of time
And into the circle of love.

– Jalal-Uddin Rumi

Foodblogging and the post-foodblogging science-blogging dinner

The three-day Foodblogging event has started, with a reading/booksigning by Michael Ruhlman at the Regulator bookshop in Durham.
Among those in the audience were Reynolds Price, local bloggers Anton Zuiker and Brian Russell, as well as Anna Kushnir, foodblogger who drove all the way from Boston (OK, via Virginia) to attend the event.
I bought The Reach of a Chef and asked him what is the best way to get a kid/teenager who is interested in cooking started. He said that hands-on experience is essential and that one should carefully pick a course that focuses on basics and not on fancy gimmicks to begin with. Then, asking to taste a dinner at home and praising the result is the next step. Anton wrote a more detailed account of the evening.
After the reading, a bunch of us went accross the street to Baba Ganoush for dinner (and even later to the sushi bar on the corner for some Guinness) – but this time we quickly switched the topic from food to science as everyone at the table was a science blogger! Anna Kushnir, who I mentioned above (and linked to her food blog) is also a science blogger on Nature Network, so check out her Lab Life blog. You also know the other locals, Sheril Kirshenbaum and Abel Pharmboy, but the special guest of the evening was Craig McClain who came all the way from California to do some work at NESCENT. Much marine science talk ensued, all interesting and I learned a lot of stuff I did not know before.
Here is one of the pictures from the dinner:
Post-foodblogging%20science-dinner.jpg

Songs not to sing at weddings

Last night at the wedding, DJ went around asking for song suggestions and I thought back about Serbian weddings and how many songs there are that are inappropriate for weddings there – so many songs are sad, melancholic romances about lost loves, about lives lost in alcohol after the only loved one got married to someone else. Heck, just a brief look at songs by Djordje Balasevic (aka George Nationale) reveals several of those, so I found a couple on YouTube and posted them under the fold for my Balkan readers – the lyrics are very difficult to translate as he loves to use localisms, archaisms and words and imagery that make sense only in the local context.
The first one is a clip from a movie made by a friend of mine Zoran Amar, which aired on Belgrade TV in the early 1980s and consisted entirely of clips of Djordje’s songs. The others are from more recent concerts (wow – he’s gotten old since I last saw him!). Of all the ex-Yugoslav artists, Djordje (with whom I apparently share the birthday) was the only one who had concerts during the 1990s (during all the wars) in all the ex-Yugoslav states: Bosnia, Croatia, Serbia, Slovenia, Macedonia…and in each of those places had thousands come and sing along – everyone over there knows every word of every song of his. I used to play all of his songs at parties. I made people cry singing the song from the second clip…certainly not for weddings!

Continue reading

Raleigh News and Observer on Anton Zuiker, Triangle bloggers, Science Blogging Conference

I was out and offline all day yesterday, so I missed this wonderful article by Dan Barkin in yesterdays’ N&O (I just took the paper out of its plastic bag a few minutes ago):
Bloggers to talk science.
It tells you where Anton Zuiker comes from and where he is going next. The killer paragraph is this one:

The Web has evolved into a tribal Internet of passionate bloggers like Zuiker, and he has become a sort-of local brand. He’s a quiet visionary. He’s a low-key doer. He’s a let’s-get-together-and-see-where-this-goes guy. It’s the Zuikers of this new, interwoven world who may play a significant role in determining how far Web 2.0 goes from being a sociable network to a social force.

That is so true! Without Anton, there would be no Triangle blogger meetups, no BloggerCon, no Podcastercon, no Foodblogging, no Storyblogging and no Science Blogging Conference. Sure, Brian, Paul, myself and others may come up with a cool idea here and there, but those ideas would go nowhere without Anton’s calm persistence (and don’t get me wrong, Anton has a dozen cool ideas before breakfast every day himself) – he makes things actually happen in the real world.
Definitely go and read the entire thing! And also read what Paul, Brian and Abel wrote about the article as well. Of course, go say Hello to Anton himself, and see all the things he’s been doing lately on BlogTogether.org.
And I hope to see you at the Foodblogging event tonight.

Today’s Carnivals

The XVIth edition of Radiology Grand Rounds is up on Sumer’s Radiology Site.
Friday Ark #157 is up on The Modulator.

ClockQuotes

It is common error to infer that things which are consecutive in order of time have necessarily the relation of cause and effect.
– Jacob Bigelow

ClockQuotes

It seems a long time since the morning mail could be called correspondence.
– Jacques Barzun

Weekend!

Wow – this was a busy and exhausting week! But Trackbacks are in place and (mostly) working.
I did not even have time to unpack everything from last weekend’s pseudo-move – the house is nice and clean but still looks like a war-zone.
And tomorrow I am teaching Lab 3 (out of 4) in the morning and going to a wedding in the afternoon.
Sunday is the beginning of the Foodblogging event and I’ll also meet some science bloggers in the evening.
Blogging? Backburner until Monday, most likely….
In the meantime, learn how to draw a magpie.

My picks from ScienceDaily

How The Brain Handles Surprise, Good And Bad:

Whether it’s a mugger or a friend who jumps out of the bushes, you’re still surprised. But your response–to flee or to hug–must be very different. Now, researchers have begun to distinguish the circuitry in the brain’s emotion center that processes surprise from the circuitry that processes the aversive or reward “valence” of a stimulus. C. Daniel Salzman and colleagues published their findings in the journal Neuron.

Official Kilogram Losing Mass: Scientists Propose Redefining It As A Precise Number Of Carbon Atoms:

How much is a kilogram? It turns out that nobody can say for sure, at least not in a way that won’t change ever so slightly over time. The official kilogram — a cylinder cast 118 years ago from platinum and iridium and known as the International Prototype Kilogram or “Le Gran K” — has been losing mass, about 50 micrograms at last check. The change is occurring despite careful storage at a facility near Paris.

The Science Of Collective Decision-making:

Why do some juries take weeks to reach a verdict, while others take just hours? How do judges pick the perfect beauty queen from a sea of very similar candidates? We have all wondered exactly why we did not win a certain award. Now, new psychological research explains how groups come to a collective decision.

Understanding The Neuron’s Green Architecture:

Being green is a lifestyle. Turns out, each of your neurons is deeply committed to that green lifestyle – and you didn’t even know it. In just a thousandth of a second, a neuron can dump up to 5,000 molecules of its chemical messenger – a neurotransmitter – into the synapse, where it will trigger an impulse in a neighboring nerve cell. The neuron is a recycler par excellence when it comes to these neurotransmitters. Neurons must not only ready neurotransmitter receptors to receive the signals coming fast and furious, but they must also recycle receptors that have been used. And you thought you had recycling problems?

Biologists Expose Hidden Costs Of Firefly Flashes: Risky Balance Between Sex And Death:

A new study by biologists at Tufts University has discovered a dark side lurking behind the magical light shows put on by fireflies each summer. Using both laboratory and field experiments to explore the potential costs of firefly courtship displays, the biologists have uncovered some surprising answers.

Bioluminescence Genes Found Through Metagenomic Study Of Deep Mediterranean:

Metagenomics is a revolutionary approach to study microbes. Rather than isolating pure cultures, the power of high-throughput sequencing is applied directly to environmental samples to obtain information about the genomes of the prokaryotic cells present in a specific habitat studied. The ocean is an ideal subject of this approach because of its enormous microbiota, whose biomass equals that of all other living organisms on earth is mostly microbial, and also because most of these microbes are extremely fastidious to cultivate.

New Strategy To Create Genetically-modified Animals Developed:

Researchers at the University of Pennsylvania School of Veterinary Medicine have demonstrated the potential of a new strategy for genetic modification of large animals. The method employs a harmless gene therapy virus that transfers a genetic modification to male reproductive cells, which is then passed naturally on to offspring.

The Petri Dish Is Taken To New Dimensions:

A team of Brown University biomedical engineers has invented a 3-D Petri dish that can grow cells in three dimensions, a method that promises to quickly and cheaply produce more realistic cells for drug development and tissue transplantation.

Scientific Nursing Top Gives Breastfeeding Babies A Brain Workout:

Breastfeeding babies could become smarter thanks to a scientifically designed ‘clever baby’ nursing top recently revealed by the University of Portsmouth.

New Understanding Of Basic Units Of Memory:

A molecular “recycling plant” permits nerve cells in the brain to carry out two seemingly contradictory functions — changeable enough to record new experiences, yet permanent enough to maintain these memories over time.

Great news from PLoS for Bloggers

Yesterday, PLoS ONE moved to the newest version of the TOPAZ platform. Rich Cave explains all the improvements that this move entails, including the citation download for articles, but one new feature that should really be exciting to bloggers are Trackbacks.
From now on, if you link to a PLoS ONE article in your post, that article will display a link back to your blog post (go to an article and look at the right side-bar, nested between the Discussions and Ratings). Thus, in addition to the conversation already going on in the commentary attached to the article itself, the readers will be able to access the responses from the blogosphere as well. And that should also bring additional traffic to the bloggers.
I have been testing the feature over the past 24 hours or so, but I need your input in order to refine and improve the Trackbacks feature.
First, for the time being, the link you use in your post has to be in the format of the full URL of the full text (i.e., not the shorter, DOI-only compression), so this is how it should look like (replace 0000000 with the actual number of the article):
http://www.plosone.org/article/info%3Adoi%2f10.1371%2Fjournal.pone.0000000
Unfortunately, for the time being (and we are working on it), this shorter form of the URL will not work:
http://www.plosone.org/doi/pone.0000000
Likewise, links to other parts of the site, e.g., to the PDF of the article, will not generate trackbacks.
So far, it appears that Trackbacks are working automatically on Drupal and MoveableType, i.e., there is no need for manual trackbacks.
In WordPress.com, it is necessary to type the trackback URL into the appropriate field in your posting form. The trackback URL is in this form:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000000/trackback
At this moment, it appears that links from Blogger/Blogspot blogs do not generate Trackbacks, but we are working on it. Test it anyway and let me know if there is a “trick” I missed so far.
Also, please let me know how it works on other platforms (e.g., Typepad, Radio Userland, Blogsome, LiveJournal, etc.)
I am not 100% sure (so tell me if I am wrong), but links posted “under the fold” will also not generate a trackback.
Also, and this may differ between platforms, I am not sure that republishing a blog (or an individual post) will trigger trackbacks from links made before yesterday. Give it a test run and let me know, please.
You can give me feedback in the comments here, or by e-mail, or by contacting the Webmaster on the PLoS ONE site itself.

My picks from ScienceDaily

Velociraptor Had Feathers:

A new look at some old bones have shown that velociraptor, the dinosaur made famous in the movie Jurassic Park, had feathers. The discovery was made by paleontologists at the American Museum of Natural History and the Field Museum of Natural History.

Personal Genomes: Mainstream In Five Years, But Who Should Have Access?:

Imagine this: you visit your clinician, undergo genetic testing, and then you are handed a miniature hard drive containing your personal genome sequence, which is subsequently uploaded onto publicly accessible databases. This may sound like science fiction, but it is scientific fact, and it is already happening.

Key To Longer Life (in Flies) Lies In Just 14 Brain Cells:

Two years ago, Brown University researchers discovered something startling: Decrease the activity of the cancer-suppressing protein p53 and you can make fruit flies live significantly longer. Now the same team reports an intriguing follow-up finding. The p53 protein, they found, may work its lifespan-extending magic in only 14 insulin-producing cells in the fly brain.

Eat Less To Live Longer: Calorie Restriction Linked To Long Healthy Lives:

For nearly 70 years scientists have known that caloric restriction prolongs life. In everything from yeast to primates, a significant decrease in calories can extend lifespan by as much as one-third. But getting under the hood of the molecular machinery that drives this longevity has remained elusive.

The Best Both Of Worlds: How To Have Sex And Survive:

Researchers have discovered that even the gruesome and brutal lifestyle of the Evarcha culicivora, a blood gorging jumping spider indigenous to East Africa, can’t help but be tempted by that ‘big is beautiful’ mantra no matter what the costs.

Basic Research Robust In Face Of More University Patenting:

As universities continue transforming scientific discoveries into potentially lucrative patents, many wonder how this might be transforming academic science itself.

Why Are Some Groups Of Animals So Diverse?:

A new study of finger-sized Australian lizards sheds light on one of the most striking yet largely unexplained patterns in nature: why is it that some groups of animals have evolved into hundreds, even thousands of species, while other groups include only a few?

Why Conservation Efforts Often Fail:

Modern conservation techniques have brought us the resurgence of American bald eagles, sustainable forest harvests and the rescue of prized lobster fisheries. So how can modern conservation strategies also have wrought such failures, from the catastrophic loss of Guatemalan forests to the economy-crippling Klamath River salmon kill in 2006?

ClockQuotes

Perfection is a waste of time.
– Kim De Coite

Welcome the new newest SciBling!

Go say Hello to the very latest addition to the Scienceblogs Universe – Coby Beck of A Few Things Ill Considered.

Today’s Carnivals

I and the Bird #58 is up on The Nightjar.
Change of Shift: Volume Two, Number 7 is up on Emergiblog.
The Carnival of Space – week 21, the XPrize edition – is up on Why Homeschool

Happy Birthday!

To Chris (an no, I am not the commenter who signed with “a sea cucumber” handle…).

Postdocs in some really good circadian labs

A post-doctoral position is available in the laboratory of Dr. Tosini to investigate the cellular and molecular mechanisms that control circadian rhythms in the mammalian retina [Tosini et al., (2007) Faseb J.; Sakamoto et al., (2004). J. Neuroscience 24: 9693-9697; Fukuhara et al., (2004) J. Neuroscience 24:1803-1811; Tosini G., Menaker, M. (1996) Science, 272: 419-421).The position is funded by a grant from the National Institute of Health.
The work will focus on the characterization of newly developed transgenic mice using physiological (ERG), molecular (Q-PCR and Laser Capture Microdissection) and bioluminescence recording from the whole retina or single photoreceptors. Previous experience in the circadian field and with retinal tissue is a plus, but not necessary.
The Neuroscience Institute at Morehouse School of Medicine is equipped with state-of-the-art equipments for research in Neuroscience and in particular on circadian rhythms and sleep disorders.
Gianluca Tosini, Ph.D.
Professor and Director
Circadian Rhythms and Sleep Disorders Program
Neuroscience Institute
Morehouse School of Medicine
720 Westview Dr. Atlanta, GA
Postdoctoral Research position available to study the control of circadian rhythms by sustained attention. Emphasis is on the ACh projection from the basal forebrain to the suprachiasmatic nucleus and the control of circadian rhythms. Ph.D. in Biopsychology, Neuroscience, or related fields is preferred. Familiarity with chronobiology and/or control of behavior through operant conditioning will be helpful. Primary responsibilities: designing and coordinating experiments to study the control of daily rhythms by a task that requires high, sustained attention; microdialysis; stereotaxic surgery; histology; managing students that will also work on this project. Salary commensurate with experience; health insurance provided. Length of appointment could be 3 yrs. Please send resume and contacts for recommendations to: Dr. Theresa M. Lee, University of Michigan, Dept of Psychology, 530 Church St, Ann Arbor, MI 48109-1043. Review of applications will begin Sept 1, 2007 and continue until the position is filled. Start date is negotiable.
Theresa M.Lee, Ph.D.
Professor, Psychology & Neuroscience Program
Chair, Department of Psychology
University of Michigan
530 Church St
Ann Arbor, MI 48109-1043

Rethinking FOXP2

Earlier studies have indicated that a gene called FOXP2, possibly involved in brain development, is extremely conserved in vertebrates, except for two notable mutations in humans. This finding suggested that this gene may in some way be involved in the evolution of language, and was thus dubbed by the popular press “the language gene”. See, for instance, this and this for some recent research on the geographic variation of this gene (and related genes) and its relation to types of languages humans use (e.g., tonal vs. non-tonal). Furthermore, a mutation in this gene in humans results in inability to form grammatically correct sentences.
This week, a new study shows that this gene is highly diverse in one group of mammals – the bats:

A new study, undertaken by a joint of team of British and Chinese scientists, has found that this gene shows unparalleled variation in echolocating bats. The results, appearing in a study published in the online, open-access journal PLoS ONE on September 19, report that FOXP2 sequence differences among bat lineages correspond well to contrasting forms of echolocation.

As Anne-Marie notes, this puts a monkey-wrench in the idea that FOXP2 is exclusively involved in language, but may be involved in vocalizations in general:

Said gene might have a new function (sensorimotor) besides the one originally attributed to it (verbal language).

Jonah Lehrer notes that the same mutation that in humans eliminates ability to use or comprehend correct grammar is also found in songbirds and the gene is expressed at high levels during the periods of intense song-learning. The story is obviously getting very interesting – does this gene have something to do with vocalizations? Or with communication? Or something totally third?
Looking forward to further responses by other blogs, hopefully Afarensis, John Hawks and Language Log?
The article on FOXP2 in bats was published yesterday on PLoS ONE so you can access it for free, read, download, use, reuse, rate, annotate and comment on.
Update: Mark Liberman explains more (and takes me to task for a mistake I made in haste last night) in this post on Language Log.
Update 2: John Hawks explains.

Anyone going to this?

Symposium Light, Performance and Quality of Life is on Thursday, 8 November 2007 in Eindhoven, the Netherlands:

Introduction
The ancient Greek already referred to the wholesome effects of the (sun)light on mankind. Ever since the industrialization, more and more people are devoid of bright daylight for a large part of the day. With the ongoing industrialization and the current information-society the number of persons that spent al large part of the day indoors further increases.
The light in these buildings is, also due to the modern trend of small windows and low lighting-levels, notably lower than the biological need for light of people. Also the energy crisis in the early seventies has been an influence on driving back sufficient light, as a result sometimes reducing the level of light inside buildings to nearly ” biological darkness”.
Rediscovery of light in relation to health.
The past 15 to 20 years light has returned to the full attention of the scientific community. Particularly visible light that reaches the retina of the human eye brings about a number of biological effects. The fact that light, besides a necessity to see, also regulates biological functions, has lead to research programs at different institutes and universities. The questions with which these centres occupy themselves are among others:
* Which bio-mechanisms are influenced by light that falls on the eye?
* What possibilities are there to use light for curative and preventive means?
In the end the increasing social importance of research and applications of light on health, have lead to the foundation of the “Stichting Onderzoek Licht & Gezondheid”, the Light & Health Research Foundation (SOLG).
The Light & Health Research Foundation is based at Eindhoven, University of Technology

Welcome the newest SciBling!

Go say Hello to Sciencewoman!

Blogrolling for Today

Lali’s Laboratory


Frog Blog


d(PhD)/dt


The Badge (SF Chronicle Police Beat Blog)


Alexipharmacopeia


Ed Boyden


The Conscience of a Liberal (Paul Krugman)


GMO Africa

Less you sleep, craziest the dreams!

There is an intriguing article in Scientific American about the consequences of sleep deprivation. When the brain is finally allowed to catch up with sleep, it tries to make-up for the loss of slow-wave sleep, but it also tries to make up for the loss of REM sleep as well – by making it more intense! As a result, the dreams are like scenes from something like “Jumanji” – wild animals running around and other crazy stuff. A very good article about various ideas on the function of sleep and dreams.

Facebook, after weeks of pressure, still bans breastfeeding photos!

I thought the LiveJournal debacle taught them a lesson. I guess not. Melissa posted about this a couple of weeks ago, and Tara did it today again because the issue has not been resolved yet. So did PZ Myers (Janet Stemwedel and Dr. Joan Bushwell also chime in). Facebook is deleting pictures of breastfeeding and banning users who post them. Now that Facebook is not just for college crowd, there are more and more moms and dads on the network, proudly showing off their offspring to the world. Including offspring in the moments of feeding bliss.
But, you know that in this country there are a lot of dirty old men who find that scene somehow sexual (what kind of sick upbringing results in such sexual perversion, I wonder?), including, apparently, someone in the upper echelons of Facebook. Join the fast-growing Facebook group and send them a message. Blog about this as well. Force them to reverse this medieval decision.

Eric Dezenhall PR memo to publishers leaked

Jim Giles, New Scientist contributor, got the memo and wrote a blog post and an article about it. You can read the actual memo here (pdf) to see what Dezenhall advised the dinosaur publishers to do to stave off the inevitable move to Open Access. So now you can see where PRISM comes from.

Tennessee bans lethal injection

Based in part on this study, lethal injection has been ruled (at least for now) unconstitutional in the state of Tennessee.
The executions by lethal injection have been on hold for several months now in North Carolina as well, until the legality of it is figured out. I hope NC follows in the footsteps of TN soon.

Happy Birthday!

To Chris (and yes, what a great birthday present!).

ClockQuotes

The best thing about the future is that it comes one day at a time.
– Abraham Lincoln, 1809 – 1865

Panda’s got some teeth!

Have you seen the new design of Panda’s Thumb?

Science Blogging Conference

2008NCSBClogo200.pngJust a reminder – watch out as I am now getting into that mode when I get on everyone’s nerves with promoting the conference almost daily – that there are now 60 amazing people already registered for the conference, so you should register soon, before we reach the cap. Don’t forget to sign yourself for the Friday dinner as well. The Program is getting closer and closer to its final shape. We’ll need volunteers (especially local drivers) and we’ll be glad to get additional sponsors if your organization is interested.

Today’s Carnivals

The 135th Carnival of Education is up on The Education Wonks.
The latest edition of the Homeschooling Carnival is up on About:Homeschooling.

Endocrine rhythms

Circadian clocks: regulators of endocrine and metabolic rhythms by Michael Hastings, John S O’Neill and Elizabeth S Maywood is a new and excellent review of the interaction between the clocks and hormones in mammals, focusing at the molecular level. The pre-print PDF of the article is freely available on the Journal of Endocrinology site.

My picks from ScienceDaily

Brain Network Related To Intelligence Identified:

A primary mystery puzzling neuroscientists – where in the brain lies intelligence? – just may have a unified answer.

The title alone should provoke a storm in the blogosphere 😉
Prehistoric Aesthetics Explains Snail Biogeography Puzzle:

The answer to a mystery that long has puzzled biologists may lie in prehistoric Polynesians’ penchant for pretty white shells, a research team headed by University of Michigan mollusk expert Diarmaid Ó Foighil has found.

Who’s Afraid Of The Big, Bad Wolf? Coyotes:

While the wily coyote reigns as top dog in much of the country, it leads a nervous existence wherever it coexists with its larger relative, the wolf, according to a new study from the Wildlife Conservation Society. In fact, coyote densities are more than 30 percent lower in areas that they share with wolves.

Gene Involved in Human Language Development Also Involved In Bat Echolocation:

When it comes to the FOXP2 gene, humans have had most to shout about. Discoveries that mutations in this gene lead to speech defects and that the gene underwent changes around the time language evolved both implicate FOXP2 in the evolution of human language.

Mortality Of Plants Could Increase By 40 Percent If Land Temperatures Increase 4 Degrees Celsius:

Scientists from the Mediterranean Institute for Advanced Studies* have formulated a universal rule that explains the equilibrium of plant communities, showing how plants assure the survival of their species whether their lives last a day or are prolonged over centuries.

ClockQuotes

Don’t let the fear of the time it will take to accomplish something stand in the way of your doing it. The time will pass anyway; we might just as well put that passing time to the best possible use.
– Earl Nightingale, 1921 – 1989

New and Exciting in PLoS ONE

There are 28 new articles up on PLoS ONE today. As always, I offer you my own picks, but you go there and look at all of them, then read, rate, comment and annotate:
Living with the Past: Nutritional Stress in Juvenile Males Has Immediate Effects on their Plumage Ornaments and on Adult Attractiveness in Zebra Finches:

The environmental conditions individuals experience during early development are well known to have fundamental effects on a variety of fitness-relevant traits. Although it is evident that the earliest developmental stages have large effects on fitness, other developmental stages, such as the period when secondary sexual characters develop, might also exert a profound effect on fitness components. Here we show experimentally in male zebra finches, Taeniopygia guttata, that nutritional conditions during this later period have immediate effects on male plumage ornaments and on their attractiveness as adults. Males that had received high quality food during the second month of life, a period when secondary sexual characteristics develop, were significantly more attractive as adults in mate choice tests than siblings supplied with standard food during this period. Preferred males that had experienced better nutritional conditions had larger orange cheek patches when nutritional treatments ended than did unpreferred males. Sexual plumage ornaments of young males thus are honest indicators of nutritional conditions during this period. The mate choice tests with adult birds indicate that nutritional conditions during the period of song learning, brain and gonad development, and moult into adult plumage have persisting effects on male attractiveness. This suggests that the developmental period following nutritional dependence from the parents is just as important in affecting adult attractiveness as are much earlier developmental periods. These findings thus contribute to understanding the origin and consequences of environmentally determined fitness components.

More under the fold….

Continue reading

New and Exciting in PLoS Medicine and PLoS Biology

There is new cool stuff published last night in PLoS Biology and PLoS Medicine, including:

Continue reading

The Best Life Science Blogs in The Scientist

The good folks at The Scientist asked a few of us to recommend some of the best and most interesting life science blogs. We have done so and the article is now online:

So, we at The Scientist are asking you to help compile the first list of the best life science blogs. Tell us what your favorite life science blogs are and why by clicking the button and leaving a comment, and we will publish a list of the most popular choices across the different areas of life sciences. With your help we hope to provide a list of who is currently hot in the science blogosphere, and why you should be reading them.

The best thing is that you can have your say as well – recommend your own favourites at this form. If a discussion about this goes on your blog, feel free to paste the URL in the form as well:

To start things off, we’ve asked some of the best known science bloggers to nominate some of their favorite blogs. Add to the list by posting your choices here, and these will appear below the list in the comments section.
In the spirit of blog-like openness, we hope people discuss their favorite science blogs elsewhere. If people on your blog are having an interesting discussion thread about this, then post a link to that page, and we’ll count those suggestions too.

So, fire away – what are your favourites?

Update:
Attila Csordas (also here), PZ Myers, Phillip Torrone, Abel PharmBoy, Alex Palazzo, Chris Patil, Mo Costandi, Tara Smith, Alan Cann, Deepak Singh, Brian Switek, John Hawks, Carl Zimmer, Orac, Terry, Bug Girl and others link to the article and in some cases suggest additional blogs.
Chad Orzel notices that not everybody is clear that the listing is of LIFE science blogs, not all science blogs. Biology and medicine only, this time around.
As expected, somebody suggested ‘Uncommon Descent’, ‘Evolution News and Views’ and ‘ID the Future’ which are, by definition, not science blogs.
Grrrlscientist, Sheril Kirshenbaum, Karmen Franklin and Zuska notice that none of the people asked are women. I wish I knew that this was going to be the case when I was asked. Although two out of my three suggestions are blogs written by women (The Anterior Commissure and Pondering Pikaia), I would have added more, starting perhaps with Notes from Ukraine, Bootstrap Analysis, Biology in Science Fiction, Dr.Petra, Bioephemera, Invasive Species Blog, Cyberspace Rendezvous, Science Made Cool, N@ked Under My Lab Coat, Easternblot, Well-Timed Period, Intueri, Emergiblog and Eye on DNA, just to begin with.
So, go there and add some female bloggers in the comments!

Yes, delay the school starting times

From the Independent:

The head has identified research which says that teenagers would be more likely to take in what they are learning if they started school two hours later. He is considering changing the school timetable for sixth-formers as a result.
“We have always assumed that learning early in the morning is best, probably because it is best for young children and adults,” he writes. ” Unfortunately, it is not true for teenagers. When teenagers are woken up at our morning time, their brain tells them they should be asleep. So they use stimulants such as coffee and cigarettes to get themselves awake. But at night, when we go to sleep, their neurological clock tells them it’s not time to sleep so they drink alcohol or take drugs to get them to sleep.
“Schools and universities only make it worse, he adds. The importance of neurological patterns of time as a factor in our learning and our lives has largely been ignored. We need to fit learning to these patterns of times. ”

(Hat-tip: nbm)
Related….

Bring back the Office of Technology Assessment!

Blog about it, contact your Senators, and contact the Presidential candidates. Let’s put some pressure on!
See what Mark Hoofnagle (and again) says.
Mike Dunford, PZ Myers (and again) and John Wilkins and their commenters have more (including all the contact information you’ll ever need).