Yearly Archives: 2007

OceanBlogging of the Fortnight

Carnival of the Blue #2 is up on Blogfish.

Kids and their genes

Gene Genie #10 (the peer-reviewed carnival of bioinformatics and computational biology) is up on Genomicron.
Paediatric Grand Rounds 2:6 are up on Breath Spa for Kids.

Net Neutrality?

I am having difficulty understanding what this is about, who is who, what are the institutional affiliations and potential biases, etc. Can someone explain it to me:
Net Neutrality: Undifferentiated Networks Would Require Significant Extra Capacity:

Using computer models, the researchers compared the current “best-effort” approach with a tiered model that separates information into two simple classes — one for most types of information and another for applications requiring service level assurance for high-bandwidth content like video games, telemedicine, and Voice over Internet Protocol (VoIP).
——-snip———
“Clearly, an undifferentiated network in this context is less efficient and more expensive,” said coauthor K.K. Ramakrishnan of AT&T Labs. “We believe understanding the real impacts of the alternative strategies is important as the debate about network architecture unfolds.”

Value of Class-of-Service (CoS) Support in the Internet Backbone:

The user expectation of Internet use has moved from best-effort connectivity to an expectation of reasonable performance & capacity for all types of applications. QoS-sensitive applications like IPTV, gaming, and VoIP could be offered over such a converged IP broadband end-to-end network. Network service providers also would like to support such applications effectively. They need to provision their networks to meet the service level agreements (SLAs). Customer experiences need to be protected and predictable despite network failures and changes in demand as well as application mix.
Currently there is a wide ranging debate on the issue of “network neutrality” which involves both economic and technical aspects. One key aspect of the net neutrality debate is whether best effort application traffic should be carried along with other (so-called “premium”) traffic for which SLA commitments have been made (or are expected, either explicitly or implicitly) without differentiation. An assertion often made in this context is that over-provisioning is an economically viable strategy due to the declining cost of capacity, instead of incurring the complexity and operational costs of running a differentiated-services network. Our study focuses on this specific question within the larger debate. We compare a classless network which is over-provisioned against an engineered network using per-class queuing to offer Class-of-Service (CoS) (i.e., differentiated-service) and meet user expectations and SLAs. In most situations a differentiated network can save significantly over a classless network.

Trees, Trees, I speak for the Trees!

Festival of the Trees #13 – Putting Down Roots – is up on Wrenaissance Reflections.

ClockQuotes

Every closed eye is not sleeping, and every open eye is not seeing.
– Bill Cosby

All Set

OK, I have scheduled to repost automatically some of the best clock-related posts. They will appear every day at 9am and 5pm from July 5th till August 12th. I hope you like them again….
Tomorrow, I’ll schedule a bunch of ClockQuotes for the next month as well, every day at 4am.

Duck testicles, beef tongues and rabbit stew – here I come!

While in San Francisco, I’d like to eat at Incanto (look around the site for their menu and progressive food and water policies, and they also have a blog). It is at 1550 Church Street, on the southwest corner of Church and Duncan Streets in San Francisco’s Noe Valley. Where is that? Anyone game to go with me?

Blogrolling for Today

The Flying Trilobite


Ljubisa Bojic


1420Mhz


Weird Science


Good Tithings


Curious Expeditions


Dandelion Diva


Cabinet of Wonders


Simplistic Art


Mixotrophy


Offal Good

Why a Populist Cannot Win?

Edwards aside, this is an excellent look at the current political landscape in the USA:
John Edwards and Dominant Media’s Selective Skewering of Populist Hypocrisy by Paul Street:

Sicko

Early reviews of the movie are coming out. Definitely read Ezra Klein’s take on it. And Amanda Marcotte’s. Also Mark Hoofnagle. And why Rob does not want to see it.
Perhaps it is my upbringing, but the fact that one has to pay for medical treatment (and/or pay health insurance) was the second most appallingly surprising thing to me when I arrived in the USA (the sincere religiosity of so many natives was the first). After 16 years here, I still cannot really wrap my mind around it. The notion that anyone but doctors, nurses and patients can have a say in medical treatment, or that anyone should make a profit out of people’s sickness is, to my mind, so atrocious, right up there with the notion of slavery. Both are extreme examples of trampling over most basic human rights.
I will go and see the movie as soon as I can.

Good News about the Bosnian “Pyramid”

It’s been a while since I last blogged about the Bosnian Pyramid (I did follow the story superficially, though, but was sick of trolls attracted to the topic), but I have to break the silence for this piece of good news:

The Culture Ministry found the “research” conducted by Osmanagic’s team to be questionable and the collaborators of Osmanagic to lack the credibility needed to allow for continued funding of their “project.” Also criticized by the Bosnian government, according to Javno, is the methods by which Osmanagic et al presented their findings, particularly the fact that they routinely kept their data from experts in relative fields.
The Bosnian Culture Ministry consulted experts including those in the fields of geology, mining, archaeology, and cultural preservation and arrived at the conclusion that Osmanagic’s foundation was not acting in the best interest of Bosnian cultural preservation and that the foundation is in violation of archaeological regulations. The Ministry even concluded that the nature of Osmanagic’s registration with the Bosnia-Herzegovina Justice Ministry may be suspect and should be “looked into.”

They are shutting Osmanagic down. Whew – that took a long time, but at least the story has (so far) a happy ending. In the end, Reason prevailed.

New on PLoS – Genetics and Computational Biology

Lots of new papers just got published in PLoS-Genetics and PLoS-Computational Biology. Here are a couple of papers that caught my eye:
From Morphology to Neural Information: The Electric Sense of the Skate:

The electric sense appears in a variety of animals, from the shark to the platypus, and it facilitates short-range prey detection where environments limit sight. Typically, hundreds or thousands of sensors work in concert. In skates, rays, and sharks, each electrosensor includes a small, innervated bulb, with a thin, gel-filled canal leading to a surface pore. While experiments have mapped single electrosensor activity, the mechanisms that integrate neural input from multiple electrosensors are still largely unknown. Here, we model the response of a precisely mapped subset of electrosensors responding in concert for a skate moving near stationary prey. Just as two ears help locate sound via time and intensity differences, we ask how a bilateral electrosensor array can contribute to electrical scene analysis. Our results show that the sensor array provides rich data for precise prey location, tuned by the morphology to render certain events, like the point of closest approach, “loud and clear.” This proof of principle makes a significant step in understanding the electric sense processing, and we recommend future experiments to compare and assess functions for the diversity of arrays found in other sharks and rays.

Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes which I have already reviewed.
The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective:

Gene expression is a process that is inherently stochastic because of the low number of molecules that are involved. In recent years it has become possible to measure the amount of stochasticity in gene expression, which has inspired a debate about the importance of stochasticity in gene expression. Little attention, however, has been paid to stochasticity in gene expression from an evolutionary perspective. We studied the evolutionary consequences of stochastic gene expression in one of the best-known systems of genetic regulation, the lac operon of E. coli, which regulates lactose uptake and metabolism. We used a computational approach, in which we let cells evolve their lac operon promoter function in a fluctuating, spatially explicit, environment. Cells can in this way adapt to the environment, but also change the amount of stochasticity in gene expression. We find that cells evolve their repressed transcription rates to higher values in a stochastic model than in a deterministic model. Higher repressed transcription rates means less stochasticity, and, hence, these cells appear to avoid stochastic gene expression in this particular system. We find that this can be explained by the fact that stochastic gene expression causes a larger delay in lactose uptake, compared with deterministic gene expression.

Mutations in gfpt1 and skiv2l2 Cause Distinct Stage-Specific Defects in Larval Melanocyte Regeneration in Zebrafish:

Programs of ontogenetic development and regeneration share many components. Differences in genetic requirements between regeneration and development may identify mechanisms specific to the stem cells that maintain cell populations in postembryonic stages, or identify other regeneration-specific functions. Here, we utilize a forward genetic approach that takes advantage of single cell type ablation and regeneration to isolate mechanisms specific to regeneration of the zebrafish melanocyte. Upon chemical ablation of melanocytes, zebrafish larvae reconstitute their larval pigment pattern from undifferentiated precursors or stem cells. We isolated two zebrafish mutants that develop embryonic melanocytes normally but fail to regenerate their melanocytes upon ablation. This phenotype suggests the regeneration-specific roles of the mutated genes. We further identified the mutations in gfpt1 and skiv2l2 and show their stage-specific roles in melanocyte regeneration. Interestingly, these mutants identify regeneration-specific functions not only in early stages of the regeneration process (skiv2l2), but also in late stages of differentiation of the regenerating melanocyte (gfpt1). We suggest that mechanisms of regeneration identified in this mutant screen may reveal fundamental differences between the mechanisms that establish differentiated cells during embryogenesis and those involved in larval or adult growth.

My Picks From ScienceDaily

First Bacterial Genome Transplantation Changes One Species To Another:

Researchers at the J. Craig Venter Institute (JCVI) have announced the results of work on genome transplantation methods allowing them to transform one type of bacteria into another type dictated by the transplanted chromosome. The work, published online in the journal Science, by JCVI’s Carole Lartigue, Ph.D. and colleagues, outlines the methods and techniques used to change one bacterial species, Mycoplasma capricolum into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome.

But, if you think about it as “transplanting the cell membrane and wall of one species onto another” than it does not sound so epochal, does it?
Cloned Pigs Help Scientists Towards A Breakthrough In Alzheimer’s:

The first pigs containing genes responsible for Alzheimer’s disease will be born in Denmark in August. This event is a landmark achivement in the effort towards finding a cure for the disease.

RNA May Play Larger Role In Cell’s Gene Activity, Researchers Find:

Large, seemingly useless pieces of RNA – a molecule originally considered only a lowly messenger for DNA – play an important role in letting cells know where they are in the body and what they are supposed to become, researchers at Stanford University School of Medicine have discovered.

ClockQuotes

Time as he grows old teaches many lessons.
– Aeschylus

A worm with an ur-hypothalamus?

Modern Brains Have An Ancient Core:

Hormones control growth, metabolism, reproduction and many other important biological processes. In humans, and all other vertebrates, the chemical signals are produced by specialised brain centres such as the hypothalamus and secreted into the blood stream that distributes them around the body.
Researchers from the European Molecular Biology Laboratory [EMBL] now reveal that the hypothalamus and its hormones are not purely vertebrate inventions, but have their evolutionary roots in marine, worm-like ancestors. In this week’s issue of the journal Cell they report that hormone-secreting brain centres are much older than expected and likely evolved from multifunctional cells of the last common ancestor of vertebrates, flies and worms.
———snip————–
Scientist Kristin Tessmar-Raible from Arendt’s lab directly compared two types of hormone-secreting nerve cells of zebrafish, a vertebrate, and the annelid worm Platynereis dumerilii, and found some stunning similarities. Not only were both cell types located at the same positions in the developing brains of the two species, but they also looked similar and shared the same molecular makeup. One of these cell types secretes vasotocin, a hormone controlling reproduction and water balance of the body, the other secretes a hormone called RF-amide.
Each cell type has a unique molecular fingerprint – a combination of regulatory genes that are active in a cell and give it its identity. The similarities between the fingerprints of vasotocin and RF-amide-secreting cells in zebrafish and Platynereis are so big that they are difficult to explain by coincidence. Instead they indicate a common evolutionary origin of the cells. “It is likely that they existed already in Urbilateria, the last common ancestors of vertebrates, insects and worms” explains Arendt.
Both of the cell types studied in Platynereis and fish are multifunctional: they secrete hormones and at the same time have sensory properties. The vasotocin-secreting cells contain a light-sensitive pigment, while RF-amide appears to be secreted in response to certain chemicals. The EMBL scientists now assume that such multifunctional sensory neurons are among the most ancient neuron types. Their role was likely to directly convey sensory cues from the ancient marine environment to changes in the animal’s body. Over time these autonomous cells might have clustered together and specialised forming complex brain centres like the vertebrate hypothalamus.
———-snip—————

“The vasotocin-secreting cells contain a light-sensitive pigment”? Why? Any connections to the mammalian SCN secreting vasopresin?

Living Vicariously

LOLafrica:
lolcat4555501.jpg
Sheril is in South Africa taking pictures of poopin’ elfants.

Do Serbian scientists need a blog of their own?

Not that it costs anything to have one…
Yet, the Konsortium of science libraries in Serbia is seriously contemplating shutting down their KOBSON blog, an invaluable tool in science communication in the region.
Danica, who the regular readers of this blog are quite familiar with as she is the Number One Champion for Open Science and Web 2.0 science in Serbia, has put a lot of effort into building the online infrastructure for Serbian scientific communication, including the KOBSON blog and the KOBSON wiki, as well as teaching and preaching to the local scientific community about the importance of catching up with the world after a decade of isolation and fully embracing the modern communication tools. She was also involved in setting up the Serbian Citation Index, from which I mined a paper that I used to demonstrate how important Open Access is to scientists in developing countries.
There is not much more that Danica alone can do in the present situation to save the KOBSON blog, but perhaps YOU all can help. How? Let’s demonstrate the power of Science 2.0 by direct example! Go to the KOBSON blog and explain the importance of such a tool in the comments of this post. Even better, if you are fluent in one or another variant of the Serbo-Croatian language, post a comment on the Serbian version of the post. Then, post a link and this plea to your own blog as well and ask your readers to do the same.

Update:
On the front page of the KOBSON home (not blog) there is “contact” information and an e-mail address:
nainfo@nbs.bg.ac.yu
Be polite and explain why hosting (and pointing to) a blog is essential for 21st century science.
The problem is not just saving the blog where it is on WordPress, but also moving it onto the Library server, or at least linking to it from the homepage so people see it and use it more. Right now, only people “in the know” use it which severely limits its usefulness.
You should also join the ‘Fight for Science Blogs‘ Cause on Facebook and invite all your friends to join it as well (the ’causes’ function is malfunctioning on Facebook right now, so try later if you cannot sign up right now).

Always wanted to go to Barcelona!

shadow%20of%20the%20wind.jpgThe Shadow of the Wind
Thank you

Referees’ Reviews on PLoS-ONE

It’s always intriguing to know what the peer-reviewers have thought and written about a particular manuscript. Now, you can find out, at least in some cases, on PLoS-ONE papers. Chris Surridge explains.

Birds and other animals

I And The Bird #52 is up on The Wandering Tattler
Friday Ark #145 is up on the Modulator

Blogswarm against Theocracy

July 1st through July 4th. Here are the detailed instructions how to participate.

My Picks From ScienceDaily

The Newest Artificial Intelligence Computing Tool: People:

A USC Information Sciences Institute researcher thinks she has found a new source of artificial intelligence computing power to solve difficult IT problems of information classification, reliability, and meaning. That tool, according to ISI computer scientist Kristina Lerman, is people, human intelligence at work on the social web, the network of blogs, bookmark, photo and video- sharing sites, and other meeting places now involving hundreds of thousands of individuals daily, recording observations and sharing opinions and information.

Book Makes Case For Using Evolution In Everyday Life:

Evolution is not just about human origins, dinosaurs and fossils, says Binghamton University evolutionist David Sloan Wilson. It can also be applied to almost every aspect of human life, as he demonstrates in his first book for a general audience, Evolution for Everyone: How Darwin’s Theory Can Change the Way We Think About Our Lives (Bantam Press 2007). Using witty, straightforward language and compelling anecdotes, Wilson outlines the basic principles of evolution in a way that can be easily understood by non-experts. He then uses the principles to explain phenomena as diverse as why beetles commit infanticide, why dogs have curly tails, and why people laugh and make art.

Bald Eagle Soars Off Endangered Species List:

Secretary of the Interior Dirk Kempthorne announced the removal of the bald eagle for the list of threatened and endangered species at a ceremony June 28 at the Jefferson Memorial in Washington, D.C. After nearly disappearing from most of the United States decades ago, the bald eagle is now flourishing across the nation and no longer needs the protection of the Endangered Species Act.

Seabird Diet History Revealed Through Analyisis Of Museum Samples:

Using feathers from museum collections all over the world, a University of Guelph integrative biology professor has tested a new hypothesis about what led to population decline of a species of seabirds in Canada.

New Study Shows How Often Juries Get It Wrong:

Juries across the country make decisions every day on the fate of defendants, ideally leading to prison sentences that fit the crime for the guilty and release for the innocent. Yet a new Northwestern University study shows that juries in criminal cases many times are getting it wrong.

ClockQuotes

Nothing valuable can be lost by taking time.
– Abraham Lincoln

Bloodthirsty carnivorous mutant sheep!

I have got to see this movie! Is it coming to the USA any time soon? Or Netflix?
black%20sheep.jpg
Thanks Peggy…I won’t be able to sleep tonight, scared of the bleating woolly terror!

PLoS on Facebook

You can now join the PLoS cause and the PLoS group if you want. If you are my friend, you can see all sorts of other groups and causes I have joined as well….

Blogrolling for Today

Sleep Apnea ED


Average Earthman


Deep Thoughts and Silliness


Three-Toed Sloth


Statistical Modeling, Causal Inference, and Social Science


The Vanity Website


The Indigestibele

Geography of Science

Stem-Cell research is easier in some places than others.
Help us locate exactly where.
When is the North Carolina/Triangle community going to try to push hard for state funding of stem-cell research? Or have I missed something?

Storm World

stormworld%20cover.jpgMy copy of the book just arrived in the mail. This answers my question of what to read in SF (at least until Harry Potter VII comes out…).

Physics of Nursing in Space

Philosophia Naturalis #11 – Powers of 11 – is up on Highly Allochthonous.
The first anniversary edition of The Change Of Shift is up on NursingLink.
Carnival of Space #9 is up on The Planetary Society Weblog

New and Exciting on PLoS-ONE

A whole bunch of papers got published on PLoS-ONE yesterday. I did not have time to check them out very closely yet, but a few titles immediatelly caught my attention:
High Costs of Female Choice in a Lekking Lizard
by Maren N. Vitousek, Mark A. Mitchell, Anthony J. Woakes, Michael D. Niemack and Martin Wikelski

The cost to males of producing elaborate mating displays is well established, but the energy females spend on mate choice is less clear. This study monitored the heart rates of female Galápagos marine iguanas (Amblyrhynchus cristatus) and found they expended almost a days’ worth of energy a month choosing a mate. More choosy females lost weight, produced smaller follicles, and were less likely to survive El Niño years.

Female Sexual Polymorphism and Fecundity Consequences of Male Mating Harassment in the Wild
by Thomas P. Gosden and Erik I. Svensson

Genetic and phenotypic variation in female response towards male mating attempts has been found in several laboratory studies, demonstrating sexually antagonistic co-evolution driven by mating costs on female fitness. Theoretical models suggest that the type and degree of genetic variation in female resistance could affect the evolutionary outcome of sexually antagonistic mating interactions, resulting in either rapid development of reproductive isolation and speciation or genetic clustering and female sexual polymorphisms. However, evidence for genetic variation of this kind in natural populations of non-model organisms is very limited. Likewise, we lack knowledge on female fecundity-consequences of matings and the degree of male mating harassment in natural settings. Here we present such data from natural populations of a colour polymorphic damselfly. Using a novel experimental technique of colour dusting males in the field, we show that heritable female colour morphs differ in their propensity to accept male mating attempts. These morphs also differ in their degree of resistance towards male mating attempts, the number of realized matings and in their fecundity-tolerance to matings and mating attempts. These results show that there may be genetic variation in both resistance and tolerance to male mating attempts (fitness consequences of matings) in natural populations, similar to the situation in plant-pathogen resistance systems. Male mating harassment could promote the maintenance of a sexual mating polymorphism in females, one of few empirical examples of sympatric genetic clusters maintained by sexual conflict.

Interethnic Differences in Muscle, Liver and Abdominal Fat Partitioning in Obese Adolescents
by David Liska, Sylvie Dufour, Tosca L. Zern, Sara Taksali, Anna M.G. Calí, James Dziura, Gerald I. Shulman, Bridget M. Pierpont and Sonia Caprio

Our study indicates that obese Hispanic adolescents have a greater IMCL lipid content than both Caucasians and African Americans, of comparable weight, age and gender. Excessive accumulation of fat in the liver was found in both Caucasian and Hispanic groups as opposed to virtually undetectable levels in the African Americans. Thus, irrespective of obesity, there seem to be some clear ethnic differences in the amount of lipid accumulated in skeletal muscle, liver and abdominal cavity.

As always, if you read the papers and have questions or comments, post them at the paper, not on this post.

My Picks From ScienceDaily

Mathematicians Discover A Simple Way To Formulate Complex Scientific Results:

A new analysis of behaviour in a structured population illuminates Darwin’s theories of co-operation and competition between kin, and provides an abstract model that could simplify scientists’ quest to map behaviour among disease-causing organisms within a cell. The study by Queen’s Mathematics and Statistics professor Peter Taylor, and co-authors Troy Day (Queen’s) and Geoff Wild (University of Western Ontario) presents a simple formula for balancing the benefit and cost in altruistic acts, allowing researchers to predict behaviour and summarize disparate results in a simple framework.

Global Climate Change And Toxic Chemicals: A Potentially Lethal Combination:

As temperature influences the toxic effects of chemicals, so does chemical exposure influence the temperature tolerance of an organism. The consequences of this harmful reciprocal relationship on four freshwater fish are explored in a new study published in the latest issue of Environmental Toxicology and Chemistry.

Letting Plants ‘Talk’ To You:

The greenhouse manager of the future walks around the greenhouse, pointing an infrared “flashlight” at potted plants. A tiny screen tells whether each plant has too much, too little, or just the right amount of nutrients. During the past three years, at a new facility in Toledo, Ohio, Agricultural Research Service (ARS) plant pathologist Jim Locke and horticulturist Jonathan Frantz have made a great deal of progress toward realizing this automated future. Frantz is testing commercial nutrient sensors with a view toward developing improved portable ones. Devices like these can give greenhouse growers a few–often critical–extra days to correct nutrient problems before their plants are seriously damaged.

Tasmanian Tiger Extinction Mystery:

A University of Adelaide project led by zoologist Dr Jeremy Austin is investigating whether the world-fabled Tasmanian Tiger may have survived beyond its reported extinction in the late 1930s. Dr Austin from the Australian Centre for Ancient DNA is extracting ancient DNA from animal droppings found in Tasmania in the late 1950s and ’60s, which have been preserved in the Tasmanian Museum and Art Gallery.

Female Iguanas Pay High Costs To Choose A Mate:

Picking a mate isn’t easy–if you are a female iguana. In a study published in the June 27th issue of PLoS ONE, Maren Vitousek of Princeton University and colleagues found that female Galápagos marine iguanas spend a lot of energy picking a mate from a wide range of suitors — energy they could otherwise spend foraging, producing eggs, or avoiding predators. Scientists have generally assumed that being choosy about potential mates carries low costs for females. These costs were thought to be particularly small when male territories are clustered together in groups, known as ‘leks’, which make it possible for females to assess many candidates without traveling far.

Study Confirms Importance Of Sexual Fantasies In Experience Of Sexual Desire:

Scientists of the Department of Personality, Evaluation and Psychological Treatment of the University of Granada have studied how some psychological variables such as erotophilia (positive attitude towards sexuality), sexual fantasies and anxiety are related to sexual desire in human beings. The researcher Juan Carlos Sierra Freire states that there are very few reliable and valid instruments in Spain to evaluate sexual desire. Due to this vacuum, the researchers have adapted the Sexual Desire Inventory by Spector, Carey and Steinberg. This inventory is a tool that enables the researcher to measure, on the one hand, the solitary sexual motivation and, on the other hand, the interest in having sexual intercourse with another person (didactic sexual desire). This fact is of a great importance because “it gives relevant information about possible disagreements in sexual desire that may appear in a couple”. Regarding figures of the Spanish Association for Sexual Health, a loss of sexual desire is one of the main factors that cause sexual dysfunction in the Spanish female population.

ClockQuotes

Blow the dust off the clock. Your watches are behind the times. Throw open the heavy curtains which are so dear to you: You do not even suspect that the day has already dawned outside.
– Aleksandr Solzhenitsyn

Summer Plans

I’ll be leaving in one week and staying in San Francisco for one month. I’ll be busy, to say the least. What should I do with the blog in the meantime? After all, it is the middle of the summer when everyone is travelling or enjoying the great outdoors and the online traffic is pitiful – my traffic is about half of what I had in April and May. So, I doubt I’ll be penning long thoughtful essays (unless I get really inspired once or twice).
I think I’ll sit down one of these days before I leave and schedule for automatic posting a Clock Quote to appear every day around 4am for the next month or so.
Perhaps I’ll pick some of my ‘greatest hits’ and repost them as well, perhaps two per day, all science, no politics. How about the entire Clock Tutorials plus some of the best from the Clock Zoo, Clock News and Friday Weird Sex Blogging categories? After all, my traffic is, even during the summer slump, double of what it was when I just joined scienceblogs.com, so there must be a bunch of readers who have not read some of the good old stuff yet.
I check ScienceDaily every night anyway, so I’ll probably continue to post my picks every or almost every day – that really takes just a few extra minutes.
I’ll meet a lot of people and take pictures, so I’ll post those whenever I find a minute and of course, I’ll let you know what I’m doing and what I’m seeing and whom I’m meeting while there (especially liveblogging the Science Foo Camp in the early August). And if you are in the area, e-mail me and we can meet in person.
I am starting to pack and I am wondering what books to take to read there. I got a bunch of Vernor Vinge books waiting to be read, but perhaps you have better ideas.
What’s the weather like in SF in July? Will I need a sweater for a chilly night? Something against rain? Or are t-shirts sufficient?

Conservatives, Animals and Cruelty

What Archy says…
Related

Blogging About Bush

Everyone always blogs about Bush…
After all, Bush is such an easy target – there is not a day that he or some of his buddies do not do something outrageously bad. And with the Media covering it as if it was OK, where else can one voice outrage if not on blogs.
bush_sad.jpg
So, it is refreshing to see people, for once, blogging about something else, for instance about bush…
burning%20Bush.jpg
Ooops, not the Burning Bush…
THE-BURNING-BUSH.jpg
And not this kind of bush either….
bush%20topiary_elephants.jpg
But bush in the sense of “hair” you know….
big%20hair.jpg
No, not that hair…
hair%20movie.jpg
No, not that hair either, this is a science blog, after all….
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But, this kind of hair and this kind of hair and this kind of hair and this kind of hair and this kind of hair

More on Framing Science

These three links have recently become freely available:
Chris Mooney’s interview with Treehugger.
Chris Mooney’s article in Harper’s Magazine/
And a report from the NYAS meeting.

Calling a Spade a Spade

Finally someone is standing up to the lunatics!
First shot was firm but polite.
The second was uncompromising – yes, they really are “crazies” and that is how we should call them. And it is high time someone stood up to them and called them on their calculated craziness and hate-speech.

Congratulations, Anton!

My friend (and the driving force behind all bloggy events in the Triangle area) Anton Zuiker has a new job! And not just any job – but a perfect job:

In August, I will take a new job at Duke University Health System as manager of internal communications. This will be a chance for me to mold a communications strategy that uses traditional tools (magazines, newsletters, posters) with new media tools (blogs, videocasts, wikis). I’m looking forward to the opportunities and challenges.

They really, really need Anton. Finding information online about anything that has to do with Duke University science and medicine has been, to put it very nicely and diplomatically now, frustrating and clunky. They have really tried over the past year to vigorously change that situation, but with very little visible results. Now, with Anton on board, I am confident that Duke Health System will soon become the example of good online communication that other schools will try to emulate in the future.

Congratulations, Robert

My friend, neighbor, blogger, frequent commenter on this blog, and fellow Edwards supporter, Robert Peterson just became a father again! Congratulations!

Condolences, Lindsay

I find it very difficult to say something nice, deep, profound or meaningful at the time of sorrow. But I am deeply saddened by the news that Lindsay Beyerstein’s father has died. Lindsay is a dear friend, a philosopher and a superb blogger (one of the rare bloggers who really became an online journalist in the best sense of the word), and her father, who I never had the fortune to meet, was an extraordinary man as well. So sorry!

Prometeo Network

Nature News just had an article announcing a new social networking site for physicians and biomedical scientists called Prometeo Network. Another one to check out and add to the ever-growing list of such new sites.

Bisphenol A – the epicenter of politicized science

Here is some chemistry of bisphenol A, but what is really interesting is this article about Fred vom Saal. It is quite revealing about the way industry produces bad science in order to protect its financial interests:

“The moment we published something on bisphenol A, the chemical industry went out and hired a number of corporate laboratories to replicate our research. What was stunning about what they did . . . was they hired people who had no idea how to do the work.”

Several of my grad school buddies worked on some aspect or other of neuroendocrinology, including environmental endocrine disruptors, including Bisphenol A itself (none of their work is cited in this article, though), so I am quite familiar with the topic through them and their manuscripts, talks, thesis defenses, seminar speakers they invited, and chat over beer. But this article reveals much, much more, e.g., :

By the end of 2004, they had identified 115 published studies on low doses of bisphenol A. They also found a troubling trend. Ninety percent of government studies found significant effects of bisphenol A at doses below the EPA’s lowest adverse effect level, but not a single industry study found any effect. Many of the industry studies, they pointed out, either used a rat strain with very low sensitivity to estrogen or misinterpreted failure to find effects with positive controls. Vom Saal and Hughes urged the EPA to conduct a new risk assessment on bisphenol A.

Yikes! Never having to work on rats before, if I got a manuscript to review and did not know that there were ties with the industry (and thus all the red flags and covering every single little detail, including re-doing the stats!), I probably would have never thought to ask my rat-friends about appropriateness of the strain used in the study and will never figured out I was duped!

After publishing her results, Hunt says, industry “paid people to read our paper and provide talking points, things they could use to say, ‘Well, we aren’t really sure about this, and well, they didn’t do that, and this is suspicious.’ It was such a learning experience for me because I had never had a piece of my work scrutinized in such detail, and I always thought my scientific peers were going to be the ones who were going to be most critical.” Hunt had been “peripherally aware” of the disputes between academics studying endocrine disruption and industry, “but you never knew whether these people were credible scientists or not, and then when you step your own foot into it and you watch, industry really did try to run damage control on our work.”

Yup, that is so typical – inject uncertainty. Chris Mooney’s “Republican War On Science” is chockfull of examples of this particular strategy.
Read the whole article – it is so revealing.
And read this related post: When Conflicts of Interest Threaten Scientific Integrity

My Picks From ScienceDaily

Foreign Herbivores May Be Key To Curbing Invasive Weeds:

Joint research with scientists in Argentina, Australia and China could lead to discovery of new biological control agents for several exotic weeds plaguing Florida and other U.S. states. Some of the worst offenders are hydrilla, Brazilian pepper, Chinese tallow and Australian pine. These and other aggressive invasive weeds occupy diverse habitats and cause many environmental problems, especially a decrease in biodiversity within infested areas.

How Fish Punish ‘Queue Jumpers’:

Fish use the threat of punishment to keep would-be jumpers in the mating queue firmly in line and the social order stable, a new study led by Australian marine scientists has found.

The Beetle’s Dilemma:

Large jaws are efficient in crushing hard prey, whereas small jaws are functional in capturing elusive prey. Researchers have suggested that such trade-offs between “force” and “velocity” could cause evolutionary diversification of morphology in animals such as birds, fish, and salamanders.

Which Came First: Primates’ Ability To See Colorful Food Or See Colorful Sex?:

The adaptive significance of the unique ability in many primates to distinguish red hues from green ones (i.e., trichromatic color vision) has always enticed debate among evolutionary biologists. The conventional theory is that primates evolved trichromatic color vision to assist them in foraging, specifically by allowing them to detect red/orange food items from green leaf backgrounds.

New Line Of Communication Between Nervous System Cells Discovered:

In a host of neurological diseases, including multiple sclerosis (MS) and several neuropathies, the protective covering surrounding the nerves — an insulating material called myelin — is damaged. Scientists at the Weizmann Institute of Science have now discovered an important new line of communication between nervous system cells that is crucial to the development of myelinated nerves — a discovery that may aid in restoring the normal function of the affected nerve fibers.

ClockQuotes

Throw out an alarming alarm clock. If the ring is loud and strident, you’re waking up to instant stress. You shouldn’t be bullied out of bed, just reminded that it’s time to start your day.
– Sharon Gold

Today’s carnivals

Grand Rounds Vol. 3, No. 40 are up on Wandering Visitor
Carnival of the Green # 83 is up on Dianovo.
Carnival of Education, The RoadTrip Edition is up on Education in Texas
Radiology Grand Rounds XIII are up on NeuroRAZiology & co.
Carnival of Homeschooling – Surgery Edition – is up on HomeschoolHacks.

Literary Medblogging Project

It’s Time for a Literary Medblogging Project…. :

Literary medblogging projects seem to occur on a semiannual basis: There was the “Dark and Stormy Night” series in December 2005, the “Literary Cheese Wheel” in July 2006, and the “Showcase” in December 2006. (Who would have thought that a website devoted to medical gadgets would link to all of these literary things?) The good Dr. Charles also hosted a travelling story, though it seems that his previous Blogger venue has been hijacked and thus, I cannot link to that literary work of art.
If you
* are a nursing student, nurse, medical student, or physician AND
* regularly maintain a blog that is considered a “medblog” AND
* enjoy storytelling AND
* would like to participate in literary medblogging project
then send me a note to express your interest.
I’m not sure what the project will entail just yet, but I’ve got a few ideas, some of which will depend on the level of medblogger interest. Maybe we’ll even make fun of the non-literary medblogs (coughKevincough). Or at least come up with a better word than “medblogger”. Yikes.

Project Exploration at Science Foo Camp

pe-logo.gifAs more and more people are slowly coming out of the woodwork and revealing they are going to Science Foo Camp, I am getting more and more excited about it! Yes, I have registered and reserved my hotel room already.
Sure, people like Neal Stephenson and Carl Djerassi are going to be there (as well as all those bloggers I linked to before – see the link above), but I am so excited to be able, for the first time, to meet in person Gabrielle Lyons, the power behind Project Exploration (the link to their site has been on my sidebar – scroll down – for about a year now). I wrote about it in more detail before.
They are gearing up for a busy summer season, taking inner-city kids to labs, museums and dinosaur digs. That, of course, costs something, but it is a cause worth supporting, so if you can, go here and see how you can help.

Blogrolling for Today

Yves Roumazeilles


Jacks of Science


Science of the Invisible


I, Platform (by Eric Rice)


CorpBlawg


Notes From Ukraine


Howard Hughes Precollege Program Summer 2007


Student Research at Duke


William Kamkwamba’s Malawi Windmill Blog

LIS BIGWIG 07 – a librarian’s dream for Facebook

Libraryman just gave a Presentation about it, and Danica likes it. Anyone using it yet?

Evolution in NY Times

You probably know by now, but you can access for free (at least for a couple of days) a whole slew of articles about evolution on the Science page of New York Times. Most are excellent, as usual (hey, it’s not the front page or some lukewarmly-pro-creationist he-said-she-said op-ed they tend to publish every now and then).
Most of the blogospheric responses are to the article by Douglas Erwin. As always, framing something as conflict sells the paper. I don’t think we are all eagerly awaiting a ‘paradigm shift’ in evolutionary biology. Much of the new thinking has been around for decades and is rapidly being absorbed into an ever-richer and ever-better scientific edifice. The best commentary comes from Larry, Greg, PZ and Jason.
Another NYT article I liked was about microbial evolution, written by my SciBling Carl Zimmer.
Finally, Jonathan is not 100% happy with the collection of quotes they put there.