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Bacterial ROS to the malaria rescue!

You've all heard of Malaria. It's bad. It infects hundreds of millions of people, mostly in developing nations. It rarely leads directly to death*, but the resulting illness can lay people out for days or weeks, increasing an already heavy economic burden on many of the poorest countries in the world. Folks from affluent regions can get medication to prevent or treat the illness, but treatments can be expensive and have nasty side effects, so it's not practical for most of the population. The good news is that Plasmodium, the parasite that causes the disease, can only be transmitted by…

A Taxonomy of Evolutionary Geneticists

Alex Palazzo managed to piss off some people with his taxonomy of biomedical disciplines. We have also learned that there are different types of physics geeks and anthropologists. (By the way, don't ever call me a geek; geeks bite the heads off of chickens. I'm a nerd.) I previously attempted to classify evolutionary biologists and named them after the important names in their particular field. It was actually a satire of the creationist ploy to call people Darwinists, so laugh. Now I'm going to further divide up the evolutionary geneticists (already a sub-set of biologists) into a bunch…

Belated news from AGBT

I've been remiss in blogging from the Advances in Genome Biology and Technology meeting here in Marco Island, Florida, primarily due to some panic-stricken last-minute changes to the slides for my own presentation last night. Fortunately the conference has been extremely well-covered by others: Sanger colleague Luke Jostins has blog posts up summarising day 1 and day 2 of the meeting; Dan Koboldt from MassGenomics has his first impressions and a review of the cancer genomics session; and Anthony Fejes is continuing the tradition of publishing extensive notes on every talk he attends.  There…

deCODEme's embarrassing data processing glitches - lessons for companies and customers

Late last week I noted an intriguing offer by personal genomics company deCODEme: customers of rival genome scan provider 23andMe can now upload and analyse their 23andMe data through the deCODEme pipeline.  On the face of it that's a fairly surprising offer. As I noted in my previous post, interpretation is what generates the real value for personal genomics companies, so giving it away for free seems a bizarre approach to business - especially for a company living on the edge of a financial precipice. However, I also argued that the intention here is likely to be to generate an opportunity…

Stormy World

It turns out that the "land hurricane" (technically, a super storm, aka extra tropical cyclone or bomb cyclone) may have been the biggest (most energetic) storm hisorically recorded for the region. Of particular interest is the pressure record (the ultimate measure for a storm) but also, the number of tornadoes and the damage due to winds was also impressive. And, there are interesting tropical things going on in the Atlantic Ocean. Is this all caused by Global Warming? Yes, probably. Gone are the days when the knee-jerk reaction must be "well, no, no one storm can be attributed to bla…

Barriers to the adoption of new surgical procedures

Last week, I wrote about factors that lead to the premature adoption of surgical technologies and procedures, the "bandwagon" or "fad" effect among surgeons, if you will. By "premature," I am referring to widespread adoption "in the trenches," so to speak, of a procedure before good quality evidence from science and clinical trials show it to be superior in some way to previously used procedures, either in terms of efficacy, cost, time to recover, or other measurable parameters. As I pointed out before, laparoscopic cholecystectomy definitely fell into that category. The popularity of the…

Global Conveyor Belt 2007: Hamster Wheel or Hemicuda?

Some new waves, pun intended, are being generated this week concerning the meridional overturning circulation (MOC). You are already familiar with the MOC as the ocean conveyor belt. To refresh your memory, the MOC is a thermohaline current, so named because currents are forced by differences in temperature and salinity both influencing the density of water, i.e. a density-driven current. So to explain the MOC, we will follow a single water mass and we'll call him Timmy. We'll start with Timmy in the equatorial Atlantic. Here, Timmy is warm and salty, like a pirate. The Gulf Stream is a…

ARCHIVE: 25 Things You Should Know About the Deep Sea: #9 The Deep-Sea Contains A Variety of Habitats

Besides the typical divisions we make for deep-sea habitats based on depth, it is important to note that the deep sea is not a homogenous landscape. Rather a variety of unique habitats, each with a specialized set of organisms, create a mosaic across the seafloor. 1. Soft-bottom benthos is the largest habitat and comprises those areas generally characterized by 'soft' sediments of silt, clay, or biogenic ooze. A variety of factors (disturbance from seafloor storms and erratic currents, patchiness in food input, sediment type, and depth) can lead to a further subset of micro- and…

On the fundaments of fantasy

Fantasy-nerd in-chief at The New York Times, Ross Douthat points me to an essay, Why is there no Jewish Narnia? As others have pointed out there are plenty of Jewish fantasy writers, including perhaps the most prominent mainstream fantasist today, Neil Gaiman. But this part caught my attention: ...and whether it is called Perelandra, Earthsea, Amber, or Oz, this world must be a truly alien place. As Ursula K. Leguin says: "The point about Elfland is that you are not at home there. It's not Poughkeepsie." Amber refers to Roger Zelazny's Amber series. Roger Zelazny's father was an immigrant…

But where does art intersect biology?

Dinner inside the belly of Iguanodon. My fellow scibling Jonah Lehrer has a new piece in SEED extending the argument from the end of his book Proust Was a Neuroscientist called "The Future of Science... Is Art?" It's pretty interesting, exploring the relation between physics and neuroscience to art, but biology (outside of the biology of the brain) is left out. I can't speak about fields like genetics and microbiology, areas where I lack expertise and a sense of history for the discipline, but as far of my own interests (particularly zoology and paleontology) art has often been essential…

Video Camera Options for video analysis

You have no idea how long I have been sitting on this one. I made some videos like a billion years ago, and still no post. Why? Oh well, here it is. I like video analysis of motion. I like looking at stuff on youtube or other video sites. But sometimes, you need to make the video yourself. What should you use? My personal favorite is a Flip Mino HD. It is small and quick. Are there other options? Sure. In this post, I will do the video analysis with the following cameras: Flip Mino HD A Canon PowerShot A470 Panasonic DMC-FZ18 Canon HV10 HD miniDV camcorder (you know, the kind that…

The speedy magma of Chaiten (and it's still going!)

Chaiten has made it back into the news in the past couple days, both with new events at the caldera and with findings from the initial blast in May 2008. Here goes: Chaiten erupting in 2008. Third Dome Spotted The latest USGS/SI Weekly Volcanic Activity Report mentions that over the last week, Chaiten experienced what was likely a significant dome collapse of one of the two domes growing in the caldera. People living close enough to the volcano to see the ash plume noticed it became larger and darker on September 29th. Afterwards, visual observations of the caldera by air confirmed that a…

What do Haeckel's embryos signify?

Casey Luskin, Disco. 'Tute spinner, has recently relaunched a fight over whether and how textbooks use embryological drawings from Ernst Haeckel's 19th century popular works. In his two posts (excerpting from a jumbled essay he wrote for a law review), he repeatedly claims that those drawings are fraudulent. To wit: textbooks in use today, in arguing for evolution, still use Haeckelâs fraudulent embryo drawings That Haeckelâs drawings were fraudulent and have been used in textbooks is essentially beyond dispute Stephen Jay Gould recognized that Haeckelâs drawings ⦠fraudulently obscured…

Spain, genes & Moors

The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula: Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations…

The Trump War on Science: Is the March for Science too political or not political enough?

Is the March for Science (and all it's satellite marches) too political or not political enough? The text on their website gives a sense of where the organizers are coming from: SCIENCE, NOT SILENCE The March for Science is a celebration of our passion for science and a call to support and safeguard the scientific community. Recent policy changes have caused heightened worry among scientists, and the incredible and immediate outpouring of support has made clear that these concerns are also shared by hundreds of thousands of people around the world. The mischaracterization of science as a…

Head, Shoulders, Knees, and Toes

Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools. If you already know all about ESTs, you might want to jump ahead and read about the activity. If…

Food poisoning and factory farm animals: caveat lector

A new study of foodborne illness has just been published and has made quite a bit of news. The typical headline is something like: "Animals Farmed For Meat Are The No. 1 Source Of Food Poisoning Bug, Study Shows." That makes it sound like most cases of food poisoning are from a particular bug and that bug comes from farm animals. Although it is inaccurate, the stories beneath the headline don't do much to dispel it: Researchers from Lancashire, England, and Chicago, IL, have discovered that animals farmed for meat are the main source of bacteria responsible for food poisoning. They suggested…

The Tet Zoo tour of Libya (part II): of larks and buntings

After a little delay, I'd like to continue regaling you with, if I may, my assorted musings on my excursion to the Great Socialist People's Libyan Arab Jamahiriya. In other words, I want to talk more about Libya... In the previous article I spoke about some of the animals I saw both in the more urban areas, and out in the countryside. If you go to north Africa (and if you're interested in ornithology), you hope to see larks. Larks (alaudids) do well in the deserts and semi-deserts of the region, and there are lots of species to see, some of which are very, very neat. If you think not, you're…

New and Exciting in PLoS ONE

There are 47 articles published in PLoS ONE this week. Here are some of the coolest titles - you go and find your own. Ultrasonic Vocalizations Induced by Sex and Amphetamine in M2, M4, M5 Muscarinic and D2 Dopamine Receptor Knockout Mice: Adult mice communicate by emitting ultrasonic vocalizations (USVs) during the appetitive phases of sexual behavior. However, little is known about the genes important in controlling call production. Here, we study the induction and regulation of USVs in muscarinic and dopaminergic receptor knockout (KO) mice as well as wild-type controls during sexual…

Visiting Darwin's Home, Part 1: Down House

tags: Sandwalk, Down House, Darwin, nature, photography, London, England, Bromley, England Darwin's Down House near Bromley, England, a short train ride away from London. This view of the house was snapped from the gardens in back of the house. If you look closely, you can see part of the cafe (under the blue umbrellas) to the right of the crooked tree in this picture. I am really proud of this photograph, by the way. Image: GrrlScientist 31 August 2008 [larger view]. Sunday, the day after the Nature Network Science Blog conference had concluded, Mike, Mo and I caught a train to Bromley,…

How the Earth moves, and how do we know?

"Nature is relentless and unchangeable, and it is indifferent as to whether its hidden reasons and actions are understandable to man or not." -Galileo Galilei All of science is rooted in the idea that natural phenomena can be explained naturally, and that if we want to know how anything in the Universe works, all we need to do is ask the Universe the right questions, and the answers will appear. So what about the question of the night sky, and why it appears to rotate the way it does? Image credit: Peter Michaud (Gemini Observatory), AURA, NSF. There are two straightforward explanations for…

Say Something Smart

"You must learn to talk clearly. The jargon of scientific terminology which rolls off your tongues is mental garbage." -Martin H. Fischer I've always thought that the Universe is absolutely amazing; that everything from the tiniest indivisible particles all the way up to the largest structures and superstructures making up the Universe has an amazing story to tell, if only we can figure out its secrets. Image credit: Boylan-Kolchin et al. (2009) for the Millenium-II simulation; MPA Garching. When I first learned some of them for myself, I was a graduate student, immersed in the minutiae and…

Messier Monday: The Triangulum Galaxy, M33

"Let the great world spin for ever down the ringing grooves of change." -Alfred Lord Tennyson Welcome back, for another Messier Monday here on Starts With A Bang! Each Monday, we've been taking a look at one of the 110 Deep-Sky Objects that make up the Messier catalogue, a mix of clusters, nebulae, galaxies and more, all visible from most locations on Earth with even the most basic of astronomical equipment. Image credit: Greg Scheckler, from his 2008 Messier marathon, where he nabbed 105/110. When you think of our local group of galaxies, you probably think of the Milky Way and Andromeda…

How can we see black holes?

"According to the special theory of relativity nothing can travel faster than light, so that if light cannot escape, nothing else can either. The result would be a black hole: a region of space-time from which it is not possible to escape to infinity." -Stephen Hawking You may have encountered objects that are the same size as one another, but have very different masses. Image credit: Basic Science Supplies / © Accelerate Media. This is because they're made out of different elements. The higher you go in the periodic table, the larger and more massive your individual atoms are, and so…

Ultra-High-Energy Cosmic Rays Explained?

I have a bunch of science news sources in my RSS feeds, and every evening, I scan through the accumulated articles to try to figure out what physics-related stories there are to talk about. Sometimes, it's hard to find anything, but other days, you get stories that lead to four press releases at EurekAlert (one, two, three, four), a write-up at Backreaction, a Physics World news story, and a Dennis Overbye piece in the New York Times. I guess I really ought to say something about the new results from the Pierre Auger Observatory, published this week in Science (Science 318, 938 (2007), if…

XMRV and Chronic Fatigue and Autism: Praise from Caesar

Thanks once again to Trine Tsouderos: Chronic fatigue and XMRV -- what one researcher (who's been there) has to say Weiss' main point is that the history of retrovirology is littered with the debris of papers finding a link between a virus and a disease that later turned out to be false results caused by contamination. "There has been a long succession of 'rumor' viruses posing as tumor viruses and promulgated as the cause of chronic human diseases," Weiss wrote. Researchers at the Whittemore Peterson Institute for Neuro-Immune Disease, which led the team that published the original paper,…

Dawkins in Maryland

Having had so much fun during my last sojourn to the University of Maryland, I decided to repeat the experience this past Wednesday. Richard Dawkins was speaking, you see. Here he is on stage during the introductions:   I attended with Douglas Gill and Clinton Jenkins, both of the University of Maryland Biology Department. And since we are all highly connected VIP's, we wound up sitting in the center of the second row. Impressed? I sure was! Dawkins had little trouble filling the venue:   There was an overflow room as well. My informal impression was that a significant majority…

Is Executive Function a Valid Construct?

Originally posted on 12/16 2006: The term "executive function" is frequently used but infrequently defined. In attempting to experimentally define executive functions in terms of their relationship to age, reasoning and perceptual speed, Timothy Salthouse reviewed the variety of verbal definitions given to construct of "executive function." Although these differ in terminology and emphasis, they are clearly addressing a similar concept: "Executive functions cover a variety of skills that allow one to organize behavior in a purposeful, coordinated manner, and to reflect on or analyze the…

Greetings from the Children of Planet Earth

In 1977, NASA sent a pair of unmanned probes named Voyager 1 and Voyager 2 into space. Among the infrared spectrometers and radio receivers included on each probe were identical copies of the same non-scientific object: the Voyager Golden Record. Sheathed in a protective aluminum jacket, the Record is a 12-inch gold-plated copper disk containing sounds and images chosen to portray the diversity of life on Earth: bird calls, whale songs, the sounds of surf, wind, and thunder, music from human cultures, and some 55 greetings in a range of languages, alive and dead. Like lonely time capsules,…

Read the Internet, Speak English

In case you didn't know, reality is science fiction. If you doubt me, read the news. Read, for example, this recent article in the New York Times about Carnegie Mellon's "Read the Web" program, in which a computer system called NELL (Never Ending Language Learner) is systematically reading the internet and analyzing sentences for semantic categories and facts, essentially teaching itself idiomatic English as well as educating itself in human affairs. Paging Vernor Vinge, right? NELL reads the Web 24 hours a day, seven days a week, learning language like a human would -- cumulatively, over…

Enjoying Florida: Experimental Prototype Community of Tomorrow

"Experimental Prototype Community of Tomorrow" - better known as EPCOT - was originally Walt Disney's vision of a perfect city, home to 20,000 people. In his words, "EPCOT... will take its cue from the new ideas and new technologies that are now emerging from the creative centers of American industry. It will be a community of tomorrow that will never be completed, but will always be introducing and testing and demonstrating new materials and systems. And EPCOT will always be a showcase to the world for the ingenuity and imagination of American free enterprise." Disney's vision was never…

The Friday Fermentable - with guest blogger, Erleichda

Welcome to our 2nd installment of The Friday Fermentable, Terra Sigillata's Friday fun-blogging feature. You can read our mission statement at the original post last week, but the goal, briefly, is to celebrate the particular class of natural products that result from the yeast-based fermentation of sugars from grapes, malted barley, and any plant-based sugar source. Our target audience is the graduate student or postdoc who, in my day, was usually pretty poor but starving for culture and knowledge (Shelley Batts' $25K graduate stipend at Michigan notwithstanding). So, I spoke last week of…

Finding a home for jaguars

A jaguar (Panthera onca). From Flickr user Prosper 973. One year ago this week Macho B was euthanized. He had been captured in mid-February of 2009, the only known jaguar living inside the United States, but after he was caught and fitted with a radio collar his health quickly deteriorated. When he nearly stopped moving he was recaptured, taken to the Phoenix zoo, and put to sleep when it was discovered that he was suffering from irreparable kidney failure. At first it seemed as if his capture was a lucky accident, but a later investigation by the Fish and Wildlife Service found that the…

A Short-Faced Bear's Mammoth Picnic

The stench emanating from the putrefying mammoth carcass carried for miles. Though kept out of the sun by the long shadows of the surrounding pine trees, the corpse reeked as the flesh, sinew, and bone of the mammoth's body were slowly parceled out into the ecosystem by scavengers. The woolly elephant's eyes had been pecked out long ago, and the intricate musculature of its trunk lay in tatters, but there was still plenty of meat to go around. The grisly death site buzzed with activity as less magisterial creatures went about their dirty work. Black birds jostled for the best access to blood-…

Calendrical Savants

Get out your stop watches. Press start, and then answer this question: What day of the week was August 17, 1932? How long did it take you? Oh, the answer is Wednesday, by the way. I cheated, and used a calculator, because I'm not very good at calendrical calculations, but some people, usually of relatively low overall intelligence, can calculate the day of the week for any date from the 20th or 21st century in fewer than three seconds (dates from other centuries take longer, with times increasing with distance from the present, especially for dates in the future)1. Over the last few years,…

When a parent won't abide by the understanding behind a non-medical exemption to school vaccine mandates

As I write this, I'm kind of beat. The reason for this is simple. Traveling sucks the energy out of me, and I just got back from almost four days in Houston for the Society of Surgical Oncology (SSO) meeting. Yes, I was a mere dozen (at most) miles from that Heart of Darkness known as the Burzynski Clinic for a few days, and I didn't even succumb to the temptation to catch a cab out there and take a selfie with the Burzynski Clinic in the background. Part of the reason was that it would just be more expense than it's worth. The other part of the reason is that it would be a bit hard to…

Muslims shouldn't be vaccinated?

Via Black Triangle, I'm made aware of another example of religious fundamentalism interfering with sound health care: A MUSLIM doctors' leader has provoked an outcry by urging British Muslims not to vaccinate their children against diseases such as measles, mumps and rubella because it is "un-Islamic". Dr Abdul Majid Katme, head of the Islamic Medical Association, is telling Muslims that almost all vaccines contain products derived from animal and human tissue, which make them "haram", or unlawful for Muslims to take. Islam permits only the consumption of halal products, where the animal has…

Homo sapiens: What We Think About Who We Are (Revised and Updated)

From De humani corporis fabrica libri septem (1543) by Andreas Vesalius In 1646, the first edition of Sir Thomas Browne's Pseudodoxia epidemica (or Vulgar Errors) first went into print, Browne's volume being an attempt to refute many of the erroneous "received tenets and commonly presumed truths" that would not go away despite their inaccuracy. Among the bevy of fallacious notions included in the book was a subject that often was a point of contention at the time; if the Biblical Eve was derived from one of Adam's ribs, from which side was the rib taken and therefore shouldn't the sexes…

90,000

Hello to my 90,000th visitor, who came in from the Culture Wars Channel, and is good at hiding wher s/he is coming from except that it is North America. Still on here right now? Say something in the comments.

A useful categorization

I like Greg Laden's taxonomy of Horwitzian Academic "Freedom" bills: "Academic Freedom" bills seem to come in two flavors: Those that protect students from the possibility of learning certain things, and those that protect subversive teachers from getting in trouble for being bad teachers.

Multicellular claymation

I'm liking these CreatureCast videos from Casey Dunn — I showed the first in this series, now here's the second. It uses very simple animation to illustrate basic concepts…like the evolution of multicellularity in this one. CreatureCast Episode 2 from Casey Dunn on Vimeo.

PLoS & Mendeley live on the Web! Science Hour with Leo Laporte & Dr. Kiki (video)

Leo Laporte and Kirsten Sanford (aka Dr.Kiki) interviewed (on Twit.tv) Jason Hoyt from Mendeley and Peter Binfield from PLoS ONE about Open Access, Science 2.0 and new ways of doing and publishing science on the Web. Well worth your time watching!

Writers' Blog Carnival Available

tags: writers, writing, blog carnival Another edition of Writers from across the blogosphere is now available for you to enjoy. Along with all the other links they have, this blog carnival includes two submissions from me that you might not have read yet.

Fossil Jewelry

These are totally cool! See the Stephaniegeology etsy store for more. What she did is get some actual fossils from Doug Grove (husband of Tatjana Jovanovic-Grove), make molds out of these fossils and then make jewelry from those molds. Fascinating!

Clock Quotes

Nature gives to every time and season some beauties of its own; and from morning to night, as from the cradle to the grave, it is but a succession of changes so gentle and easy that we can scarcely mark their progress. - Charles Dickens

Joe P. II

Joe P. is ok For PSU & xPSU: heard from him today, they're still out in hostile country and took some more casualties. He appreciates hearing from people, just casual chat stuff. More care packages wouldn't hurt either, he can always share.

Viper Eating A Shrew

Came across this viper on a bike path one evening in July. It got shy when we stood around admiring it, so it disengaged from the shrew and slithered off into the greenery. May have saved it from getting run over by a bike.

Faking Evolution is Hard Work

"The Fossil-Maker's Blues", by Steven Brust. Inspired by a comment in this post about paleoarcheology. It's calcium and marrow and mix 'em fine I'm on the job from nine to nine Oh lord won't someone set me free From the Devil's Fossil Factory.

Non-Dorky Poll: Distressing Public Art

A quick photo poll question: Which of these statues seen on the street in Japan is more disturbing? This chubby nude saxophonist from Himeji: Or this small child riding a giant carp from Takayama: Leave your answer in the comments. You can only pick one.

Unhealthy Diet in Ancient Near East

This is an old story being resurrected wiht new data: Biblical diet 'unhealthy' A new study into the diet of ancient Israel has revealed that far from being 'the land of milk and honey', its inhabitants suffered from the lack of a balanced diet.