In the wake of the sequencing of the human genome in the early 2000s, genome pioneers and social scientists alike called for an end to the use of race as a variable in genetic research. Unfortunately, by some measures, the use of race as a biological category has increased in the postgenomic age. Although inconsistent definition and use has been a chief problem with the race concept, it has historically been used as a taxonomic categorization based on common hereditary traits (such as skin color) to elucidate the relationship between our ancestry and our genes. We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way. - An editorial in Science exploring the conundrum facing genomic researchers where race is both fundamentally flawed as a scientific model and violently dangerous but still the only consistent lens through which study participants understand the information they have about their own connection to human diversity [more inside]
"Don't look at them directly,” Rie Henriksen whispers, “otherwise they get suspicious.” The neuroscientist is referring to a dozen or so chickens loitering just a few metres away in the car park of a scenic observation point for Opaekaa Falls on the island of Kauai, Hawaii. As the two try to act casual by their rented car, a jet-black hen with splashes of iridescent green feathers pecks its way along a trail of bird feed up to a device called a goal trap. Wright tugs at a string looped around his big toe and a spring-loaded net snaps over the bird. After a moment of stunned silence, the hen erupts into squawking fury. Biologists see in the feral animals an improbable experiment in evolution: what happens when chickens go wild?[more inside]
As the West African Ebola epidemic stretches into its 10th month: researchers have identified the likely cause of the initial outbreak: a young boy playing with bats in a village in Guinea. The NY Times considers how the opportunity to contain the epidemic was missed and the effects of Ebola on West African economies. Vanity Fair takes a look at the failure to contain the disease within Guinea, Frontline goes to "Ground Zero" in Guinea, and searches for a missing Ebola patient. Meanwhile, West Africans welcomed Christmas (previously) and the New Year. Africa Stop Ebola!
In this paper, we examine a first-year torque and angular acceleration problem to address a possible use of the forelimbs of Tyrannosaurus rex. A 1/40th-scale model is brought to the classroom to introduce the students to the quandary: given that the forelimbs of T. rex were too short to reach its mouth, what function did the forelimbs serve? This issue crosses several scientific disciplines including paleontology, ecology, and physics, making it a great starting point for thinking “outside the box..." Lipkin and Carpenter have suggested that the forelimbs were used to hold a struggling victim (which had not been dispatched with the first bite) while the final, lethal bite was applied. If that is the case, then the forelimbs must be capable of large angular accelerations α in order to grab the animal attempting to escape. The concepts of the typical first-year physics course are sufficient to test this hypothesis... Naturally, student love solving any problem related to Tyrannosaurus rex.
"If a woman is objectified in a relationship, the research indicates, it's more likely that her male partner will sexually coerce and pressure her." [more inside]
Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. Naturalists first became aware of our invisible lodgers in the 1600s, but it wasn’t until the past few years that we’ve become really familiar with them. This recent research has given the microbiome a cuddly kind of fame. We’ve come to appreciate how beneficial our microbes are — breaking down our food, fighting off infections and nurturing our immune system. It’s a lovely, invisible garden we should be tending for our own well-being. But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example.[more inside]
"For many a female octopus, laying eggs marks the beginning of the end (pdf, 1.11MB). She needs to cover them and defend them against would-be predators. She needs to gently waft currents over them so they get a constant supply of fresh, oxygenated water. And she does this continuously, never leaving and never eating. (via)."
Bacterial diseases cause millions of deaths every year. Most of these bacteria were benign at some point in their evolutionary past, and we don’t always understand what turned them into disease-causing pathogens. In a new study, researchers have tracked down when this switch happened in one flesh-eating bacteria. They think the knowledge might help predict future epidemics. [more inside]
Harvard University and XVIVO have come together again (Previouslyw/ a commercial focus, Previouslierw/an Academic focus) to add to the growing series of scientific animations for BioVisions -- Harvard's multimedia lab in the department of Molecular and Cellular Biology. 'Protein Packing' strives to more accurately depict the molecular chaos in each and every cell, with proteins jittering around in what may seem like random motion. Proteins occupy roughly 40% of the cytoplasm, creating an environment that risks unintentional interaction and aggregation. Via diffusion and motor protein transport, these molecules are directed to sites where they are needed.
Much of this is no doubt inspired by the beautiful art and explained illustrations of David Goodsell, a biologist at Scripps who has been accurately portraying the crowdedness of the cellular landscape for a long time now.[more inside]
This Video Will Hurt
A detailed explanation of a fascinating field of science and medicine by the always interesting C.G.P. Grey.[more inside]
Because who is perfect? Disabled mannequins will be eliciting astonished looks from passers-by on Zurich's Bahnhofstrasse today. Between the perfect mannequins, there will be figures with scoliosis or brittle bone disease modelling the latest fashions. One will have shortened limbs; the other a malformed spine. The campaign has been devised for the International Day of Persons with Disabilities by Pro Infirmis, an organisation for the disabled.
Busty Mannequins and an Inflated Sense of Beauty in Venezuela In Venezuela, women are confronted with a culture of increasingly enhanced physiques fueled by beauty pageants and plastic surgery. - The New York Times [more inside]
Busty Mannequins and an Inflated Sense of Beauty in Venezuela In Venezuela, women are confronted with a culture of increasingly enhanced physiques fueled by beauty pageants and plastic surgery. - The New York Times [more inside]
"On a sunny day in 1998, Maura Gillison was walking across the campus of Johns Hopkins University in Baltimore, Maryland, thinking about a virus. The young oncologist bumped into the director of the university's cancer centre, who asked politely about her work. Gillison described her discovery of early evidence that human papillomavirus (HPV) — a ubiquitous pathogen that infects nearly every human at some point in their lives — could be causing tens of thousands of cases of throat cancer each year in the United States. The senior doctor stared down at Gillison, not saying a word. “That was the first clue that what I was doing was interesting to others and had potential significance,” recalls Gillison."
Human papillomavirus is causing a new form of head and neck cancer— leaving researchers scrambling to understand risk factors, tests and treatments.[more inside]
Abstract: Cycling is popular among children, but results in thousands of injuries annually. In recent years, many states and localities have enacted bicycle helmet laws. We examine direct and indirect effects of these laws on injuries. Using hospital-level panel data and triple difference models, we find helmet laws are associated with reductions in bicycle-related head injuries among children. However, laws also are associated with decreases in non-head cycling injuries, as well as increases in head injuries from other wheeled sports. Thus, the observed reduction in bicycle-related head injuries may be due to reductions in bicycle riding induced by the laws. [FULL TEXT PDF] [more inside]
False memories of fabricated political events [ABSTRACT]. In the largest false memory study to date, 5,269 participants were asked about their memories for three true and one of five fabricated political events. Each fabricated event was accompanied by a photographic image purportedly depicting that event. Approximately half the participants falsely remembered that the false event happened, with 27% remembering that they saw the events happen on the news. Political orientation appeared to influence the formation of false memories, with conservatives more likely to falsely remember seeing Barack Obama shaking hands with the president of Iran, and liberals more likely to remember George W. Bush vacationing with a baseball celebrity during the Hurricane Katrina disaster. A follow-up study supported the explanation that events are more easily implanted in memory when they are congruent with a person's preexisting attitudes and evaluations, in part because attitude-congruent false events promote feelings of recognition and familiarity, which in turn interfere with source attributions. [FULL TEXT PDF AVAILABLE HERE] [more inside]
"Hundreds (maybe thousands) of spiders congregate between poles in the town of Santo Antonio de Plantina / PR." [more inside]
The practice of lying to one's children to encourage behavioral compliance was investigated among parents in the US (N = 114) and China (N = 85). The vast majority of parents (84% in the US and 98% in China) reported having lied to their children for this purpose. Within each country, the practice most frequently took the form of falsely threatening to leave a child alone in public if he or she refused to follow the parent. Crosscultural differences were seen: A larger proportion of the parents in China reported that they employed instrumental lie-telling to promote behavioral compliance, and a larger proportion approved of this practice, as compared to the parents in the US. This difference was not seen on measures relating to the practice of lying to promote positive feelings, or on measures relating to statements about fantasy characters such as the tooth fairy. Findings are discussed with reference to sociocultural values and certain parenting-related challenges that extend across cultures. [HTML] -- [PDF] [more inside]
This week the FDA announced that they were approving a new kind of flu vaccine. Nestled in the articles was an odd fact: unlike traditional flu vaccines, the new kind, called Flublok, is produced by the cells of insects. This is the kind of detail that you might skim over without giving it a thought. If you did pause to ponder, you might be puzzled: how could insects possibly make a vaccine against viruses that infect humans? The answer may surprise you. To make vaccines, scientists are tapping into a battle between viruses and insects that’s raging in forests and fields and backyards all around us. It’s an important lesson in how to find new ideas in biotechnology: first, leave biologists free to explore the weirdest corners of nature they can find. [more inside]
The Norovirus: A Study in Puked Perfection, "Each norovirus carries just nine protein-coding genes (you have about 20,000). Even with that skimpy genetic toolkit, noroviruses can break the locks on our cells, slip in, and hack our own DNA to make new noroviruses. The details of this invasion are sketchy, alas, because scientists haven’t figured out a good way to rear noroviruses in human cells in their labs. It’s not even clear exactly which type of cell they invade once they reach the gut. Regardless of the type, they clearly know how to exploit their hosts. Noroviruses come roaring out of the infected cells in vast numbers. And then they come roaring out of the body. Within a day of infection, noroviruses have rewired our digestive system so that stuff comes flying out from both ends." [more inside]
Woese once said of himself and his work that when a wise man points out the moon, only a fool looks at the finger. Let us all be fools if just for a moment .
Microbiology's Scarred Revolutionary(PDF), Carl Woese (pron.: /ˈwoʊz/), a biophysicist and evolutionary microbiologist whose discovery 35 years ago of a “third domain” of life in the vast realm of micro-organisms altered scientific understanding of evolution, died on Sunday at his home in Urbana, Ill. He was 84. [more inside]
Association of Coffee Drinking with Total and Cause-Specific Mortality [FULL TEXT HTML]: "We used data from a very large study, the National Institutes of Health (NIH)–AARP Diet and Health Study (ClinicalTrials.gov number, NCT00340015), to determine whether coffee consumption is associated with total or cause-specific mortality. The current analysis, involving more than 400,000 participants and 52,000 deaths, had ample power to detect even modest associations and allowed for subgroup analyses according to important baseline factors, including the presence or absence of adiposity and diabetes, as well as cigarette-smoking status." [more inside]
Deciphering the Tools of Nature’s Zombies: The ability of parasites to alter the behaviour of their hosts fascinates both scientists and non-scientists alike. One reason that this topic resonates with so many is that it touches on core philosophical issues such as the existence of free will. If the mind is merely a machine, then it can be controlled by any entity that understands the code and has access to the machinery. This special issue of The Journal of Experimental Biology highlights some of the best-understood examples of parasite-induced changes in host brain and behaviour, encompassing both invertebrate and vertebrate hosts and micro- and macro-parasites. Full issue annotated inside: [more inside]
Contesting the “Nature” Of Conformity: What Milgram and Zimbardo's Studies Really Show [FULL TEXT] [more inside]
An influential US advocacy group has set a deadline to beat breast cancer by 2020. But it puts public trust at risk by promising an objective that science cannot yet deliver. [more inside]
In just a few weeks single-celled yeast have evolved into a multicellular organism, complete with division of labour between cells. This suggests that the evolutionary leap to multicellularity may be a surprisingly small hurdle. More from Scientific American blogs. [Full Text PDF of the Publication of Note] [more inside]
What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. [more inside]
Our study, “Bicyclists’ Injuries and the Cycling Environment” (the BICE Study), examined which route types are associated with higher and lower cycling injury risk. It examined the association between bicyclists’ injuries and the cycling environment (e.g., route types, intersection types). Taking place in Toronto and Vancouver between May 2008 and November 2009, the participants were adults who were injured while bicycling and who attended hospital emergency departments for treatment. Five hospitals recruited participants, 690 in total. [more inside]
One of the many problems farmers of various kinds of legumes need to deal with is the pea aphid. They reproduce incredibly fast and live by sucking the sap out of the plants, an electron micrograph of one in action. However, while they are terrifying parasites of legumes, they have their own yet more horrific parasites, a parasitoid wasp. Here is a really nice close up picture of one doing its thing, a video of the act, and here is a brain meltingly horrific video of a dissection of the mummified aftermath 8 days later. Essentially, these wasps deposit their eggs in a pea aphid and the growing larva feeds on it, developing there for about a week, and then consuming the host from the inside out like a Xenomorph. When it’s done, the wasp larva dries the aphid’s cuticle into a papery brittle shell and an adult wasp emerges from the aphid mummy. Legume farmers love them, and you can even order their mummies online these days. However, farmers noticed that the wasps didn't work as effectively on all of the aphids, and so researchers went to work figuring out why. It turns out that all aphids have a primary bacterial endosymbiont living inside their cells, in addition to and just like a mitochondria, and that many have some combination of five other secondary endosymbionts. Interestingly, two of those other five, Hamiltonella defensa and Serratia symbiotica have been shown to confer varying levels of resistance to the parasitoid wasp, allowing the aphid to survive infection. However, it turns out that there is yet one more layer to this story, [more inside]
The Puzzle of Plastid Evolution: A comprehensive understanding of the origin and spread of plastids remains an important yet elusive goal in the field of eukaryotic evolution. Combined with the discovery of new photosynthetic and non-photosynthetic protist lineages, the results of recent taxonomically broad phylogenomic studies suggest that a re-shuffling of higher-level eukaryote systematics is in order. Consequently, new models of plastid evolution involving ancient secondary and tertiary endosymbioses are needed to explain the full spectrum of photosynthetic eukaryotes. [Full Text HTML] [Full Text PDF] [more inside]
Mitigating Mutational Meltdown in Mammalian Mitochondria PLoS Biol 6(2): e35. [The PDF, where you can read the paper in its much prettier intended format.]
Mitochondria are remarkable microorganisms. About two billion years ago, their distant free-living ancestors hooked up with a truly foreign lineage of archaebacteria and started a genomic merger that led to the most successful coevolved mutualism on the planet: the eukaryotic cell. Along the way, evolving mitochondria lost a lot of genomic baggage, entrusted their emerging hosts with their own replication, sorted out genomic conflicts by following maternal inheritance, and have mostly abstained from sex and recombination. What mitochondria did retain was a subset of genes that encode critical components of the electron transport chain and ATP synthesis enzymes that carry out oxidative phosphorylation. Because mitochondria house the biochemical machinery that requires us to breathe oxygen, it was first assumed that mitochondrial genes would show very slow rates of molecular evolution. So it was big news almost 30 years ago when mitochondrial DNA (mtDNA) evolution was observed to be quite rapid . How could the genes for a highly conserved and critical function sustain the consequences of high mutation pressure and permit rapid rates of nucleotide substitution between species? Without the benefits of recombination, where offspring can carry fewer mutations than either parent, mutations should accumulate in mitochondrial genomes through the random loss of less-mutated genomes, a process referred to as Muller's ratchet [2,3]. How have mitochondria avoided a mutational meltdown, or at least significant declines in fitness?Here is a jaw droppingly beautiful 3D animation of what Mitochindria look like in action. [more inside]
Constitutive formation of caveolae in a bacterium. [Full Text]
Caveolin plays an essential role in the formation of characteristic surface pits, caveolae, which cover the surface of many animal cells. The fundamental principles of caveola formation are only slowly emerging. Here we show that caveolin expression in a prokaryotic host lacking any intracellular membrane system drives the formation of cytoplasmic vesicles containing polymeric caveolin. Vesicle formation is induced by expression of wild-type caveolins, but not caveolin mutants defective in caveola formation in mammalian systems. In addition, cryoelectron tomography shows that the induced membrane domains are equivalent in size and caveolin density to native caveolae and reveals a possible polyhedral arrangement of caveolin oligomers. The caveolin-induced vesicles or heterologous caveolae (h-caveolae) form by budding in from the cytoplasmic membrane, generating a membrane domain with distinct lipid composition. Periplasmic solutes are encapsulated in the budding h-caveola, and purified h-caveolae can be tailored to be targeted to specific cells of interest.Elio Schaechter writes in plain English about how fantastically amazing and unexpected the researchers actually pulling this off is, and he also talks about it in more detail in his podcast.
Provirophages and transpovirons as the diverse mobilome of giant viruses
Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7 in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.[Full Text PDF] and two explanations in English [more inside]
There are fewer microbes out there than you think. New estimate reduces the number of microbes on Earth by around half. [more inside]
Does anesthesiology have a problem? Final version of report suggests Fujii will take retraction record, with 172
In the wake of a very thorough and damning statistical analysis of 168 of his papers, published in March, Japanese investigators have concluded that Yoshitaka Fujii, fabricated his results in at least 172 published studies; shattering the previous record for most retracted papers. Considered an expert in postoperative nausea and vomiting, his "incredibly nice" findings drew scrutiny in 2000, but he continued to publish prolifically for more than a decade. Here are the published results of the Japanese Society of Anesthesiology's Special Investigation Committee, with an annotated list of all of his papers (PDF). The Retraction Watch also considers not only the depth of Fujii's betrayal but also whether the discipline of anesthesiology itself has a problem as it weighs in. [more inside]
What if a deadly epidemic was burgeoning and almost nobody noticed? In the latest issue of PLoS Neglected Tropical Diseases, a distinguished group of virologists, epidemiologists and infectious-disease specialists say that’s not a hypothetical question. They argue that Chagas disease, a parasitic infection transmitted by blood-sucking insects, has become so widespread and serious — while remaining largely unrecognized — that it deserves to be considered a public health emergency. [more inside]
Traffic jams without bottlenecks—experimental evidence for the physical mechanism of the formation of a jam
The mathematical theory behind shockwave traffic jams was developed more than 20 years ago using models that show jams appearing from nowhere on roads carrying their maximum capacity of free-flowing traffic - typically triggered by a single driver slowing down. After that first vehicle brakes, the driver behind must also slow, and a shockwave jam of bunching cars appears, traveling backwards through the traffic. The theory has frequently been modeled in computer simulations, and seems to fit with observations of real traffic, but had never been recreated experimentally until recently (PDF of SCIENCE). The authors also released video of their experiments which has since been posted to YouTube. [more inside]
How Corporations Corrupt Science at the Public's Expense: Report looks at methods of corporate abuse, suggests steps toward reform [Full Report (PDF)] [Executive Summary (PDF)] [more inside]
As reported by Agence France Presse, the Guardian and the New York Times, last week four families in Kano, Nigeria received $175,000 each as compensation for the deaths of their children, who participated in a drug trial conducted by Pfizer Inc. (Wikileaks links inside) [more inside]
"On the surface, it looks as if our identity as male or female is determined in the womb. The decision seems final – a genetic switch flicks towards either setting, and locks into place for the rest of our lives." [more inside]
Who would have ever thought that Gila monster saliva would be a good place to look for a type 2 diabetes drug?
Improving Peptides: Small firms develop better peptide drug candidates to expand this pharmaceutical class and attract big pharma partners
With the help of Bill Gates, the World's efforts to eradicate polio (PDF) have over the last few years gained a great deal of new hope (TED) [more inside]
So far this year there have been 118 cases of measles reported in the United States. [more inside]
Health ministers from the World Health Organization's (WHO's) 193 member states will meet this week to debate when to destroy the two last known remaining stocks of the virus that causes smallpox. [more inside]
In a recent paper published in Nature Hansen et al. show the efficacy of their unusual vaccine strategy against SIVMAC239 in rhesus macaques. While the goal is not necessarily to produce a human vaccine against HIV using this exact strategy, this paper is now reigniting the debate over the progression of HIV infections and the mechanism(s) by which the virus skirts the human immune system.