Outmaneuvering Antibiotic Resistance

A groundbreaking study published in PLOS ONE offers hope that scientists can reverse the development of antibiotic resistance among bacteria with the help of “a mathematical model that pinpoints optimal antibiotic cycling patterns.” On The Pump Handle, Kim Krisberg writes, “the research comes at a time of widespread concern that without a coordinated, well-funded response to growing antibiotic resistance, medicine could lose some of its most effective, life-saving tools.” The collaboration between biologists and mathematicians yielded a piece of software dubbed “Time Machine” that “computes which antibiotic goes with which mutation at which point in time to best manage the evolution of resistance.”

The promise of this software comes as the problem of antibiotic resistance becomes ever more urgent. On The Pump Handle, Liz Borkowski details a WHO report that documents strains of resistant pneumonia, E. coli, staph, tuberculosis, malaria, and flu worldwide. Borkowski also covers the recent outbreak of a “nightmare bacteria” called CRE due to contaminated medical equipment at a Los Angeles hospital. Meanwhile, last year, the CDC issued a warning about the threat of drug-resistant gonorrhea.

On Aetiology, Tara C. Smith provides some historical perspective, noting that the discoverer of penicillin warned about evolving resistance in 1945. Smith considers the possibility of moving beyond traditional antibiotics entirely, instead using viruses to consume bacteria, or using antimicrobial peptides like those produced by our immune systems to mutilate bacterial cell walls. But as Smith writes, “the peptides of our innate immune system are one of our first lines of defense against an immense variety of pathogens, and we don’t know what the outcome may be if we compromise this essential level of protection.”

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DNA: The Web Inside the Strands

Only 1% of the human genome codes for proteins, which might make you wonder what the rest of the nucleotide sequence is good for. In 2012 the Encyclopedia of DNA Elements (or ENCODE) announced that a full 80% of the genome played a biochemical role, interacting with proteins in some way. But a new study says it takes only about 8% of our non-protein-coding genes to make us human. This is the percentage of genes that are ‘conserved’ by the human species: change one of these genes, and you’ll alter the fitness of the individual. These genes evolve slowly (although not as slowly as protein-coding genes). The rest of the genome is free to drift about and see what happens.

On Pharyngula, PZ Myers wonders why, when you tame a canine species (thus reducing the size of its adrenal gland), you automatically get floppy ears, spotted coats, and neoteny. PZ Myers says of genes, “everything is tangled together in interacting patterns of connectivity, so you often get unexpected results from single inputs.” A new paper argues that an embryonic population of cells known as the neural crest explains why domestication causes changes throughout a mammal’s body.

Last Week on ResearchBlogging.org

For the first time, researchers have transformed induced pluripotent stem cells (iPSCs) into specialized bladder cells. Meanwhile the development of iPSCs from normal cells has been shown to depend on two proteins necessary for the induction of a glycolytic state. In order to make iPSCs, researchers have previously needed to collect significant amounts of skin, bone marrow, or blood from a donor, but researchers have demonstrated a new method that requires only a single drop of blood.  In the future, you may be able to prick your finger, send a drop of blood to the lab, and have them grow a new bladder for you.

Paleontologists digging in the Dakotas have discovered “a giant crested bird-like dinosaur that the experts liken variously to an outsized cassowary, or a ‘chicken from hell.'”  The new genus of oviraptorosaur was named Anzu after a Mesopotamian bird-demon.

By coating gallium nitride semiconductors with “a layer of phosphonic acid derivatives,” researchers increased the brightness and longevity of LEDs without having to increase energy input.

Human appetite for conch snails has reduced the size of mature specimens by 2/3 in the last seven millennia.

A study of dioxin exposure via breast milk in Vietnam showed a correlation between levels of the chemical and development of autism in children.

Regardless of how long you spend playing, video games (especially those played with others) may help you relax after a long day at work.

Mexico now beats the U.S. as the most obese country in the world; they also drink the most Coca-Cola.  With Coke expanding aggressively in developing nations, chronically undernourished people are faced with too much of a good thing.

Getting less sleep is associated with having less ‘gray matter’ in the brain, but researchers can’t determine the direction of causality.  In another study, autistic children demonstrated shorter sleep duration than control groups.

Among sex-changing fish, the largest females are known to replace dominant males in a pinch, but male-to-female transitions are much more rare.  By studying a bunch of widowed male wrasses, researchers observed that the males would pair up with the next individual they encountered–whether male, female, or juvenile–and when two widowed males paired up, the smaller would become a female.

Baseline risk of ACL and other ligament injury may be genetically determined.

To accelerate word learning in young children, read them a story and then put them down for a nap.

Lithium-air batteries use the atmosphere as a cathode and could boost the range of electric vehicles to 300 miles or more.

Computational research has postulated the structure of electromagnetic knots that satisfy Maxwell’s equations.

And finally, a study of stem cell therapy for Lou Gehrig’s disease (or ALS) showed that the cells can be safely transplanted into the spinal cord and do not accelerate progression of the disease, providing a green light for further research.

The Carte Blanche of Intelligent Design

As an alternative to biblical creationism, Intelligent Design infers a less obtrusive God to explain life on Earth. This deity doesn’t hurl bolts of lightning, unless it’s with the express purpose of sparking abiogenesis in the primordial soup. On EvolutionBlog, Jason Rosenhouse dismisses probabilistic arguments against the likelihood of complex organisms, explaining that even the most improbable-seeming outcome of natural selection is more or less inevitable. As a flawed analogy, he imagines flipping a coin 500 times. This will always manifest a sequence of heads and tails that only had a one in gazillion chance of occurring. But of course, nature has no mercy upon arbitrary outcomes. Rosenhouse writes, “The prolonged action of natural selection ensures that most gene sequences have a probability close to zero of ever occurring (or persisting for long if they do occur) while the small percentage of functional sequences have a relatively high probability.” On Pharyngula, PZ Myers aces a quiz that was meant for him to fail. PZ writes that ID “was intentionally formulated in response to court decisions that prohibited gods and faith-based arguments — they literally rewrote their texts to exclude god to circumvent church-state conflicts.” No surprise: it’s hard to sway skeptics with a true believer’s plan B.

Thus it was an uphill battle that Ken Ham lost in his debate against Bill Nye the Science Guy.  Nye was widely perceived as the winner, even in religious circles.  Greg Laden sums up Ken Ham’s argument as “We know everything, we understand the most important issues of origins, creation, and evolution, and all of this information comes mainly from the Bible.”  This in contrast to Nye, who presented “science, science, science and more science” clearly and convincingly.  Greg continues “During the few moments when we were allowed to see the evangelical audience during Bill Nye’s presentation they looked, frankly, charmed.”  PZ Myers sounds a note of dissonance amongst the praise for Nye, saying “Nye is good at communicating a passion for science, but fails to note the conflict when he pretends that science is about being a better, more employable widget maker for Big Widget, Inc.”  In other words, Nye focused on the economic advantages of scientific understanding to the exclusion of aesthetic and philosophic advantages.  PZ sees science as an art, and argues we should practice science for science’s sake.

As for Ken Ham, with even Pat Robertson disavowing biblical creationism, he may have been flogging a dead horse.  The invention of Intelligent Design as a shield for traditional religious beliefs may have backfired on creationism. The faithful are comfortable abandoning the idea of a Young Earth to embrace geology and evolution, as long as they have the carte blanche of Intelligent Design to provide a hypothetical role for the Almighty.