Start codons in DNA may be more numerous than previously thought

Yet again, genetics is more complicated than we thought. Start codons in DNA may be more numerous than previously thought

Genetic code is typically represented via sequences of four letters—A, C, G, and T or U—which correspond to the molecular units known as adenine, cytosine, guanine and thymine (for DNA code) or uracil (for RNA code). Fifty years ago, the best available research tools indicated that there were only a few start codons (with sequences of AUG, GUG and UUG) in most living things. Start codons are important to understand because they mark the beginning of a recipe for translating RNA into specific strings of amino acids (i.e., proteins).

NIST specializes in the process of precision measurement, and the start codon challenge proved irresistible to the JIMB team. The collaboration was formed in 2016 with the goal of advancing biomeasurement science and facilitating the process of discovery by bringing together experts from academia, government labs and industry for collective scientific investigations.

With the use of GFP and nanoluciferase, the team measured translation initiation in the bacteria E. coli from all 64 codons. They were able to detect initiation of protein synthesis from 47 codons. The implications of the work could be quite profound for our understanding of biology.

Astronaut Twin Study Hints at Stress of Space Travel

Nature reports Astronaut twin study hints at stress of space travel "Preliminary results are in from NASA’s unprecedented twin study — a detailed probe of the genetic differences between astronaut Scott Kelly, who spent nearly a consecutive year in space, and his identical twin Mark. Measurements taken before, during and after Scott Kelly’s mission reveal changes in gene expression, DNA methylation and other biological markers that are likely to be attributable to his time in orbit."

We don't have a lot of details yet, but apparently the findings are interesting.

A Woman Was Killed By a Superbug Resistant to All 26 American Antibiotics

The Atlantic reports A Woman Was Killed By a Superbug Resistant to All 26 American Antibiotics

Funny—by which we all mean scary—because yesterday afternoon, the CDC also released a report about a Nevada woman who died after an infection resistant to 26 antibiotics, which is to say all available antibiotics in the U.S. The woman, who was in her 70s, had been previously hospitalized in India after fracturing her leg, which led to an infection of the bone. There was nothing to treat her infection—not colistin, not other last-line antibiotics. Scientists later tested the bacteria that killed her, and found it was somewhat susceptible to fosfomycin, but that antibiotic is not approved in the U.S. to treat her type of infection.

The most worrisome kind of colistin resistance is caused by a single gene called mcr–1. The bacteria that killed this woman did not have mcr–1; it’s still unclear how they became resistant. Other cases of colistin resistance have emerged before though. What makes mcr–1 special is that sits on a loop of free-floating DNA called a plasmid, which bacteria of different species can pass back and forth. And there are many plasmids out there with genes that confer resistance to this or that class of antibiotics.

Bugs on Screen

Science published a paper that's pretty amazing. Bugs on Screen: "Scientists film bacteria’s maneuvers as they become impervious to drugs".

A time-lapsed video reveals how bacteria develop resistance to increasingly higher doses of antibiotics in a matter of days.

In a creative stroke inspired by Hollywood wizardry, scientists from Harvard Medical School and Technion-Israel Institute of Technology have designed a simple way to observe how bacteria move as they become impervious to drugs.

The experiments, described in the Sept. 9 issue of Science, are thought to provide the first large-scale glimpse of the maneuvers of bacteria as they encounter increasingly higher doses of antibiotics and adapt to survive—and thrive—in them.

The Evolution of Bacteria on a "Mega-Plate" Petri Dish from Harvard Medical School on Vimeo.

And, an obligatory movie connection:

Senior study investigator Roy Kishony, of HMS and Technion, had seen a digital billboard advertising the 2011 film Contagion, a grim narrative about a deadly viral pandemic. The marketing tool was built using a giant lab dish to show hordes of painted, glowing microbes creeping slowly across a dark backdrop to spell out the title of the movie.

“This project was fun and joyful throughout,” Kishony said. “Seeing the bacteria spread for the first time was a thrill. Our MEGA-plate takes complex, often obscure, concepts in evolution, such as mutation selection, lineages, parallel evolution and clonal interference, and provides a visual seeing-is-believing demonstration of these otherwise vague ideas. It’s also a powerful illustration of how easy it is for bacteria to become resistant to antibiotics.”

Some Science Stories

io9 reports New Cancer Therapy Leaves Three Dead "Clinical trials of a promising new therapy, in which white blood cells are reprogrammed to attack cancer cells, has resulted in the deaths of three patients. In response, the US Food and Drug Administration has ordered a temporary halt to the trial."

It’s an incredibly promising new approach to battling cancer—but now there’s been a major setback. Three patients, all under the age of 25, have died in a Juno Therapeutics Phase II clinical trial that’s been using the CAR-T cells to treat ALL. The patients died after excess fluids accumulated in their brains (cerebral edemas). In all cases, the deaths happened after a chemotherapy drug, fludarabine, was added to the treatment regimen.

stat news has more, What's next for CAR-T after Juno's clinical misstep?

The Verge reports This robot stingray is propelled by rat heart cells, and it’s teaching us about underwater robotics. "A team of scientists have developed a robot that mimics the motion of a stingray by using the cardiac muscles from a rat mounted on a stingray-shaped skeleton. The robot, detailed in a study published in the journal Science, is a wonderfully weird hybrid of biological and mechanical engineering that could be the first step towards a new class of underwater robots."

This robot uses a single layer of muscle allowed for downward contraction to mimic movement. While live creatures have another layer of muscle to pull their wings upward, the skeleton of this robot is designed to rebound after such a contraction, simplifying the overall structure. When the muscles were stimulated with light, the combined actions allowed the robot to swim forward.

FIveThirtyEight reports, The Loudest Sound In The World Would Kill You On The Spot. "Consider this piece of history: On the morning of Aug. 27, 1883, ranchers on a sheep camp outside Alice Springs, Australia, heard a sound like two shots from a rifle. At that very moment, the Indonesian volcanic island of Krakatoa was blowing itself to bits 2,233 miles away. Scientists think this is probably the loudest sound humans have ever accurately measured. Not only are there records of people hearing the sound of Krakatoa thousands of miles away, there is also physical evidence that the sound of the volcano’s explosion traveled all the way around the globe multiple times."

Are reports, HTTPS crypto’s days are numbered. Here’s how Google wants to save it. "In the coming months, Google servers will add a new, experimental cryptographic algorithm to the more established elliptic curve algorithm it has been using for the past few years to help encrypt HTTPS communications. The algorithm—which goes by the wonky name "Ring Learning With Errors"—is a method of exchanging cryptographic keys that's currently considered one of the great new hopes in the age of quantum computing. Like other forms of public key encryption, it allows two parties who have never met to encrypt their communications, making it ideal for Internet usage."

Gene Therapy’s First Out-and-Out Cure Is Here

Gene Therapy’s First Out-and-Out Cure Is Here

A treatment now pending approval in Europe will be the first commercial gene therapy to provide an outright cure for a deadly disease. The treatment is a landmark for gene-replacement technology, an idea that’s struggled for three decades to prove itself safe and practical. Called Strimvelis, and owned by drug giant GlaxoSmithKline, the treatment is for severe combined immune deficiency, a rare disease that leaves newborns with almost no defense against viruses, bacteria, or fungi and is sometimes called ‘bubble boy’ disease after an American child whose short life inside a protective plastic shield was described in a 1976 movie. The treatment is different than any that’s come before because it appears to be an outright cure carried out through a genetic repair. The therapy was tested on 18 children, the first of them 15 years ago. All are still alive."

Scientists regenerate spinal cord in injured rats with stem cells

Ars Technica reports Scientists regenerate spinal cord in injured rats with stem cells "While previous studies have shown progress in regenerating certain types of nerve cells in injured spinal cords, the study is the first to coax the regrowth of a specific set of nerve cells, called corticospinal axons. These bundles of biological wiring carry signals from the brain to the spinal cord and are critical for voluntary movement. In the study, researchers were able to use stem cells from rats and humans to mend the injured rodents."

Scientists May Have Accidentally Found the Cure For Cancer

TomoNews reports, Scientists may have accidentally found the cure for cancer. "Malaria researcher Professor Ali Salanti from UCPH in collaboration with cancer researcher Mads Daugaard from UBC have revealed that the carbohydrate the malaria parasite attaches itself to in the placenta in pregnant women is identical to a carbohydrate present in cancer cells. Scientists have created the protein that the malaria parasite uses to attach to the placenta in a laboratory and have added a toxin. The combination of malaria protein and toxin finds cancer cells, is absorbed, then the toxin is released inside, causing the cancer cells to die."

"For decades, scientists have been searching for similarities between the growth of a placenta and a tumor. The placenta is an organ, which within a few months grows from only few cells into an organ weighing approx. two pounds, and it provides the embryo with oxygen and nourishment in a relatively foreign environment. In a manner of speaking, tumors do much the same, they grow aggressively in a relatively foreign environment," says Ali Salanti from the Department of Immunology and Microbiology at the University of Copenhagen. Research groups from the two universities have tested thousands of samples from brain tumors to leukemias and have found that the malaria protein is able to attack more than 90% of all types of tumors.

Oral Argument

Tor published Oral Argument "We’re thrilled to have the opportunity to publish internationally bestselling author Kim Stanley Robinson’s first stand-alone short story in twenty-five years. In it, we get a glimpse of a very green future through the lens of a Supreme Court transcript."

It's a short and fun story about science and patents and the supreme court. The prior cases he references are real.

The Past, Present, and Future of DNA

Last month I went to a Harvard Symposium on The Past, Present, and Future of DNA. They’ve posted the video of the event so here are my raw notes from it (any mistakes are mine).

• Science Symposium at Radcliffe 10/2/2015
• website
• #raddna

The one-day science symposium will focus on the explosion of knowledge about past and present DNA, and will include discussions about possible directions and applications for future research. The event will include experts in ancient DNA, de-extinction, human origins, population genetics, forensic science, ethics, business, future synthetic life, and the personal genome.

9:30am WELCOME

• Lizabeth Cohen, Dean of the Radcliffe Institute and Howard Mumford Jones Professor of American Studies, Department of History, Harvard University
• First isolated in 1869
• Microbes Hunters and The Eighth Day of Creation books

INTRODUCTION

• Janet Rich-Edwards, Codirector of the Science Program, Radcliffe Institute; Associate Professor of Medicine, Harvard Medical School; Associate Professor in the Department of Epidemiology, Harvard T.H. Chan School of Public Health
• Adding nucleotides to code more codons
• Mitochondria have their own DNA, inherit item just from mom. Have less repair mechanisms than nuclear DNA.
• Mitochondrial Eve, 150,000 years ago in Ethiopia
• Spider-goat - transgenic goat whose milk can be strung into fibers 10x stronger than steel.

10am MAMMOTHS, NEANDERTHALS, AND YOUR ANCESTORS

video

Moderator: George Church

• Robert Winthrop Professor of Genetics, Harvard Medical School

John Hawks

• Vilas-Borghesi Distinguished Achievement Professor of Anthropology, University of Wisconsin-Madison
• Has a blog, runs a MOOC
• Goram caves, sites of Neanderthals
• In last 20 years we have finally agreed on role of Neanderthals in our evolution
• Living people today have Neanderthal ancestors, regionally distributed in surprising ways
• East Asians more, then European, then African
• Neanderthals come from European as well as central Asian sites
• Denisova caves show a new humanoid species, that coexisted with Neanderthals
• Field guide to Pleistocene Hookups
• Every archaic human group interbred with each other
• Every population before 40,000 years ago has been through a period of very high inbreeding
• Neanderthals did not survive unaltered for 100,000s years. Much more dynamic
• Europe has more mixing in it than we thought. Lots of colonization from other places, post-farming
• Today’s populations are a mixture of ancient progenitor populations that no longer exist
• Interbreeding with ancient populations provided raw materials for human adaptations
• Changing excavation practices to get DNA

Beth Shapiro

• Associate Professor, Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
• How to Clone a Mammoth
• Sequencing the Dead
• Found DNA in old stuff, like dinosaur DNA in Amber, wasn’t real. DNA decays
• Organisms have DNA repair processes but of course these require energy
• Cold helps. Oldest known DNA from Dawson Yukon, 700,000 years old (ash layer from volcano eruptions). In bad condition but were able to sequence whole genome. A horse.
• Field is Ancient DNA. She started in 1999. Works in Beringia (Alaska, Russia)
• Collect bones from animals, with DNA can find population size over time
• Modern sequencers can do amazing things with short fragments. Other fields don’t like this, but these guys only have short fragments
• Found a new camel species
• Looked at horse domestication history
• Can we clone a mammoth? No.
• Asian elephants are closest relative to mammoth. 6 millions years of difference , not very much, just 1%
• Hemoglobin difference is in three places, expressed these, found mammoths were better at delivering oxygen when it’s cold
• Pleistocene Park. Guy introduced big animals like were there and just their presence over a few summers has brought back grass.

Spencer Wells

• Scientist, author, entrepreneur, and former explorer-in-residence and director of the Genographic Project at National Geographic
• The Human Journey -migration patterns
• Apes 23m yrs ago
• ~16m years ago africa bumped into Asia and species spread
• Humans are 99.9% same genetically
• African Adam and Eve 140,000–200,000 years ago
• Only left Africa 60,000 years ago
• The Genographic Project
• 700,000 participants

Questions

• While we each might have 3% Neanderthal genome, we each have different parts of it. Combine people in this room and you probably get close to half of Neanderthal genome.
• ~75,000 years ago humans had a near extinction event, down to just 10,000 of us and we came back, so that’s a reason there’s so little variation.

1pm FORENSIC DNA INVESTIGATION

video

Introducer: Ronald S. Sullivan, Jr.

• Clinical Professor of Law; Director, Criminal Justice Institute, Harvard Law School

Greg Hampikian

• Professor, Department of Biological Sciences, Joint appointment in Department of Criminal Justice, Director of the Idaho Innocence Project, Boise State University
• Happy Wrongful Convictions Day
• Average time on death row before exoneration is 9 years
• We know the genes and base pairs that do eye color (blue and brown, hazel is a little more difficult)
• Databases with DNA, crime scene DNA, can look for exact match, but if none, look for half match to find family members.
• Y-STRs are tied to last name, mitochondrial DNA is tied to mother. Public genealogy database combine these.
• Sperm cells are different from other cells and we can separate them from others in samples
• Given a profile, is a sample included or excluded or inconclusive. A statistics problem and it’s not always clear
• Given tests to different labs, get back wildly different results

1:45pm THE ETHICAL FRONTIER OF DNA

video

Introducer: Danielle Allen

• Director, Edmond J. Safra Center for Ethics, and Professor, Department of Government and Graduate School of Education, Harvard University

Arthur Caplan

• Drs. William F. and Virginia Connolly Mitty Professor of Bioethics; Director, Division of Medical Ethics, Department of Population Health, NYU Langone Medical Center, NYU School of Medicine
• Genetic Testing For Neurological Disorders: Ethical Challenges
• We can test for Down’s syndrome and have been able for a while
• It’s faced the ethical challenges that other testing will face
• Given a prenatal tests, parents could do a lot of different things, some good some bad
• Lookup Down’s on web, get different answer per website, Down’s, CDC, WebMD
• Some states with laws about informing parents about down fetus and some banning aborting of down fetuses
• Future is a big abortion battle based on testing

2:45pm THE FUTURE UTILITY OF DNA SCIENCE

video

Moderator: Christine Seidman

• Thomas W. Smith Professor of Medicine, Harvard Medical School

Jacob Corn

• Scientific Director, Innovative Genomics Initiative; Assistant Adjunct Professor of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley
• The Genome Editing Revolution
• Passed around a model of some enzyme (Cas9)
• Reading DNA is faster than writing. Reading is growing faster than Moores law.
• 1990s Zinc Fingered clueless
• 2009 TAL Effector Nuclease - protein based recognition engineered Nuclease
• 2012 CRISPR/Cas9 - targeting RNA endogenous Nuclease $100 and < 1 week
• Cas9 is a bacterial immune system
• Cas9 does a double stranded cut, not the edit
• Gene editing to cure blood diseases
• Seems to work everywhere, bacteria, virus, yeast, mice, chickens, cows, humans, etc.
• Good for science testing. On organisms that we don’t know much about can use this to edit genes and see effects.
• A German man was cured of HIV by getting a transplant from someone with a particular mutation (by coincidence), now looking to do this via editing

Alison Murdoch

• Professor of Reproductive Medicine and Head of Department, Institute of Genetic Medicine, International Fertility Centre for Life, Newcastle University (United Kingdom)
• The Science and Politics of Mitochondrial Donation (In the UK)
• Large variety of mtDNA caused diseases
• Nuclear DNA encode 32,000 genes
• mtDNA encodes 37 genes
• Mitochondrial transfer in embryos idea is 5 years old
• Done in monkeys in 2009
• Still not legal in UK on humans, is it ethical?
• Just became legal in Oct 2015, treatment in a few months

Floyd Romesberg

• Professor, Department of Chemistry, The Scripps Research Institute
• Expanding the Genetic Alphabet
• Predominantly hydrophobic nucleotides
• Details of finding bases that pair well and don’t interfere with existing ones

4:15pm CLOSING REMARKS

Janet Rich-Edwards

4:30pm RECEPTION AND POSTER SESSION

Cure for cancer might accidentally have been found, and it could be malaria

The Independent reports Cure for cancer might accidentally have been found, and it could be malaria

Scientists might have accidentally made a huge step forward in the search for a cure for cancer — discovering unexpectedly that a malaria protein could be an effective weapon against the disease.

Danish researchers were hunting for a way of protecting pregnant women from malaria, which can cause huge problems because it attacks the placenta. But they found at the same time that armed malaria proteins can attack cancer, too — an approach which could be a step towards curing the disease.

Scientists have combined the bit of protein that the malaria vaccine uses to bury into cells and combined it with a toxin — that can then bury into cancer cells and release the toxin, killing them off.

The scientists have found that in both cases the malria protein attaches itself to the same carbohydrate. It is the similarities between those two things that the cure could exploit."

So this is really early and the tests have only been in mice and lots of things that work in mice don't work in humans, but it's interesting.

Scientists Successfully Turn Human Cancer Cells Back to Normal in Process That Could ‘Switch Off’ Disease

This sounds promising, U.S. scientists successfully turn human cancer cells back to normal in process that could ‘switch off’ disease

"The scientists discovered that the glue which holds cells together is regulated by biological microprocessors called microRNAs. When everything is working normally, the microRNAs instruct the cells to stop dividing when they have replicated sufficiently. They do this by triggering production of a protein called PLEKHA7 which breaks the cell bonds. But in cancer that process does not work.

Scientists discovered they could switch on cancer in cells by removing the microRNAs from cells and preventing them from producing the protein. And, crucially, they found that they could reverse the process, switching the brakes back on and stopping cancer."

Mucus is gross. But here are 9 things you should know about it

I learned a lot from this Vox article Mucus is gross. But here are 9 things you should know about it.

The U.S. government is poised to withdraw longstanding warnings about cholesterol

Wonkblog reports The U.S. government is poised to withdraw longstanding warnings about cholesterol.

"The new view on cholesterol in the diet does not reverse warnings about high levels of 'bad' cholesterol in the blood, which have been linked to heart disease.  Moreover, some experts warned that people with particular health problems, such as diabetes, should continue to avoid cholesterol-rich diets.

But the finding, which may offer a measure of relief to breakfast diners who prefer eggs, follows an evolution of thinking among many nutritionists who now believe that for a healthy adult cholesterol intake may not significantly affect the level of cholesterol in the blood or increase the risk of heart disease. The greater danger, according to this line of thought, lies in foods heavy with trans fats and saturated fats."

They also have a Q&A, Should I binge on eggs for breakfast? Here’s what you need to know.

The Independent Discovery of TCP/IP, By Ants

The Independent Discovery of TCP/IP, By Ants.

Neat article. It turns out that the way harvester ants determine if it's safe to look for food is very similar to the way TCP deals with network congestion.

Individual harvester ants would forage for seeds to bring back to the colony. Once they’d left, they would not come back until they found something. As you might imagine, this didn’t work out for some ants: ants would often perish before ever finding food, or carrying a seed back to the nest, particularly on the hottest and driest of days. Gordon had noticed that colonies had adapted to their desert environment by not “sending out” as many foragers on extremely hot and dry days, subsisting on the seeds they had stored up instead.

Through careful observation and experimentation, Gordon discovered that would-be foragers wait at a narrow tunnel entrance to the colony. Whenever another forager ant returns with food, it drops off its load, and touches antennae with waiting ants. Whether or not any individual forager sallies forth depends on the number of interactions it has with returning foragers, and the timing of those interactions -- so a complex collective behavior is governed solely through simple individual interactions.

That's one of the important points, there's no "manager" that everyone reports to that determines how many ants to send out. TCP works the same way, there isn't a special manager computer on the network (since it would be bad if that one machine crashed). Instead they all work via a set of rules so that they collectively figure out a good thing to do.

Transmission Control Protocol, also known as TCP, is a big part of what makes the Internet possible. The Internet involves a lot of machines sending each other files including websites, videos, text documents, audio -- over a vast network of hardware including routers, cables, satellites, cellphone towers, and of course computers. The problem is that sometimes parts of the network fail -- hardware can break, or become overloaded and slow down dramatically.

If a source hosting a file is using TCP, it breaks the file down into smaller chunks, called “packets”. It sends out a bunch of packets to the requester, and monitors the acknowledgements of receipt, called “acks”, to calibrate how quickly to send the rest of the packets.

The article also includes this table of other technical problems we've solved in a similar way to low level biological systems:

Researchers Discover Key to Lung Cancer's Spread

Researchers Discover Key to Lung Cancer's Spread "In a breakthrough in the understanding of how cancer spreads, researchers at the University of Virginia School of Medicine have identified a substance secreted by lung cancer cells that enables them to metastasize, beginning their deadly march to other sites in the body. By blocking that process in lab studies, the researchers were able to confine cancer cells to a single tumor site, offering hope that drugs could one day block the spread of cancers in people."

"We found that when you blocked Activin A expression, the cancer cells would grow, and they would form a primary tumor, but they wouldn’t metastasize," Mayo said. "We did protein analysis to see if Activin A protein was over-expressed in human lung cancer tissue samples, and the answer was yes. We believe this protein is expressed in many other types of cancer as well, including colon and breast cancer."

9 surprising facts about the sense of touch

I really don't like Vox's Buzzfeed headlines but I found 9 surprising facts about the sense of touch to actually be surprising.

A new antibiotic kills pathogens without detectable resistance

Nature published: A new antibiotic kills pathogens without detectable resistance. Here's the abstract:

Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.

Kelly Service explains a little more in Science, Microbe found in grassy field contains powerful antibiotic.

Many existing antibiotics, including penicillin, were identified by cultivating naturally occurring microorganisms—bacteria often try to kill each other with chemical warfare, it turns out. But the supply of novel microbes that will grow in a lab has been largely tapped out. In 2002, microbiologist Kim Lewis, along with his colleague at Northeastern University in Boston, microbial ecologist Slava Epstein, described a new technique for coaxing bacteria to grow: Put soil samples into tiny chambers sandwiched between permeable membranes and return these contraptions to the ground. The bacterial strains confined in the chambers will form colonies—thanks in part, the team suspects, to growth factors from neighboring organisms that cross the membranes. The resulting “domesticated” colony can then be removed from the chamber and sometimes will more readily call a petri dish home.

The researchers used a version of this approach to isolate and grow new bacterial colonies—many scooped out of soil in the backyard of microbiologist Losee Ling, who leads research and development at the startup company NovoBiotic Pharmaceuticals, formed to commercialize their approach. To test the antibacterial properties of these soil microbes, the team let each of them duel in a lab dish with Staphylococcus aureus, a cause of serious skin and respiratory infections. Then they isolated and tested individual compounds—10,000 in all—from the bacteria that most effectively killed the staph bacteria.

One bacterium, from a grassy field in Maine, produced a compound with powerful abilities to kill a variety of other bacterial species, including many human pathogens. Moreover, these pathogens failed to develop resistance to the compound: There were no surviving individuals that had evolved to withstand its attack. (Resistance usually develops when a small percentage of microbes escape an antibiotic because of a mutation and then those bacteria multiply.) Lewis initially took this total devastation as a discouraging sign—the mark of “another boring detergent.” (Bleach, after all, is a strong antibiotic, but it’s a little too effective at killing any surrounding cells.) However, it turned out that the new compound, which the group named teixobactin, was not toxic to human cells in a dish.

One of the biggest science breakthroughs of 2014 never really happened

Vox reports One of the biggest science breakthroughs of 2014 never really happened "Although it's never encouraging to see scientific misconduct, the speed with which this was caught shows how researchers are now using social media to unearth shoddy science. For example, PubPeer, which basically hosts comments sections for papers, played a huge role in picking these papers apart, as did Knoepfler's blog."

The Revolution in Biology is Here, Now

Mike Loukides wrote in O'Reilly Radar about the BioFabricate summit, The revolution in biology is here, now.

"What I saw, instead, was real products that you might never notice. Bricks made from sand that are held together by microbes designed to excrete the binder. Bricks and packing material made from fungus (mycelium). Plastic excreted by bacteria that consume waste methane from sewage plants. You wouldn’t know, or care, whether your plastic Lego blocks are made from petroleum or from bacteria, but there’s a huge ecological difference. You wouldn’t know, or care, what goes into the bricks used in the new school, but the construction boom in Dubai has made a desert city one of the world’s largest importers of sand. Wind-blown desert sand isn’t useful for industrial brickmaking, but the microbes have no problem making bricks from it. And you may not care whether packing materials are made of styrofoam or fungus, but I despise the bag of packing peanuts sitting in my basement waiting to be recycled. You can throw the fungal packing material into the garden, and it will decompose into fertilizer in a couple of days."

"Several people spoke about their work as “collaboration with biomaterial.” This is a unique and exciting perspective. In computing, we write programs that make computers do things. If the program doesn’t do what we want, we’ve made a mistake. We driving the process: the machine always does what it’s told. In electronics, we assemble parts that, again, do what we want (or not); they have no will of their own. We make things out of metal and concrete by bending and pouring. The metal never decides how to be bent, and the concrete never decides how to pour. Biology is fundamentally different. Biology has been creating and building for billions of years. Its creativity is quite distinct from human creativity; it has evolved extraordinarily efficient systems. So, it’s an act of hubris to talk about designing biological systems. We need to collaborate with biological systems and enable them to design themselves. We need to let them teach us what they are able to do, and build around that. Otherwise, fungus is just a bunch of mushrooms. Maybe tasty, but not a building material."