BLOGS

(a) Schematics of the word INFORMATION is written on a material in binary code using magnetic recording. Red denotes magnetization pointing out of the plane and blue is magnetization pointing into the plane. (b)–(d) Time evolution of the digital magnetic recording information states simulated using micromagnetic Monte Carlo. (b) Initial random state. (c) INFORMATION is written (t = 0 s). (d) Iteration 930 (t = 1395 s) showing the degradation of information states. Reproduced with permission from M. M. Vopson and S. Lepadatu, AIP Adv. 12, 075310 (2022). Copyright 2022 AIP Publishing.

Topics: Chemistry, DNA, General Relativity, Genetics, Nucleotides, Thermodynamics

Reference: Electronic Orbitals, Chem Libre Text dot org

As Morpheus describes, “You take the blue pill, the story ends. You wake up in your bed and believe whatever you want to believe. You take the red pill; you stay in Wonderland. And I show you how deep the rabbit hole goes.” Neo takes the red pill and wakes up in the real world. Source: Britannica Online: Red Pill and Blue Pill Symbolism

The simulation hypothesis is a philosophical theory in which the entire universe and our objective reality are just simulated constructs. Despite the lack of evidence, this idea is gaining traction in scientific circles as well as in the entertainment industry. Recent scientific developments in the field of information physics, such as the publication of the mass-energy-information equivalence principle, appear to support this possibility. In particular, the 2022 discovery of the second law of information dynamics (infodynamics) facilitates new and interesting research tools at the intersection between physics and information. In this article, we re-examine the second law of infodynamics and its applicability to digital information, genetic information, atomic physics, mathematical symmetries, and cosmology, and we provide scientific evidence that appears to underpin the simulated universe hypothesis.

Introduction

In 2022, a new fundamental law of physics has been proposed and demonstrated, called the second law of information dynamics or simply the second law of infodynamics.¹ Its name is an analogy to the second law of thermodynamics, which describes the time evolution of the physical entropy of an isolated system, which requires the entropy to remain constant or to increase over time. In contrast to the second law of thermodynamics, the second law of infodynamics states that the information entropy of systems containing information states must remain constant or decrease over time, reaching a certain minimum value at equilibrium. This surprising observation has massive implications for all branches of science and technology. With the ever-increasing importance of information systems such as digital information storage or biological information stored in DNA/RNA genetic sequences, this new powerful physics law offers an additional tool for examining these systems and their time evolution.² 

The second law of infodynamics and its implications for the simulated universe hypothesis, Melvin M. Vopson, AIP Advances

A mathematical tool called a fast Fourier transform maps the structure in a way that reveals the 12-fold symmetry of the quasicrystal. The fast Fourier transform of the electron microscope image of the quasicrystal is shown on the left, while the transform of the simulated crystal is shown on the right. Image credit: Mirkin Research Group, Northwestern University, and Glotzer Group, University of Michigan.

Topics: Biology, DNA, Nanoengineering, Nanomaterials, Nanotechnology

ANN ARBOR—Nanoengineers have created a quasicrystal—a scientifically intriguing and technologically promising material structure—from nanoparticles using DNA, the molecule that encodes life.

The team, led by researchers at Northwestern University, the University of Michigan, and the Center for Cooperative Research in Biomaterials in San Sebastian, Spain, reports the results in Nature Materials.

Unlike ordinary crystals, which are defined by a repeating structure, the patterns in quasicrystals don’t repeat. Quasicrystals built from atoms can have exceptional properties—for example, absorbing heat and light differently, exhibiting unusual electronic properties such as conducting electricity without resistance, or their surfaces being very hard or very slippery.

Engineers studying nanoscale assembly often view nanoparticles as a kind of ‘designer atom,’ which provides a new level of control over synthetic materials. One of the challenges is directing particles to assemble into desired structures with useful qualities, and in building this first DNA-assembled quasicrystal, the team entered a new frontier in nanomaterial design.

“The existence of quasicrystals has been a puzzle for decades, and their discovery appropriately was awarded a Nobel Prize,” said Chad Mirkin, the George B. Rathmann Professor of Chemistry at Northwestern University and co-corresponding author of the study. “Although there are now several known examples, discovered in nature or through serendipitous routes, our research demystifies their formation and, more importantly, shows how we can harness the programmable nature of DNA to design and assemble quasicrystals deliberately.”

Nanoparticle quasicrystal constructed with DNA, Kate McAlpine, University of Michigan

Researchers from the University of Connecticut and colleagues have created a highly durable, lightweight material by structuring DNA and then coating it in glass. The resulting product, characterized by its nanolattice structure, exhibits a unique combination of strength and low density, making it potentially useful in applications like vehicle manufacturing and body armor. (Artist’s concept.)

Topics: Biotechnology, DNA, Material Science, Nanomaterials

Researchers have developed a highly robust material with an extremely low density by constructing a structure using DNA and subsequently coating it in glass.

Materials possessing both strength and lightness have the potential to enhance everything from automobiles to body armor. But usually, the two qualities are mutually exclusive. However, researchers at the University of Connecticut, along with their collaborators, have now crafted an incredibly strong yet lightweight material. Surprisingly, they achieved this using two unexpected building blocks: DNA and glass.

“For the given density, our material is the strongest known,” says Seok-Woo Lee, a materials scientist at UConn. Lee and colleagues from UConn, Columbia University, and Brookhaven National Lab reported the details on July 19 in Cell Reports Physical Science.

Strength is relative. Iron, for example, can take 7 tons of pressure per square centimeter. But it’s also very dense and heavy, weighing 7.8 grams/cubic centimeter. Other metals, such as titanium, are stronger and lighter than iron. And certain alloys combining multiple elements are even stronger. Strong, lightweight materials have allowed for lightweight body armor and better medical devices and made safer, faster cars and airplanes.

Scientists Create New Material Five Times Lighter and Four Times Stronger Than Steel. Sci-Tech Daily

Reference: “High-strength, lightweight nano-architected silica” by Aaron Michelson, Tyler J. Flanagan, Seok-Woo Lee, and Oleg Gang, 27 June 2023, Cell Reports Physical Science.
DOI: 10.1016/j.xcrp.2023.101475

Image Source: MedPage Today

Topics: Biology, Biotechnology, Civilization, COVID-19, DNA, Epidemiology

Currently authorized bivalent COVID-19 boosters demonstrated similar protection against symptomatic illness from the XBB/XBB.1.5 Omicron subvariants as from BA.5-related subvariants, according to a CDC study.

From December 2022 to January 2023, the bivalent boosters' vaccine effectiveness (VE) against symptomatic infection was a similar 48% versus XBB/XBB.1.5-related strains and 52% versus BA.5-related sublineages, reported Ruth Link-Gelles, Ph.D., of the CDC's National Center for Immunization and Respiratory Diseases, and colleagues in Morbidity and Mortality Weekly Report (MMWR).

Meanwhile, Pfizer's updated booster demonstrated superior neutralizing antibody activity compared with the company's original product against all the latest Omicron subvariants, including XBB.1, according to Kena Swanson, Ph.D., of Pfizer Vaccine Research and Development in Pearl River, New York and colleagues, writing in the New England Journal of Medicine. Their findings contradict earlier research from other labs that found no significant difference in neutralizing activity with the bivalent over the monovalent vaccine.

According to the latest estimates from the CDC, XBB.1.5 is responsible for 49.1% of new COVID-19 cases in the U.S., while XBB is responsible for another 3.3%.

CDC: Bivalent COVID Vaccines Stop Illness From XBB.1.5

— And Pfizer lab data show better neutralization against the latest variants with the bivalent shot, Ingrid Hein, Staff Writer, MedPage Today

The proportion of disruptive scientific papers, such as the 1953 description of DNA’s double-helix structure, has fallen since the mid-1940s.Credit: Lawrence Lawry/SPL

Topics: DNA, Education, Philosophy, Research, Science, STEM

The number of science and technology research papers published has skyrocketed over the past few decades — but the ‘disruptiveness’ of those papers has dropped, according to an analysis of how radically papers depart from the previous literature¹.

Data from millions of manuscripts show that, compared with the mid-twentieth century, research done in the 2000s was much more likely to incrementally push science forward than to veer off in a new direction and render previous work obsolete. Analysis of patents from 1976 to 2010 showed the same trend.

“The data suggest something is changing,” says Russell Funk, a sociologist at the University of Minnesota in Minneapolis and a co-author of the analysis published on 4 January in Nature. “You don’t have quite the same intensity of breakthrough discoveries you once had.”

Telltale citations

The authors reasoned that if a study were highly disruptive, subsequent research would be less likely to cite its references and instead cite the study itself. Using the citation data from 45 million manuscripts and 3.9 million patents, the researchers calculated a measure of disruptiveness called the ‘CD index,’ in which values ranged from –1 for the least disruptive work to 1 for the most disruptive.

The average CD index declined by more than 90% between 1945 and 2010 for research manuscripts (see ‘Disruptive science dwindles’) and more than 78% from 1980 to 2010 for patents. Disruptiveness declined in all analyzed research fields and patent types, even when factoring in potential differences in factors such as citation practices.

‘Disruptive’ science has declined — and no one knows why, Max Kozlov, Nature.

Topics: Civics, Civil Rights, Civilization, Democratic Republic, DNA, Existentialism, Fascism

The genesis of grievance

The man who was least deserving of the Presidential Medal of Freedom in history is the beginning of the roots of white fragility. It wasn't that he might have had learning disabilities or wasn't suited for college. He turned his focus outward to "others": immigrants, feminists, the LGBT, and minorities. Once he settled into a syndicated broadcast on AM Talk Radio that proved more lucrative than what his WWII veteran father earned as a fighter pilot, lawyer, and legislator, he founded a cottage industry of handling that fragility by blaming others for personal shortcomings with no sense of hypocrisy in the party he championed labeling itself the "party of personal responsibility and family values."

In 1969 Limbaugh graduated from Cape Girardeau Central High School, where he played football and was a Boys State delegate.^{[15][16][17][18]} At age 16, he worked his first radio job at KGMO, a local radio station. He used the air name Rusty Sharpe having found "Sharpe" in a telephone book.^[12][19] Limbaugh later cited Chicago DJ Larry Lujack as a major influence on him, saying Lujack was "the only person I ever copied."^[20] In deference to his parents' desire to attend college, he enrolled at Southeast Missouri State University but dropped out after two semesters. According to his mother, "he flunked everything [...] he just didn't seem interested in anything except radio."[12][21] Biographer Zev Chafets asserts that Limbaugh's life was largely dedicated to gaining his father's respect.^[22] Source: Wikipedia/Rush_Limbaugh

The high priest of gridlock

In the 1994 campaign season, to offer an alternative to Democratic policies and to unite distant wings of the Republican Party, Gingrich and several other Republicans came up with a Contract with America, which laid out ten policies that Republicans promised to bring to a vote on the House floor during the first 100 days of the new Congress if they won the election.^[61] Gingrich and other Republican candidates for the House of Representatives signed the contract. The contract ranged from issues such as welfare reform, term limits, crime, and a balanced budget/tax limitation amendment, to more specialized legislation such as restrictions on American military participation in United Nations missions.^[62]

In the November 1994 midterm elections, Republicans gained 54 seats and took control of the House for the first time since 1954. Long-time House Minority LeaderBob Michel of Illinois had not run for re-election, giving Gingrich, the highest-ranking Republican returning to Congress, the inside track at becoming Speaker. The midterm election that turned congressional power over to Republicans "changed the center of gravity" in the nation's capital.^[63]Time magazine named Gingrich its 1995 "Man of the Year" for his role in the election.^[3] Source: Wikipedia/Newt_Gingrich

The apotheosis of grift

"Government is not the solution to our problem; government is the problem." President Ronald Reagan's inaugural address.

Despite the propaganda from the "Never-Trumper" folks, Saint Ronnie Reagan wasn't: a saint. Reagan had a racist conversation with Richard Nixon, mocking an African delegation as "monkeys." He was famous for referencing African Americans with the terms "young bucks" and "welfare queens." Ironically, the Nixon administration came after Donald and his father for discriminatory housing practices. TO THIS DAY and with DNA evidence, he still wants the Central Park Exonerated Five rearrested and executed. Trump came down that escalator in his Ivory Tower and talked like a racist white man from Queens, famous for attacking black children in the 1970s. Reagan did his racism with winks and nods, plausible denial for any blacks who supported him: Trump was, and is, who he has always been.

After railing before the election about inflation and gas prices, they immediately, on a DIME, switched to Hunter Biden's laptop, A.K.A. Benghazi 2.0, without a SHRED of shame or cognizance of hypocrisy. They had no political platform in 2020 and none in the midterms. They eeked a majority out of gerrymandered districts and refused to campaign about the fifty-year project of overturning Roe vs. Wade. Because when you have no policies or a framework to govern, trolling is what you do. If Elon kills Twitter, that might be the best thing he’s ever done. It’s dumbed down our public discourse and allowed conspiracy theories to run rampant as “free speech.”

The fact that Trumpism is largely a reincarnation of the German American Bund is beyond dispute. To paraphrase Thom Hartmann's latest article, we are in late-stage Reaganism. Lauren Boebert and Matt "pedo" Gaetz refused to stand or applaud during Voldemyr Zelinski's address to Congress (you know, like normal humans), and "Boe" is on the outs with the former Mrs. Marjorie Taylor "Nazi Barbie, Secret Jewish Space Lasers" Greene. There was no "red wave," but elections were razer close: we almost got Herschel Walker as a Senator from Georgia, and the aforementioned mean girls got reelected. We are FAR from out of the authoritarian woods yet. If January 6, 2021, isn't punished, including Trump and other plotters, it was a dry run practice before the next bloody coup.

We went from a B-Movie actor whose film credits included "Bedtime with Bonzo" to a reality television star that was a carefully-crafted public fiction by Jeff Zucker and NBC. Mark Burnett had to replace his office furniture that had long succumbed to Entropy. We as a nation are at the endpoint of the Lewis Powell memo. Before it, lobbyists were rare to nonexistent. The confluence of government and corporations hasn't always been our "normal." We have to decide IF we're a "nation of laws and not of men" or if the only men that will count in the opposite of a democratic republic are wealthy, white, male, cisgender American oligarchs. “Fascism should more properly be called corporatism because it is the merger of state and corporate power.” — Benito Mussolini; however, it's unlikely he ever said this, but what it outlines is disturbing nonetheless. We give far too much attention and power to narcissists with itchy Twitter fingers and deep pockets to corrupt politicians.

We can have either a functioning Constitutional Republic or we can have the Hunger Games. We cannot have both.

1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and are reversible. (Courtesy: Davide Michieletto)

Topics: Biology, Biotechnology, DNA, Molecules

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naive, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment with it, I tried to pipette some of the solutions out, but they didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh, UK

A nurse prepares a COVID-19 vaccine in Guwahati, India, on 10 April. A new subvariant named BA.2.75 that was first detected in India has surfaced in many other countries. ANUPAM NATH/AP IMAGES

Topics: Biology, COVID-19, DNA, Economics, Environment, Evolution, Existentialism

Ed Rybicki, a virologist at the University of Cape Town in South Africa, concentrated his article in Scientific American on the viruses dominating the news cycle in the early 2000s: Ebola, Marburg, and HIV. Not comforting, but he said, "HIV, which is thought to have first emerged in humans in the 1930s, is another kind of virus, known as a retrovirus." Not mentioned, but the H1N1 comes from the 1918 Flu Pandemic, and a friend in Texas lost his girlfriend to it also in the early 2000s. Retro means "a process that reverses the normal flow of information in cells" and relates to a bridge between the first forms of life on this planet. In an e-brief, I wrote my first year at JSNN, an article in Nature: Education posits that viruses are not ‘alive’ because they don’t have metabolic processes, one of the four criteria for life (“organized, metabolism, genetic code, and reproduction”). The last part is important: they cannot reproduce asexually (unicellular division), or sexually with genders, spermatozoa, and an incubation period before birthing a copy. In other words, they aren't "alive," but they aren't dead either. They manage to replicate themselves by invading a host. Usually us.

It DOES mention three possible mechanisms as to origins: The Progressive Hypothesis, i.e., “bits and pieces” of a genome gained the ability to move in and out of cells (retroviruses like HIV given as an example); The Regressive Hypothesis, meaning the viruses evolved from some common ancestor to their current state (reductio ad absurdum), lastly The Virus-First Hypothesis, which puts any anthropocentric notions away and their hypothesis that viruses existed before mortals as “self-replicating units.”

I am as ready for this pandemic to be over as anyone else. However, this read from AAAS didn't give me hope that a societal "all-clear" will be uttered, or that we'll overcome our shared arrogance and stupidity:

In the short history of the COVID-19 pandemic, 2021 was the year of the new variants. Alpha, Beta, Gamma, and Delta each had a couple of months in the Sun.

But this was the year of Omicron, which swept the globe late in 2021 and has continued to dominate, with subvariants—given more prosaic names such as BA.1, BA.2, and BA.2.12.1—appearing in rapid succession. Two closely related subvariants named BA.4 and BA.5 are now driving infections around the world, but new candidates, including one named BA.2.75, are knocking on the door.

Omicron’s lasting dominance has evolutionary biologists wondering what comes next. Some think it’s a sign that SARS-CoV-2’s initial frenzy of evolution is over and it, like other coronaviruses that have been with humanity much longer, is settling into a pattern of gradual evolution. “I think a good guess is that either BA.2 or BA.5 will spawn additional descendants with more mutations and that one or more of those subvariants will spread and will be the next thing,” says Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center.

But others believe a new variant different enough from Omicron and all other variants to deserve the next Greek letter designation, Pi, may already be developing, perhaps in a chronically infected patient. And even if Omicron is not replaced, its dominance is no cause for complacency, says Maria Van Kerkhove, technical lead for COVID-19 at the World Health Organization. “It’s bad enough as it is,” she says. “If we can’t get people to act [without] a new Greek name, that’s a problem.”

As Omicron rages on, scientists have no idea what comes next, Kai Kupferschmidt, American Association for the Advancement of Science

Credit: Getty Images

Topics: Biology, COVID-19, DNA, Research

Note: I have friends who thankfully survived infection now affected by this phenomenon. The article thus grabbed my attention.

SARS-CoV-2 appears to travel widely across the cerebral cortex

“Brain fog” is not a formal medical descriptor. But it aptly describes an inability to think clearly that can turn up in multiple sclerosis, cancer, or chronic fatigue. Recently, the condition has grabbed headlines because of reports that it afflicts those recovering from COVID-19.

COVID’s brain-related symptoms go beyond mere mental fuzziness. They range across a spectrum that encompasses headaches, anxiety, depression, hallucinations, and vivid dreams, not to mention well-known smell and taste anomalies. Strokes and seizures are also on the list. One study showed that more than 80 percent of COVID patients encountered neurological complications.

The mystery of how the virus enters and then inhabits the brain’s protected no-fly zone is under intensive investigation. At the 50th annual meeting of the Society for Neuroscience, or SFN (held in virtual form this month after a pandemic hiatus in 2020), a set of yet-to-be-published research reports chronicle aspects of the COVID-causing SARS-COV-2 virus’s full trek in the brain—from cell penetration to dispersion among brain regions, to disruption of neural functioning.

How COVID Might Sow Chaos in the Brain, Gary Stix, Scientific American

A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

Topics: Biology, DNA, Evolution, Research

In her laboratory in Barcelona, Spain, Miki Ebisuya has built a clock without cogs, springs, or numbers. This clock doesn’t tick. It is made of genes and proteins, and it keeps time in a layer of cells that Ebisuya’s team has grown in its lab. This biological clock is tiny, but it could help to explain some of the most conspicuous differences between animal species.

Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged, and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

“I’m interested in biological time,” says Ebisuya, a developmental biologist at the European Molecular Biology Laboratory Barcelona. “But lifespan or gestation period, they are too long for me to study.” The swift speed of the segmentation clock makes it an ideal model system, she says.

These cellular clocks help explain why elephants are bigger than mice, Michael Marshall, Nature

Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants

Topics: Biology, Chemistry, DNA, Nobel Prize, Research, Women in Science

This year’s (2020) Nobel Prize in Chemistry has been awarded to two scientists who transformed an obscure bacterial immune mechanism, commonly called CRISPR, into a tool that can simply and cheaply edit the genomes of everything from wheat to mosquitoes to humans. 

The award went jointly to Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens and Jennifer Doudna of the University of California, Berkeley, “for the development of a method for genome editing.” They first showed that CRISPR—which stands for clustered regularly interspaced short palindromic repeats—could edit DNA in an in vitro system in a paper published in the 28 June 2012 issue of Science. Their discovery was rapidly expanded on by many others and soon made CRISPR a common tool in labs around the world. The genome editor spawned industries working on making new medicines, agricultural products, and ways to control pests.

Many scientists anticipated that Feng Zhang of the Broad Institute, who showed 6 months later that CRISPR worked in mammalian cells, would share the prize. The institutions of the three scientists are locked in a fierce patent battle over who deserves the intellectual property rights to CRISPR’s discovery, which some estimate could be worth billions of dollars.

“The ability to cut DNA where you want has revolutionized the life sciences. The genetic scissors were discovered 8 years ago, but have already benefited humankind greatly,” Pernilla Wittung Stafshede, a chemical biologist at the Chalmers University of Technology, said at the prize briefing.

CRISPR was also used in one of the most controversial biomedical experiments of the past decade, when a Chinese scientist edited the genomes of human embryos, resulting in the birth of three babies with altered genes. He was widely condemned and eventually sentenced to jail in China, a country that has become a leader in other areas of CRISPR research.

Although scientists were not surprised Doudna and Charpentier won the prize, Charpentier was stunned. “As much as I have been awarded a number of prizes, it’s something you hear, but you don’t completely connect,” she said in a phone call with the Nobel Prize officials. “I was told a number of times that when it happens, you’re very surprised and feel that it’s not real.”

At a press briefing today, Doudna noted she was asleep and missed the initial calls from Sweden, only waking up to answer the phone finally when a Nature reporter called. "She wanted to know if I could comment on the Nobel and I said, Well, who won it? And she was shocked that she was the person to tell me."

CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel, Jon Cohen, Science Magazine, AAAS

1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and reversible. (Courtesy: Davide Michieletto)

Topics: Biology, DNA, Physics, Polymer Science, Research

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naïve, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment on it, I tried to pipette some of the solution out, but it didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh

MGM/VICTOR TANGERMANN

Topics: Biology, Computer Science, DNA

Why cannot we write the entire 24 volumes of the Encyclopedia Britannica on the head of a pin? Dr. Richard P. Feynman, "There's Plenty of Room at the Bottom," said to be the seminal talk that started the concept of atomic-level engineering, soon known as nanotechnology, (named by Professor Norio Taniguchi, 1974, of the Tokyo Science University).

The intricate arrangement of base pairs in our DNA encodes just about everything about us. Now, DNA contains the entirety of “The Wonderful Wizard of Oz” as well.

A team of University of Texas Austin scientists just vastly improved the storage capacity of DNA and managed to encode the entire novel — translated into the geek-friendly language of Esperanto — in a double strand of DNA far more efficiently than has been done before. DNA storage isn’t new, but this work could help finally make it practical.

Big tech companies like Microsoft are already exploring DNA-storage technology, as the biomolecule can encode several orders of magnitude more information per unit volume than a hard drive. But DNA is particularly error-prone. It can easily be damaged and erase whatever’s stored on it.

“The key breakthrough is an encoding algorithm that allows accurate retrieval of the information even when the DNA strands are partially damaged during storage,” molecular biologist Ilya Finkelstein said in a UT Austin press release.

Scientists Stored "The Wizard of Oz" on a Strand of DNA, Dan Robitzgi, Futurism

Image Source: Link below

Topics: Biology, DNA, Genetics

"Like Horoscope Readings!": The Scammy World of DNA Startups, Dan Robitzki, Futurism

Callao Cave, Luzon Island, The Philippines Image credits: Callao Cave Archaeology Project

Topics: Biology, DNA, Evolution, History, Research

Image Source: Homo luzonensis

Researchers Find a New Ancient Human Species in the Philippines
Charles Q. Choi, Live Science