Quantum biology: Algae evolved to switch quantum coherence on and off

Quantum biology: Algae evolved to switch quantum coherence on and off: "Most cryptophytes have a light-harvesting system where quantum coherence is present. But we have found a class of cryptophytes where it is switched off because of a genetic mutation that alters the shape of a light-harvesting protein.
"This is a very exciting find. It means we will be able to uncover the role of quantum coherence in photosynthesis by comparing organisms with the two different types of proteins."

Proteins 'ring like bells'

Proteins 'ring like bells': Using modern laser spectroscopy, the scientists have been able to measure the vibrational spectrum of the enzyme lysozyme, a protein that fights off bacteria. They discovered that this enzyme rings like a bell with a frequency of a few terahertz or a million-million hertz. Most remarkably, the ringing involves the entire protein, meaning the ringing motion could be responsible for the transfer of energy across proteins.

The experiments show that the ringing motion lasts for only a picosecond or one millionth of a millionth of a second. Biochemical reactions take place on a picosecond timescale and the scientists believe that evolution has optimised enzymes to ring for just the right amount of time. Any shorter, and biochemical reactions would become inefficient as energy is drained from the system too quickly. Any longer and the enzyme would simple oscillate forever: react, unreact, react, unreact, etc...

New Double Helix Visualization Revises What We Know About DNA

New Double Helix Visualization Revises What We Know About DNA: Results reaffirmed the structure first suggested by Watson and Crick in 1953. But surprisingly, the single-molecule images showed major variations in the depths and grooves in the double helix structure.

The symphony of life, revealed - News Center

The symphony of life, revealed - News Center: Using a technique they developed based on terahertz near-field microscopy, scientists... have for the first time observed in detail the vibrations of lysozyme, an antibacterial protein found in many animals.

The team found that the vibrations, which were previously thought to dissipate quickly, actually persist in molecules like the “ringing of a bell...”

To observe the protein vibrations, Markelz’ team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb...

Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed.

Speed limit on a superfluid helium nano-highway

Speed limit on a superfluid helium nano-highway: The new research has now shown that even in tiny nanodroplets, helium still exhibits superfluidity...


The result of the experiment was quite astonishing: the measured velocity is always the same. It does not matter whether the impurity is a metal atom, a diatomic molecule or a polyatomic molecule with a cage structure: they all leave the droplet with the same speed. Mass or size thus does not matter. Even the repulsive force (which could be tuned with the laser pulse) turned out not to be of any influence.

Imaging most of a worm’s brain activity at high resolution and in a single operation | KurzweilAI

Imaging most of a worm’s brain activity at high resolution and in a single operation | KurzweilAI: Visualizing the neurons also requires tagging them with a fluorescent protein that lights up when it binds to calcium, signaling the nerve cells’ activity.

“The neurons in a worm’s head are so densely packed that we could not distinguish them on our first images...”

“Our solution was to insert the calcium sensor into the nuclei rather than the entire cells, thereby sharpening the image so we could identify single neurons.”

How neurons ‘decide’ to create axons or dendrites | KurzweilAI

How neurons ‘decide’ to create axons or dendrites | KurzweilAI: They found that embryonic nerve cells manufacture a signaling enzyme called Atypical Protein Kinase C (aPKC) in two varieties: a full-length one and a shorter one...
When the researchers blocked the production of the short form, the nerve cell grew multiple axons and no dendrites. When they created an artificial abundance of the short form, dendrites formed at the expense of axons.

What does mercury being liquid at room temperature have to do with Einstein’s theory of relativity? | The Curious Wavefunction, Scientific American Blog Network

What does mercury being liquid at room temperature have to do with Einstein’s theory of relativity? | The Curious Wavefunction, Scientific American Blog Network:  From Niels Bohr’s theory of atomic structure we know that the velocity of an electron is proportional to the atomic number of an element. For light elements like hydrogen (atomic number 1) the velocity is insignificant compared to the speed of light so relativity can be essentially ignored. But for the 1s electron of mercury (atomic number 80) this effect becomes significant; the electron approaches about 58% of the speed of light, and its mass increases to 1.23 times its rest mass. Relativity has kicked in. Since the radius of an electron orbit in the Bohr theory (orbital to be precise) goes inversely as the mass, this mass increase results in a 23% decrease in the orbital radius. This shrinkage makes a world of difference since it results in stronger attraction between the nucleus and the electrons, and this effect translates to the outermost 6s orbital as well as to other orbitals. The effect is compounded by the more diffuse d and f orbitals insufficiently shielding the s electrons. Combined with the filled nature of the 6s orbital, the relativistic shrinkage makes mercury very reluctant indeed to share its outermost electrons and form strong bonds with other mercury atoms.

The bonding between mercury atoms in small clusters thus mainly results from weak Van der Waals forces which arise from local charge fluctuations in neighboring atoms rather than the sharing of electrons.

Muscles act as metamaterials due to collective behavior, physicists show

Muscles act as metamaterials due to collective behavior, physicists show: Upon further search for possible mechanisms of negative stiffness, scientists in a new study have found that biological muscles exhibit a mechanical response that also qualifies them as metamaterials: when a tetanized (maximally contracted) muscle is suddenly extended, it comes loose, and if it is suddenly shortened, it tightens up...

Quite surprisingly, the cooperation at the nanoscale in muscles was found to be similar to magnetism; moreover, the critical point at which muscles seem finely tuned to perform near is, in this case, a direct analog of the ferromagnetic Curie point.

A Near-Whole Brain Activity Map in Fish

A Near-Whole Brain Activity Map in Fish:  The zebrafish larvae, whose bodies are transparent and brains are tiny, were genetically engineered to produce a protein in their neurons that glows in response to the chemical changes that occur when that neuron fires...

With the modified fish and microscopy methods, the researchers were able to capture the activity of at least 80 percent of the baby fish’s 100,000 neurons over a time period of just 1.3 seconds.  

The Swiss Army Knife Robot | MIT Technology Review

The Swiss Army Knife Robot | MIT Technology Review: The device is called a milli-motein—a reference to its millimeter-sized components and a motorized design inspired by proteins, which naturally fold themselves into incredibly complex shapes. "It’s effectively a one-dimensional robot that can be made in a continuous strip, without conventionally moving parts, and then folded into arbitrary shapes," says Neil Gershenfeld...

To build it, the research team had to invent an entirely new kind of motor: one that is not only small and strong but also able to hold its position firmly even with the power switched off. (When an ordinary electric motor is switched off, its shaft can rotate freely.) The researchers met these needs with a new system called an electropermanent motor.

Researchers Build First Complete Computer Model of an Entire Organism

Researchers Build First Complete Computer Model of an Entire Organism: A team at Stanford created the model, basing it on more than 900 scientific papers. M. genitalium has the smallest genome of any living organism--a mere 525 genes--but even for an organism of its size, it takes that much information to account for every interaction it will undergo in its lifespan. Researchers tallied the number of experimentally determined parameters in the model at more than 1,900; those were split up into 28 algorithms, which stepped in for biological processes.

Evolution could generate new semiconducting structures

Evolution could generate new semiconducting structures: The team chose silicateins – proteins that build the silica skeletons of marine sponges – as the basis for their work. Using DNA amplification techniques, they grew millions of strands of DNA that code for silicateins. Mutations arise naturally during the process, so the final pool of DNA contained enough variation to ensure that some of the silicateins would build different kinds of mineral structures.

The researchers then attached the DNA to polystyrene microbeads and placed them in a solution containing a silicon-rich compound. Bawazer's team was looking to select proteins that could draw silicon out of the solution to build silica structures around the beads, while still allowing access to the DNA on the surface of the bead. This would make it easy to collect and amplify the DNA that made the most promising structures. The end product? Proteins that built silica structures unlike any seen in nature.

Scientists switch mouse's genes off and on with radio waves

Scientists switch mouse's genes off and on with radio waves: Friedman and his colleagues coated iron oxide nanoparticles with antibodies that bind to a modified version of the temperature-sensitive ion channel TRPV1, which sits on the surface of cells. They injected these particles into tumours grown under the skins of mice, then used the magnetic field generated by a device similar to a miniature magnetic-resonance-imaging machine to heat the nanoparticles with low-frequency radio waves. In turn, the nanoparticles heated the ion channel to its activation temperature of 42 °C. Opening the channel allowed calcium to flow into cells, triggering secondary signals that switched on an engineered calcium-sensitive gene that produces insulin. After 30 minutes of radio-wave exposure, the mice's insulin levels had increased and their blood sugar levels had dropped...
Even better, the researchers have already developed a way to achieve similar, albeit weaker, results without having to inject nanoparticles at all. They have developed cells that can grow their own required nanoparticles, meaning there would be no need to give patients strange chemicals or molecules.

Enzymes grow artificial DNA : Nature News & Comment

Enzymes grow artificial DNA : Nature News: The artificial polymers, dubbed XNAs, carry the normal genetic 'alphabet' on a backbone made using different sugars. Scientists have previously developed XNAs that recognize and bind genetic sequences for experimental and biomedical applications, but is it difficult to make them in large quantities.

“Any time you want another XNA molecule, you’ve got to make more, but you can’t copy what you already made — until now,” says Gerald Joyce, a biochemist at the Scripps Research Institute in La Jolla, California.

Holliger and his team engineered enzymes that helped six types of XNA to assemble and replicate genetic messages. The enzymes transcribed DNA into the various XNAs, then back into new DNA strands — with 95% accuracy or more.

More evidence found for quantum physics in photosynthesis

More evidence found for quantum physics in photosynthesis: In an experiment published Dec. 6 in Proceedings of the National Academy of Sciences, a connection between coherence—far-flung molecules interacting as one, separated by space but not time—and energy flow is established.

..."Here we can watch the relationship between coherence and energy transfer. This is the first paper showing that coherence affects the probability of transport. It really does change the chemical dynamics."

...Energy from incoming photons could simultaneously explore every possible chlorophyll route from a protein's surface to the reaction center at its core, then settle on the shortest path.


...a team... analyzed the fluctuation of lasers as they passed through antenna proteins. Depending on how they shifted, the researchers could track what happened inside.

They found a clear mathematical link between energy flows and fluctuations in chlorophyll coherence. The link was so clear it could be described in derivative sines and cosines, mathematical concepts taught in college trigonometry.

Synthetic yeast will evolve on command - life - 14 September 2011 - New Scientist

Synthetic yeast will evolve on command: Biologists have built two artificial chromosome arms and put them to work in a living yeast. They plan to replace the entire yeast genome over the next five years and then evolve new strains to order...
The artificial yeast are similar to Craig Venter's synthetic cells, announced last year. Venter replaced the entire genome of a bacterium with a synthetic genome – but the task is far harder in yeast, because it is a more complex organism and has a bigger genome...

First life: The search for the first replicator - New Scientist - New Scientist

First life: The search for the first replicator: Sutherland was being deliberately messy by including the phosphate from the start, but it gave the best results. That's encouraging: the primordial Earth was a messy place and it may have been ideal for making nucleotides. Sutherland now suspects there is a "Goldilocks chemistry" - not too simple, not too complex - that would produce many key compounds from the same melting pot.

"Sutherland had a real breakthrough," Holliger says. "Everyone else was barking up the wrong tree."

Lasers Made from Human Cells - Technology Review

Lasers Made from Human Cells - Technology Review: Living lasers have a few basic parts that are drawn from the same list as any laser. First, the researchers genetically modified human liver cells so that they produce large amounts of green fluorescent proteins that are scattered throughout the cell. A cell carrying these proteins acts as the "gain medium"—the part of the laser that amplifies light energy. '

Like any laser, the cell laser needs an energy source to "pump" it and increase the power of the light it can emit. The researchers pumped the living lasers by pulsing the cells with light through a microscope. As light bounces around inside the cell and is re-emitted by the fluorescent proteins, it's amplified, increasing in power before being emitted in a coherent beam. To keep the light bouncing around as long as possible, to gain as much power as possible, the Boston group placed these cells inside a biocompatible optical cavity—essentially a tiny, highly reflective, cell-shaped hole.

New algorithm helps engineers choose self-assembling proteins | KurzweilAI

New algorithm helps engineers choose self-assembling proteins | KurzweilAI: "The researchers’ algorithm works in three steps that successively eliminate proteins that will not produce the right shape. The elimination criteria are based on traits like symmetry, periodicity of binding sites, and similarity to protein “motifs” found in nature.

The result is a list of thousands of candidate proteins."