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Wednesday, 27 March 2013

The Spooky World Of Quantum Biology : New Horizon of Molecular Biology

Animated Slides of Quantum Biology

The Spooky World Of Quantum Biology  By: Michael Garfield

The new science of quantum biology is teaching us about how the actual behavior of evolution is governed by disconcertingly spooky processes – time travel being one of them. Will quantum computation finally be realized by biomimicry, in organic systems?  Evolution is the new (old) computation…and we’re about to take the reins.

World Of Quantum Biology

One hundred and fifty years ago, paleontologist Thomas Henry Huxley (an autodidact and philosopher who coined the term “agnostic” and was known as “Darwin’s Bulldog” for his passionate defense of natural selection) asserted that humankind would eventually take the processes of evolution into our own hands. Within a few decades of his proclamation, a cadre of equally brilliant scientists including Werner Heisenberg, David Bohm, and Max Planck began to unravel the mysterious properties of quantum mechanics. These two theories –- evolutionary and quantum dynamics — can each be considered among the most important discoveries of all time. Taken together, they have changed almost everything about the way we understand reality. However, in spite of the popularity of interdisciplinary research and unifying theories over the last hundred years (despite, even, quantum physicist Erwin Schröedinger’s 1944 book, What Is Life?), it was only recently that the relationship between these two vastly important domains was even considered. Now, a new kind of science, called “quantum biology,” is beginning to emerge –- and it could change everything we know, again..

The premise is simple. Life is a molecular process; molecular processes operate according to the quantum playbook; therefore, life is a quantum process. And yet, it wasn’t until the nineties that anyone suggested biology could be better understood by looking at it through the lens of quantum theory. (The seminal paper was D.V. Nanopoulos’ "Theory of brain function, quantum mechanics and superstrings.”)  Not long after that, the idea caught on – particularly in the neurosciences, where the idea of the brain as a quantum computer quickly became a topic of fierce debate.

Quantum computation, a science still in its infancy, promises swiftness and efficiency vastly superior to anything possible with conventional silicon chips. Rather than relying on binary bits like contemporary systems, quantum computers use “qubits” that include all possible superpositions of a particle’s classical state. Instead of being “trapped” in a single configuration, the logic gates of a quantum computer employ multiple possibilities in synchrony – using the entire set of alternative outcomes to arrive at an answer.

Scientists have recently discovered that quantum energy transfers allow plants and cynobacteria to convert sunlight into chemical energy nearly instantly, and with almost 100 percent efficiency. "As energy passes between molecules involved in photosynthesis, a newly observed ‘wavelike characteristic’ allows the energy to ‘simultaneously sample all the potential energy pathways and choose the most efficient one,’" our   worid science co-bloggers observe. They liken it to the "sci-fi trope" in which "a digital consciousness" is split "into several ‘forks’ that simultaneously explore different courses of action before telling a central consciousness what to do

It’s a promising avenue for people with big plans for strong AI or virtual reality. The only complication is that coherence –- in which the many possible states of a particle or group of particles stay hung in superposition –- is something scientists have only been able to study under extremely controlled conditions. It’s only possible when that system doesn’t interact with anything else that might “collapse the wave function,” and so most of the major options for quantum computing involve impractical scenarios like creating a supercooled vacuum.

This is one of the reasons that many scientists have considered quantum biology both unlikely and unscientific. The thermal noise of biological systems seemed too great to allow for quantum weirdness; and even if it could, how on Earth would we study it?  But science is the story of ingenuity’s victory over shortsightedness – and one research team, led by Gregory S. Engel at UC Berkeley, has devised way to directly detect and observe quantum-level processes within a cell using high-speed lasers.

They were trying to establish exactly how organic photosynthesis approaches 95% efficiency, whereas the most sophisticated human solar cells operate at only half that. What they discovered is nothing short of remarkable. Using femtosecond lasers to follow the movement of light energy through a photosynthetic bacterial cell, Engel et al. observed the energy traveling along every possible direction at the same time. Instead of following a single trajectory like the electrons on a silicon chip, the energy in photosynthesis explores all of its options and collapses the quantum process only after the fact, retroactively “deciding” upon the most efficient pathway.

What does this all mean? Not only does quantum phenomena occur in living systems, but the basic processes of life we take for granted rely on the transfer of information backward in time. Life is so magical because it cheats.

Although the mechanisms by which a living cell can prevent decoherence by dampening its own chemical “noise” remain utterly mysterious, findings such as Engels’ conclusively demonstrate that room-temperature quantum computing is possible (and knowing how something works isn’t always necessary in order to use it). And Engel’s group isn’t the only team to detect it: other laboratories have implicated a phenomenon called electron tunneling (micro-teleportation, in which an electron disappears in one location and instantaneously appears somewhere else without having traveled the intermediate distance) at work behind a range of organic phenomena, from our sense of smell and the activities of our enzymes to the neutralization of free radicals with anti-oxidants…  possibly even consciousness itself. Paul Davies (Arizona State University) and JohnJoe McFadden (The University of Surrey) have independently suggested that computation in the netherworld of quantum coherence might explain how the earliest self-replicating molecules overcame the inestimable odds against them –- life’s very existence may be the consequence and continued operation of a quantum computer. We may ultimately have to accept our human quest for qubit calculation as a kind of biomimicry, rather than something new and unique.

Quantum biology stands to answer other big questions, as well –- questions that many contemporary biologists prefer to ignore. McFadden, in his excellent primer Quantum Evolution, cites several experiments that suggest certain mutations are “intelligent,” even “anticipatory.”  For example, bacterial cultures have been observed to evolve clever responses to lab toxins at speeds that – just like the emergence of DNA from a primordial soup – defy astronomical odds.  Can biological quantum calculation account for this?  McFadden thinks so. (His hypothesis was itself anticipated in the science fiction of Greg Egan, whose novel Teranesia featured some very “spooky” retrocausal mutations – including the instantaneous appearance of entire new ecosystems via competing future evolutionary scenarios. Whether such extreme examples of quantum biological principles are possible remains to be seen.)

Quantum Computer

As we continue to probe biological phenomena that beat quantum computer scientists to the punch, a new picture emerges of evolutionary computing and design. Huxley’s prophecy that we will eventually take the reins of our own evolution might come true sooner than predicted by establishment geneticists. But by appealing to the quantum oracle, we may be acting in service of something far older and more intelligent than we can even guess. Ultrafast computing, accelerated by our explorations into the new science of quantum biology, could well be the critical technology that pushes us over the edge into the Singularity – a timeless and transcendent event in which we already live, because it is the nature of life itself – a vast sentience beyond human comprehension, and we are merely the newest avenue for its expression in the world. Classical or quantum, human or ecological, natural selection still gets the last laugh.

Everywhere in a Flash: The Quantum Physics of Photosynthesis

The Quantum Physics of Photosynthesis

By hitting single molecules with quadrillionth-of-a-second laser pulses, scientists have revealed the quantum physics underlying photosynthesis, the process used by plants and bacteria to capture light’s energy at efficiencies unapproached by human engineers.

The quantum wizardry appears to occur in each of a photosynthetic cell’s millions of antenna proteins. These route energy from electrons spinning in photon-sensitive molecules to nearby reaction-center proteins, which convert it to cell-driving charges.

Almost no energy is lost in between. That’s because it exists in multiple places at once, and always finds the shortest path.

Molecular  Pathway of Photosynthesis

“The analogy I like is if you have three ways of driving home through rush hour traffic. On any given day, you take only one. You don’t know if the other routes would be quicker or slower. But in quantum mechanics, you can take all three of these routes simultaneously. You don’t specify where you are until you arrive, so you always choose the quickest route,” said Greg Scholes, a University of Toronto biophysicist.

Scholes’ findings, published Wednesday in Nature, are the strongest evidence yet for coherence — the technical name for multiple-state existence — in photosynthesis.

Bacterial Photosynthesis

he LH2 pigment-protein from Rhodopseudomonas acidophila. Views are parallel (left) and perpendicular (right) to the plane of the membrane. The protein scaffold comprises concentric cylinders of nine  (inner), and nine ß (outer) polypeptides (teal and purple ribbons, respectively). The 18 B850 BChls (which absorb strongly at 850 nm) are shown as spheres, in alternating red and orange, and the nine B800 BChls (which absorb strongly at 800 nm) are shown as green sticks (with the central Mg shown as a sphere). The macrocycles of the B850 and B800 BChls are arranged perpendicular and parallel, respectively, to the plane of the membrane. The figure was constructed using using Protein Data Bank (PDB) file 1NKZ (Papiz et al., 2003).

Two years ago, researchers led by then-University of California at Berkeley chemist Greg Engel found coherence in the antenna proteins of green sulfur bacteria. But their observations were made at temperatures below minus 300 degrees Fahrenheit, useful for slowing ultrafast quantum activities but leaving open the question of whether coherence operates in everyday conditions.

The Nature findings, made at room temperature in common marine algae, show that it does. Moreover, similar results from an experiment on another, simpler light-harvesting structure, announced by Engel’s group last Thursday on the pre-publication online arXiv, suggest that photosynthetic coherence is routine.

The findings are wondrous in themselves, adding a new dimension to something taught — incompletely, it now seems — to every high school biology student. They also have important implications for designers of solar cells and computers, who could benefit from quantum physics conducted in nonfrigid conditions.

“There’s every reason to believe this is a general phenomenon,” said Engel, now at the University of Chicago. He called Scholes’ finding “an extraordinary result” that “shows us a new way to use quantum effects at high temperatures.”

Scholes’ team experimented on an antenna protein called PC645, already imaged at the atomic scale in earlier studies. That precise characterization allowed them to target molecules with laser pulses lasting for one-quadrillionth of a second, or just long enough to set single electrons spinning.

By analyzing changes to a laser beam sent through the protein immediately afterwards, the researchers were able to extrapolate what was happening inside — an ultra-high-tech version of shadows on a screen. They found that energy patterns in distant molecules fluctuated in ways that betrayed a connection to each other, something only possible through quantum coherence.

“It’s the same as when you hit two tuning forks at the same time, and hear a low-pitched oscillation in the background. That’s the interference of sound waves from the forks. That’s exactly what we see,” said Scholes.

According to Scholes, the physics of photosynthetic proteins will be further studied and used to improve solar cell design. Engel suggested their use in long-promised but still-unworkable quantum computing. “This allows us to think about photosynthesis as non-unitary quantum computation,” he said.

Quantum-physical processes have been observed elsewhere in the biological realm, most notably in compass cells that allow birds to navigate by Earth’s geomagnetic fields. Researchers have also proposed roles for quantum physics in the animal sense of smell and even in the brain. Engel predicts the emergence of an entire field of quantum biology.

“There are going to be some surprises,” said Scholes. “Who knows what else there is to discover?”

Reverse-Engineering the Quantum Compass of Birds

Quantum Compass of Birds

Scientists are coming ever closer to understanding the cellular navigation tools that guide birds in their unerring, globe-spanning migrations.The latest piece of the puzzle is superoxide, an oxygen molecule that may combine with light-sensitive proteins to form an in-eye compass, allowing birds to see Earth’s magnetic field.

“It connects from the subatomic world to a whole bird flying,” said Michael Edidin, an editor of Biphysical Journal, which published the study last week. “That’s exciting!”The superoxide theory is proposed by Biophysicist Klaus Schulten of the University of Illinois at Urbana-Champaign, lead author of the study and a pioneer in avian magnetoreception. Schulten first hypothesized in 1978 that some sort of biochemical reaction took place in birds’ eyes, most likely producing electrons whose spin was affected by subtle magnetic gradients.

In 2000, Schulten refined this model, suggesting that the compass contained a photoreceptor protein called cryptochrome, which reacted with an as-yet-unidentified molecule to produce pairs of electrons that existed in a state of quantum entanglement — spatially separated, but each still able to affect the other.

According to this model, when a photon hits the compass, entangled electrons are scattered to different parts of the molecule. Variations in Earth’s magnetic field cause them to spin in different ways, each of which leaves the compass in a slightly different chemical state. The state alters the flow of cellular signals through a bird’s visual pathways, ultimately resulting in a perception of magnetism.

Avian Compass Experiment : Published in Nature

Far-fetched as it sounds, subsequent research from multiple groups has found cellular evidence of such a system. Molecular experiments suggest that it’s indeed sensitive to Earth’s geomagnetics, and computational models suggest a level of quantum entanglement only dreamed of by physicists, who hope to use entangled electrons to store information in quantum computers.

Birds Flight

But though cryptochrome is likely part of the compass, the other part is still unknown. In April, another group of magnetoreception researchers showed that oxygen could interact with cryptochrome to produce the necessary electron entanglements. Schulten’s latest proposed role for superoxide, an oxygen anion found in bird eyes, fits with their findings.Edidin cautioned that “this is still not an experimental demonstration. It’s a possibility.”As for the perceptual result of the compass, it remains a mystery. Some researchers think birds might see a dot at the edge of their vision, swiveling according to the direction they’re facing. Others think it might produce effects of color or hue. Perhaps migrating birds fly towards the light.

Google Earth Reveals Sixth Sense of Cattle, Deer

Sixth Sense of Cattle, Deer

Though my farm-raised father insists differently, there’s something a bit spooky about cows standing in a field. They’re just a bit too placid; I’ve always suspected that those limpid eyes hide strange secrets.And what do you know — I was right! German and Czech biologists have shown that cattle, along with deer, instinctively stand in a north-south direction. They appear to possess a sixth sense of magnetism.After studying Google Earth satellite images of cattle herds, along with their own observations of roe deer, the researchers realized that the animals routinely stood along a north-south axis."The magnetic field is the only common and most likely factor responsible for the observed alignment," write the researchers in a study published today in the Proceedings of the National Academy of Sciences. "Our analysis … clearly provides the crucial proof in favor of the Earth’s magnetic field being the responsive cue."

They think the ability evolved to help guide the animals’ ancestors during migrations (which could explain why the results are stronger in deer than cattle, which having been domesticated and restrained no longer migrate.) What’s the physiological mechanism? That’s not yet known. "Our findings … challenge neuroscientists and biophysics to explain the proximate mechanisms," the researchers write.You hear that, neuroscientists and biophysics? You got served!

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