Wednesday, May 6, 2009

479)From Green Leaves To Bird Brains, Biological Systems May Exploit Quantum Phenomena; Quotes Of Noble Quran, Prophet Muhammad, Aga Khans And Others

Chapter 2, Verse 242: Kathalika yubayyinu Allahu lakum ayatihi la'allakum ta-'aqiloona: "Allah thus makes clear to you His Signs that you may intellect"(Noble Quran)

"One hour of contemplation on the works of the Creator is better than a thousand hours of prayer"(Prophet Muhammad, circa 632CE)

"Every particle of the Creation has a share of the Command of God, because every creature shares a part of the Command of God through which it has come to be there and by virtue of which it remains in being and the light of the Command of God shines in it. Understand this!"(Abu Yakub Al Sijistani, 10th century Fatimid Ismaili cosmologist, d971, Kashf al-Mahjub("Unveiling of the Hidden"))

"Tarkib' is composition as in the compounding of elements in the process of making more complex things, that is, of adding together two things to form a synthesis, a compound. Soul composes in the sense of 'tarkib'; it is the animating force that combines the physical elements of the natural universe into beings that move and act. Incorporating is an especially apt word in this instance. It means to turn something into a body, as in 'composing'. But it is actually the conversion of an intellectual object, a thought, into a physical thing. Soul acts by incorporating reason into physical objects, the natural matter of the universe and all the things composed of it"(Abu Yakub Al-Sijistani,10th century Fatimid Ismaili cosmologist, d971CE, from the book, 'Abu Yakub Al-Sijistani: Intellectual Missionary', by Paul Walker)

"O brother! You asked: What is the [meaning of] `alam [world] and what is that entity to which this name applies? How should we describe the world in its entirety? And how many worlds are there? Explain so that we may recognize. Know, O brother, that the name `alam is derived from [the word] `ilm(knowledge), because the traces of knowledge are evident in [all] parts of the physical world. Thus, we say that the very constitution (nihad) of the world is based on a profound wisdom"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet, from his book "Knowledge and Liberation")

"In fact this world is a book in which you see inscribed the writings of God the Almighty"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

"The God of the Quran is the One whose Ayats(Signs) are the Universe in which we live, move and have our being"(Aga Khan III, April 4th 1952)

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

The above are 10 quotes and excerpts taken from Blogpost Four Hundred, a collection of around 100 quotes on the subjects of Knowledge, Intellect, Creation, Science and Religion:

Living Physics

From Green Leaves To Bird Brains, Biological Systems May Exploit Quantum Phenomena

By Susan Gaidos
May 9th, 2009; Vol.175 #10 (p. 26)

EnlargePHOTOSYNTHESIS GOES QUANTUMHi-Res (Click twice to zoom in) Plants and certain bacteria capture energy from light and use it to make food through the process of photosynthesis. The initial stage of the process is remarkably efficient — so efficient, in fact, that scientists are looking to quantum phenomena to explain what’s happening.Illustration by Nicolle Rager Fuller

Until a century or so ago, nobody had any idea that there even was such a thing as quantum physics. But while humans operated for millennia in quantum darkness, it seems that plants, bacteria and birds may have been in the know all along.

Quantum effects, human researchers have only recently discovered, may explain how the first steps of photosynthesis convert light to chemical energy with such high efficiency. Other studies suggest that quantum tricks may enable migratory birds to navigate using Earth’s magnetic field lines.

Through studies like these, scientists are beginning to understand how quantum mechanics — weirdness supposedly confined to the realm of subatomic physics — affects everyday biology.
On one level, it seems perfectly natural that quantum mechanics would serve a function at life’s foundation. After all, quantum principles define the properties of atoms, from which living matter is made. And yet the quantum rules, which allow particles like electrons to exist in two places at once and sometimes behave like waves rather than particles, seem an unlikely driver of life’s tightly regulated processes. Bizarre quantum properties are supposed to govern objects such as individual atoms, not great clumps of matter like redwoods or robins.

Now, with growing evidence that quantum weirdness indeed exists in biological systems, scientists are looking for ways to tell how, or even if, nature exploits these effects to confer an advantage.

“We can’t tell nature to ignore quantum mechanics, so we might need to measure it and see what happens,” says Graham Fleming, a chemist at the University of California, Berkeley, who coauthored a paper in the 2009 Annual Review of Physical Chemistry outlining recent studies showing quantum effects in photosynthesis.

Understanding how natural systems use quantum effects to their advantage might help researchers find ways to control, and ultimately harness, such processes. By copying the quantum tricks used by plants, for example, researchers might be able to develop new technologies, such as more efficient solar cells.

Making waves in the lab

Photosynthesis is carried out by molecular machinery embedded in membranes in the interior of plant cells and some bacteria. Like all chemical reactions, it relies on the action of electrons.
In green plants, light particles are absorbed by pigment molecules — primarily chlorophyll — found in leaves. An incoming light particle, or photon, boosts an electron in the chlorophyll into a mobile state. Once excited, the electron is quickly shuttled from the chlorophyll to a nearby “acceptor” molecule, setting off a series of electron transfers. Moving from one molecule to another, the electron ultimately reaches the “reaction center,” where the energy is converted into a form the cell can use to make carbohydrates.

It’s these initial, near instantaneous energy transfers that are so remarkably efficient — scientists estimate that more than 95 percent of the energy in the light hitting a leaf reaches the photosynthesis reaction center. Although each of the biochemical steps that follow adds a loss in energy efficiency, the first steps in the process closely approach the ideal of one photon leading to one electron transfer.

Previous models of photosynthesis assumed that the light energy stored in excited electrons found its way to the reaction center via random hops, particles moving in a step-by-step manner to successively lower energy levels. But some scientists seeking to explain plants’ superefficient energetics have considered the notion that plants may have a way to exploit the quantum behavior of electrons.

In the odd quantum world, particles can behave like waves. Rather than simply moving from one chlorophyll to another, electrons can exist as whirling clouds of energy, jostling back and forth between the molecules. In this wavelike state, the electrons become connected, or coupled, and act in a concerted manner so the excitation is actually “sloshing around” between the molecules, Fleming says.

Scientists theorized that this and other quantum effects could allow for more efficient movement of energy but were faced with a problem in trying to capture evidence of such effects in the lab. In the classical world, either molecule A or B is excited, and scientists can track the transfer of excitation by measuring changes in the molecules over time. But in the quantum world, things appear to exist in a multitude of states, making measurements more complicated. Besides measuring changes of excitation in A and B over time, the scientists needed a way to measure simultaneous excitations of A and B — a signature of a quantum effect called coherence.

In 2005, Fleming and his colleagues developed a way to capture these simultaneous excitations, or oscillations, in a photosynthetic protein found in green sulfur bacteria. Using ultrafast lasers, the scientists flashed the sample with three pulses from different beams to stimulate energy absorption and transfer. A fourth pulse was then delivered to amplify the signal.
The timing of the flashes allowed the scientists to follow energy flow in two dimensions, watching it in time and space as it moved from one chlorophyll to another.

EnlargeGOING FOR A SPINView Larger Version Studies suggest that migrating birds exploit quantum effects in their visual systems to sense magnetic fields. Illustration by Nicolle Rager Fuller

The method provided a way to follow a system’s vibrational state, tracking its many wavelengths to see when they are what scientists call “in phase.” When numerous particles such as electrons move in phase, all atoms are moving, spinning and tipping in synchronicity. Such a system is in a coherent state.

Uncertain he would find such wavelike behavior in a photosynthetic bacterium, Fleming nonetheless considered it possible. “What changed is that we could stop considering [the quantum effect] as a possibility and actually measure it,” Fleming says.

In 2007, a sharp-eyed postdoc using the two-dimensional laser technique spotted the telltale signature in a sample of green sulfur bacteria after blasting it with the laser.

When the scientists repeated the experiment, their data showed the oscillations meeting and interfering constructively, forming wavelike motions of energy flowing through the system.
Fleming’s team, publishing in Nature, noted that quantum coherence could explain the extreme efficiency of photosynthesis by enabling electrons to simultaneously sample all the various potential pathways to the reaction center and choose the most efficient one (SN: 4/14/07, p. 229). Rather than hopping from one molecule to another in a step-by-step manner, the electrons could try various routes to find the path of least resistance.

Intelligent design

Photosynthetic organisms are designed for efficiency. The light-absorbing chlorophyll molecules found in leaves, for example, aren’t just arbitrarily scattered throughout the cell, but are tightly packed into tiny organelles, crammed into spaces where they touch each other frequently. So when excited by a photon, the chlorophylls no longer act as individuals, but band together to create a system that works in concert, says Thorsten Ritz, a theoretical physicist at the University of California, Irvine.

And acting in concert has advantages. For one, it allows plants to absorb energy in different ranges of light. Such a system also permits other light-absorbing pigment molecules, such as carotenoids, to transfer energy into the system in an efficient manner.

Early this year, scientists in Ireland and England used an ultrafast laser with multiple color wavelengths to get an even closer view of energy moving through a photosynthetic system. Ian Mercer of University College Dublin, along with researchers at Imperial College London, flashed a light-absorbing protein from purple bacteria with a series of pulses lasting less than one ten-thousandth of a billionth of a second each.

When it hit the bacterial protein, the light energized a series of reactions that ultimately led the protein to emit light of its own. Because the laser pulses were made up of a broad spectrum of colors, with each color corresponding to a specific energy, the light emitted by the sample provided a clear view of the different energies at play inside the protein. The resulting map showed how individual electrons coordinated their movements as they jostled energy back and forth: Shifts to the left or right showed electrons connecting, while vertical shifts indicated energy was being passed or received.

The methods allowed the scientists to distinguish random hopping of energy, or particle behavior, from the wavelike movements of electrons behaving collectively. The study, published in the Feb. 6 Physical Review Letters, will help scientists better model how quantum effects such as coherence influence energy transfer in photosynthesis, Mercer says.

“We’ve been needing a better pair of eyes to see how molecules are doing the tricks that they do,” he says.

Going for a spin

Birds may give scientists another pair of eyes in which to view quantum effects in living cells. Studies suggest that migratory birds about to embark on their seasonal journeys may tap into a quantum property called spin to help them “see” Earth’s magnetic field using photosensitive proteins in their eyes.

The idea that birds rely on some sort of biochemical reaction to orient themselves during migration was first proposed more than 30 years ago. Eleven years ago, Ritz and his colleagues identified cryptochrome, a protein containing a light-sensitive pigment, as a candidate molecule capable of creating such a reaction.

Cryptochrome is found in the nerve layers of birds’ eyes. Research shows that when cryptochrome interacts with a specific wavelength of blue-green light it can trigger a cascade of electron transfers similar to those that occur in photosynthesis.

Normally, the electrons in cryptochrome exist in pairs. The energy from light, however, can rip the electrons apart, leaving one electron on the original molecule and sending the other off to another molecule. The result is two charged molecules, or ions.

Initially, the electrons in these molecules spin in opposite directions. In the presence of an external magnetic field, however, the dynamics of the spins will change, altering their orientation relative to each other. The veering spins create a biochemical reaction allowing the birds to perceive the Earth’s magnetic lines as patterns of color or light superimposed on their surroundings, Ritz speculates, similar to a dashed line in the middle of a road.

Though scientists have yet to prove that cryptochrome can create this reaction in birds, evidence for the theory is mounting.

In a 2004 Nature study, Ritz and his colleagues showed that disrupting the local magnetic field around captive birds preparing to migrate interfered with the birds’ internal compasses. By disrupting the field, for example, the scientists could induce the birds to take off in the wrong direction.

Last spring, in a proof-of-theory trial published in Nature, researchers at the University of Oxford in England and Arizona State University in Tempe showed how a cryptochrome-like molecule could respond to the direction of a weak magnetic field, such as the Earth’s.

The scientists created a synthetic molecule made up of three light-absorbing pigments. When flashed with a laser beam, electrons in the molecule first separated briefly, as predicted, then recombined. The amount of time the electrons spent in a separated state varied with the angle of the magnetic field. When the electrons returned to their paired state, the energy caused a change in the shape of the molecule.

Ritz is now looking for ways to isolate cryptochrome in fruit flies to test these effects in animals. Though the light-absorbing pigments in cryptochrome trigger a different cascade of electron transfers than those generated in photosynthesis, Ritz says both systems appear to be influenced by the wavelike nature of quantum mechanics. But how biological systems can maintain what most consider such a fragile effect is still a puzzle.

“The same questions that I asked about photosynthesis are true here, as well,” Ritz says. “How does this system maintain coherence when you have all kinds of fluctuations that could, in principle, disrupt it? It’s a big open question that we don’t have good answers to at this point.”

A higher standard of proof

While coherent quantum states can be maintained in controlled laboratory settings, most scientists have been dismissive of the idea that such coherence could be achieved in the hot, messy realm of living cells. Atoms and molecules in such a system are continually assailed by influences from their environment. And the slightest insult can mangle the phases of their waves, causing them to lose their coherence.

When Fleming measured the persistence of these wavelike states in photosynthetic bacteria, he found that the coherence lasted surprisingly long — up to 660 billionths of a second. On the timescale of molecular events, that’s an eternity.

“For some reason it seems that nature has maybe coordinated the movement or done something else to let this coherence survive,” Ritz says. “And what that reason is would be very interesting to find out because it may give us a clue of how we could control processes at that level.”
While recent work has found evidence for the presence of quantum effects in living systems, researchers have yet to demonstrate that those effects can actually influence the efficiency of photosynthesis or migrating birds’ ability to navigate.

“Would plants not work so well if this didn’t happen?” Fleming asks. “I think we need to be a bit cautious about answering that at this point. It’s a complicated question. You have to be very sophisticated in how you model things to show that the quantum effect is really making the system work better. You can’t just turn it on and off.”

Not yet, anyway. Fleming, who says he is looking for “a higher standard of proof,” has worked out two new theoretical models that will allow scientists to perform experiments and better simulate bioquantum effects in the lab. The new models will appear in an upcoming issue of the Journal of Chemical Physics.

“Once you have a really good theory, you can turn things off to see what happens,” he says.
Discovering how quantum effects play out in photosynthesis and bird navigation may point scientists to other examples of the quantum in biological systems.

“Photosynthesis, after all, is one of the oldest processes around,” Ritz says. “If we see that nature learned at the very beginning, when they were still bacteria, to control quantum processes, there’s no reason why nature should have forgotten that in the future for more complex things.”

Susan Gaidos is a science writer in Maine.

Easy Nash

The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)