Saturday, February 23, 2013

Quantum Biology

If quantum mechanics hasn’t profoundly shocked you, you haven’t understood it yet. 
-Neils Bohr
There was a time when the newspapers said that only twelve men understood the theory of relativity. I do not believe there ever was such a time. There might have been a time when only one man did, because he was the only guy who caught on, before he wrote his paper. But after people read the paper a lot of people understood the theory of relativity in some way or other, certainly more than twelve. On the other hand, I think I can safely say that nobody understands quantum mechanics.
-Richard Feynman
 The quotes above are more reflective of the nature of the quantum world than of any fundamental disagreement between the two great physicists. The quantum world does not conform to classical logic, but instead resembles some Buddhist teachings as suggested below: (if this interests you check out this fascinating post)
Anything is either true,
Or not true,
Or both true and not true,
Or neither true nor not true;
This is the Buddha's teaching.

--Nagarjuna (second century Buddhist monk and philosopher), the Mulamadhyamakakarika, Chapter XVIII, verse 8

In my last post (Complementarity and Wave/Particle Duality ) I attempted to describe the strangeness of quantum mechanics. Until recently it was thought that quantum effects could only occur at extreme (cold) temperatures and therefore would not play a role in living systems. In this article for Nature, Phillip Ball describes how this assumption is changing.

"Or so everyone thought. But discoveries in recent years suggest that nature knows a few tricks that physicists don't: coherent quantum processes may well be ubiquitous in the natural world. Known or suspected examples range from the ability of birds to navigate using Earth's magnetic field to the inner workings of photosynthesis — the process by which plants and bacteria turn sunlight, carbon dioxide and water into organic matter, and arguably the most important biochemical reaction on Earth"
"Biology has a knack for using what works, says Seth Lloyd, a physicist at the Massachusetts Institute of Technology in Cambridge. "

 In 2007 Graham Fleming reported on direct evidence of quantum effects in biology leading to near 100% efficiency in the photosynthesis process.

"Our results suggested that correlated protein environments surrounding pigment molecules (such as chlorophyll) preserve quantum coherence in photosynthetic complexes, allowing the excitation energy to move coherently in space, which in turn enables highly efficient energy harvesting and trapping in photosynthesis,"

A more recent study has identified entanglement as a natural feature in this quantum process.
"This is the first study to show that entanglement, perhaps the most distinctive property of quantum mechanical systems, is present across an entire light harvesting complex," (Mohan Sarovar).
There are potentially great implications for this research especially in the area of renewable non-polluting energy.
 "We hope to be able to learn from the quantum proficiency of these biological systems," says Lloyd. A better understanding of how quantum effects are maintained in living organisms could help researchers to achieve the elusive goal of quantum computation, he says. "Or perhaps we can make better energy-storage devices or better organic solar cells."
"These effects, in turn, suggest practical uses. Perhaps most obviously, says Scholes, a better understanding of how biological systems achieve quantum coherence in ambient conditions will "change the way we think about design of light-harvesting structures". This could allow scientists to build technology such as solar cells with improved energy-conversion efficiencies. Seth Lloyd considers this "a reasonable expectation"
 To see a short video that explains some birds may make use quantum effects in flight navigation click here ( The Quantum Robin video ).

And another excellent video by the above mentioned Seth Loyd - Quantum Life

Lee H, Cheng YC, Fleming GR(2007) Coherence dynamics in photosynthesis: Protein protection of excitonic coherence. Science 316:1462–1465
Sarovar M, Ishizaki A, Fleming GR, Whaley KB(2010) Quantum entanglement in photosynthetic light-harvesting complexes. Nat Phys 6:462–467.

Monday, February 18, 2013

Complementarity and Wave/Particle Duality

Quantum mechanics involves the study of the natural world on the smallest of scales. While quantum mechanics has never failed an experimental test, and makes extremely accurate predictions there is no universally accepted interpretation of the wave particle duality which arises from the famous double slit experiment . To best understand the double slit paradox take a look at this short video. 



Beams of light behave like waves when aimed through slits. This in and of itself is not surprising. When single photons (light particles) or electrons are sent through the slits they arrive as particles but in the pattern of a wave. This defies logic as it seems each particle is going through both slits and then interfering with itself to produce the pattern.

Physicists then changed the experiment to observe each slit to see what the photon/electron particles were doing. The simple act of observation however changed the behavior of the particles. When experimentally observed, no wave like behavior occurred.
Neils Bohr (the father of the atom) interpreted this paradox with his philosophy of complementarity.




Bohr's principle of complementarity claims that objects of knowledge contain complementary properties. Knowledge of a property depends upon the reference frame of the observer, and knowledge of one property excludes the simultaneous knowledge of the other. Here are some quotes from Bohr who won the Nobel prize for physics in 1922:


"Two sorts of truth: profound truths recognized by the fact that the opposite is also profound truth, in contrast to trivialities where opposites are obviously absurd. The opposite of a correct statement is a false statement. But the opposite of a profound truth may well be another profound truth. "   

"How wonderful that we have met with a paradox. Now we have some hope of making progress."

 Werner Heisenberg who developed the uncertainty principle was also an advocate for complementarity. Here is a quote by Heisenberg:


"There is a fundamental error in separating the parts from the whole, the mistake of atomizing what should not be atomized. Unity and complementarity constitute reality."

The views of Bohr and Heisenberg came to be known as the Copenhagen Interpretation of quantum mechanics. This interpretation assumed the nature of reality was uncertain and probabilistic rather than causally deterministic. For Bohr, quantum mechanics was a complete description of reality despite it's fundamental uncertainty. There is a non-material wave of probability that precedes physical manifestation. Einstein could not accept this arguing that 'God does not play dice'. Quantum mechanics also implied an even stranger phenomenon known as 'quantum entanglement'.

In quantum entanglement pairs of fundamental particles can become interdependent even when separated at great distances. When one entangled particle is measured the state of it's pair is known simultaneously. Einstein refrered to this as 'spooky action at a distance', and felt that there must be some hidden variables that quantum mechanics had not been accounted for. Since the time of Bohr and Einstein however, quantum entanglement has proven to be a true phenomena, first by theory and more recently by experiment. For once Einstein appeared to be wrong, there could be no (local) hidden variables.

Quantum mechanics has since been extended to what is now known as the 'Standard Model of Fundamental Particles'. According to the standard model and quantum field theory each fundamental particle is really just a special case of an underlying field.  Fields are not stuff, but relations spread out in space. This goes for all fundamental particles such as photons, electrons, quarks (which make up protons), and the recently discovered Higgs boson. This short video by Sean Carroll provides a concise description of how the universe is made of fields.


Currently the physics community is divided over the proper interpretation of quantum foundations. The Copenhagen interpretation may still be the most favored, but there are many theories that can explain the experimental results. The interpretations seem to break down into metaphysical preferences. In the link above Sean Carroll prefers a 'Many Wolrds' interpretation which suggests that infinite universes underly the quantum waves of probabilities. This is a deterministic theory that preserves causality and suggests infinte branches off each quantum state although we only experience one. Another nobel prize winner Richard Feynman, suggested a varient sometimes referred to as 'Many Paths' described in this quote by Physicist Freeman Dyson:
‘Thirty-one years ago [1949!], Dick Feynman told me about his "sum over histories" version of quantum mechanics. "The electron does anything it likes," he said. "It just goes in any direction at any speed, forward or backward in time, however it likes, and then you add up the amplitudes and it gives you the wave-function." I said to him, "You're crazy." But he wasn't.’ 
Feynman was also quoted however as stating that nobody really understands quantum mechanics. If Feynman was right than us non-physicists should feel free to help ourselves to our own preferred meta-physical interpretation so long as it agrees with the experimental results. Currently my preferred interpretation is Bohr's complementarity. This brings us back to the concept of duality and my motivation for composing the post.
In the west we have a long history of focusing on the separation between 'things' and characterizing them as distinct dualities. One example is Descartes dualism with regard to the separation of mind and body. Another example would be the separation of man (or woman) from nature. For example free will in western philosophy has historically  been conceived as mans ability to transcend his natural environment. More recent trends in the west have been to focus on the foundational reality of material things perhaps at the expense of the non-material. 

The elimination of the non-material has been very successful in physics to a point. Even at the quantum level we can make precise predictions of what will emerge physically if we know the initial experimental conditions (which is an important caveat). Physical descriptions alone however do not move us closer to understanding hard problems like value, meaning, purpose, and consciousness. In his book 'Incomplete Nature',the evolutionary biologist Terrence Deacon makes an intruiging argument that it will be necessary to understand the contribution of 'what is not realized' or what is 'absent' in order to even to begin to understand the emergence of life. In making this argument Deacon borrows in part from Taoist philosophy and chapter 11 of the Tao Te Ching which describes the utility of emptiness.
"Thirty spokes share the wheel's hub;
It is the center hole that makes it useful.
Shape clay into a vessel;
It is the space within that makes it useful.
Cut doors and windows for a room;
It is the holes which make it useful.
Therefore profit comes from what is there;
Usefulness from what is not there."

(translation by
Gia-fu Feng and Jane English)

This is an example of the Taoist version of complementarity. No-thing is fundamentally intrinsic to and of itself. Instead it is from the complementary relationship of apparently distinct things or concepts that would seem to oppose each other that usefulness emerges. Deacon would say that in self-organizing systems the physical structure that keeps things from being realized is what has important and useful implications. For example, we have as system of blood vessels that constrains where our blood can flow. If the blood could go anywhere it would not efficiently get where it needs to go. The vessels also need an emptiness within for the blood to flow smoothly.


There are different ways of at looking at what is fundamental. The deterministically inclined physicist might say that fundamental particles encompass the stuff from which all the other sciences emerge. Quantum field theory however suggests to others (see Ladyman & Ross) that it is relations, as opposed to stuff, that are fundamental. This resonates with me as relations in the form of complementary oppostion seem to have a great reach in their usefulness across the sciences and the humanities.

 Life emerged from non-life and is not separate from fundamental physics. Man emerged from the simple living organisms, and in some ways we manifest distinct qualities such as the potential for consciousness foresight. It was likely the evolution of stable relationships rooted in seeming opposites such as safety and exploration, competition and cooperation, self-interest and altruism that led to our distinct qualities. Ultimately however we are part of nature and cannot transcend our conflicts with the natural world by focusing only on what makes us distinct.

I believe this approach allows us to see the necessity of conflict. We cannot transcend conflict by denial of it's necessity. Instead perhaps we can see how conflict and opposition can serve the quest for unity.

Update:

Just to be clear, by recognizing the necessity of conflict I am not suggesting we promote it's celebration. Similarly the embracing of a degree of uncertainty does not give warrant to wallow in ignorance. On the contrary I think it is necessary to have the humility to recognize where our fundamental uncertainties lie so that we may stimulate our curiosities to increase our ways of knowing to reduce those uncertainties. This is an example of what I intended by allowing opposition to serve the quest for unity.

Here are some fascinating followup articles :


Time’s Arrow Traced to Quantum Source

A Jewel at the Heart of Quantum Physics

Fluid Tests Hint at Concrete Quantum Reality