Friday, 20 April 2012

Information and entanglement in DNA

Deoxyribonucleic acid or DNA is the biological molecule that carries genetic information in all known organisms except for certain viruses. It is a nucleic acid consisting of two long chains, or strands, of basic units called nucleotides. The two strands are arranged in a twisted ladder structure known as a double helix, and is shown below.

Each nucleotide is composed of a nitrogen-containing base attached to a sugar phosphate molecule.  (The sugar in DNA is deoxyribose, which is a sugar with five carbon molecules, hence the name.)

There are four types of DNA bases: adenine(A), guanine (G), cytosine (C), and thymine (T). It is the sequence of these four bases that carry genetic information along segments of DNA called genes. That is, the 'language' of genes uses an alphabet with these four letters.

Wednesday, 18 April 2012

A quantum compass for birds

During migration, birds like the European robin use the earth's natural magnetic field to know which direction to go. Like with a compass, such migratory birds can sense if the earth's magnetic field changes direction as they fly. But beyond that, they can also detect subtle differences in the strength of magnetic field. This ability to perceive magnetic fields and use them for navigation is called magnetoreception. It is an ability shared by other organisms such as sea turtles, fruit flies, honey bees, and even certain bacteria. Because different organisms detect magnetic fields in different ways, we focus on the case of birds, where a simple hypothesis is known.

The most widely accepted explanation for magnetoreception in birds is called the radical pair (RP) mechanism. If it's proven correct, it demonstrates one of the ways in which a living system exploits quantum effects to perform certain biological tasks.

Photosynthesis is partly a quantum process

Photosynthesis is the process by which plants use energy from sunlight to convert carbon dioxide into organic compounds such as sugars. It is also the first biochemical process where the presence of quantum effects has been experimentally verified. 

Photosynthesis involves two kinds of reactions called light and dark reactions. 

Light reactions are the chemical processes where sunlight is needed. In particular, sunlight is absorbed by light-harvesting pigments such as chlorophyll, and substances within those pigments react with light and water to produce the standard energy-storage molecule ATP, oxygen and the co-enzyme NADPH. 

Dark reactions are processes that do not depend on light and part of what is known as the Calvin cycle, a series of biochemical processes which use NADPH and ATP from light reactions to turn carbon dioxide into sugar-phosphate molecules.      

The truly quantum effects, as far as we know, only appear in light reactions.

The quantum physics of smell

When I first heard about how quantum effects might be involved in the process of smelling, I was immediately fascinated by it. So much so that I searched for the original paper making such a proposal and studied what role quantum mechanics plays in the nose's ability to recognize odors. This entry is an attempt to explain what I've learned, in the simplest possible terms that I can make it.

To start, it is worth mentioning that much is already known about the smelling process. The 2004 Nobel Prize in Physiology or Medicine was awarded to Richard Axel and Linda Buck for their discoveries on odor receptors and how the signals from these receptors are amplified and processed. The basic idea is that odor molecules, or odorants, attach onto receptors that match their size and shape, in what is called a lock-and-key mechanism. Just as a lock can only be opened with a key of the right shape, an odor receptor is activated only if the right odor molecules comes along and 'plugs' it.

Is quantum mechanics relevant for biological systems?

It is commonly believed that you don’t need quantum mechanics to properly describe how biological systems work. They are simply too large, too hot and too messy for any fragile quantum effects to matter. But over the past few years, some scientists have come to realize that this might not necessarily be the case. Our ability to recognize odours might involve phonon-assisted quantum tunnelling. The way some birds navigate during flight might include perceiving subtle differences in magnetic fields in a quantum coherent way. The stability of DNA double helix structure might possibly depend on quantum entanglement between neighbouring nucleic bases. We know of at least one example where the presence of quantum effect is indisputable: the coherent transport of light energy in photosynthetic systems. I will attempt to describe that in a later article.

For now, it seems we are quite uncertain as to how significant quantum effects are in the phenomena I mentioned, so perhaps the first question to address is, how do we even know it is possible for quantum effects to survive in organic systems?

Quantum refrigerators and biological cooling

In a colloquium last week at PI, Sandu Popescu talked about the smallest possible refrigerators. He was motivated to explore this question by considering how biological systems manage to regulate temperatures despite their exposure to various elements of their external environment. The thinking was some form of biological cooling process might be involved.  This entry is an attempt to explain his most fascinating ideas on small cooling engines.

The logical place to start, of course, is to define what a refrigerator is. If you can still recall what you learned in basic thermodynamics, then you'll know that when you have two objects in contact, one hot and one cold, then heat will naturally flow from the hot object to the cold object until the two settle at the same temperature.

Physics and computational complexity

Scott Aaronson is an accomplished computer scientist whose research work focuses mainly on computational complexity. Computational complexity has to do with how difficult it is for a computer to solve a particular class of problems that you can ask it. It seems that you can ask your PC anything you want as long as you're a competent enough programmer but there are at least three ingredients that characterize the sorts of questions suitable for a computer: (i) you have some input information available to you at the start, (2) there is a known procedure or algorithm for attacking the problem (the simplest of which will be some type of brute-force approach), and (3) you desire a particular kind of output. 

Quantum foundations: what is real?

A few terms ago, I took a course called "Foundations and Interpretations of Quantum Theory". It's a physics course officially listed as an applied mathematics course although its content is more philosophy than math. The purpose of such a course is to clarify the meaning of quantum mechanics in terms of concrete physical ideas. We believe this can always be done because physics supposedly isn't just about doing some fancy mathematics. Ultimately, we would like physics to explain to us how Nature works, in terms of unambiguous laws that dictate how physical objects must behave in a variety of real-life situations.

Writing science

Science writing in its highest form isn't shrouded in mystifying jargon meant to segregate the uninitiated commoners from the scientifically-literate elite. Perhaps only a fool would think that science will one day be expressed entirely in colloquial terms but I believe we should always strive to come close to that ideal. A real understanding of science should mean that it is possible to communicate the most important ideas of a scientific concept with language comprehensible to an educated audience. Einstein once said, "you do not really understand something unless you can explain it to your grandmother." That's probably setting the bar too high but the point is we should at least try to make science as accessible to many as we can.

Why can't time run backwards

(Nobel Laureate Public Lecture by Tony Leggett)

This is really one of the great unanswered questions in physics. It is our common experience that time seems to "flow" only from the past to the future. We say this because we remember only our past and we can affect only our future. This is not just a semantic issue because we can all agree that there is such a thing as the past and such a thing as the future. Why such a divide exists is not at all easy to explain.

Our current understanding of physics doesn't seem to help us much. Why? Because all the laws of physics we know so far are totally symmetric with respect to the flow of time. If you let time run backwards in our equations, equally valid systems result. This is true for Newton's physics as it is for relativity or quantum mechanics.