May 31, 2007

Radio Waves from the Big Bang

Arno A. Penzias and Robert W. Wilson, A Measurement of Excess Antenna Temperature at 4080 Mc/s, 1965

Robert H. Dicke, P. James E. Peebles, Peter G. Roll, and David T. Wilkinson, Cosmic Black-body Radiation, 1965

Science teachers often present established facts and theories about the world around us without giving much information about the observations and evidence that require these explanations. Perhaps this is necessary simplification for the sake of educating without overwhelming, but paring things down to the bare conclusions, however true they may be, always leaves doubt about their accuracy. To really believe in some of the more astonishing things we've discovered about the universe, it helps to know what real people saw with their own eyes that forced them to these conclusions. The Big Bang is one of these discoveries.

In 1964 Bell Laboratories turned over a sensitive radio receiver, originally designed to detect signals bounced off of Echo, NASA's first communications satellite, to Arno Penzias and Bob Wilson, who planned to use it to study radio emissions from our galaxy. No ordinary radio receiver, the Horn Antenna is a freakish looking contraption, 15m long and 10m high, its form entirely determined by its function. (Go look at the pictures!) It is an exquisitely sensitive instrument, able to detect ridiculously tiny signals, amplify them, and filter out background noise. The horn itself acts much like the more familiar dish antennas in concentrating faint signals. Background noise is quantified and filtered out by repeatedly switching the detector between the signal from the horn and a null radio source (a bath of liquid helium kept at -269°C). Background noise remains constant while the signal varies with the same timing as the switch. The signal is amplified by a maser, also cooled by liquid helium to reduce internal static.

From July 1964 through April 1965, Penzias and Wilson struggled to quantify all the sources of background noise in their antenna at a radio frequency of 4,080 megacycles per second. They calculated the amount of radio emission being received from the atmosphere. They calculated the amount of radio emission received from the ground. They calculated the amount of radio emission generated by the telescope itself. (Practically anything that has a temperature emits small amounts of radio, along with much larger amounts of infrared radiation.) They set up a radio transmitter nearby to measure the effects of man-made radios, and pointed the antenna at major cities such as New York. They measured the static generated in every component of the detector. They rebuilt the maser, finding it blameless. They carefully cleaned and realigned the joints in the telescope, and put aluminum tape over the rivets and seams to help eliminate any possible noise from these imperfections in the telescope. They even evicted some pigeons which had taken to roosting in the horn and cleaned up their mess.

Throughout this process, a residual signal equivalent to a radio temperature of 3.5°±1.0°K remained unexplained. It did not vary with direction. It did not vary with time, even over the course of several months. Penzias and Wilson were confident that they had identified every source of noise generated by their equipment, and the invariance of the signal ruled out any possibility that it could come from a single source in the sky, or even a large source like the Milky Way. They concluded that the whole universe must be permeated by this tiny glow of background radiation.

A chance discussion put them in contact with Robert Dicke, a theoretician with an explanation. Since Hubble's work on redshifted galaxies we've known that the universe is expanding. Extrapolating backwards and taking things to an extreme suggests that at some point in the past everything might have been crammed into a very small amount of space. At sufficiently high densities, the average temperature of all matter in the universe would be high enough to prevent atoms from forming. Unlike the universe of today, where a photon can travel billions of light-years without hitting anything, all the light in a high density universe regularly hits free-roaming electrons, meaning that all the light in such a universe quickly reaches black-body equilibrium. When the temperature drops below ~3,000°K, atoms can form, at which point collisions between photons and electrons decrease significantly, an event that physicists refer to as "the decoupling of light and matter". From that point on, the 3,000°K black-body spectrum of most of the universe's light is largely unaffected by anything except the expansion of the universe, which steadily redshifts it down the spectrum.

So, to sum up: Penzias and Wilson made the first measurement of what is now called the Cosmic Microwave Background (CMB), which turns out to look like a black-body spectrum from light interacting with matter at a temperature of 2.726°K. The fact that it's there at all tells us that the universe must at some point have had a density high enough to give everything in it a temperature of at least 3,000°K. The fact that it has been redshifted down to 2.726°K tells us that the universe has expanded by a factor of ~1100 since then.

May 30, 2007

The Structure of Proteins

Max Perutz, et al., Structure of Haemoglobin: a Three-Dimensional Fourier Synthesis at 5.5-Å Resolution, Obtained by X-Ray Analysis, 1960

The unravelling of the structures of the first proteins is a great example of the way scientific discoveries are built on and interlock with each other. Proteins like Haemoglobin are the workhorses of living systems. They are created by the translation of strands of DNA into chains of amino acids, while almost all other types of molecules in cells are assembled by proteins. They perform a myriad of functions, acting as targeted chemical messengers (hormones), enzymes which speed the rate of otherwise improbable chemical reactions, structural components of cells, pumps, valves, and turbines embedded in cell membranes, contractile fibres in muscles, and many other roles. Until the three-dimensional structure of a protein is worked out, scientists can only know what a protein does, not how. Understanding of protein structures leads to some unifying principles that help explain their diverse properties.

Haemoglobin is a relatively small protein, at only 10,000 atoms, that transports oxygen from the lungs of vertebrate animals to their cells, there to be fed into the Krebs Cycle. It's formed of four chains of amino acids of roughly equal length, all of which are quite similar to each other and to another protein called Myoglobin. Myoglobin is the second stage of oxygen transport in the body: where Haemoglobin binds strongly to oxygen at the concentration found in blood near the lungs and releases it at the concentrations found in blood near oxygen consuming cells, myoglobin binds strongly at the concentrations where Haemoglobin releases, and only relinquishes oxygen when very low concentrations are present, inside active cells.

The chemical similarity between Haemoglobin's four amino acid sub-chains and Myoglobin makes the difference between their oxygen binding properties mysterious. As it turns out, it is the three-dimensional arrangement of the four sub-chains that makes all the difference. To figure out the structure of Haemoglobin, Max Perutz and his team used (and improved) X-ray crystallography. This involved making crystals of the oxygenated and deoxygenated forms of Haemoglobin (actually Haemoglobin crystallized in a matrix of much smaller molecules), taking pictures of the diffractions produced by shining X-rays through them at several hundred different angles, repeating this process many times with specific atoms in the Haemoglobin crystal replaced with heavier atoms (to help locate particular parts of the amino acid chain), and putting all the results together with what computing power was available in the UK in the 1950s (including Cambridge's Edsac II).

The diffraction pictures produced were much larger than von Laue's initial trials. They contained thousands of spots of differing intensities, each of which had to be quantified one-by-one, by eye, in much the same way that Henrietta Leavitt determined the brightness of stars by comparing spots on a photographic plate. And the mathematical effort required to combine all this data into a three-dimensional model was staggering. The whole process took more than a decade the first time around. (Not including WWII, during which Perutz, an Austrian living in Britain, was imprisoned, then banished to Newfoundland. On the way across the Atlantic, the liner he was travelling on, the Arandora Star, was torpedoed by a U-boat, killing almost all of the 1,800 aboard. Perutz was one of the few to be fished out of the water alive. Needless to say, no work on Haemoglobin got done during this interlude.)

The payoff was a plastic model, built up slice-by-slice, showing the way the four sub-chains fold up and fit together.

The circular plates are heme groups, non-protein molecules that serve as the actual binding sites for oxygen. Many proteins have bits and pieces of non-amino-acid molecules embedded in them, often to act as binding sites, while the bulk of the protein acts as structural support. In Haemoglobin's case, when oxygen is bound to a heme group, the structure of the whole molecule shifts in a small but significant way, making its binding properties different from Myoglobin. (Animated GIF)

These days, with massively improved automation and computer support, thousands of protein structures are mapped every year (although understanding of their significance, as always, still takes time), and there are some indications that we may someday be able to predict the configuration of a protein from its amino acid sequence alone (and therefore from the DNA that encodes it).