Out of the Shadows

Here is a copy of a blog I provided for the Yale University Press website, in connection with my book Out of the Shadow of a Giant.  More details will be at   http://blog.yalebooks.com/2017/10/22/out-of-the-shadows-robert-hooke/ ‎from 22 October.

Who was the first person to realise that gravity is a universal force possessed by every object in the Universe, which attracts every other object? Isaac Newton, right?  Wrong! Newton got the idea, and other insights which fed in to his theory of gravity, from Robert Hooke, a seventeenth century polymath whose work has been overshadowed by the giant figure of Newton. Hooke was both an experimenter and observer, and a theorist.  His insight about gravity came partly from his telescopic observations of the Moon.  He studied lunar craters, and noticed that they are formed of nearly circular walls, around a shallow depression.  They looked, in his words “as if the substance in the middle had been digg’d up, and throw on either side.”  So he carried out experiments, dropping bullets onto a mixture of water and pipe-clay, making miniature craters which, when illuminated from the side by a candle, looked just like lunar craters.  He realised that the material thrown up from the centre of the craters of the Moon was pulled back down by the Moon’s own gravity, independent of the Earth’s gravity.  He pointed out that apart from small irregularities like craters, the Moon is very round, so that “the outermost bounds. . . are equidistant from the Center of gravitation”, tugged towards the center by gravity, and concluding that it had ”a gravitating principle as the Earth has.”  This was published in 1665, when Newton was just completing his degree at the University of Cambridge.  Hooke went on to suggest that planets are held in orbit by an attractive gravitational force from the Sun. This was a revolutionary idea. Hooke’s contemporaries argued that the planets were whirled around in vortices in some mysterious invisible fluid, like chips of wood in whirlpools on a river. When Newton convinced them that this was wrong, and gravitational attraction was right, they remembered him and forgot who gave Newton the idea!

Hooke wasn’t the only seventeenth century scientist overshadowed by Newton. Edmond Halley, of comet fame, was another. It was Halley, in fact, who not only persuaded Newton to write his great book, the Principia, but paid for its publication! The most astonishing forgotten achievement of Halley, though, is that he was given command of a Royal Navy ship to make a scientific voyage of exploration to the southern ocean. Literally given command.  He was the captain and navigator (in Royal Navy language, Master and Commander), not a passenger. The ship, Paramore was just 52 feet long, with a crew of 24.  It sailed on 16 September 1699, and Halley took it as far south as the edge of the Antarctic ice pack, making observations of magnetism and winds long the way.  At their furthest south, 52 degrees 24 minutes latitude, they were nearly crushed by icebergs.On his return to England, Halley was lauded by Samuel Pepys as “the first Englishman (and possibly any other) that had so much, or (it might be said) any competent degree (meeting in them) of the science and practice (both) of navigation.” His navigational skills were also used by the British in secret surveying of the French side of the English channel, to make charts for use in time of war. When Halley became Savilian Professor of Astronomy in Oxford, the Astronomer Royal, John Flamsteed, complained that he “talks, swears, and drinks brandy like a sea captain.” He was indeed a sea captain, and proud of it; not your average Oxford Professor, even by eighteenth century standards.




Cosmic chemistry and the Origin of Life

Recent experiments suggesting that the origin of life may have happened in warm little pool four billion years ago made a splash in the media. The idea is relatively old, but the “news” was that precursors to life might have been brought down to Earth by meteorites and laced those ponds with the chemicals necessary to kickstart life. But all these stories missed an even more significant possibility, that life itself may have been brought down to Earth by comets. If that scenario is correct, the Universe is teeming with life. To put it all in perspective, here is an adapted extract from my book Alone (aka The Reason Why).

Carbon atoms have an unusual ability to combine strongly with up to four other atoms at a time, including other atoms of carbon. The simplest way to picture this is to imagine that a carbon atom has four hooks sticking out from its surface, and each of these can latch on to another atom to make a chemical bond. In the simplest example, each molecule of the compound methane is made of a single carbon atom surrounded by four hydrogen atoms which are attached to it by bonds – CH4. But carbon atoms can also link up with one another fore and aft to form chains, linking each carbon atom in the chain with two other carbon atoms, but leaving two bonds free to hook up with other kinds of atoms, and leaving the two carbon atoms at the ends of the chain each with three spare bonds. Or the chain may become a ring, with carbon atoms forming a closed loop, still with two bonds available for each atom in the ring to form other linkages. Even complex carbon-based molecules, including other rings and chains, can attach to other carbon chains or to other rings. It is this rich potential for carbon chemistry which makes the complexity of life possible. Indeed, when chemists first began to study the complexity of life, and realised that it involves carbon so intimately, the term “organic chemistry” became synonymous with “carbon chemistry.”
There are two key components of the chemistry of life. To non-biologists, the most widely known life molecule is DNA, or deoxyribonucleic acid. This is the molecule within the cells of living things, including ourselves, which carries the genetic code. The genetic code contains the instructions, rather like a recipe, which tell a fertilised cell how to develop and grow into an adult. But it also contains the instructions which enable each cell to operate in the right way to keep the adult organism functioning – how to be a liver cell, for example, or how to absorb oxygen in the lungs. The mechanism of the cell also involves another molecule, ribonucleic acid, or RNA. As the name suggests, molecules of DNA are essentially the same as molecules of RNA but with oxygen atoms removed.
The “ribo” part of the name comes from “ribose” (strictly speaking the names should be ribosenucleic acid and deoxyribosenucleic acid). Ribose (C5H10O5) is a simple sugar, but it lies at the heart of DNA and RNA. Each molecule of ribose is made of a core of four carbon atoms and one oxygen atom linked in a pentagonal shape. Each of the four carbon atoms in the pentagon has two spare bonds with which to link up with other atoms or molecules. In ribose itself, these attachments link the pentagon to hydrogen atoms, oxygen atoms, and one more carbon atom, making five in all, which is itself joined to more hydrogen and oxygen; but any of these attachments can be replaced by other links, including links to complex groups which themselves link up with other rings or chains. In DNA and RNA, each sugar ring is attached to a complex known as the phosphate group, which is itself attached to another sugar ring. So the basic structure of both of the life molecules is a chain, or spine, of alternating sugar and phosphate groups, with interesting things sticking out from the spine. It is the interesting things that carry the code of life, spelling out the message in what is in effect a four-letter alphabet with each letter corresponding to a different chemical group. But that is not a story to go into here; from the point of view of interstellar chemistry, it is the basic building block of DNA, the ribose molecules, that are significant.
Nobody has yet detected ribose in space. But astronomers have detected the spectroscopic signature of a simpler sugar called glycolaldehyde. Glycolaldehyde is made up of two carbon atoms, two oxygen atoms and four hydrogen atoms (usually written as H2COHCHO, which reflects the structure of the molecule), and is known, logically enough, as a “2-carbon sugar.” Glycolaldehyde readily combines, under conditions simulating those in interstellar clouds, with a 3-carbon sugar, making the 5-carbon sugar ribose. We have not yet found the building blocks of DNA in space; but we have found the building blocks of the building blocks.
The other kind of “life molecule” is protein. Proteins are the structural material of the body; they always contain atoms of carbon, hydrogen, oxygen, and nitrogen, often sulphur, and some contain phosphorus. Things like hair and muscle are made of proteins in the form of long chains, not unlike the long chains of sugar and phosphate in DNA and RNA molecules; things like the haemoglobin that carries oxygen around in your blood are forms of protein in which the chains are curled up into little balls. Other globular proteins act as enzymes, which encourage certain chemical reactions that are beneficial to life, or inhibit chemical reactions that are detrimental to life. There is such a variety of proteins because they are built up from a wide variety of sub-units, called amino acids.
Amino acid molecules typically have weights corresponding to a hundred or so units on the standard scale where the weight of a carbon atom is defined as 12, but the weights of protein molecules range from a few thousand units to a few million units on the same scale, which gives you a rough idea how many amino acid units it takes to make a protein molecule. One way of looking at this is that half of the mass of all the biological material on Earth is in the form of amino acids. But even though a specific protein molecule may contain tens of thousands, or hundreds of thousands, of separate amino acid units, all the proteins found in all the forms of life on Earth are made from combinations of just twenty different amino acids. In the same way, every word in the English language is made up from different combinations of just 26 sub-units, the letters of the alphabet. There are many other kinds of amino acid, but they are not used to make protein by life as we know it.
If a chemist wishes to synthesise amino acids in the laboratory, it is relatively easy and quick to do so by starting out with compounds such as formaldehyde (HCHO), methanol (CH3OH) and formamide (HCONH2), all of which will be to hand in any well-stocked chemical lab. With such materials readily available, it would be crazy to start out from the basics – water, nitrogen and carbon dioxide. But the chemistry lab isn’t the only place you will find such compounds. One of the most dramatic results of the investigation of molecular clouds is the discovery that all of the compounds used routinely in the lab to synthesise amino acids (including the three just mentioned) are found in space, together with others such as ethyl formate (C2H5OCHO) and n-propyl cyanide (C3H7CN). In a sense, the molecular clouds are well-stocked chemical laboratories, where complex molecules are built up not atom by atom, but by joining together slightly less complex sub-units.
There have also been claims that the simplest amino acid, glycine (H2NH2CCOOH), has been detected in space. It is very difficult to pick out the spectroscopic signature of such a complex molecule, let alone those of even more complex amino acids, and these claims have not been universally accepted by astronomers, even though amino acids have been found in rocks from space left over from the formation of the Solar System, which occasionally fall to Earth as meteorites. The claims have been bolstered, though, by the recent detection in space of amino acetonitrile (NH2CH2CN), which is regarded as a chemical precursor of glycine. But even if we take the cautious view and leave these claims to one side, that still means that, echoing the situation with DNA, with the identification of compounds such as formaldehyde, methanol and formamide, although we have not yet found the building blocks of protein in space, we have found the building blocks of the building blocks.
Complex organic molecules can only be built up in the molecular clouds because those clouds contain dust as well as gas. If all the material in the clouds were in the form of gas, even if by some unimaginable process a complex molecule such as NH2CH2CN did exist, how could it grow? You might imagine that a collision with a molecule of oxygen, O2, would provide an opportunity to capture some of the additional atoms needed to make glycine, H2NH2CCOOH. But the impact of the oxygen molecule would be more likely to break the amino acetonitrile apart, rather than encouraging it to grow. But tiny solid grains, coated with a snowy layer of ice (not just water ice, but also things like frozen methane and ammonia) provide sites where molecules can stick and be held alongside each other for long enough for the appropriate chemical reactions to take place.
Old stars swell up near the end of their lives, and eject material out into space. Spectroscopic studies show that this material includes grains of solid carbon, silicates, and silicon carbide (SiC), which is the most common solid component definitely identified in the dust around stars, although there are many as yet unidentified spectral features as well. Laboratory experiments simulating the conditions on the surfaces of such particles in space have confirmed that they provide places where the kinds of chemical reactions needed to make the kinds of complex organic molecules we detect in space can take place. Some of these studies suggest that the grains may not simply provide a surface where the reactions can take place, but that there may be chemical bonds between the molecules and the surface itself. That would explain how the molecules stick around for long enough for the reactions to take place even in relatively warm parts of a molecular cloud. As long as they do stick, there is plenty of time for the reactions to take place, because molecular clouds may wander around the Galaxy for millions – even billions – of years before part of the cloud collapses to form a group of new stars. When the grains are warmed by the heat from a newly forming star, the complex molecules can be liberated and spread through the molecular cloud, where they can be detected by our radio telescopes.
In this context, it is almost an anticlimax, but still significant, that a simple organic molecule, methane, was detected in the atmosphere of one of the hot jupiters in 2008. This was no surprise – methane is an important component of the atmosphere of Jupiter itself. But it was still regarded as a landmark event. For the record, the planet is the same one where water was identified earlier, orbiting the star HD 189733. Astronomers working with the Spitzer Space Telescope have also found large amounts of hydrogen cyanide, acetylene, carbon dioxide and water vapour in the discs around young stars where planets form. And a team from the Carnegie Institution used the Hubble Space Telescope to analyse light from a star known as HR 4796A, 270 light years away in the direction of the constellation Centaurus, to determine that the red colour of the dusty disc around the star is caused by the presence of organic compounds known as tholins. Tholins are large, complex organic molecules that are manufactured by the action of ultraviolet light on simpler compounds such as methane, ammonia and water vapour. They can be synthesised in the lab, but do not occur naturally on Earth today because they would be destroyed by reacting with oxygen in the atmosphere as fast as they formed. But their presence explains the reddish-brown hue of Saturn’s moon Titan, they are present in comets and on asteroids, and they may well have been present on Earth when it was young. Tholins are widely regarded as precursors of life on Earth, which made their discovery in the disc around HR 4796A hot news.
This is not the same, though, as finding such compounds on a planet. When planets like the Earth form by the accretion of larger and larger lumps of rock, they get hot, because of the kinetic energy released by all those rocks smashing together. A rocky planet starts its life in a sterile, molten state, certainly hot enough to destroy any organic molecules present in the material from which it formed. The importance of all the observations of organic material in space is that they tell us that there is a great reservoir of such material available to fall down on to the planets after they are cool enough for the complex molecules to survive. Life does not have to be “invented” from scratch on each new planet from the basics of water, carbon dioxide and nitrogen, any more than an organic chemist has to synthesise amino acids from the basics of water, carbon dioxide and nitrogen. In which case, every “Earth-like” planet in the Galaxy should have been seeded with life — all of it based on the same chemistry as life on Earth.