Category: Science

Science, usually research I have done or topics on which I have lectured

Sep 20 2010

Wallpaper paste and the giant death ray

Starch_kernel Nature is good a growing fancy structures. It takes air and water and turns them into sugar, a small molecule, which it then stitches together in chains to form starch and these starch chains arrange themselves into starch granules: organised structures with a diameter about that of hair, found in plants. The electron micrograph to the right* shows one that has been eroded to show some of its internal structure.I have my name on a couple of pieces of work on starch. I played a small part in the piece of work described here:

Waigh, T. A., I. Hopkinson, A. M. Donald, M. F. Butler, F. Heidelbach, and C. Riekel. “Analysis of the native structure of starch granules with X-ray microfocus diffraction.” MACROMOLECULES 30, no. 13 (June 30, 1997): 3813-3820. (pdf)

Tom Waigh was a PhD. student in the group I worked in, he was studying starch granule structure. This meant visits to the ESRF in Grenoble; source of mighty x-rays and a micro-focus beam-line, to do experiments. Tom had several days of beam-time, with experiments which essentially required continuous attention (a starch granule in the x-ray beam lasted 15 seconds), therefore a collection of warm bodies were required to press buttons and stuff through the night. Mike Butler and I stayed up late and pressed buttons. Florian Heidelbach and Christian Riekel designed and built the beam-line, and Athene Donald was the boss – supervising Tom’s PhD. and raising money to do the work. Starch granule structure is interesting and funding-worthy for several reasons: we eat lots of starch based things both natural like potatoes and not so natural, like Cheesy Wotsits; it’s used in processing paper and fabric and as a glue. There’s also work going to make plastics from starch, little extruded starch worms can also be found as a replacement for expanded polystyrene packing. Understanding starch granule structure is useful to people who run industrial processes, better knowledge of the granule structure leads to a better understanding of its processing properties which might lead to seeking out or breeding plants, which produce different sorts of starch granule, with different or better properties.There are two types of starch: amylose and amylopectin. Amylose makes shorter, less branched chains, whilst amylopectin makes longer branched chains. Starch granules are onion-like structures with alternating crystalline and amorphous regions. (Crystalline means nicely ordered, amorphous means not nicely ordered). Crystallisation in polymers is one of those puzzling things, how does all that long stringy polymer get folded up into such a nice neat structure. Blind physics is the answer, it’s broadly understandable but when I was active in the field it still wasn’t clear how it got started; once the nucleus of a crystal had formed, its growth was understandable but the formation of the nucleus was not so clear. X-rays tell us about the structure of things on very small length scales, since we’re interested in the variations in structure of an object only 0.1mm across we need to use an x-ray beam much smaller than this. The beam at the ESRF is only 0.002mm across so we can get a very detailed picture of the crystalline and amorphous regions of the starch granule. If you want to find the structure of a car by poking it with a stick, then you need a stick which is much smaller in diameter than the car. All we know of starch granule structure is summarised below:

Starch Schematic illustration of the starch granule structure*

The experimental procedure was entertaining: the starch granules were deposited on an electron microscope grid – a very fine wire mesh with numbers and letters allowing you to identify where you were on the grid. The starch granules were visible under a low power optical microscope, as were the numbers and letters. The numbers and letters were visible under the harsh stare of the x-ray beam but not the starch granules. So we would print out an optical micrograph, and take it off to the instrument hutch where we would get a shadowograph of the grid from the x-ray beam (sans starch granules). Then there would be a process of half-blind navigation, this was far from leisurely since once the x-ray beam was shining on the starch granule it lasted a few seconds before becoming irreversibly damaged. Once we’d found a starch granule we would take sets of closely spaced scattering patterns in a quest to discover the structure of the crystalline and amorphous bits of the granule.  It was like Battleships but rather more sophisticated expensive. To make a microfocus beam line you take the output of a synchrotron – a big wide beam of x-rays and direct it down a cone – known as a capillary. At some point we decided to be cunning and reduce the power of the micro-focused x-ray beam by offsetting the capillary so that the incoming x-ray beam didn’t hit the open end fully. This failed, because it turns out the beam wobbles up and down very slightly. What we should have done was put the attenuators in, but we were a bit tired. These experiments didn’t solve the structure of the starch granule, they filled in another little corner of the big picture. This is how much of science works. The story of the starch granule structure is one of a repeating theme in nature: it can do subtle things with structure without a large machinery to make it happen.
Update: Athene Donald has written on her side of this story -“Am I having impact?” some nice detail on the origins of the work and the problem of impact. *Images from Braukaiser.com

Sep 15 2010

Science is Vital – history repeating 1667

I’m reading Thomas Sprat’s “History of the Royal Society of London, for the improving of Natural Knowledge“* published in 1667. He’s just mentioned that following the return of Charles II much spending has been made on public works and goes on to say:

This general Temper being well weigh’d; it cannot be imagin’d that the Nation will withdraw its Assistance from the Royal Society alone; which does not intend to stop at some particular Benefit but goes to the Root of all noble Inventions, and proposes an infallible Course to make England the Glory of the Western World.

This seems terribly relevant to current circumstances, he does spoil it slightly by going on to say:

There is scarce any Thing has more hindered the true Philosophy than a Vain Opinion, that men have taken up, that Nothing could be done in it, to any purpose, but upon a vast Charge, and a mighty Revenue.

 Old Sprat had a fine way with words!

*Quotes are from p78-79

Sep 11 2010

Book Review: The Fellowship by John Gribbin

an_experiment_on_a_bird_in_an_air_pump_by_joseph_wright_of_derby_1768 I’ve written previously about the Royal Society via the medium of book reviews: Seeing Further, Joseph Banks and Age of Wonder, and also in a data mangling exercise. This post is about “The Fellowship: The Story of the Royal Society and a Scientific Revolution” by John Gribbin, it describes the scientific world before the Society and the founding of the Royal Society. As with many books about this period, the front cover of my copy features “An experiment on a bird in the Air pump” by Joseph Wright of Derby and so that is the image I use to decorate this post. Following my usual scheme this review is really an aide memoire as much as a review.

The book opens with a set of brief biographies, starting with William Gilbert of Colchester (1544-1603), and his scientific study of magnetism: de Magnete (1600). This work on magnetism was unusual for it’s time in that it was very explicitly based on experimental observation, rather than the “philosophising” of Aristotelian school which imputed that the world could be understood simply by thinking. William Gilbert is relatively little known (ok – I didn’t know about him!), perhaps because his work was in a relatively narrow field and was superseded in the 18th century by work of people like Michael Faraday furthermore Gilbert seems to have spent most of his life practicing as a doctor with his scientific work playing only a small part of his life.

Next step is Galileo Galilei (1564-1642). He continued in the tradition of William Gilbert, eschewing the philosophical approach for experiment. In contrast to Gilbert, Galileo made contributions across a wide range of science for a long period – promulgating technology such as telescopes, microscopes and computing devices. This likely explains his greater fame. A detail that caught my eye was that as a professor of mathematics at the University of Pisa he was paid 60 crowns per year, whilst the Professor of Medicine gained 2000 crowns. For many early scientists, medical training appears to be the major scientific training available.

Francis Bacon (1561-1626) was more important as a parliamentarian, lawyer and courtier than a scientist. I link reluctantly to wikipedia in this instance, since in the opening paragraph they seem to be repeating the myth that he met his end through stuffing snow into a chicken to see if this helped preservation. His fame as a founding father of modern science is based largely on a book he didn’t write in which he intended to describe how a scientist should work – a scientific method. Perhaps more notably he had a vision as to how science might function in society at a time when there was no such thing as a scientist. It is apparently from Bacon that Isaac Asimov got his “Foundation”; it is the name of an organisation of scientific Fellows found in Bacon’s fictional work New Atlantis. Finally we are introduced to William Harvey (1578-1657), who identified the circulatory system for blood in the human body by a process of observation and experiment (published in De Motu Cordis (1628)) he was primarily a physician.

The point of this preamble is to say that, as the founding of the Royal Society approached, a number of people had started doing or proposing to do a new kind of science (or rather natural philosophy as it would have been called). The new natural philosophy involved doing experiments, and thinking about them – it was experimental science in contrast to the “received wisdom” from the ancient Greeks which was certainly interpreted to mean at the time that thinking was all that was required to establish true facts about the physical world. It’s not really accurate to say that one person did this and everything changed: rather that a shift had started to take place in the middle years of the 16th century. The foundation of the Royal Society can be seen as the culmination of that shift.

The Royal Society was founded at Gresham College in London on 28th November 1660, although it’s origins lay in Oxford where many of the group that would go on to form the Society had been meeting since the 1640’s. The Royal charter of the Society was agreed a couple of years later. The central figure in the Oxford group was John Wilkins (~1614-1672). The original Society included Christopher Wren, Robert Boyle and Robert Hooke amongst others. What striking is the political astuteness of the founding fathers as the monarchy returned to England in the form of Charles II, the first President, Viscount Brouncker, was a Royalist and the Society clearly identified that a Royal seal of approval was what they required from the very beginning. The Society had an air of purposefulness about it, not of airy philosophising for the amusement of gentlemen. The Society started publishing the worlds first scientific journal, “Philosophical Transactions”, and commissioning a history of their founding by Thomas Sprat only a few years later.  As a scientist I have picked out those names that mean most to me, however it’s very clear that the Royal Society was more than a group of scientists meeting to talk about science and the other less scientifically feted Fellows were equally important in the success of the Society.

Gribbin’s book then goes on to consider three men important in the early life of the Royal Society. Firstly: Robert Hooke (1636-1703), originally scientific assistant to Robert Boyle (1627-1691) who became the Society’s first “Curator of Experiments”. Prior to his appointment the Fellows appeared to be poorly organised in terms of providing weekly demonstration experiments for the Society’s education. Hooke was a really outstanding scientist, a skilled draftsman and maker of scientific equipment. The reason Hooke is not better known is largely down to Isaac Newton, with whom he had a longstanding feud and who outlived him. Newton (1643-1727) does not need further introduction as a scientist, his role in the Royal Society was to provide scientific gravitas (after Hooke had died) he was also President of the Society for the period 1703-27. Edmond Halley (1656-1742) was more important to the Society on the administrative side, he is chiefly remembered from the scientific point of view for his prediction of the return of a comet calculated using Newton’s theory of gravitation. He also spent a great deal of time persuading Newton to publish and trying to extract data from Flamsteed (the Astronomer Royal). In addition to this he invented a diving bell, wrote the first article on life annuities, published on the trade winds and monsoons, made observations of the stars of the Southern hemisphere and went on several scientific expeditions.

Some miscellaneous thoughts that arose as I read:

  • Royal patronage, in this instance by Charles II, was important for the Society in this period and later by George III – as described a little in Age of Wonder.
  • On the face of it astronomy is blue-skies research, but at the time the precise measurement of the position of the stars was seen as a route to determining the longitude – an important practical problem.
  • It’s notable that the persistent anecdotes about the scientists mentioned here i.e. Francis Bacon and the frozen chicken, Newton and the apple falling from the tree and Galileo dropping things from towers, originate from the earliest biographies often written by people who knew them personally. These anecdotes have later been found to be rather fanciful, but nevertheless have persisted.
  • There was serious feuding going between scientists in the early years of the Society!

Overall I enjoyed this book, although it does sometimes have the air of a collection of short biographies of men who are already relatively well known. The most interesting part to me was the core part around the founding of the Society, bringing in some of the lesser known members and also highlighting the importance of the non-scientific aspects of the Society in it’s success.

In terms of scientific history reading, where next? “God’s Philosophers” by James Hannam seems relevant to understanding scientific activities prior to those covered in this book. A deeper investigation into Edmond Halley seems worthwhile, and I should also make another attempt at the Thomas Sprat history of the Royal Society.

Further reading

  1. “Joseph Banks” by Patrick O’Brian.
  2. “Seeing Further” edited by Bill Bryson.
  3. “God’s Philosophers” by James Hannam.
  4. “Age of Wonder” by Richard Holmes.
  5. “The Curious Life of Robert Hooke” by Lisa Jardine.
  6. “Hostage to fortune” by Lisa Jardine and Alan Stewart, which is a biography of Francis Bacon.
  7. “The History of the Royal Society of London, for the Improving of Natural Knowledge” by Thomas Sprat.
  8. “Isaac Newton: The Last Sorcerer” by Michael White.

Sep 05 2010

God and the scientist

Recently I observed that Stephen Hawking* had introduced God into his book “The Grand Design” as a way of gaining sales. Last weeks story on Hawking and God irritated me for two reasons. Firstly, the idea that a new idea that Stephen Hawking has introduced in his forthcoming book either proves or disproves the existence of God is fatuous nonsense. Secondly, revealing some intellectual snobbery on my part, this is a popular science book – such an important idea would have been published in peer-reviewed literature first – most likely Nature! On the first point Mary Warnock covers the philosophical side of this well in a short article in The Observer this week, in summary: proof / not proof of the existence of God is a hoary old chestnut.

As an atheist and scientist, I’m quite clear that my demand for evidence for the existence of God is what makes me an atheist. You don’t need evidence if you have faith. Although many scientists are atheists, this is by no means a pre-requisite. Many scientists in the past have been professed strong religious beliefs, no doubt in large part because of the spirit of the time they lived in. It’s only for particular variants of theism and particular topics that the two things are in direct collision: Creationism and the study of evolutionary biology are not happy bedfellows. The degree of cognitive dissonance required to accommodate a religious view of the world and a scientific view is really rather minor. Many scientists in the past have seen their scientific work as revealing the mechanism that God has created.

A further element to this is the degree to which modern cosmology requires a degree of faith. As an experimental soft condensed matter physicist the world of cosmologists is very far away. The things I study are essentially testable in the lab, you can put your hands on them, prod and poke them. Modern cosmology has a large degree of internal logical consistency and mathematical beauty, but it has close to zero contact with observations. At times it feels like any experimental test is wilfully pushed into timescales, or size scales that are simply impossible to observe (and not just impossible in practice, but impossible in principle). This is not to say they are wrong, but simply that their correctness must be taken on faith.

*Pointless name dropping/anecdotage: I had dinner with Stephen Hawking at Gonville and Caius College, he’s not very dynamic.

Aug 22 2010

More colours than the rainbow

500px-CIE1931xy_blank.svg
This post is about making the bridge between how a physicist understands colour, and something a bit more useful.

Light is a collection of electromagnetic waves; for a physicist the most important property of a wave is its wavelength, its “size”. The wavelengths of visible light fall roughly in the range 1/1000 of a millimetre to 1/2000 of a millimetre. (1/1000 of a millimetre is a micron). Blue light has a shorter wavelength than red light.

Things have colour either because they generate light or because of the way they interact with light that falls upon them. The light we see is made of many different wavelengths, the visible spectrum. Each wavelength has a colour, and the colour we perceive is a result of adding all of these colours together.

The diagram to the right summarises this: it’s called a chromaticity diagram, the numbers around the edge are wavelengths in nanometres (a millionths of a millimetre), pure, single wavelength light falls on this line; any point inside the line is formed from the mixture of wavelengths. The line represents “all the colours of the rainbow”; colours inside the line are not in the rainbow. The chromaticity diagram is the “periodic table” for colour scientists, it’s iconic and it summarises the world of colour.
This chromaticity diagram is just a slice through a volume, we could draw another one a little bit dimmer, and a little bit dimmer than that until we reached black.

How do we get to this diagram? The central issue to understanding perceived colour is that although the light in the environment comes as a mixture of a multitude of wavelengths, our eyes are limited by the light sensitive cells they contain, known as “cones”. In humans cones come in three types, which are sensitive in three different ranges of the spectrum. Roughly there are red-, blue- and green sensitive cones. So the eye gives just three readings in terms of colour description. The chromaticity diagram comes from a calculation trying to predict these three values and combining them to fit on a flat page (which only gives you two dimensions to play with).

Some other animals don’t have three sorts of cones. Birds, for example, have four – this is known as tetrachromacy which sounds to me like some sort of wizardry involving chairs (I’m reading Terry Pratchett at the moment). Birds have an extra type of cone in the ultra-violet part of the spectrum – so they are sensitive to wavelengths which we are not. Most mammals are dichromatic, but other primates, like humans, are also trichromatic. Dichromatic animals will be able to perceive a smaller range of colours than us. The evolutionary implication here is that earlier mammals lost some colour sensing ability, possibly for a gain in low light sensitivity but some mammals subsequently regained the ability.

The chromaticity diagram is still something of a physicists play-thing, it’s useful for doing calculations. There are other ways of describing colour which are related to human perception, they are developments based on the first steps used in constructing the chromaticity diagram. The aim of these methods is to similar numbers to colours that look similar; make those numbers reasonably easy to explain from a conceptual standpoint and try to give numbers twice as big to colours that are twice as bright. My favoured system in this respect is the CIE LAB system. The colours are expressed as three numbers L, a and b: L tells you something about overall brightness, a tells you the point on a scale between red and green and b tells you a point on the scale between yellow and blue.

But all of this is a bit of a fraud, because actually the colours you’re seeing on your monitor aren’t the real colours I’m trying to show you. The problem is that display devices contain red, green and blue elements but they don’t fall anywhere near the extremes of the chromaticity diagram and we can only get colours inside the the triangle defined by the red, green and blue elements in the monitor. A typical monitor gamut is shown here.

All this is based on the study of ideal colour stimuli (little square patches) on grey backgrounds, things get an awful lot more complicated if we start to worry about context. This is best illustrated with an image:

Adelson

As far as my computer is concerned squares A and B have the same colour, my brain and your brain are interpreting the scene context and giving them different colours. This is called Adelson’s checker shadow illusion.