Tag Archives: science

Crystallography: past, present and future (Science Week 2014)

This post was contributed by Dr Clare Sansom, Senior Associate Lecturer in Birkbeck’s Department of Biological Sciences

Prof Paul Barnes sets the scene for one of the experiments he carried out in the Crystallography lecture

The second of the Science Week lectures from the Department of Biological Sciences, which was presented on 2 July 2014, was a double act from two distinguished emeritus professors and Fellows of the College, Paul Barnes and David Moss. Remarkably, they both started their working lives at Birkbeck on the same day – 1 October 1968 – and so had clocked up over 90 years of service to the college between them by Science Week 2014.

The topic they took was a timely one: the history of the science of crystallography over the past 100 years. UNESCO has declared 2014 to be the International Year of Crystallography in recognition of the seminal discoveries that started the discipline, which were made almost exactly 100 years ago; a number of the most important discoveries of that century were made by scientists with links to Birkbeck.

The presenters divided the “century of crystallography” into two, with Barnes speaking first and covering the first 50 years. In giving his talk the title “A History of Modern Crystallography”, however, he recognised that crystals have been observed, admired and studied for many centuries. What changed at the beginning of the last century was the discovery of X-ray diffraction. Wilhelm Röntgen was awarded the first-ever Nobel Prize for Physics for his discovery of X-rays in 1896, but it was almost two decades before anyone thought of directing them at crystals. The breakthroughs came when Max von Laue showed that a beam of X-rays can be diffracted by a crystal to yield a pattern of spots, and the father-and-son team of William Henry Bragg and William Lawrence Bragg showed that it was possible to derive information about the atomic structure of crystals from their diffraction patterns. These discoveries also solved – to some extent – the debate about whether X-rays were particles or waves, as only waves diffract; we now know that all electromagnetic radiation, including X-rays, can be thought of as both particles and waves.

Von Laue and the Braggs were awarded Nobel Prizes for Physics in 1914 and 1915 respectively, and between 1916 and 1964 no fewer than 13 more Nobel Prizes were awarded to 18 more scientists for discoveries related to crystallography. Petrus Debye, who won the Chemistry prize in 1936, showed how to quantify the thermal motion of atoms as vibrations within a crystal. He also invented one of the first powder diffraction cameras, used to obtain diffraction patterns from powders of tiny crystallites. Another Nobel Laureate, Percy Bridgman, studied the structures of materials under pressure: it has been said that he would “squeeze anything he could lay his hands on”, often up to intense pressures.

Scientists and scientific commentators often argue about which of their colleagues would have most deserved to win the ultimate accolade. Barnes named three who, he said, could easily have been Nobel Laureates in the field of crystallography. One, Paul Ewald, was a theoretical physicist who had studied for his PhD under von Laue in Munich, and the other two had strong links with Birkbeck. JD “Sage” Bernal was Professor of Physics and then of Crystallography here; he was famous for obtaining, with Dorothy Crowfoot (later Hodgkin) the first diffraction pattern from a protein crystal, but his insights into the atomic basis of the very different properties of carbon as diamond and as graphite were perhaps even more remarkable. He took on Rosalind Franklin, whose diffraction patterns of DNA had led Watson and Crick to deduce its double helical structure, after she left King’s College, and she did pioneering work on virus structure here until her premature death in 1958.

Barnes ended his talk and led into Moss’s second half-century with a discussion of similarities between the earliest crystallography and today. Then, as now, you only need three things to obtain a diffraction pattern: a source of X-rays, a crystalline sample, and a recording device; the differences all lie in the power and precision of the equipment used. He demonstrated this with a “symbolic demo” that ended when he pulled a model structure of a zeolite out of a large cardboard box.

David Moss then took over to describe some of the most important crystallographic discoveries from the last half-century. His talk concentrated on the structures of large biological molecules, particularly proteins, and he began by explaining the importance of protein structure. All the chemistry that is necessary for life is controlled by proteins, and knowing the structure of proteins enables us to understand, and potentially also to modify, how they work.

Even the smallest proteins contain thousands of atoms; in order to determine the position of all the atoms in a protein using crystallography you need to make an enormous number of measurements of the positions and intensities of X-ray spots. The process of solving the structure of a protein is no different from that of solving a small molecule crystal structure, but it is more complex and takes much more time. Very briefly, it involves crystallising the protein; shining an intense beam of X-rays on the resulting crystals to produce diffraction patterns, and then doing some extremely complex calculations. The first protein structures, obtained without the benefit of automation and modern computers, took many years and sometimes even decades.

Thanks to Bernal’s genius, energy and pioneering spirit, Birkbeck was one of the first institutes in the UK to have all the equipment that was needed for crystallography. This included some of the country’s first “large” computers. One of the first electronic stored-program computers was developed in Donald Booth’s laboratory here in the 1950s. In the mid-1960s the college had an ATLAS computer with a total memory of 96 kB. It occupied the basements of two houses in Gordon Square, and crystallographers used it to calculate electron density maps of small molecules. Protein crystallography only “took off” in the 1970s with further improvements in computing and automation of much of the experimental technique.

Today, protein crystallography can almost be said to be routine. The first step, crystallising the protein, can still be an important bottleneck, but data collection at powerful synchrotron X-ray sources is extremely rapid and structures can be solved quite easily with user-friendly software that runs on ordinary laptops. There are now over 100,000 protein structures freely available in the Protein Data Bank, and about 90% of these were obtained using X-ray crystallography. The techniques used to obtain the other 10,000 or so, nuclear magnetic resonance and electron microscopy, are more specialised.

Moss ended his talk by describing one of the proteins solved in his group during his long career at Birkbeck: a bacterial toxin that is responsible for the disease gas gangrene. This destroys muscle cells by punching holes in their membranes, and its victims usually have to have limbs amputated to save their lives. Knowing the structure has allowed scientists to understand how this toxin works, which is the first step towards developing drugs to stop it. But you can learn even more about how proteins work if you also understand how they move. Observing and modelling protein motion in “real time” still poses many challenges for scientists as the second century of crystallography begins.


The evolutionary secrets of garden flowers described at Birkbeck’s Science Week

This post was contributed by Tony Boniface a member of the University of the Third Age.

Science Week logo

Science Week logo

On 3 July, Dr Martin Ingrouille, of Birkbeck’s Department of Biological Sciences, began his talk by pointing out that Darwin had studied plants for 40 years and had published books on pollination. However, Darwin knew nothing of genes and chromosomes and could not explain the rapid origin of flowering plants in the Cretaceous period.

Dr Ingrouille continued by emphasising that garden plants are sterile and exotic plants without their natural pollinators. They have been selected for showiness, many being artificial hybrids. He referred to Goethe, who stressed the essential unity of floral parts, which have all evolved from leaves.

Dr Ingrouille explained how genetic control, in its simplest form, consists of three classes of genes: A, B and C. Class A genes control sepals and petals, class B genes control petals and stamens, and class C genes control stamens and carpels. Mutations of these genes result in parts being converted into others.

Floral evolution in plants could have been the result of duplication of basic genes allowing one to perform its normal function while the other could give rise to a novel structure or function. New plant species have often arisen by chromosome doubling in a sterile hybrid as seen in the formation of Primula kewensis.

Dr Ingrouille then explained how much insight into plant evolution arose from the work of John Gerard (gardener to William Cecil), John Ray (author of the first modern text book of botany) and the Jussieus family (three generations of gardeners to the king of France). These people put plants into groups that were the first natural classification of the angiosperms.

Now DNA sequencing has resulted in a detailed understanding of the phylogeny or evolutionary history of these plants in which many of the families have survived such as the umbellifers and legumes but some such as the figwort family have been split. The result was the arrangement of the plants into two main groups namely the Eudicots, with three  grooves on their pollen grains, and the Basal Angiosperms, with only one groove. Within the Eudicots are the Core Eudicots including the Rosids and the Asterids whilst the Monocots are within the Basal Angiosperms. The first ancestor was Amborella trichopoda, a weedy shrub from New Caledonia in the Pacific – a place Dr Ingrouille hopes to visit on his retirement.

Dr Ingrouille finished  by urging his audience – all members of the University of the Third Age (a movement for retired and semi-retired people to come together and learn together) – to examine their garden plants in detail to look for the variations, which suggest their origins.


The Art of Writing; Or the Science of Writing

This post was contributed by Clare Brown, a student on Birkbeck’s MA History of Art. Clare also blogs at Renaissance Utterances.

‘Stop it with all the damn metaphors’
Kirk to ‘Bones’ McCoy in irritated exasperation 
Star Trek: Into Darkness (2013)

Science writing has held a peculiar interest for me this week, given my Trekkie credentials. I’ve seen the new Star Trek movie twice and have contemplated buying the original ‘Wrath of Khan’ to compare the change in writing and production styles. However for the purposes of these notes, the quote above is the perfect introduction to the Birkbeck Science and Writing Symposium, 21 May 2013.

A rare group of people – two poets, a playwright, an astronomer, a science/history/cultural academic, two actors and a cartoonist – were brought together not just to discuss the way they communicate their ideas but to actually demonstrate and showcase their skills. I’m not going to simply narrate what each person said but try to highlight themes. What I must say is, so often at academic symposia the emphasis is on the presentation of paper after paper with little or no presenter animation. No matter how interesting the topic, my eyes glaze over eventually but not here, not this time, we were off; starting with the Big Bang. Before I come on to the themes, I want to dwell a little on the poets and their poetry.

Anyone who has written poetry is aware of the painstaking care that goes into the selection of words, creation of sentences and the presentation of it on paper. Simon Barraclough is instantly ‘get-able’ with his ability to have words fall out of his subconscious. He is currently working on various projects; the first is penning a contribution to a collection of poems inspired by Light Show, the recent Hayward gallery exhibition, as well as his own Sun inspired collection. He entertained with his series of From Big Bang To Heat Death, my favourite being this one, because of the perfect combination of religion, science and cultural reference:

Our fusion
Which art in heaven
From evil 

However Rosie Sheppard is a different kind of poet. With her scientific background and a fascination with DNA she uses the everyday, such as food, as a way of conveying the complex patterns and processes of nature and science. Earlier I was rereading one of the poems she recited and her astonishing images conjured by words and situations are tightly structured in a way that is suggestive of the double helix. But only because she told me it was there. Which is like telling a person who likes flowers purely for their scent that behind all the pretty smell is a complicated list of chemicals and chemical reactions. Interesting but without the specialised knowledge, some of the clever stuff goes over my head.

The themes which predominated were roughly these:

  • Science fiction is the absolute favourite way of linking writing and science. From wildly speculative space travel to the sci-fi closer to home, as demonstrated by Nick Payne with ‘Constellation’, the enduring popularity of the incorporation of science into fiction will continue. Science provides a way into a story, writers can play with it, laugh at it, imagine all possibilities and explore what would otherwise be difficult topics. As Nick said, the cosmologists he spoke to rubbished his multiverse theory but he has none-the-less produced a wondrous ‘what if’ play about death.
  • Rise in popular science and the use of accurate and clear summaries of contentious science to inform the public. Darryl Cunningham, cartoonist/graphic novelist has used the power of the image to blast bad science such as the MMR Scandal.
  • Scientists spend a lot of time writing, whether it is grant applications, reports or articles, communicating with the public, so a number of different styles are required. The Public Astronomer Marek Kukula emphasised the importance of getting precisely the right words, which was then immediately echoed by the poets. Another interesting linguistic point Marek made was the importance of foreign scientists working in English, for example, returning to home institutions and having to create new words in their own language to explain new concepts.
  • A continuing collaboration between the writers of art and science. The more theoretical and exploratory areas of science are perhaps more aligned to the arts; financially speaking they may not have a direct payoff but it’s culturally vital to have that inspiration and ‘blue sky’ understanding of our infinitely complex world. Scientists are working on imagining unimaginably abstract ideas, multiverses, esoteric maths, string theory, god particles, black holes. Some writers use art to explain science and this scientific language in turn enriches art. Science provides new metaphors. As Laura Salisbury stated, this is a hybrid language, a juxtaposition of communications ‘abraiding’ with one another.
  • An undeveloped theme was science as a new faith. For the majority of us, we live in a world in which we have to trust because we don’t understand the science behind every-day objects. Laura Salisbury in her cool articulate way outlined the importance of cultural assumptions, drawing on the ideas of French sociologist of science anthropologist Bruno Latour. Interestingly he said that we only become truly modern when we separate the rational from the irrational/superstitious. Scientists and their theories are often found to be wrong and the conservative religious right suggest this is a flaw. But all theories and ideas are incomplete and the enquiring mind is happy to uncover layers of truth.
  • Unrealistic expectation in medical science was also touched upon with examples of illness and resuscitation on television discussed. Marek says that there is no problem with fiction bending  scientific rules but when you’re on a real operating table you want it right. This takes us back to the way that hard science is communicated and the style that the doctor, scientists selects when disseminating methods, procedures etc. No art or metaphor required there.
  • There is a perception that science is dull because of the way it is taught in school and this raised some interesting points. Nick in his role as everyman said he had no clue what he was getting into with cosmology and multiverses but he spoke with people who did know. It was suggested that scientists are like dancers – they have learnt the basics and practiced and practiced – they use their knowledge, analytic thinking, and experience to put on their performance. School children are still learning; exercising at the barre, not yet ready to perform and what they need is ‘cool science’ to inspire.

The evening generated plenty of interesting discussion, each one easily a separate essay topic. There was a final note of caution from Laura on the dangers of metaphor, not just as a Star Trek character devise, but that it may cause a blurring in the precision of scientific language. But despite this, the most important feeling to take away was the acknowledgement that science and art are actually of equal importance; certainly the language of each, informs and enriches the other.