Category Archives: Science

Investigating the moon and meteorites

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This post was contributed by Dr Jennifer Harris, postdoctoral researcher in Birkbeck’s Department of Earth and Planetary Sciences. Dr Harris attended two Birkbeck Science Week 2016 events on Tuesday 12 April: Analysing the Moon (led by Dr Louise Alexander); and Looking Inside (led by Natasha Almeida)

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What small fragments of rocks can tell us about the moon, the formation of the Solar System and even the early Milky Way was the subject of the second half of Birkbeck Science Week 2016’s Planetary Science evening on Tuesday 12th April.

Dr Louise Alexander, a postdoctoral researcher and Birkbeck student alumna based in the UCL/Birkbeck Centre for Planetary Sciences, and Natasha Almeida, a Birkbeck PhD student and Meteorite Curation Assistant at the Natural History Museum spent an entertaining and informative hour detailing just how much could be gleaned from tiny fragments of extra-terrestrial rocks, and how exactly they go about doing this in their own research.

Apollo Moon samples

Dr Louise Alexander

Dr Louise Alexander

The first half of the session was dedicated to the Moon with Louise Alexander giving us an introduction to the lunar samples brought back by the Apollo astronauts that she uses in her research.

As anyone who’s ever spent any time looking at the full moon can tell you, the moon can be divided into two rough units, one bright and one dark. Lunar samples also fall into these two categories representing the dark Mare basalts and the brighter highland rocks together with a third category of pyroclastic samples. Information from these samples can be used to provide evidence to support the Giant Impact Formation theory of the moon, tell us about the moons internal structure and help to validate surface age estimates from crater counting techniques.

The particular samples that Louise’s work has focused on are all Mare Basalts and are fragments only millimetres in size. Key instruments for extracting data from such small samples are Electron Microprobes, like the one housed by Birkbeck Department of Earth and Planetary Sciences, and Gas Mass Spectrometers.

These instruments enable scientists to peer inside tiny fragments of rock and identify the different mineral crystals that comprise it. Despite the size of each sample, by looking at a large number of them Louise and her collaborators are able to build up a picture of the petrological variety that exists within the Apollo 12 site.

It’s now been over 40 years since the last samples were brought back from the moon and so it’s in the interests of those scientists lucky enough to be in possession of any of them to squeeze as much data out of them as possible. Having used them to gain an understanding of the history of the moon Louise and her colleagues are now investigating the possibility that these samples could have recorded evidence of high energy galactic events over the past few billions of years as the moon has moved through the Milky Way.

This research is still in its infancy and Dr Alexander was keen to point out that the best samples for doing this would be ones from several metres beneath the lunar surface. Sadly for this research no such samples have ever been collected, but if we were to send people back to the moon they could be!

Mapping inside meteorites

Natasha Almeida

Natasha Almeida

An important consideration of the analysis that was described in the first half of the session was that many of the techniques resulted in the destruction of the sample. However not all analysis has to be destructive as we would find out from Natasha Almeida. As a curator Natasha has a professional bias towards preserving her unique and precious samples, whilst as a researcher, still wanting to exploit them as much as possible.

The Natural History Museum in London is home to the oldest collection of meteorites in the world and makes crucial loans of their 4870 samples to researchers across the globe. These meteorites are fragments of the surfaces of Mars and the Moon, and surfaces and interiors of numerous asteroids, some of which have been identified and some of which have not. In order to analyse these rare rocks Natasha uses equipment most of us will have some experience of, an X-Ray scanner, more specifically a micro-CT scanner. Just like a medical CT the NHM’s micro-CT makes use of X-rays to scan through the rock and build up a 3D picture of its interior.

There are some clear differences however; primarily the strength of the beam and the duration of the scan. Rock is more impervious to X-Rays than flesh and bone requiring a much stronger beam and a longer scan time. Each scan results in a 3D image with a resolution of down to 5mm/voxel (a voxel is a 3D pixel) and around 20 – 30Gb of data.

With these images Natasha has extracted a variety of information from numerous meteorites including spotting internal structures and features that would otherwise only be found by cutting into the sample, tracing cracks to establish the possibility of internal contamination by the atmosphere of the Earth and mapping out internal fractures and pores. This final result is especially key for meteorites as the historical methods for working out the porosity of a rock sample involve dunking it in a bucket of water. This method is a purely quantitative one that tells you how much space is in the rock but not how it is distributed unlike micro-CT.

In addition submerging your sample in a tank of water definitely counts as a high contamination risk, something meteoriticists and curators try and avoid like the plague! Unlike the electron microprobe analysis discussed in the first half of this session micro-CT for meteorite analysis is a technique that is still in its infancy but it certainly holds a lot of promise, especially if we have to wait another 40 years for people to bring us back more samples from another planetary body.

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Life Story: The Race for the Double Helix

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This post was contributed by Professor Nick Keep, Executive Dean of the School of Science. Professor Keep attended the Birkbeck Science Week 2016 film screening of “Life Story: The Race for the Double Helix” on Monday April 11 at the Birkbeck Cinema.

DNA

“Life Story: the race for the Double Helix”is a 1987 BAFTA award winning film length TV dramatisation of the story of the discovery of the structure of DNA. The film screening was co-introduced by Dr Richard Hamblyn from the Dept of English and Humanities, who works at the interface of science and literature, and Dr Tracey Barrett from the Dept Biological Sciences, a female protein crystallographer in a Birkbeck tradition that goes back to Rosalind Franklin.

Richard described the film as having two classic odd couples; Crick and Watson in a glossy tourist Cambridge, and Wilkins and Franklin in a rainy London, contrasting with Franklin’s former sunny life in Paris and the easy going relationship with her previous collaborator Vittorio Luzzati, the inventor of the Luzzati plot.

The search for truth in science

Tracey outlined the importance of the science and the changes for women in Science. There are no longer men-only common rooms, such as Franklin encountered at Kings, but there are still problems. They also discussed the interplay between the search for truth in science and competition to be first and famous. Birkbeck is mentioned in the film as the place of refuge Franklin can relocate to escape the oppressive atmosphere at Kings. Richard quoted Rosalind Franklin as writing that she “will be moving from a palace” (Kings) “to a slum” (Birkbeck)” but I’m sure I will find Birkbeck pleasanter all the same”.

The film itself was excellent with Juliet Stevenson as Franklin, Alan Howard as Wilkins, Tim Piggot-Smith as Crick and Jeff Goldblum as the ambitious Watson. I found Clive Panto very convincing (if a little overweight) as Max Perutz, the only character that I knew in person, albeit later in his life. The widespread smoking was an authentic period touch that stood out for me. Whether a 2017 production would do that I am not sure.

Discussing the injustice

The Race for the Double Helix.jpg

By Source, Fair use, https://en.wikipedia.org/w/index.php?curid=46189683

After the showing, the audience discussed the injustice of Rosalind Franklin not winning the Nobel Prize. Firstly the prize is never awarded to more than three people so a decision had to be made and by this time Rosalind Franklin had tragically died. Interestingly, checking afterwards, the ban on posthumous prizes was only formalised in 1974, well after the 1962 award for DNA (See section on Posthumous Nobel Prizes), although observed in practice for Science awards until it was discovered that one of the 2011 winners for Physiology and Medicine had died three days before the announcement, but this was not known to the Swedish Academy when they released the names.

The 1961 Peace prize, just a year before the Medicine and Physiology award to Crick, Watson and Wilkins, was knowingly awarded to the UN Secretary General, Dag Hammarskjöld, who had recently died in an air crash, as was the 1931 Literature Prize to a Swedish Poet. Whether Rosalind Franklin is better known now for not having been awarded the Nobel Prize, than she would have been if she had received it is a matter for debate. Birkbeck, where she worked at the end of her life, remembers her via the Rosalind Franklin Laboratory built in 1996 and, from this year, the annual Rosalind Franklin lecture by a leading woman scientist in a field Birkbeck researches in.

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Computational modelling of the mind

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This post was contributed by Nick Sexton, PhD student in the Department of Psychological Sciences

Prof Rick Cooper

Prof Rick Cooper

How can computer simulations help us understand the human mind? That was the main topic of the Rick Cooper Inaugural Lecture, in which Professor Cooper outlined 15 years of research on cognitive computational modelling.

Cognitive computational modelling boils down to designing computer simulations of how the mind processes information. While computers that appear to think in a human-like-way (whatever that means) are increasingly commonplace in our everyday lives – driverless cars, the Google Deepmind model which learns to play Atari games, and intelligent personal assistants, are all examples – the talk revealed that a more difficult challenge is not only to mimic (or improve on) human behaviour, but to produce it in the same way that humans do – using the same types of mental process.

For example, certain computer programs have succeded in being indistinguishable from humans on Alan Turing’s classic test of artificial intelligence: however, when one digs under the surface, it is readily apparent that their responses are generated in a not remotely human-like way.

So if modelling how the human mind actually works is tricky, how does one go about doing it? Cooper’s approach is to build on theories of how the mind works, from cognitive psychology, often pieced together through painstaking use of behavioural experiments on human participants. These theories, describing how the mind processes information, often resemble flow-chart-like schematics – but often the details are left vague.

This is where cognitive modelling comes in – a fully operational computational model must provide exact details on the inputs, outputs, and algorithms computed, at every stage of mental processing, so the modeller must fill in details that the theorist has left blank. It is a test of whether the psychological theory really is sufficient to explain what it purports to explain, and if not, suggest what details it might be missing.

One element that makes Cooper’s research stand out is his focus, not just on abstract tasks conducted in a sterile psychology or neuroscience lab, or even on a less defined realm of behaviour, as in the Atari game player – but on distinctively human, often startlingly everyday behaviour.

For instance, a large amount of what we consider normal human behaviour is routine – habitual actions, like preparing meals or hot drinks, dressing, commuting. One particular branch of Cooper’s modelling work has been on developing a computational theory of how the mind accomplishes routine actions with minimal attentional oversight, and how this mental apparatus can be applied to non-routine situations.

One model of routine everyday actions simulated preparing drinks. It manipulated objects in its (virtual) environment, like utensils (cups, knives, juicers) and resources (such as hot water, coffee, tea, milk, sugar, oranges )- to achieve an end goal – such as preparing coffee(milk no sugar). The model needed to account for normal human behaviour – successful preparation of the drink most of the time, with occasional lapses – sometimes forgetting to put milk in the coffee, or adding sugar when it wasn’t required.

So what is interesting about a model which prepares drinks (sometimes badly)?
Well, the model was also able to explain what happens when normal mental processes break down – say, in the event of brain damage. With certain setttings, the model not only simulated the lapses of neurotypical people, but also the more extreme lapses observed in
patients with particular types of brain damage – putting butter in the coffee, or forgetting to add water, say.

The model was also able to simulate the behaviour of patients with specific conditions – Ideational apraxic patients struggle to retain a sense of an object’s purpose – say, trying to use a fork to cut an orange. Patients with utilisation behaviour tend to perform actions
appropriate to a given object, but inappropriately to the current situation – take off your glasses and hand them to the patient, and they are liable to put them on.

Here, a cognitive model is rather more use than more everyday artificial intelligences which perform everyday tasks, such as Siri – because Siri might ‘think’ in a way completely differently to humans, there is no reason to believe that if we deliberately damage part of the program, she will produce behaviour typical of people with brain damage. However, because Cooper’s model was based on  neuropsychological theories where routine actions depend on the correct interaction of different cognitive processes – simulating damage to specific processes in the model was able to account well for the
differrent patterns of behaviour typical of different neural conditions.

This approach isn’t just useful for understanding what might be damaged in people unfortunate enough to suffer brain damage, then – it is also a powerful tool for trying to understand what role those cognitive processes play in the human mind when it is functioning normally, and whereabouts in the brain they might take place.

The hour-long talk gave a fascinating glimpse into how – as the knowledge gained from the brain and mind sciences continues to accelerate – computational cognitive modelling has an important role to play in drawing together different disciplines – taking cutting-edge research in psychology, neuroscience, and machine learning – showing how the individual pieces fit together, to give us a better glimpse of the overall picture of how our minds work.

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Microtubules and Microscopes: Exploring the Cytoskeleton

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This post was contributed by Clare Sansom, Senior Associate Lecturer at the Department of Biological Sciences

"The binding site for End Binding protein 1 (highlighted in green) on the microtubule lattice at the corner of four tubulin dimers, visualised using cryo-electron microscopy" (Credit Cell by Maurer et al (2012))

“The binding site for End Binding protein 1 (highlighted in green) on the microtubule lattice at the corner of four tubulin dimers, visualised using cryo-electron microscopy” (Credit Cell by Maurer et al (2012))

Electron microscopist Carolyn Moores, the most recently appointed professor in the Department of Biological Sciences at Birkbeck, gave her inaugural lecture at the college on June 1.

Moores arrived at Birkbeck in 2004 to start her research group and has risen rapidly and steadily up the academic ladder ever since. Introducing the lecture, the Master of Birkbeck, David Latchman, explained that Moores’ CV stood out in every way; she was clearly as gifted a teacher and administrator as she was a researcher. Furthermore, as she has won several awards for science communication, he predicted that the audience would be in for a treat. We were not disappointed.

Educational journey

Moores began her lecture by saying that she would talk about three different things: her own career development; her group’s research into the structure and function of microtubules; and the advancement of women in science, a cause that is close to her heart.

She remembered that she had wanted to work as a scientist as soon as she knew what a laboratory was, and she started young, as an intern in a research lab at Middlesex Hospital while still in the sixth form. School was followed by a BSc in Biochemistry at Oxford and a PhD in John Kendrick-Jones’ lab at the world-famous Laboratory for Molecular Biology (LMB) in Cambridge. She then moved to work as a post-doc with Ron Milligan at the Scripps Research Institute in La Jolla, California, USA, and it was there that she began her studies on microtubules.

Coming to Birkbeck

The award of a David Phillips research fellowship in 2004 gave her the opportunity to return to the UK as an independent researcher. She explained that there were three reasons – or more accurately three people – that led her to choose to come to Birkbeck. Working in electron microscopy, she was inspired by the work of Helen Saibil, one of the UK’s principal exponents of that technique; she had known Nicholas Keep, then a lecturer in Biological Sciences, as a friend since her time at the LMB; and she knew that she would value the interdisciplinary working environment of the Institute for Structural Molecular Biology under the ‘inspired’ leadership of Gabriel Waksman.

Research into microtubules

Moores then moved on to discuss the main topic of her group’s research: the three-dimensional structure, function and role in disease of tiny cylindrical structures known as microtubules. These are one of the building blocks of the cytoskeleton, which forms a framework for our cells in the same way that our skeletons form a framework for our bodies. They are about 25nm in diameter, which puts them firmly into the ‘nano-scale’ of biology that is easily studied using electron microscopy.

There is a cytoskeleton in every living cell, and it, and the microtubules that form it, are involved in many important cellular processes including shape definition, movement and cell division. Diseases as diverse as cancer, epilepsy, neurodegeneration and kidney disease have been linked to microtubule defects. Understanding their fundamental structure and function, as Moores’ group aims to, should help in understanding these disease processes and perhaps also in developing effective treatments.

Microtubules are built up from many copies of a small protein called tubulin, which, in turn, is a dimer of two similar proteins called alpha and beta tubulin. These tubulin dimers make contacts with each other both head-to-tail and side-to-side to create the cylindrical microtubule wall, fuelled by energy derived from the molecule GTP. Each tubulin unit has a definite “top” and a “bottom” and, as the units are oriented in parallel, so has the complete microtubule.

Microtubules are dynamic structures; they continue to grow by the addition of tubulin units to one end as long as GTP is available, and then begin to unravel and shrink. This dynamism, which allows them to respond to the changing needs of the cell, is essential for their function in healthy cells. In particular, microtubules organise chromosome structures during cell division and are therefore necessary for cell proliferation. As cancer is a disease of uncontrolled cell proliferation, it is possible to imagine that a molecule that could specifically block microtubule growth and assembly in the nucleus might be useful as an anti-cancer drug.

Moores and her group are aiming to understand the process of microtubule growth at as high resolution as possible, using electron microscopy. Unfortunately, however, the most detailed images can only be obtained if the specimen is at very low temperatures (in so-called cryo-elecron microscopy) and using this means that the dynamics of the specimens must be “frozen” into a still image. While it is now possible to see the individual tubulin subunits in the static microtubule images, many details of their structure can only be inferred from computational analysis.

Understanding growth

Moores went on to describe one project in her lab in a little more detail. This was an investigation of the structure and role of proteins that bind only to growing microtubule ends, falling off when the growth stops. It is possible to obtain low-resolution images of microtubules in which these molecules have been made to fluoresce, so only growing microtubules are tracked.

In order to understand the growth process in detail, the group developed an analogue of the GTP “fuel” molecule which can bind to the tip of a microtubule that is extending but not break down to release its energy, so the microtubule does not in fact grow. This forms a static analogue of a growing microtubule that retains all the characteristics of the dynamic structure but that can be studied at low temperatures.

Images of this structure have shown that the end binding proteins bind at the corner of four of the tubulin units. They have explained a lot of the properties of growing microtubules, but there is still more to learn. A full understanding will need structures that are at even higher resolution, where the positions of individual atoms can be made out. Following many years of technical development, today’s most powerful electron microscopes are now making this possible.

Women in science

In the last section of the lecture, Moores left the topic of research to talk briefly about another of her passions: the promotion of women in science. She explained that although 65% of under-graduates in the biological sciences are now women, the proportion of women drops to 40% at any academic grade and 25% for full professors.

A study cited by the European Molecular Biology Organisation has suggested that the barriers for women scientists to progress are set so high that at the current rate of progress full equality would never be achieved. Birkbeck has signed up to the Athena SWAN Charter, set up to encourage higher education institutions to transform their culture and promote gender equality. She described her work with the Athena SWAN team that has so far resulted in the college gaining a bronze award as being as exciting as, but also as challenging as, her studies of microtubules.

Nicholas Keep, Dean of the Faculty of Science and, as Moores had stated, a personal friend, gave the vote of thanks after the lecture. He paid tribute in particular to her value as a colleague, her administrative skills, and the importance of her contribution to the college’s application for the Athena SWAN award.

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