Computational modelling of the mind

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

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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Spatial Distortion in Perception and Cognition

This post was contributed by Elena Azañón and Luigi Tamè, postdoctoral fellows in Birkbeck’s BodyLab

matthew-longoProf Matthew Longo gave his inaugural lecture about “Spatial Distortions in Perception and Cognition” on June 4th. He has been a lecturer in the Department of Psychological Sciences at Birkbeck, University of London, since 2010, and has recently been appointed Professor of Cognitive Neuroscience in the same Department.

He completed his PhD at the University of Chicago in 2006 and spent several years at the Institute of Cognitive Neuroscience at University College London as a postdoctoral researcher before joining Birkbeck. The main focus of his research concerns the psychological and neural mechanisms underlying body representations, and how these affect all aspects of our mental lives.

Longo’s inaugural lecture was introduced by the Master of Birkbeck, Prof David S Latchman, who commented on Longo’s exceptional achievements during his remarkable career. Professor Latchman highlighted the high quality of his research and impressive publication record in high impact journals. Indeed, Longo has been recently awarded by two of the major internationally recognised early career awards, in Europe (i.e., the 2014 Experimental Psychology Society Prize) and overseas (i.e., the American Psychological Association Distinguished Scientific Award for Early Career).

Pathological conditions

Longo started his lecture by highlighting that in many situations healthy people appear to have distorted representations of their bodies. However, despite these distortions, people are able to appropriately interact with the environment. Longo continued by describing several bizarre pathological conditions characterised by distortions in the representations of the body.

The underlying idea is that pathology is a continuum and, in one way or another, healthy people might share some features of these deficits. One of the paradigmatic examples he mentioned was the phantom limb experience, a condition in which a patient who has suffered the amputation of a limb, continues to experience the limb. In this respect, he recounted an elegant historical anecdote about Horatio Nelson’s phantom limb experience after loss of his arm, which was described by the admiral as proof of the immaterial soul.

He finally mentioned a patient, described by Oliver Sacks, who repeatedly fell out of her bed. When asked the reason of this behaviour, the patient complained that the nurses were secretly introducing a severed arm in the bed with her. The nurses finally realized that the patient was affected by somatoparaphrenia (i.e., the lack of awareness of a part of the body). It was the patient’s own left arm, which she believed was somebody else’s arm that she was throwing out of the bed!

Spatial distortions in perception

Before starting to describe his own work, he explained more about the idea of spatial distortions in perception. This is somehow a counterintuitive concept considering that the goal of perception is to create a veridical model of the world.

If people perceive a distorted world, how can they possibly act on it in an appropriate way? As an example of normal distortions, he described the representations at the level of the primary sensory and motor cortices in which the body parts are represented with different levels of magnification. Longo explained that these distortions are necessary steps to achieve complex behaviours.

Indeed, if we had homogenous tactile sensitivity across the body, then apparently simple tasks such as lacing up our shoes would be impossible. What allows us to perform everyday actions, which seem simple to us but are incredibly complex from a motor control perspective, is that different bits of the skin are represented differently in the brain. That is, bits of the skin able to produce fine-grained movements, such as the fingers, have extremely high tactile sensitivity, while others, such as the back of the leg have much less sensitivity.

Examining distortions

In the second half of the lecture he demonstrated that body representations are not only distorted at the level of the primary cortices, but also, though to a lesser degree, at higher levels of perceptual processing. Across several experiments, Longo made use of Weber’s illusion. In this illusion, the perceived distance between two touches is larger on skin regions of high tactile sensitivity than on those with lower acuity. His research suggests that the dorsum of the hand, but not the palm, is implicitly represented wider and squatter than it actually is. He argued that these distortions are partly explained by the shape of the tactile receptive fields of cortical neurons on the different parts of the hand.

Longo continued describing similar distortions of the representation of our bodies that are independent from touch. In order to isolate and measure this implicit body representation, Longo developed, jointly with his former supervisor, Professor Patrick Haggard from UCL, an elegant, simple and effective paradigm.

Participants used a long baton to judge the location of the knuckle and tip of each finger of their own occluded hand. By comparing the relative location of each landmark, he was able to construct implicit maps of the represented shape and size of the hand, which could then be compared to the actual hand shape. He found that these maps were drastically distorted, and in a highly consistent manner across individuals. In particular, across a number of studies, Longo revealed a general underestimation of finger length and an overestimation of hand width. These distortions are similar to those he found in the tactile modality. He further noted that this pattern of results was highly stable across body parts.

The event concluded with a final speech by Professor Martin Eimer. He thanked Longo for his exciting and entertaining lecture. He further highlighted the high productivity and creativity of Longo’s research during his early career, exalting the elegance of his experimental approach and design. He also highlighted that despite being a great scientist, he is likewise an excellent colleague, who is always available and willing to perform mundane duties that despite being unexciting, are fundamental for the department’s life.

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