Sunday, 20 December 2009

Research proposal for dummies

Here you go, as promised a rewritten project proposal written for beginners to neuroscience. Not quite a plain English rewording, but simplified and with key terms defined. This is what I will be doing up until September...

The way in which the brain that processes our main senses, such as sight and hearing (and by the way, don’t go thinking you only have the 5 senses we all know about, there are far more!) is fascinating. They are what we call ‘topographically organised’. Which basically means that the surface of the brain, the cortex, acts as a little map of what we perceive. For example, if you could look down on the main visual area of your brain, called V1, and see what each brain cell is processing, it would look more or less the same as the picture you see out of your eye (although this is a hugely simplified explanation, but you get the general idea).

The hearing process is slightly different. In another simplified explanation, sound is processed in terms of what we perceive as the ‘pitch of a sound’, or how ‘high or low’ it sounds; its frequency. Each frequency (or note, if that makes it simpler) is processed by a separate part of the primary auditory cortex, or A1. These areas of the A1 are also organised by frequency, a bit like the keys of a piano going from low up to high pitch notes. So if you were to scan the brain and run your hand down a piano, you would see a ripple of activation move along A1. The range of frequencies that each auditory brain cell responds to is called it’s ‘receptive field’.

If you read to the entry I wrote recently about neuroplasticity you will know that the organisation of the brain, or its ‘wiring’ can be changed. When this occurs to our sensory areas we can think of this as ‘remapping’. Research in animals has shown that the receptive fields of neurons in AI can undergo these ‘plastic’ changes very rapidly, as a result of what the animals learns to associate particular sounds with. Amazingly, these changes occur within minutes.

If something happens to make the animal associate a particular frequency with something external, the tone acquires behavioral relevance and a large number of these AI cells shift their preferred frequency and begin to respond more to the new frequency. This effect has been shown to depend on the animal paying direct attention to the stimulus. In one experiment, two groups of rats were trained to respond to musical tones. One group responded to the frequency and the second group responded to the volume of the tone. So, each were played a series of tones at either different frequencies or different volumes, and had to respond only to the frequency or volume to which they were trained to respond. The frequency rats demonstrated changes to the frequency map in the A1, with more cells firing in response to the trained tone. This didn’t happen in the rats who were trained to respond to loudness, but they did have an increase in the type of cells that respond to volume rather than frequency. This would support the idea that brain cells can be changed depending on what an animal needs them for, and what sounds hold a particular relevance for the animal. Other studies have achieved the same result without training the animal, instead electrically stimulating parts of the brain, such as the nucleus basalis, when the animal heard a particular frequency.

However, very little work has been done in humans on this subject. So our study aims to determine whether conditioning of a particular frequency can lead to improved performance in detection and/ or discrimination of that frequency amid others, as would be predicted if human receptive fields show similar plasticity to that documented in animals.

What we are planning to do is to compare the ability of people to detect a particular frequency as well as to discriminate between the frequency and others close by. In the detection task subjects will have to decide which of two successive bursts of white noise contained a ‘hidden’ embedded auditory tone. In the discrimination experiment participants will be required to decide whether the second of two successively presented pure tones was higher or lower than the first.
After this initial detection / discrimination task, subjects will undergo a training method known as ‘classical conditioning’, repeatedly pairing one distinct target frequency tone with an electric shock to the forearm so the participant comes to associate that frequency with receiving a physical shock. After this association is established, the detection / discrimination tasks are repeated, with an occasional “topping up” of the shock conditioning. After 40 minutes, the detection / discrimination task will continue without further conditioning. The absence of reinforcement of the target frequency will then lead to what is called “extinction” of the association between frequency and shock. We will then compare the ability of participants to spot the tone to which they were conditioned before and after the task.

If the animal studies are applicable to humans there is likely to be a greater number of brain cells in A1 detecting the target frequency, because it has become associated with the electric shock. More cells responding to that frequency should make people better at spotting it. If we find a significant effect we may then go on to repeat the experiment while monitoring brain activity using a method known as MEG, to see what is going on in the brain during the experiment.

Saturday, 19 December 2009

Oh, and I'll post a simplified explanation of that last post soon!

Friday, 18 December 2009

Research Proposal

Today I had to submit my research proposal for my thesis project. Here it is, written by myself and Dr Christian Kluge:

Rapid plastic changes in Auditory Cortex: a classical conditioning paradigm

Chris Fassnidge, Dr Christian Kluge and Professor Jon Driver


This study seeks to determine whether detection and/or discrimination of a pure auditory tone can be improved by classical conditioning, pairing a target frequency with an electric shock

Literature Review

Work by Merzenich, Weinberger, Irvine and others has shown that receptive field properties of neurons in primary auditory cortex (AI) can undergo rapid plastic changes in response to behavioral learning in animals (reviewed in Weinberger 2004, Weinberger 2007, Irvine 2007). Remarkably, these changes occur within minutes. During learning, when a target frequency acquires behavioral relevance a large number of AI pyramidal cells shift their best frequency towards this distinct frequency. This effect has been shown to depend on attention , i.e. behavioural relevance (Polley et al., 2006). Two groups of rats underwent operant conditioning with identical stimulus sets. One group responded to a target frequency and demonstrated tonotopic changes resulting in an increased representation of the target frequency, while the second group performed the task (with exactly the same stimuli) in response to a target loudness which led to changes in the topographic organisation of neurons’ preferred loudness. In non-human primates, Blake et al. (2006) demonstrated a crucial role for active cognitive control and involvement needed for tonotopic re-mapping to occur.

Later mechanistic assessment has revealed that the neurotransmitter acetylcholine (ACh) is crucially involved in these plastic processes. Pairing brief ACh infusions with the purely passive presentation of tones induced changes in the AI tonotopic maps similar to the ones observed in the experiments described above. In addition, stimulation of the nucleus basalis, the main source of corticopetal cholinergic projections, led to identical remapping. These findings are intriguing because they strongly argue against the long-held view that primary sensory cortices are merely passive input structures in which plastic changes of receptive fields occur only during early ontogeny. Instead, the studies summarised indicate that the sensitivity and perhaps even local network resonance patterns can be dynamically adapted to current behavioural requirements.

Very little work has been done in humans on this subject. Thus, we aim to behaviourally determine whether conditioning of one or another frequency can lead to improved performance in detection and/ or discrimination of pure tones, as would be predicted if human receptive fields show similar plasticity to that documented in animals.

Materials and Method

In a within-subject design (with conditioned frequencies counterbalanced over subjects), we will compare the detection (experiment A) as well as the discrimination (experiment B) of pure tones. The detection task will employ a two alternative forced choice (2AFC) scheme in which subjects have to decide which of two successively presented white noise stimuli actually contained a pure tone. In the discrimination experiment, participants will be required to decide whether the second of two successively presented pure tones was higher or lower than the first one. In both experiments tones of a range of frequencies will be used and this part of the experiment will last about 15 minutes.

After this initial detection / discrimination block, subjects will undergo classical conditioning, pairing one distinct target frequency tone with an electric shock to the forearm. After this association is established, the detection / discrimination 2AFC routines are repeated, interleaved with further conditioning blocks (“topping up”). After 40 minutes, the detection / discrimination task will cease to be interupted by further conditioning. The absence of reinforcement of the target frequency will then lead to extinction of the association between frequency and shock (extinction).

A number of potential follow-up studies are conceivable. First, the work by Blake and colleagues (2006) suggests that operant conditioning might be more effective in inducing tonotopic changes. Thus, modifications of the paradigm employing reward or punishment depending on performance are possible. Also, there are potential MEG versions of all experiments described which would, through analysis of early latency auditory components of the evoked magnetic fields, allow for a direct assessment of the underlying neurophysiological principles.

Predicted Outcomes

This series of experiments allows for three possible outcomes:
1. Conditioning may improve tone detection performance but not tone discrimination. This situation would allow for the conclusion that a greater number of neurons areresponding to the target frequency after conditioning but that this improvement does not involve a sharpening of best frequency tuning curves.
2. Conditioning may improve tone discrimination performance but not tone detection. This outcome could be interpreted as a potential increased local signal-noise ratio. This situation seems somewhat unlikely, however, since previous studies reported best frequency shifts in large numbers of cells rather than sharpening of existing tuning curves.
3. Finally, if conditioning leads to performance improvements in both detection and discrimination our interpretation would be that although there was an increase in the number of neurons responding to the target frequency, this change does not come at the expense of frequencies around it. In this situation it would be interesting to study the underlying compensatory mechanisms in a later MEG experiment.


The data will be analyzed with ANOVA (random effects) using the SPSS statistics software package. Further analysis may be required depending on results.


Preparatory work: January - March 2010
(generation of stimuli, programming of the actual experiment, pilot measurements)
Data collection: March - June 2010
(16 to 20 subjects each group)
Analysis and write up: June - July 2010


Participants will be reimbursed for their time and effort using existing research grants of the ICN attention group. No investment in equipment or software will be neccessary.


Full ethical approval will be sought from the Graduate School Research Ethics Committee prior to pilot data collection. The ethics application will be submitted in early January 2010.


Blake, D. T., Heiser, M. A., Caywood, M., & Merzenich, M. M. (2006). Experience-dependent adult cortical plasticity requires cognitive association between sensation and reward. Neuron, 52(2), 371-381.

Irvine, D. R. F. (2007). Auditory cortical plasticity: Does it provide evidence for
cognitive processing in the auditory cortex? Hearing Research, 229(1-2), 158-170.

Polley, D. B., Steinberg, E. E., & Merzenich, M. M. (2006). Perceptual Learning Directs Auditory Cortical Map Reorganization through Top-Down Influences. The Journal of Neuroscience, 26(18), 4970–4982.

Weinberger N. M. (2004) Specific long-term memory traces in primary auditory cortex. Nature Reviews Neuroscience, 5(4), 279-290.

Weinberger N. M. (2007). Associative representational plasticity in the auditory cortex: a synthesis of two disciplines. Learning & Memory, 14(1-2) 1-16.

Thursday, 10 December 2009

My apologies, but this may be a rather lengthy, self-indulgent entry.

There are times on this course when I really need to take a deep breath and swallow down the surge of inadequacy that I feel building up inside me. It is something akin to those moments in life when one almost throws up but somehow at the last second manages to swallow down the noxious brew. Both avoid leaving oneself in an unpleasant position, but equally leave you with a revolting taste in your mouth.

A tad overdramatic? Perhaps.

It is fair to say, however, that I often feel out of my depth on this course. Those of you who have read my past entries in this blog will know that my school record was far from exemplary. You will also know that I have felt more than a slither of trepidation at being accepted to study at such a prestigious institution, a world leader no less.

It has not been the finest of weeks. Monday started off optimistically enough, with a meeting at the Institute of Cognitive Neuroscience (ICN) to discuss my upcoming research project with my soon-to-be collaborator, Dr Christian Kluge. I left the ICN buzzing at having drawn up an exciting and original piece of research with Dr Kluge, and feeling a lot more confident about what would in the new year become the embryonic stage of my thesis.

How crushed I was then, on returning home to see in my inbox the following words from Dr Kluge:

“There is an ongoing project with quite similar designs that i did not know of. Therefore, we will probably have to re-think what we want to do”.

A lesson in expectations management, perhaps. That’ll teach me to curb my enthusiasm!

Anyway, there was little time to waste, as in seven days I time I would be required to make a brief presentation to my peers and the course administrators outlining my research project. What Dr Kluge proposed was we meet with Professor Jon Driver, one of the directors of the ICN and the man who would be supervising the project that myself and Dr Kluge will spend the next nine months on.

It didn’t go well.

I came across as a bumbling, poorly read amateur. Prof Driver was clearly unimpressed, and Dr Kluge was visibly embarrassed at having brought me into his office. Nevertheless, between us we managed to thrash out a viable research project which certainly has potential to be an exciting piece of work.

The one advantage of making such a poor first impression on such an important figure within the ICN is that there is now only one direction in which his opinion of me can go. The last thing professor Driver asked of me, as he was on his way into a two hour meeting, was to draw up the slides for my presentation on Monday, and to do it before Friday so he could take a look at it.

It was in his inbox by the time he left the meeting.

The best thing about fighting down those feelings of inadequacy is that it resets ones perspective in order that we may replace them with feelings of pride and self-congratulation; quite rare for me to feel and even rarer to voice. But if I am honest I have done bloody well to get here. It can be off-putting at times to hear some of my fellow students list their accomplishments, to reel off terminology that leaves me perplexed, and to have to take the time to explain things to me in simple terms.

I should not lose sight of the fact that I came into this course without a single science A-level, and ten years after a decidedly average performance at GCSE science. In addition, contrary to what some may think, a psychology degree is far from the ideal prerequisite for a cognitive neuroscience MSc, let alone one with as little scientific content as my bachelors degree had. But then again, I had no experience of psychology before undertaking my degree, and emerged with first class honours.

This may all be new to me now, and I may have to endure some snobbery, condescending comments and pangs of self-doubt, but I will learn fast, improve exponentially and come out the other side with one heck of a valuable qualification.

And then, just maybe, repeat the whole cycle again with a PhD.

Thursday, 3 December 2009

Some people are just ahead of their time.

"Men ought to know that from nothing else but the brain come joys, delights, laughter and sports, and sorrows, griefs, despondency, and lamentations. And by this, in an especial manner, we acquire wisdom and knowledge, and see and hear, and know what are foul and what are fair, what are bad and what are good, what are sweet, and what unsavoury... And by the same organ we become mad and delirious, and fears and terrors assail us... All these things we endure from the brain"

Hippocrates, 400 B.C