Wednesday, 18 March 2020

Memory and The Brain Module


A few weeks ago a long discussion followed a tweet about the start of my “Memory & The Brain” module. I promised to provide a summary of the content of the module, as several people seemed to be interested. So here it is.

First, the context. This is an “advanced module” that final year undergraduates (and some Masters students) take after completing core 1st and 2nd year modules in “perception and cognition” and “brain and behaviour”. They therefore have a relatively strong background in undergraduate psychology, and the module is designed to push them beyond this core knowledge. It consists of eight 2-hour seminars. In several seminars (2, 3, 5, 6, & 7), I provide a 1-hour lecture and then the students present two key papers on the topic. The idea is for them to digest and then present the material to the other students, and to promote a discussion on the broader theoretical topic. This can often lead to stimulating discussion among the students where they learn how to critically evaluate the studies (and sometimes it can lead to awkward silences).

In each seminar I typically choose 2-3 “key papers” on the broader topic. Some of these papers I have chosen because they are clearly the key papers in the area. Some I have chosen because they are important, but also are written well, and have a clear experimental design, to ensure the students are not overly stretched. I often include my papers, not necessarily because I think they are THE key papers, but because (1) students seem to like reading and discussing lecturer’s work and (2) it allows them to understand that scientists are able to critically evaluate their own work to the same degree as others. All this means that there will undoubtedly be key papers related to the topic that aren’t covered. These are the choices we sometimes must make when teaching.

Finally, the module has now run for 4 years with relatively little change to the content (some tweaks to which papers the students present), so this is perhaps a good moment to reflect on whether anything needs changing or updating. If you have any suggestions along these lines, please feel free to email me. With all that out of the way, here is the content. Note, the content is largely taken from the online material the students have access to, in italics is my narrative/summary of each seminar and how they link together.

Module overview


Our memories make us who we are. They allow us to delve into our past and project ourselves into the future. How does the brain support something so complex, subjective and personal?

This module will explore the cognitive neuroscience of long-term memory, with a specific focus on episodic and spatial memory. We will explore this topic from a wide variety of methodologies - from traditional experimental psychology, to neuropsychology, to brain imaging, to eletrophysiological recordings.

Learning outcomes


On completing this module, the student will be able to:
  • Appreciate the complexities involved in the study of long-term memory
  • Discuss memory research at multiple scales, from individual neurons, to cortical networks, to behaviour
  • Critically appraise research related to episodic and spatial memory
  • Identify different regions of the medial temporal lobe (MTL), including subfields of the hippocampus
  • Describe the main theoretical accounts of the medial temporal lobe and hippocampus

Seminar 1 – Memory systems and declarative memory


The purpose of this lecture is to teach and/or revise what is commonly taught at the undergraduate level – primarily Squire’s taxonomy of memory, and the possible “types” of memory that have been identified by neuropsychology and neuroimaging studies. Many of the students will have covered some aspects of this before (i.e., the distinction between episodic and semantic memory). Here I want to present the material in such as way as to prepare them for the remainder of the module. In particular, I want them to think carefully about what a “type” of memory might be, and whether this is a good way of conceptualising long-term memory.

Learning outcomes


After the lecture, the student will be able to:
  • Discuss evidence for multiple memory systems
  • Understand the different sources of evidence provided by neuropsychology and functional brain imaging
  • Explain the role of the medial temporal lobes in long-term declarative memory

Key Reading


  1. Squire, L.R., & Zola-Morgan, S. (1991) The Medial Temporal Lobe Memory System, Science, 253(5026), 1380-1386.
  2. Scoville, W.B., & Milner, B. (1957) Loss of recent memory after bilateral hippocampal lesions, Journal of Neurology, Neurosurgery & Psychiatry, 20(11), 11-21.

Further Reading


  1. Chapter 7: Long-term memory systems, in Eysenck & Keane, Cognitive Psychology: A Student's handbook

Seminar 2 – Episodic and semantic memory


Here we discuss the distinction between episodic and semantic memory. We start off with evidence that seemingly provides a double dissociation between episodic and semantic memory – MTL amnesic patients vs semantic dementia patients. We then discuss how this difference may stem from that fact that episodic memory tests typically assess anterograde memory (learning of new material) whereas semantic memory tests typically assess retrograde memory (retrieval of material learnt prior to brain injury/degeneration). Because of this, we focus on research that assesses whether amnesic patients with damage to the hippocampus/MTL can learn new semantic information.

Learning outcomes


After the lecture, the student will be able to:
  • Give clear real-world examples of episodic and semantic memory
  • Discuss evidence for possible dissociations between episodic and semantic memory
  • Report the key brain regions involved in episodic and semantic memory

Key Reading


  1. Vargha-Khadem et al., (1997) Differential effects on early hippocampal pathology on episodic and semantic memory, Science, 227, 376-380.
  2. Tulving et al., (1991) Long-lasting perceptual priming and semantic learning in amnesia: a case experiment, Journal of Experimental Psychology: Learning, Memory & Cognition, 17(4), 595-617.
  3. Hodges et al., (1992) Semantic dementia. Progressive fluent aphasia with temporal lobe atrophy, Brain, 115(6), 1783-1806.
  4. Hamann & Squire, (1995) On the acquisition of new declarative knowledge in amnesia, Behavioural Neuroscience, 109(6), 1027-1044.

Further Reading


  1. Squire & Zola (1998) Episodic memory, semantic memory and amnesia, Hippocampus, 8(3), 205-211.

Seminar 3 – Recollection and familiarity


We next focus on episodic memory, and the distinction between familiarity and recollection. We cover the strengths and weaknesses of three different approaches to dissociating between these two plausibly distinct processes – the remember/know procedure, the process dissociation procedure, and signal detection theory/ROC curves. We then discuss neuropsychological data for/against this distinction.

Learning outcomes


After the lecture, the student will be able to:
  • Explain the distinction between recollection and familiarity
  • Appreciate how signal detection theory has contributed to the recollection/familiarity distinction
  • Report the key brain regions involved in recollection and familiarity

Key Reading


  1. Yonelinas (1994) Reciever-operating characteristics in recognition memory: evidence for a dual-process model, Journal of Experimental Psychology: Learning, Memory & Cognition, 20(6), 1341-1354.
  2. Bowles et al. (2010) Double dissociation of selective recollection and familiarity impairments following two different surgical treatments for temporal-lobe epilepsy, Neuropsychologia, 48(9), 2640-2647.
  3. Wais et al. (2006) The hippocampus supports both the recollection and the familiarity components of recognition memory, Neuron, 49(3), 459-466.
  4. Horner et al., (2012) A rapid, hippocampus-dependent, item-memory signal that initiates context memory in humans, Current Biology, 22(24), 2369-2374.

Further Reading:


  1. Aggleton & Brown, (1999) Episodic memory, amnesia, and the hippocampal-anterior thalamic axis, Behavioural Brain Sciences, 22(3), 425-444.
  2. Brandt et al., (2009) Impairment of recollection but not familiarity in a case of developmental amnesia, Neurocase, 15(1), 60-65.

Seminar 4 – Medial temporal lobe architecture


Prior to seminar 4, we discuss the hippocampus, perirhinal cortex, and the medial temporal lobes but students have learnt little of the underlying architecture of these regions. We therefore cover the major inputs into the perirhinal and parahippocampal cortices, the entorhinal cortex, and the trisynaptic loop. This is covered at this point, given the following seminar requires knowledge of the individual subfields of the hippocampus (in particular CA3 and DG). The emphasis of this seminar is to understand how knowledge of the underlying architecture provides clues as to what the functions of each region might be (e.g., if perirhinal cortex receives major input from ventral visual stream, it is likely to process object/item information relative to parahippocampal cortex).

The format of this seminar is slightly different from other seminars, in that I give a 1-hour lecture and then students go through a workbook of brain diagrams/images in groups, identifying key regions (this replaces student presentations).

Learning outcomes


After the lecture, the student will be able to:
  • Discuss the principal inputs into the medial temporal lobes
  • Identitify the subfields of the hippocampus
  • Explain the circuitry of the hippocampal trisynaptic loop

Key Reading


  1. Preston & Wagner, (2007) The medial temporal lobe and memory, in Kestner & Martinez (Eds) The Neurobiology of Learning and Memory, 305-337.
  2. Amaral (1999) Introduction: what is where in the medial temporal lobe? Hippocampus, 9(1), 1-6.
  3. Lavenex & Amaral (2000) Hippocampal-neocortical interaction: a hierachy of associativity, Hippocampus, 10(4), 420-430.

Further Reading


  1. Amaral & Lavenex, (2007) Hippocampal neuroanatomy, in Per Andersen et al (Eds) The Hippocampus Book, 37-109.

Seminar 5 – Pattern separation and pattern completion


We cover the two computational processes of pattern separation and pattern completion, and how these are likely supported by DG and CA3 respectively. We then cover the related concept of attractor dynamics, and how this might relate to pattern separation/completion. The key readings are human fMRI study, though we start to cover more rodent electrophysiology work from this point. We focus on how pattern separation/completion might be useful computations in relation to episodic memory.

Learning outcomes


After the lecture, the student will be able to:
  • Explain how pattern separation and pattern completion might support memory
  • Report the hippocampal subfields that support pattern separation and pattern completion
  • Discuss research in rodents and humans that provide evidence for these computations

Key Reading


  1. Horner et al., (2015) Evidence for holistic episodic recollection via hippocampal pattern completion, Nature Communications, 6(7462), 1-11.
  2. Berron et al. (2016) Strong evidence for pattern separation in the human dentate gyrus, Journal of Neuroscience, 36(29), 7569-7579.

Further Reading


  1. Wills et al. (2005) Attractor dynamics in the hippocampal represention of the local environment, Science, 308(5723), 873-876.
  2. Neunuebel & Knierim, (2014) CA3 retrieves coherent representations from degraded input: Direct evidence for CA3 pattern completion and Dentate Gyrus Pattern Separation
  3. Bakker et al., (2008) Pattern separation in the human hippocampal CA3 and dentate gyrus, Science, 319(5870), 1640-1642.
  4. Nakazawa et al., (2002) Requirement for hippocampal CA3 NMDA receptors in associative memory recall, Science, 297(5579), 211-218.
  5. Steemers et al., (2016) Hippocampal attractor dynamics predict memory-based decision making, Current Biology, 1-8.

Seminar 6 – Functional neurons in the medial temporal lobe


Prior to seminar 6, we have primarily covered fMRI and neuroimaging in humans, and as such know little about what individual neurons in the MTL do. Here we cover the major “functional neurons” in the MTL, as revealed by single-unit electrophysiology in rodents and humans – place cells, head-direction cells, grid cells, boundary/border cells, and “concept” cells. Towards the end of the seminar we discuss how these cells are responding to (e.g.,) the rodent’s current position or heading-direction, so seem not to serve an obvious “memory” function. At this point, it is simply to think about this possible disconnect – patients with MTL damage clearly show memory deficits, however individual neurons in the MTL respond to stimuli in the present (i.e., appear somewhat more “perceptual” in nature).

Learning outcomes


After the lecture, the student will be able to:
  • Report the main functional neurons in the hippocampus
  • Describe the firing characteristics of these neurons
  • Appreciate how these neurons contribute to spatial and episodic memory

Key Reading


  1. O'Keefe & Dostrovsky (1971) The hippocampus as a spatial map. Preliminary evidence from unity activity in the freely-moving rat, Brain Research, 34(1), 171-175.
  2. Hafting et al., (2004) Microstructure of a spatial map in the entorhinal cortex, Nature, 436(7052), 801-806.
  3. Quiroga et al., (2005) Invariant visual representation by single neurons in the human brain, Nature, 435(7045), 1102-1107.

Further Reading


  1. Solstad et al. (2008) Representation of geometric borders in the entorhinal cortex, Nature, 322(5909), 1865-1868.
  2. Lever et al. (2009) Boundary vector cells in the subiculum of the hippocampal formation, Journal of Neuroscience, 29(31), 9771-9777.
  3. Taube et al. (1990) Head-direction cells recorded from the postsubiculum in freely moving rats. I. Description and quantitative analysis, Journal of Neuroscience, 10(2), 420-435.

Seminar 7 – Process vs representational accounts of the medial temporal lobes


Building on the content from seminar 6, we cover two dominant theories in the literature in relation to how to best characterise the medial temporal lobes – namely process vs representational accounts. We discuss the key research in humans that provided some of the first clear evidence in favour of representational accounts. We finish by trying to reconcile the representational account with the “memory” deficits that patients with MTL damage present with. In particular, we discuss how certain processes (e.g., episodic memory) may rely more heavily on specific representations (e.g., complex configural representations supported by the hippocampus) than other representations.

Learning outcomes


After the lecture, the student will be able to:
  • Appreciate the distinction between process and representational accounts
  • Critically appraise evidence for and against these differing accounts

Key Reading


  1. Ranganath et al. (2001) Medial temporal lobe activity associated with active maintenance of novel information, Neuron, 31(5), 865-873.
  2. Hartley et al. (2007) The hippocampus is required for short-term topographical memory in humans, Hippocampus, 17, 34-48.
  3. Lee et al. (2005) Specialization in the medial temporal lobe for processing of objects and scenes, Hippocampus, 15(6), 782-797.
  4. Barense et al (2007) The medial temporal lobe processes online representations of complex objects, Neuropsychologia, 45(13), 2963-2974.

Further Reading

  1. Lee et al. (2008) Activating the medial temporal lobe during oddity judgement for faces and scenes, Cerebral Cortex, 18(3), 683-696.
  2. Wang et al. (2010) The medial temporal lobe supports conceptual implicit memory, Neuron, 68(5), 835-842.
  3. Schnyer et al. (2006) Rapid response learning in amnesia: delineating associative learning components in repetition priming, Neuropsychologia, 44(1), 140-149.
  4. Nadel & Hardt. (2011) Update on memory systems and processes, Neuropsychopharmacology Reviews, 36(1), 251-273.

Seminar 8 – The medial temporal lobe beyond episodic memory


In the last seminar, I present some of the studies I think are most interesting in relation to the medial temporal lobes – suggesting they play a role in episodic future thinking, scene construction, imagined navigation, decision-making, and moral judgements. For the second half of the seminar, the students split into groups and go over the 8 seminars discussing content they found most challenging. We then have a group revision session where I help to clarify any material they may not understand, or we discuss topics that they find particularly interesting. After this, they leave with smiles on their faces and lead productive, happy, successful lives (this has nothing to do with that fact they completed my module though).


Learning outcomes


After the lecture, the student will be able to:
  • Appreciate that the medial temporal lobes aren't solely a 'memory' structure
  • Evaluate research showing medial temporal lobe involvement in non-memory tasks
  • Discuss what role the medial temporal lobes play in our mental lives

Key Reading


  1. Addis et al. (2007) Remembering the past and imagining the future: Common and distinct neural substrates during event construction and elaboration, Neuropsychologia, 45(7), 1363-1377.
  2. Hassabis et al. (2007) Patients with hippocampal amnesia cannot imagine new experiences, Proceedings of the National Academy of Science, 104(5), 1726-1731.
  3. Wimmer et al. (2012) Preference by association: How memory mechanisms in the hippocampus bias decisions, Science, 338(6104), 270-273.

Further Reading


  1. McCormick et al. (2016) Hippocampal damage increases deontological responses during moral decision making, Journal of Neuroscience, 36(48), 12157-12167.
  2. Zeithamova et al. (2012) Hippocampal and ventral medial prefrontal activation during retrieval-mediated learning supports novel inference, Neuron, 75(1), 168-179.
  3. Horner et al. (2016) Grid-like processing of imagined navigation, Current Biology, 26, 842-847.

Areas not currently covered (but could be)


The module is necessarily selective, and there are some topics I would like to cover but don’t feel I have the time. These include:

  • Systems consolidation – we mention this in passing, but don’t cover it systematically. However, there is another advanced module that focusses on sleep and memory, so if I were to include it there might be too much overlap between modules.
  • Brain networks – the module is heavily focussed on the medial temporal lobes. That partly reflects my research interests, but it also reflects my desire for the students to focus more on the broader theoretical questions (e.g., process vs representational accounts) as opposed to the neuroscience.
  • Memory and emotion – this is a big topic, but one students would definitely find interesting. If students are taking this module as part of a Masters level degree, they do have the option of reading some of this literature.
  • Hippocampal longitudinal axis – the module focusses on hippocampal subfields at the expense of the anterior-posterior axis of the hippocampus. As in (3), if students are taking this module as part of a Masters level degree, they do have the option of reading some of this literature.
  • Forgetting – this reflects my own shifting research interests but forgetting is a fascinating topic with a rich psychological and neuroscientific history.


I’m sure there are other topics as well, but these are the ones I have thought about including previously. As above, if you have any thoughts or suggestions, feel free to email me. I think that just about covers it. I hope this is useful to some – possibly just as a way of figuring out what NOT to teach. Happy teaching to you all.

Monday, 26 March 2018

Excuses for not taking extended paternity leave


Men usually get 2 weeks of paternity leave in the UK. Most men I know have taken this leave when their child was born, and gone straight back to full time work following this. Perhaps they took holiday days following this when needed. This compares to women who are allowed up to 1 year of maternity leave (pay depends on your employer, but typically decreases over this time and the final 3 months are usually unpaid). Most women I know have taken somewhere between 6 months to 1 year, with 9 months being quite common. It goes without saying that this results in a big difference in parental roles in the first year of a child’s life in the UK, with a host of demonstrable knock-on effects in terms of career progression and pay that can last a lifetime.

There is provision for men to take off more time, through shared parental leave. This has been available since 2015, and allows the couple to share up to 50 weeks of leave in a relatively flexible manner. I am currently 1 month into a 3-month stint of parental leave (from 9 months to 1 year) and my wife went back to work at 9 months. However, I know few men who have committed to more paternity leave than the usual 2 weeks despite this legal entitlement.

Below is a list of a few “excuses” that I have heard in relation to this. A few caveats first though. First, I am assuming you are committed to equality between men and women. If you’re not, take a long walk off a short pier. Second, I am writing as someone in a heterosexual relationship, to other men in a similar relationship. This is because it is what I have experience with, and it’s probably where most change needs to occur in terms of questioning gender roles. Third, I am presuming you are eligible for shared parental leave in the UK. If you’re not, this is a pretty good excuse for not taking shared parental leave. Finally, this is not meant to be judgmental, or if it is I apply it equally to myself as well as others. I think I have probably used most of these excuses either implicitly or explicitly when making decisions about the length of my paternity leave for both my daughters (~2 months for the first on a relatively ad hoc basis, 3 months for the second). Finally, some of these excuses are legitimate in certain situations, which is perhaps why they are easy to use as a post hoc way of justifying your decision. The point of this list is to identify these common excuses so we can question them more thoroughly next time we’re making a decision.

1. I didn’t know I could
This one is easy to deal with. It isn’t an excuse. If you wanted to take extended paternity leave, you would have googled it. Ignorance isn’t an excuse.

2. It isn’t part of my work culture
You happen to be in a job where men don’t typically take long periods of paternity leave? What are the chances of that happening? Well, fairly high given that’s the current norm in UK society. I would ask yourself two questions though: (1) do I think this culture should change, and (2) have I previously pushed for change at work in other ways (not related to paternity leave)? If you answered yes to both of these questions, or just yes to the first one, then perhaps you’re realising this isn’t a great excuse either. You are legally entitled to shared parental leave. The only way it becomes part of work culture is for men to start taking advantage of this opportunity.

3. I earn more than my wife
So what? If anything, this is a reason to take more time off, so maternity leave has less of an effect on your wife’s pay packet. You taking time off might help to redress the balance, or at least not exacerbate it.

4. We can’t afford it
This may be a completely legitimate excuse. However, it’s still important to question this. For example, you are presumably already taking a financial hit with your wife being on maternity leave. Why did you decide this was affordable but you taking time off wasn’t? Did you sit down and carefully do the sums, or did you decide relatively quickly that whatever financial cost associated with your wife taking maternity leave was worth the sacrifice but somehow it wasn’t with you taking time off?

This obviously interacts with excuse 3. If you earn more, you will take more of a financial hit by taking time off. However, it might be worth asking why you are earning more. Did your wife not apply for that dream job during early pregnancy because she had better maternity cover at her current job? Did you move city for your job and not hers even before you were considering having children?

5. It would affect my career progression
Good. It’s about time men risked taking a hit, given the sacrifices women have been making in terms of career progression and pay. Ultimately though, I think it unlikely that (e.g.) 3 months away from work is really going to have a massive effect on your career. The mere fact that you are having a child is going to affect your career in some way, so taking a bit of time off isn’t going to make things much worse. A related excuse is "it's not a good time career-wise". It never is, get over it.

6. My wife wants to take the full year of maternity leave
This is a trickier one. I completely understand why someone might want to take a full year of maternity leave (leaving you with no “shared” time to take off). There are a few things to ask though. First, how much of this desire is based on societal expectations? I have seen pregnant women questioned when they say they’re planning on taking “only” 6 months off. Second, do you always acquiesce to your wife’s wishes, or do you typically talk things through and arrive at a mutual decision that takes into account both your wishes? I would hope that any equal partnership would be able to deal with this amicably, and your wife would be able to see the positives in you spending more time with your child.

7. I’m scared, and not very good at looking after my baby
It’s OK to be scared. I was terrified when I made the decision. You have to make it relatively early on though, and then by the time it comes around you’re already committed so can’t do anything about it. You will mess things up. You will find it hard. You will find it rewarding though, and you will enjoy yourself (at least some of the time).


***EDIT***
I'll keep adding to the list based on suggestions from Twitter.

8. My wife is breastfeeding our baby
Thanks to Catherine Manning and Jenni Rodd for pointing this out. This is potentially a good excuse for not taking paternity leave early in the first year, but doesn't apply as much to taking time off later in the year. This can certainly make things logistically difficult if your wife is still breastfeeding when she goes back to work. There are ways around this though. I have talked to female colleagues who have gone back to work relatively early. They have got by through pumping as well as the man bringing the child to work once a day to be breastfed. As I said, logistically difficult but not necessarily a deal breaker. If this just isn't feasible, consider taking the final few months off, where your child is likely to be eating mostly solids and can much more easily be fed occasionally with a bottle. 

Thursday, 12 October 2017

Being an academic

This blog post was prompted by a long twitter conversation on science careers, number vs quality of publications, and the inevitable inclusion of the term ‘glam mags’. Although twitter is great for an immediate exchange of ideas, it isn’t good for nuance. Here are some of my thoughts on a career in academia.

First, if you want to be an academic in the long-term, you probably can be. It may not be the academic career you dreamt of, or at the university you wanted to be at. You may not be teaching exactly what you want. You may not have much time for research at all. However, if you decide to be an academic, you work hard, and you aren’t precious about your definition of ‘success’, then it’s a career like any other. There are plenty of people out there without glittering CVs who are grafting and getting by, but ultimately are fully fledged academics who do amazing jobs day-after-day for little praise or reward.

Much of the conversation on twitter relates to academic ‘success’ rather than simply what it takes to be an academic long-term. People obviously have high expectations, and want to be successful. I get that. I want to do amazing science with clever supportive colleagues, teach happy engaged students, and have a vibrant well-funded lab. Where I think there might be an issue is the expectation that this is what it means to be an ‘academic’. To me, this is what it means to be a high-flying successful academic. None of us have a right to expect such a career. I am grateful that I have a good solid job in a university I like. If I have success over-and-above this, it is a massive bonus. I will of course be under pressure from those above me to be that high-flying academic, and I will work towards that as best as I can, but I can’t expect it and it certainly isn’t a right.


So what is my advice to those more junior than myself? During your PhD, do the best possible science you can and try to ensure you publish at least one good solid paper. This is clear evidence that you can push a project from start to finish, and that you have developed a set of experimental/methodological skills. If you feel you have time, apply for fellowships that might propel your career into the stratosphere, but don’t bank on it. Concentrate on finding a postdoc in a lab where you feel you would fit in, you can further your skills set, and you can do good science. Join twitter and read conversations about careers, glam mags, etc. but don’t let it get under your skin. Understand the system you are trying to navigate, but appreciate that there is a huge amount of inherent noise such that there is no one-size-fits-all recipe for career success. Most importantly, enjoy yourself as much as possible. If you do commit to academia and don’t get that dream job, you will probably look back on your PhD and postdoc positions rather fondly. If you do stay in academia though, well done you. Regardless of what your CV looks like, you’re a success.

Friday, 16 December 2016

My first year as a lecturer (actually 11 months)

A few months ago I blogged about my first 6 months as a lecturer. This is the (almost) one year since starting follow up. Last time I confessed to feelings of loneliness as I was tasked with writing grants and setting up a lab before the teaching and administrative load started to ramp up. Well, the latter has now happened. I have been given a relatively substantial administrative position (though certainly not the most arduous) and although I am yet to deliver lectures, this term I have dedicated a significant amount of time to activities related to teaching. This means I have had virtually zero time to do research, but all is not lost on this front (see good news below).

Administratively I am now “strand-leader” of the neurosciences strand of the Natural Sciences programme at York. This does take up a reasonable amount of time, but certain aspects of the job are actually quite fun. I have spent several afternoons interviewing incredibly bright A-level students (most are expected to get straight A/A*s), asking them about their scientific interests and trying to get them to think laterally about topics/questions they may not have encountered before. The sheer enthusiasm of many of these students is tonic for the soul. On the other hand, I had to sit through a 3 hour board of studies meeting the other day.

Teaching this term has consisted of supervising “literature surveys” – talking to final year students in small groups (~7) about their topic of interest, helping them frame their specific question/topic, and providing feedback on their plans. I have also started to supervise 3rd year empirical projects, though the bulk of that occurs next term. Finally, as I am teaching two modules next term, I have spent a considerable amount of time reading around certain topics, and preparing lectures. This can be rewarding as it forces you to go back to basics in a particular area, but it is hugely costly in terms of time and is relatively open-ended. As a new lecturer how do I know when I have read “enough” to teach the topic to 2nd or 3rd year BSc students? My conclusion was if I care enough to worry about it, I’m conscientious enough to do a good job, but time will tell.

Finally, although I currently have very little time for research, I am fortunate in that I managed to secure a (smallish) grant to employ a postdoc over the next 2 years. That, alongside a PhD student who started in October, means data will be accruing whilst I am teaching next term. It could be a lot worse, and to be honest it couldn’t get much better.

The contrast between the first and second 6 months has been stark. The increased administrative and teaching load has been a shock to the system, and for a 3-4 week period I really felt like I was drowning. I am just as busy now, but I seem to be learning to deal with it a bit better. I am getting better at trusting that I can get things done relatively last minute if necessary (this goes against my innate nature, so has been difficult to learn). The upside to this increased stress has been a sense of increased belonging. The negative way of putting this would be “siege mentality”, but I feel these is a sense of camaraderie with colleagues that I haven’t felt before. Alongside this is an increased awareness of the “big picture” - understanding how the university and department function and how the nitty-gritty of day-to-day teaching/research/administration works. This helps in generating distance from the minor setbacks one receives. As with last time, a few possible words of advice:
  1. If you have time before teaching starts, get grants in ASAP. Smaller ones in particular that have a faster turnaround time and potentially have a higher chance of success. Concentrate on getting money for personnel – having individuals to collect data will reap rewards when you’re teaching; an expensive bit of kit that you have no time to use won't.
  2. As I suggested last time, talk to colleagues as much as possible. Get their advice when you’re struggling. Ask questions about the department and how it functions. Turn up to meetings and talks. Become part of the academic community.
  3. Realise that your first lecture isn’t going to be perfect. Cover a sensible amount of material as clearly as possible. Don’t worry too much about whether the students walk away thinking you’re amazing. Make sure they have learnt something in the 1-2 hours you have with them.
  4. Accept that you won’t have control of everything at all times. Allow some things to slip if you have to. Prioritise your time as effectively as possible. It may feel like you’re constantly putting out fires (that’s certainly how I feel), but as long as nothing develops into an inferno then I count that as a success. 

Thursday, 7 July 2016

My first (almost) six months

In February I became a lecturer, with all that it entails. I have a permanent contract, I have responsibilities, I have my own office, and I have undergraduates to teach. In short, things have changed. Given I am approaching the six month mark in my new job, I thought I would write a post reflecting on what I have done and what I have learnt. The short answer to both being: (subjectively) not very much.

First, what have I done? Or perhaps the more informative question should be: what should I have done? I am in the fortunate position that I have minimal teaching responsibilities until January 2017. I realise I am lucky in this regard. As such, I have been given the opportunity to set up my lab and get my research up and running unencumbered by the responsibilities associated with teaching.

I think my job at present broadly falls into three categories: (1) finish up postdoc work, (2) get new projects up and running and (3) apply for grants for future projects. As such, I have to balance demands from the past, present and future. Which one is more important? The simple answer is none. I have to try to make progress on all fronts in the long-run, but concentrate on one of these aspects in the short term to actually make some form of progress. I have tried to not make too many long-term “deadlines”, instead I simply try to come in everyday and get something meaningful done. If I’m feeling less inspired, I tackle easier jobs but still make sure I tackle them. If I’m feeling more inspired, I tackle harder jobs. It’s amazing how much you can achieve by simply getting stuck in. This approach has potentially worked. I have managed to resubmit a postdoc paper (now fully published), write and submit a short grant proposal, and collect some preliminary data on a more short-term research project. My hope is I can continue with this policy until the postdoc work tapers off over the next year.

One difficulty I found initially was actually getting started on a job. This was largely driven by the inevitable feeling of being alone relative to when I was a postdoc. I was accustomed to sharing an office with other postdocs and constantly discussing science. I was accustomed to having regular discussions with my PI about what I had done and what I was going to do. Despite the fact that I had relative freedom in my postdoc, the continual everyday input from other scientists shaped what I did on a day-to-day basis. I didn’t fully realise this at the time. Although my PI never directly told me what to do, I did not appreciate how much he steered me in the appropriate direction. I now have very supportive colleagues who I speak to regularly, but the onus is definitely on me to do what I think is best. Essentially I now have to fully rely on my frontal lobes to makes day-to-day decisions.

Although I am yet to fully immerse myself, the other stark contrast is the amount of administration involved in a faculty position. Again, as a postdoc I was relatively sheltered from the bureaucratic side of academia. Now, the small jobs, and associated paper work, are already starting to affect my day-to-day work schedule. No longer can I rely on my brain to remember all the small administrative jobs I am required to do and when I need to do them. This is before I have even been given a ‘proper’ administrative role in the department, such as contributing to a departmental committee. At present it feels a bit like the calm before the storm. I have the ominous feeling that things will only get worse. As such, I am trying to be much more organised, using Google Calendar to dictate what I need to do and when.

I sum, it’s been fascinating, overwhelming, scary, fun, boring, lonely, engaging, and many other adjectives. A bit like any other day in the life of an academic. Would I do anything differently? Probably not. It’s too early to tell whether I’ve made the most of my first 6 months, or whether I should have done things differently. Here’s a few thoughts that might prove useful to some though:

  1. Get stuff done. As academics we are prone to thinking things over and questioning ourselves. Don’t let this get in the way of doing something. Start a small experiment, analyse some old data. Just do something.
  2. Talk to others. Starting a faculty position can be lonely. Talk to as many colleagues as you can. Go for lunch, go for coffee, ask for feedback on a grant, discuss new experimental ideas. They went through the same process once, and know how difficult it can be. Ultimately, they want you to succeed just as much as you do.
  3. Act in the short-term but plan for the long-term. Think about big projects and grants. Mull over how different experimental ideas might fit into a larger question. Push ideas further than you have before. Thank bigger and longer-term than you did as a postdoc. But don’t wait around for grant money to start these projects. Don’t let (3) get in the way of (1).
  4. Don’t listen to me, I’ve only been in the job for less than six months.

Thursday, 22 October 2015

Computational modelling courses

Recently on twitter I asked for advice on computational modelling and/or computational neuroscience courses, in particular summer schools for early career researchers. I received quite a few suggestions so thought I would create a list for anyone else who is interested. Note, I only know about these courses through recommendations and/or the information on their website. For some, the link is for a previous years course, so I can't guarantee they are definitely still running. Still, I hope the list proves useful for some.

Computational modelling of cognition with applications to society

http://escop.eu/news/conferences-news/third-european-summer-school-on-computational-modeling-of-cognition-with-applications-to-society-/

Advanced course in computational neuroscience

http://www.accn.pt/venue/lisbon-portugal/previous-course-editions

Computational psychiatry course (Zurich)

http://translationalneuromodeling.org/cpcourse/

Computational psychiatry course (London)

https://sites.google.com/site/comppsychcourse/2015schedule

Summer school in computational sensory-motor neuroscience (CoSMo)

http://www.compneurosci.com/CoSMo/

Model-based neuroscience summer school

http://www.modelbasedneuroscience.com/

OIST computational neuroscience course

https://groups.oist.jp/ocnc

Brains, minds and machines

http://www.mbl.edu/education/special-topics-courses/brains-minds-and-machines/

Computational neuroscience and the hybrid brain

http://www.nncn.de/en/news/events/computational-neuroscience-hybrid-brain

ACT-R spring school and master class

http://act-r.psy.cmu.edu/?post_type=announcement&p=15589

If anyone else has further suggestions, I'm happy to continue to update this list. Just leave a comment with the link and name of the course.

Thursday, 2 July 2015

Research briefing: Evidence for holistic episodic recollection via hippocampal pattern completion


Horner, A.J., Bisby, J., Bush, D., Lin, W-J., & Burgess, N. (2015) Evidence for holisitic episodic recollection via hippocampal pattern completion, Nature Communications, 6:7462 doi: 10.1038/ncomms8462


Think back to your last birthday. Perhaps you were at home, eating good food. Perhaps you were in a pub, drinking good beer. Perhaps you were in a club, dancing to terrible music.

When we recall events like these from our past we are able to re-immerse ourselves in the experience, as if we were there once again. You might remember being in your dining room, eating birthday cake, whilst your friends sing happy birthday. You might even remember incidental details, like what you were thinking at the time or the music playing in the background. How do we remember and re-experience these complex events?

A long-standing theory, originally proposed by Marr but developed by many others, suggests that the individual elements of a complex event are represented in distinct neocortical regions. For example, the faces of our friends might be represented in visual regions in the ventral temporal lobe whilst the background music might be represented in auditory regions in the lateral temporal lobe. These distinct elements are thought to be bound in a single coherent memory – what Tulving referred to as an ‘event engram’. It is the hippocampus, receiving input from multiple neocortical regions (acting as a ‘convergence zone’ in the words of Damasio), that is thought to form these event engrams when we first experience an event.

What happens when remembering this event at a later date? Perhaps you meet a friend who attended your birthday party. This friend acts as a ‘cue’ to retrieve the previous event. Importantly, with a single cue we are able to retrieve the entire event. In this case, we see our friend and that enables us to remember the room we were in, our birthday cake, the background music etc. This retrieval of a complete memory from a partial cue is known as ‘pattern completion’ and is thought to be a key function of the hippocampus (and particularly subfield CA3 of the hippocampus). Following this pattern completion process in the hippocampus, all the retrieved elements are thought to be ‘reinstated’ in the neocortex. In other words, the same representations that were active when we first experienced an event become active at retrieval. It is this hippocampal pattern completion process, followed by reinstatement of all event elements in the neocortex, that is thought to underpin ‘recollection’ – our ability to subjectively re-experience a previous life event.

Despite a wealth of evidence for the involvement of the human hippocampus in episodic memory, and recollection in particular, evidence has not been presented for this pattern completion process in relation to the retrieval of complex events.

Participants learnt pairwise associations of locations (e.g., kitchen), famous people (e.g., Barack Obama), objects (e.g., hammer) or animals (e.g., dog). Importantly, each pairwise association overlapped with other associations, forming complex ‘associative structures’ (see Figure 1). For example, you might learn ‘Kitchen-Obama’ on one trial, ‘Obama-hammer’ on a second trial and ‘hammer-kitchen’ on a third trial. As such, we build relationships between multiple elements across separate encoding trials. This is an example of a ‘closed-loop’ structure, where each element is paired with each other element (forming a triangle of associations). This closed-loop condition is compared to ‘open-loop’ structures, where a chain of three associations is formed between four elements (see Figure 1). Importantly, both conditions are formed from three pairwise associations across three encoding trials. Participants are asked to vividly imagine the two elements for each association ‘interacting in a meaningful way’.



At retrieval we tested each pairwise association. For example, we cued with ‘Obama’ and participants were required to retrieve ‘kitchen’. They were shown six elements of the same type (locations in this example) and asked to select the element (kitchen) originally paired with the cue (Obama). The retrieval trials were identical for both the closed-loop and open-loop condition.

How does this allow us to look for pattern completion? If pattern completion is present then when retrieving a single element, all other elements should also be retrieved. In our example, when cued with ‘Obama’ and retrieving ‘kitchen’ the object associated with these two elements (‘hammer’) should also be retrieved. This is despite ‘hammer’ being task-irrelevant during this trial.

This retrieval should have behavioural consequences – retrieval accuracy for any two elements within an event should be related (called ‘behavioural dependency’). If you successfully retrieve ‘kitchen’ when cued with ‘Obama’, you should be more likely to retrieve ‘hammer’ when cued with ‘Obama’. This is because your retrieval success for one element is based on the strengths of all the associations for a single event. We provide evidence for this ‘behavioural dependency’ in our closed-loop, but not open-loop, condition (see Figure 2). This suggests, despite their similarity at both encoding and retrieval, that pattern completion is present in the closed-loop but not the open-loop condition.

If pattern completion is present in the closed-loop condition we should see reinstatement of all elements in the neocortex – including the ‘non-target’ element. Using fMRI, we identified neocortical regions associated with the encoding/retrieval of individual elements. Locations were associated with the parahippocampal gyrus, famous people with the medial prefrontal cortex and objects/animals with lateral occipital cortex. We next looked for ‘reinstatement’ of non-target elements. If cuing with a location, and retrieving a person, we should also see reinstatement in the region associated with objects/animals. We found greater activity in non-target regions for closed-loops relative to open-loops, again consistent with pattern completion in the closed-loop but not open-loop condition (see Figure 3). Importantly, we also show this ‘behavioural dependency’ and retrieval of non-target element in a computational model of the hippocampus (an attractor network model), further demonstrating the presence of pattern completion in the closed-loop but not the open-loop condition.

Finally, we correlated this ‘non-target’ reinstatement with the BOLD response across the whole brain to see what other regions correlated with reinstatement. This revealed the hippocampus (see Figure 4). The BOLD response in the hippocampus correlated (across participants) with the amount of neocortical reinstatement for the non-target element. This result supports the idea that the hippocampus is performing pattern completion, retrieving all event elements, allowing for the reinstatement of these elements in the neocortex.

What is critical to our study is that we always compare the closed-loop relative to the open-loop condition. In both conditions participants have learnt a series of overlapping pairwise associations and are successfully performing pairwise associative retrieval. As such, all our results are related to processes over-and-above simple pairwise associative retrieval. It is this careful experimental design that we believe is critical to our ability to infer the presence of pattern completion in our data.

To summarise, we have presented behavioural, computational modelling and fMRI evidence for hippocampal pattern completion and neocortical reinstatement in humans, and related these processes to the retrieval of complex events. We believe this is the first evidence to support a long-standing mechanistic account of recollection – our ability to subjectively re-experience previous life events.