Here’s an official announcement that I will no longer be maintaining this blog. ‘Official’ because the blog hasn’t seen an update in a long time. This is just the full stop that ends the sentence.
Blogging has been a valuable exercise for me. An exercise that started during my postdoc in St Louis, and continued through setting up and establishing my own lab in St Andrews. I always intended it to be a series of notes to myself that I could make public for others to benefit from. This, from the first post in 2010:
I hope that this blog helps me to gather to one place many of the bits and pieces, both on- and off-line, that have helped me over the past couple of years. I also hope that I get into the habit of updating it in a way that is useful when I need to find out how I tackled a particular problem in the past, or even when I simply need to find a web-site I know was previously useful to me. If it proves to be useful to anyone else in the process, then that will be a marvelous outcome too.
There are still times when I google an SPM error, to find the top hit from my own blog on how I overcame it years before. Judging by the emails I also still receive about historic blog posts, I think the blog has served its purpose of being useful to others. Marvelous.
You’ll still find me on twitter: @akiraoc, and I’ll keep updating the various non-blog pages on this site. Here though, I’ll end with some posts that, for all sorts of different reasons, remain particularly important to me.
In recent years, déjà vu has become of great interest in cognition, where it is mostly seen as a memory illusion. It can be described as having two critical components: an intense feeling of familiarity and a certainty that the current moment is novel. As such, déjà vu could be described as a dissociative experience, resulting from a metacognitive evaluation (the certainty) of a lower-level memory process (familiarity). There are currently a number of proposals of how déjà vu arises which receive empirical support from paradigms which attempt to reproduce déjà vu in laboratory settings. Further information about déjà vu comes from neuropsychological populations and the use of neuroscientific methods, where again the focus is on memory, and in particular the involvement of temporal lobe structures. In this Special Issue, we will draw together the state of the art in déjà vu research, and develop and evaluate the idea that déjà vu can be seen as a momentary memory dysfunction. We are seeking empirical papers and brief theoretical statements which consider the nature of déjà vu and how it may be induced experimentally, as well as studies of déjà vu in pathological groups, and studies investigating the neural basis of déjà vu. We are also interested in associated dissociative phenomena, such as jamais vu, presque vu, prescience and other metacognitive illusions, where their relation to contemporary memory theory (and déjà vu) are clear.
We will consider all types of empirical article, including short reports and neuropsychological cases. Theoretical statements and reviews should make a genuine novel contribution to the literature. First drafts should be submitted by the end of July 2017 through the Memory portal, https://mc.manuscriptcentral.com/pmem, please select special issue ‘Deja vu’. All submissions will undergo normal full peer review, maintaining the same high editorial standards as for regular submissions to Memory.
If you are considering submitting an article please contact one of the editorial team stating the title of you intended submission.
A happy consequence of the media exposure I have received is that all sorts of people contact me when they have questions about déjà vu. Often, people want to find out about personal experiences they or those they know have had, but every now and again, school students will contact me for help with their projects.
One student who contacted me earlier this year was Cyril Vivek Subramanian, from Sydney. Cyril Vivek was researching a video to enter for the University of Sydney Sleek Geeks Science Eureka Prize, and I had a couple of conversations with him and his mother via email and Skype to help him with this. He was keen to do a lot of background research himself, and I found myself thankful for being able to refer him to the Frontiers for Young Minds article I’d previously written with Julia Teale.
The video didn’t end up being shortlisted, but I was thoroughly impressed with it, and delighted to be able to share it here. It is always great to be able to guide and work with young people, and a privilege to see students like Cyril Vivek excited about science and able to communicate it so well. Bravo!
At the International Conference on Memory last month, I presented some new work from my lab, a 21 participant, fMRI-scanned, memory experiment. We imaged people’s brains as they underwent a procedure that generates sensations likened to déjà vu (based on Josie Urquhart’s procedure, published in 2014, that you can find here). What makes this work particularly exciting is that, to our knowledge, this is the first time people undergoing an experimental analogue of déjà vu have been imaged. It lead to some pretty neat results.
Embedded within that article is the following video, which distills the essence of what we’re excited about – brain regions associated with memory conflict, rather than false memory, appear to be driving the déjà vu experience. This is consistent with our idea of deja vu as the conscious awareness of a discrepancy in memory signals being corrected. This in turn sheds some light on why déjà vu occurrence appears to decline with age despite the fact that memory errors tend to increase with age. If it’s not an error, but the prevention of an error, this makes a lot more sense.
A few other news organisations have since reported the story:
Is it possible to reliably generate déjà vu in participants? Is it possible to get participants to reliably report déjà vu? These very similar questions are not necessarily as closely linked as we might think.
A paper I wrote with Radka Jersakova (@RadkaJersakova) and Chris Moulin (@chrsmln), recently published in PLOS ONE, reports a series of experiments in which we tried to stop people reporting déjà vu. Why? Because even in simple memory experiments that shouldn’t generate the sensation, upwards of 50% of participants will agree to having experienced déjà vu when asked about it. On the one hand, it’s a pretty strange set of experiments in which we are chasing non-significant results. On the other, it’s really important for the field of subjective experience research. If we can’t reliably assess the absence of an experience, how can we trust reports of its presence (OR if your null hypothesis isn’t a true null, don’t bother with an alternative hypothesis)?
Over the past couple of days, I have been archiving published fMRI projects, and copying data from SD cards to start new ones. I have written previously about ways in which I have copied and verified copied files, and this is a quick update to that post to document another tool for verifying copies.
As far as the copying itself is concerned, I still swear by Teracopy. As far as verifying that copies have been successfully made though, I have recently started using Exactfile. The tagline “Making sure that what you hash is what you get” sums up the procedure for using Exactfile, once you have installed it on a Windows machine.
Create a single file checksum, or, if you are comparing all the files and subfolders within folders (even massive folders containing gigabytes of fMRI data) a checksum digest (illustrated above). This will be saved as a file using which you can…
Test your checksum digest. You locate your digest file and the copied data you wish to compare against the checksums, and it runs through making sure each file is identical.
That’s it – pretty straightforward. Step 1 takes a little longer than Step 2, and if you’re comparing hundreds of thousands of files, you should prepare to have this running in the background as you get on with other stuff.
Please email (email@example.com) or tweet (@akiraoc) me if you’d like to speak more about this project. If you’d like to speak to anyone about doing a PhD with me, please get in touch with Mags Pitt (3rd yr PhD), Bjorn Persson (3rd yr PhD) or Ravi Mill (completed PhD) via the People section of the blog.
BBSRC Theme: Word class underpinning Bioscience
Adaptive cognition involves both the completion of a set of mental operations and the awareness that these operations have been completed so that the next stage of cognition can be engaged. During successful memory decision-making these two steps, memory retrieval and retrieval awareness, go hand in hand. However, they can occasionally fragment, leading to a set of experiences termed introspective memory phenomena (IMPs; e.g. déjà vu and jamais vu). During déjà vu positive retrieval awareness arises in the absence of true retrieval, yielding the overall sensation of inappropriate familiarity (O’Connor & Moulin, 2010). Jamais vu is the opposite–negative retrieval awareness in the presence of true retrieval. IMPs signal conflict within the cognitive system, and thus may play a crucial role in error correction (we do not act on IMPs in the way that we do act on false memories). However, beyond some curious demographic associations (they occur more in those who are well-travelled and well-educated), IMP occurrence is not known to be associated with any existing cognitive or psychological traits.
IMPs are not experienced uniformly across the population but peak in those in their mid-20s, before declining with age thereafter. They are also thought to be driven by dopaminergic over-activity such that some pharmacological and recreational drugs (e.g. dopaminergic flu medications) have been reported as causing persistent déjà vu (Taiminen & Jääskeläinen, 2001). Interestingly, these characteristics mirror what is known about neurophysiological markers of inhibitory control and response monitoring more generally (e.g. Strozyk & Jentzsch, 2012), which show the same lifespan trajectory with an age-related decrease in the dopaminergic functions mediated by the frontal cortex. These links suggest that IMP occurrence may be underpinned by basic neurocognitive characteristics integral to healthy cognition. Thus, the importance of IMPs may not lie in the fragmentation of the memory decision-making system, but in the capacity for our response monitoring systems to detect it and stop us making decisions based on faulty information.
We propose a systematic programme of research to establish the role of error-monitoring in the generation of IMPs. Using i) retrospective questioning to verify the recent occurrence of IMPs and ii) established procedures for their laboratory generation, we will explore individual differences in IMP experience and neurophysiological markers of response monitoring. These experiments will be a) developed in young adults and extended to b) primary school children (age 8-11; the age at which IMPs are first reported by children) and c) older adults (age 55 and older). We will also conduct opportunistic case-studies on d) patients who present themselves to Dr O’Connor over the course of the PhD (UK-based patients typically get in touch at a rate of 1-2/year). This systematic programme will allow us to establish any potential links between basic neurocognitive characteristics and the tendency to experience dissociative memory sensations which are not known to have any other psychological correlates.
This project will benefit from the joint multi-disciplinary expertise of Dr O’Connor, an internationally recognized expert in the area of metacognition and introspective memory phenomena and Dr Jentzsch, a biophysicist and electrophysiologist by training, who specialized in studying the neural underpinnings dopaminergic functions such as action and conflict control. Together, we will provide the prospective student conceptual knowledge of metacognitive models of memory and changes to these functions with healthy ageing integrating behavioural methods and physiological measures of brain function in humans. The student will learn about experimental design, programming (Matlab), data collection and behavioural analysis techniques such as signal detection theory. In addition, the student will learn how to design, conduct and analyse electrophysiological experiments using EEG. Acquisition of generic skills such as team-working, time-management and communication skills amongst many others will also be an important part of the students training.
This project is eligible for the EASTBIO Doctoral Training Partnership: View Website
This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body.
Apply by 5.00pm on the 14th December 2015 following the instructions on how to apply at: View Website
Informal enquiries to the primary supervisor are very strongly encouraged.
O’Connor, A.R. & Moulin, C.J.A. (2010). Recognition without identification, erroneous familiarity, and déjà vu. Current Psychiatry Reports, 12(3), 165-173.
Strozyk, J.V. & Jentzsch, I. (2012). Weaker error signals do not reduce the effectiveness of post-error adjustments: Comparing error processing in young and middle-aged adults. Brain Research, 460, 41-49
Taiminen, T. & Jääskeläinen, S.K. (2001). Intense and recurrent déjà vu experiences related to amantadine and phenylpropanolamine in a healthy male. Journal of Clinical Neuroscience, 8, 460-462.
The Journal of Cognitive Neuroscience have just invoiced me $985 for a paper they agreed to publish earlier this year. This wasn’t unexpected – not only did we sign away our copyright, allowing MIT Press to make money from our work, but we did so knowing that we would pay a hefty sum to allow them to do this. It still came as a bit of a shock though.
Paying the invoice will curtail some of my research activities next year, like going to conferences to present data. I put this to the journal, asking if they’d hear my case for a reduction or a waiver. Here’s their response:
JOCN does not provide fee waivers. Page costs are stated on the submission guidelines page, as well as on the last page of the online manuscript submission so that all authors are aware of the financial obligation required if your paper is accepted for publication. These fees pay for the website, submission software, and other costs associated with running the journal. If you are unable to pay the page fees, please let us know so that we can remove your manuscript from the publication schedule.
Journal of Cognitive Neuroscience
What did I expect though? We willingly submitted to this journal knowing that they would charge us $60 per page. And the Journal of Cognitive Neuroscience certainly isn’t alone in doing this. Most cognitive neuroscience journals are pretty good at making money out of authors (see table below – I haven’t included OA megajournals in the table). Imagers tend to have money and junior imagers, like all junior academics, still need to publish journals that have a reputation.
For what it’s worth, Elsevier journals keep their noses pretty clean. Cerebral Cortex’s publishing house Oxford Journals though… pretty much every stage of that process is monetised. Just. Wow.
Journal of Neuroscience
Neuroimage / Cortex / Neuropsychologia
Journal of Cognitive Neuroscience
Cognitive, Affective and Behavioral Neuroscience
Society for Neuroscience
Taylor & Francis
6.13 / 6.04 / 3.45
Open Access Supplement
2200 / 2200 / 1800
Black and white figures are without cost in all the listed journals. IF is Impact Factor. The paper for which the 'Our paper' costs are calculated had 3 authors, 16 pages, 3 colour figures, and no Open Access Supplement.
* There is a one-off charge for all colour figures, regardless of number.
This is a guest post from Radka Jersakova (@RadkaJersakova), who did her undergraduate degree in my lab and is now working on her PhD at the University of Leeds. Radka has previously written on this blog about how to conduct online studies. Here she discusses the merits of travelling during your doctoral training.
I am writing this as I near the end of the second lab visit abroad of my PhD. While I know many students who like me have managed to acquire the ‘visiting scholar’ status on extended lab visits, the number is far smaller than I believe it should be. This is even though visiting other labs and collaborating with other researchers, having external input into the work you are doing and having an idea what others in your field are doing right now is invaluable. It doesn’t matter if it is a visit of few weeks or few months; either way it is worth it and a lot easier to make happen than you would expect. Researchers are mostly very open to hosting and there is a lot of support and funding for such visits. It is a great learning experience and it makes academia seem smaller and friendlier. There are also the practical benefits such as having a travel grant on your CV, being able to show that you are capable of forging international collaborations and increasing the opportunity of knowing someone with post-doc funding.
The purpose of this post is to address the question of how one goes about organizing a visit of any length to another lab (ideally abroad although it doesn’t have to be!). However, the motivation for writing anything on this topic at all is to encourage PhD students – especially at the beginning of their studies – to consider in what ways can they make the most of it and travelling is definitely one way to do that.
WHAT TO DO AND HOW LONG TO GO FOR
The obvious first step is deciding what would you like to get out of a visit to another lab. This can be as generic as ‘networking’ or as specific as learning a particular analysis method. Ideally a visit should involve a collaboration of some kind although whether the visit should be used to plan a project or to actually carry out the data collection and analysis is open to discussion. This will naturally determine how long the visit is. Ideally, you’d look for funding to finance the type of visit you have in mind but sometimes the funding sources available to you might shape – to an extent – how long a visit you undertake. Some of the funding opportunities outlined below are aimed at visits of 6 months or longer; others at 2-3 months and a few start at a couple of weeks. As such it is important to know from the start what options are available to you.
WHERE TO GO
Most commonly, students make use of their supervisor’s network. This is by far the easiest way to organize a visit as it builds on collaborations that already exist. It is also the best way to identify a researcher with relevant experience to help you develop new ideas in the context of the topic of your thesis. As such, the first step is talking to your supervisor; they might already have someone in mind and can initiate the contact.
It is also possible there already is a researcher that you want to work with for an extended period. If you are going to a conference and they are going as well, try to talk to them there. You can contact them before the conference to suggest you meet to discuss your work with them. Having met them in person makes it much easier to talk to them about visiting their lab. If there isn’t an opportunity to meet in person, it is also fine to email the researcher you are interested in working with and ask them whether this could be arranged.
There is more funding available for research visits than might seem at first. Below is a list of some useful starting places for researching funding options. Everyone’s background is unique and the opportunities will vary accordingly.
(i) Funding organizations: It is very likely the organization or research council funding your PhD also has funding for travel visits. What is more, they are probably very keen to fund such a visit. The Economic and Social Research council in the UK is a great example of this as they place great emphasis on international research links through their Overseas Institutional Visits scheme.
(ii) Universities: There is a chance that the institution you want to visit has a ‘visiting scholars’ program that you can apply for to fund the visit. Similarly, your own institution might have ‘travel abroad’ schemes with funding for going abroad to an institution of your choice. Further, there are partnership networks between universities that also offer funding. An example is the Worldwide Universities Network which supports mobility for students and researchers between its partner institutions. It is best to ask your university or someone in the department whether you belong to one.
(iii) National grants: Some countries have grants for their nationals to go on study visits – a great example is the German Academic Exchange Service, which also offers a lot of support for international students to come to Germany. Similarly, France funds visits of 6-10 months to any of its institutions through the Eiffel Excellence Scholarship. There are also bilateral agreements between countries to fund exchanges such as the Fulbright Commission which focuses on mobility between the US and (according to their website) a list of more than 155 countries.
The key thing is to give yourself enough time to plan a visit. It is important to have an idea of what funding is available to you, when the funding deadlines are, what the application process is like, what documents you need, and what the interval is between submission and final decision.
We had an fMRI paper accepted to the Journal of Cognitive Neuroscience earlier this week. Having got the science out the door, I was able to turn my attention to the fun stuff – a cover image. The cover image for my first fMRI publication was selected by the Journal of Neuroscience and I wanted to go with something similar.
In the past 6 months or so, @alby has tweeted some of the images he generated using @lowpolybot, a twitter bot that returns low-polygon renderings of images tweeted to it. I tweeted a figure from the accepted paper to @lowpolybot and got this back:
There are a range of operations @lowpolybot can perform on your images (detailed on the @lowpolybot tumblr), but if you give no instructions you will get a random combination of operations applied to your image. This was what I had done. I was happy with the picture so, having checked with @lowpolybot’s creator @quasimondo that he was happy for me to do this, I submitted it to the journal.
Sadly though, there’s no chance this image will b e used as a cover image. I received an email the next day from a journal administrator informing me that they have stopped printing cover images. Ah well.