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 (firstname.lastname@example.org) 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.
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.
When I submit my work, all of the variables at play, including the quality of the thing being judged, combine to give me a probability that a positive outcome will occur e.g. 0.4 – 2 out of 5 times, a good thing will happen. BUT, probabilities produce lumpy strings of outcomes. That is, good and bad outcomes will appear to us pattern-spotting humans to be clustered, rather than what we would describe as “random”, which we tend to think of as evenly spaced (see the first link above).
To illustrate, I did something very straightforward in Excel to very crudely simulate trying to publish 8 papers.
Column A: =RAND() << (pseudo)randomly assign a number between 0 and 1; in the next
Column B: =IF(Ax>0.4, 0,1) << if the number column A (row x) exceeds .4, this cell will equal 0, otherwise it will equal 1.
Thus, column B will give me a list of successes (1s) and failures (Os) with an overall success rate of ~.4. It took me four refreshes before I got the following:
Although the rejections look clustered, they are all independently determined. I have almost certainly had strings of rejections like those shown above. The only thing that has made them bearable is that I have switched papers, moving on to a new project after ~3 rejections, at the same time giving up on the thrice-rejected paper I assume to be a total failure. As a result, I am almost certainly sitting on good data that has been tainted by bad luck.