Top 200 terms in cognitive neuroscience according to neurosynth

Tonight I was playing around with some of the top features in neurosynth (the searchable terms with the highest number of studies containing that term). You can find the list here, just sort by the number of studies. I excluded the top 3 terms which are boring (e.g. “image”, “response”, and “time”)  and whose extremely high weights would mess up the wordle. I then created a word-cloud weighted so that the size reflects the number of studies for each term.

Here are the top 200 terms sized according to number times reported in neurosynth’s 5809 indexed fMRI studies:

wordle

Pretty neat! These are the 200 terms the neurosynth database has the most information on, and is a pretty good overview of key concepts and topics in our field! I am sure there is something useful for everyone in there 😀

Direct link to the wordle:

Wordle: neurosynth

Surely, God loves the .06 (blob) nearly as much as the .05.

Image Credit: Dan Goldstein

“We are not interested in the logic itself, nor will we argue for replacing the .05 alpha with another level of alpha, but at this point in our discussion we only wish to emphasize that dichotomous significance testing has no ontological basis. That is, we want to underscore that, surely, God loves the .06 nearly as much as the .05. Can there be any doubt that God views the strength of evidence for or against the null as a fairly continuous function of the magnitude of p?”

Rosnow, R.L. & Rosenthal, R. (1989). Statistical procedures and the justification of knowledge in psychological science. American Psychologist, 44, 1276-1284.

This colorful quote came to mind while discussing significance testing procedures with colleagues over lunch. In Cognitive Neuroscience, with it’s enormous boon of obfuscated data, it seems we are so often met with these kinds of seemingly absurd, yet important statistical decisions. Should one correct p-values over the lifetime, as often suggested by our resident methodology expert? I love this suggestion; imagine an academia where the fossilized experts (no offense experts) are tossed aside for the newest and greenest researchers whose pool of p-values remains untapped!

Really though, just how many a priori anatomical hypothesis should one have sealed up in envelopes? As one colleague joked, it seems advantageous to keep a drawer full of wild speculations sealed away in case one’s whole-brain analysis fails to yield results. Of course we must observe and follow best scientific and statistical procedures to their maximum, but in truth a researcher often finds themselves at these obscure impasses, thousands of dollars in scanning funding spent, trying to decide whether or not they predicted a given region’s involvement. In these circumstances, it has even been argued that there is a certain ethical need to explore one’s data and not merely throw away all non-hypothesis fitting findings. While I do not support this claim, I believe it is worth considering. And further, I believe that a vast majority of the field, from the top institutions to the most obscure, often dip into these murky ethical realms.

This is one area I hope “data-driven” science, as in the Human Genome and Human Connectome projects, can succeed. It also points to a desperate need for publishing reform; surely what matters is not how many blobs fall on one side of an arbitrary distinction, but rather a full and accurate depiction of one’s data and it’s implications. In a perfect world, we would not need to obscure the truth hidden in these massive datasets while we hunt for sufficiently low p-values.

Rather we should publish a clear record, showing exactly what was done, what correlated with what, and also where significance and non-significance lie. Perhaps we might one day dream of combing through such datasets, actually explaining what drove the .06’s vs the .05’s. For now however, we must be careful not to look at our uncorrected statistical maps; for that way surely voodoo lie! And that is perhaps the greatest puzzle of all; two datasets, all things being equal. In one case the researcher writes down on paper, “blobs A, B, and C I shall see” and conducts significant ROI analyses on these regions. In the other he first examines the uncorrected map, notices blobs A, B, and C, and then conducts a region of interest analysis. In both cases, the results and data are the same. And yet one is classic statistical voodoo– double dipping- and the other perfectly valid hypothesis testing. It seems thus that our truth criterion lay not only with our statistics, but also in some way, in the epistemological ether.

Of course, it’s really more of a pragmatic distinction than an ontological one. The voodoo distinction serves not to delineate true from false results but rather to discourage researchers from engaging in risky practices that could inflate the risk of false-positives. All-in-all, I agree with Dorothy Bishop: we need to stop chasing the novel, typically spurious and begin to share and investigate our data in ways that create lasting, informative truths. The brain is simply too complex and expensive an object of study to let these practices build into an inevitable file-drawer of doom. It infuriates me how frustratingly obtuse many published studies are, even in top journals, regarding the precise methods and analysis that went into the paper. Wouldn’t we all rather share our data, and help explain it cohesively? I dread the coming collision between the undoubtably monolithic iceberg of unpublished negative findings, spurious positive findings, and our most trusted brain mapping paradigms.

Google Wave for Scholarly Co-authorship: excerpt from Neuroplasticity and Consciousness Abstract

Gary Williams and I are working together on a paper investigating the consciousness and neuroplasticity. We’re using Google wave for this collaboration, and I must say it is an excellent co-authorship tool. There is nothing quite so neat as watching your ideas flow and meld together in real time. There are now new built in document templates that make these kinds of projects a blast. As an added bonus, all edits are identified and tracked in real time, letting you keep easy track of who wrote what. One of the most suprising things to come out of this collaboration is the newness of the thoughts. Whatever it is we end up arguing, it is definetely not reducible to the sum of it’s parts. As a teaser, I thought I’d post a thread from the wave I made this morning. This is basically just me rambling on about consciousness and plasticity after reading the results of our wave. I wish I could post the movie of our edits, but that will have to wait for the paper’s submission.

I have an idea I want to work in that was provoked by this paper:
http://www.jneurosci.org/cgi/content/abstract/30/18/6205

Somewhere in here I still feel a nagging paradox, but I can’t seem to put my finger on it. Maybe I’m simply trying to explain something I don’t have an explanation for. I’m not sure. Consider this a list of thoughts that may or may not have any relationship to the kind of account we want to make here.

They basically show that different synthesthetic experiences have different neural correlates in the structural brain matter. I think it would be nice to tie our paper to the (likely) focus of the other papers; the idea of changing qualia / changing NCCs. Maybe we can argue that, due to neural plasticity, we should not expect ‘neural representations’ for sensory experience between any two adults to be identical; rather we should expect that every individual develops their own unique representational qualia that are partially ineffable. Then we can argue that it this is precisely why we must rely on narrative scaffolding to make sense of the world; it is only through practice with narrative, engendered by frontal plasticity, that we can understand the statistical similarities between our qualia and others. Something is not quite right in this account though… and our abstract is basically fine as is.

So, I have my own unique qualia that are constantly changing- my qualia and NCCs are in dynamical flux with one another. However, my embodiment pre-configures my sensory experience to have certain common qualities across the species. Narrative explanations of the world are grounded in capturing this intersubjectivity; they are linguistic representations of individual sense impressions woven together by cultural practices and schema. What we want to say is that, I am able to learn about the world through narrative practice precisely because I am able to map my own unique sensory representations onto others.

I guess that last part of what I said is still weak, but it seems like this could be a good element to explore in the abstract. It keeps us from being too far away from the angle of the call though, maybe. I can’t figure out exactly what I want to say. There are a few elements:

  • Narratives are co-created, coherent, shareable, complex representations of the world that encode temporality, meaning, and intersubjectivity.
  • I’m able to learn about these representations of the world through narrative practice; by mapping my own unique dynamic sensory experience to the sensory and folk psychological narratives of others.
  • Narrative encodes sensory experience in ways that transcend the limits of personal qualia; they are offloaded and are no longer dynamic in the same way.
  • Sensory experience is in constant flux and can be thrown out of alignment with narrative, as in the case of most psychopathy.
  • I need some way to structure this flux; narrative is intersubjective and it provides second order qualia??
  • Narrative must be plastic as it is always growing; the relations between events, experiences, and sensory representations must always be shifting. Today I may really enjoy the smell of flowers and all the things that come with them (memory of a past girlfriend, my enjoyment of things that smell sweet, the association I have with hunger). But tommorow I might get buried alive in some flowers; now my sensory representation for flowers is going to have all new associations. I may attend to a completely different set of salient factors; I might find that the smell now reminds me of a grave, that I remember my old girlfriend was a nasty bitch, and that I’m allergic to sweet things. This must be reflected in the connective weights of the sensory representations; the overall connectivity map has been altered because a node (the flower node) has been drastically altered by a contra-narrative sensory trauma.
  • I think this is a crucial account and it helps explain the role of the default mode in consciousness. On this account, the DMN is the mechanism driving reflective, spontaneous narrativization of the world. These oscillations are akin to the constant labeling and scanning of my sensory experience. That they in sleep probably indicates that this process is highly automatic and involved in memory formation. As introspective thoughts begin to gain coherency and collude together, they gain greater roles in my over all conscious self-narrative.
  • So I think this is what I want to say: our pre-frontal default mode is system is in constant flux. The nodes are all plastic, and so is the pattern of activations between them. This area is fundamentally concerned with reflective-self relatedness and probably develops through childhood interaction. Further, there is an important role of control here. I think that a primary function of social-constructive brain areas is in the control of action. Early societies developed complex narrative rule systems precisely to control and organize group action. This allowed us to transcend simple brute force and begin to coordinate action and to specialize in various agencies. The medial prefrontal cortex, the central node, fundementally invoked in acts of social cognition and narrative comprehension, has massive reciprocal connectivity to limbic areas, and also pre-frontal areas concerned with reward and economic decision making.
  • We need a plastic default mode precisely to allow for the kinds of radical enculturation we go through during development. It is quite difficult to teach an infant, born with the same basic equipment as a caveman, the intricacies of mathematics and philosophy. Clearly narrative comprehension requires a massive amount of learning; we must learn all of the complex cultural nuances that define us as modern humans.
  • Maybe sensory motor coupling and resonance allow for the simulation of precise spatiotemporal activity patterns. This intrinsic activity is like a constant ‘reading out’ of the dynamic sensory representations that are being constantly updated, through neuroplasticity; whatever the totality of the connection weights, that is my conscious narrative of my experience.
  • Back to the issue of control. It’s clear to me that the prefrontal default system is highly sensitive to intersubjective or social information/cues. I think there is really something here about offloading intentions, which are relatively weak constructions, into the group, where they can be collectively acted upon (like in the drug addict/rehab example). So maybe one role of my narration system is simply to vocalize my sensory experience (I’m craving drugs. I can’t stop craving drugs) so that others can collectively act on them.

Well there you have it. I have a feeling this is going to be a great paper. We’re going to try and flip the whole debate on it’s head and argue for a central role of plasticity in embodied and narrative consciousness. It’s great fun to be working with Gary again; his mastery of philosophy of mind and phenomenology are quite fearsome, and we’ve been developing these ideas forever. I’ll be sure to post updates from GWave as the project progresses.

A defense of vegetarian fMRI (1/2)

Recently there’s been much ado about a newly published fMRI study of empathetic responding in vegetarians, vegans, and omnivores. The study isn’t perfect, which the authors admit, but I find it interesting and relatively informative for an fMRI paper. The Neurocritic doesn’t, rather he raises some seemingly serious issues with the study. I promised on twitter I’d defend my claim that the study is good (and that neurocritic could do better). But first, a motivated ramble to distract and confuse you.

As many of you might realize, neuroscience could be said to be going through something like puberty. While the public remains infatuated with every poorly worded research report, researchers within the neurosciences have to view brain mapping through an increasingly skeptical lens. This is a good thing: science progresses through the introduction and use of new technologies and the eventual skeptical refinement of their products.

And certainly there is plenty of examples shoddy neuroscience out there, whether it’s reports of voodoo correlations or inconsistencies between standard fMRI analyses packages. Properly executed, attention to these issues and a healthy skepticism of the methods will ultimately result in a refined science. Yet we must also be careful to apply the balm of skepticism in a refined manner: neuroscientists are people to, and we work in an increasingly competitive field where there are few well-defined standards and even less clarity.

Take an example from my lab that happened just today.  We’re currently analyzing some results from a social cognition experiment my colleague Kristian Tylen and I conducted last year. Like many fMRI results, our hypotheses (which were admitable a bit vague when we made them) were not exactly supported by our findings. Rather we ended up with a scattered series of blobs that appeared to mostly center on early visual areas. This is obviously boring and unpublishable, and after some time we decided to do a small volume correction on some areas we’d discussed in a published paper. This finally revealed some interesting findings somewhere around the TPJ, which brings me to the point of this story.

My research has thus far mostly focused on motor and prefrontal regions. We in neuroimaging can often fall victim to what I call ‘blob blind sight’ where we focus so greatly on a single area or handful of areas that we forget there’s’ a wide world of cortex out there. Imagine my surprise when I tried to get clear about whether our finding was situated in exactly the pSTS, TPJ, or nearby inferior parietal lobule (IPL) only to discover that these three areas are nearly indistinguishable from one another anatomically.

All of these regions are involved in different aspects of social cognition, and across the literature there are no clear anatomical differentiation between them. In many cases, researchers will just lump them together as pSTS/TPJ, regardless of the fact that a great deal of research has gone on explicitly differentiating them. Now what does one do with a blob that lands somewhere in the middle, overlapping all three? More specifically, imagine the case where your activation foci lands smack dab in the middle, or a few voxels to the left. Is it TPJ? Or IPL? Or is it really the conjunction of all three, and if so, how does one make sense of that given the wide array of functions and connectivity patterns for these areas. IPL is a part of the default mode, whereas TPJ and pSTS are not. It’s really quite a mess, and the answer you choose will likely depend upon the interpretation you give, given the vast variety of functions allocated to these three regions.

The point of all this, which begins to lead to my critique of TNC critique, is that it is not a simple matter of putting ones foot down and claiming that the lack of an expected activation or the presence of an unexpected one is damning or indicative of bad science. It’s an inherent problem in a field where hundreds of papers are published monthly with massive tables of activation foci. To say that a study has gone awry because they don’t report your favorite area misses the point. What’s more important is to evaluate the methods and explain the totality of the findings reported.

So that’s one huge issue confronting most researchers. Although there are some open source ‘foci databases’ out there, they are underused and hard to rely on. One can of course try to pinpoint the exact area, but in reality the chance that you’ll have such a focused blob is pretty unlikely. Rather, researchers have to rely on extra-scanner measures and common sense to make any kind of interesting theoretical inferences from fMRI. This post was meant to be a response to The Neurocritic, who took issue with my taking issue of his taking issue with a certain vegetarian fmri study… but I’m already an hour late coming home from work and I’m afraid I’ve failed to deliver. I did take the time this afternoon to go thoroughly through both the paper and TNC’s response however, and I think I’ve got a pretty compelling argument. Next time: why the neurocritic is plain wrong 😉

Synaptic Adaptation to Environmental Alteration

From Quartz & Sejnowski: Neural Basis of Cognitive Development (1997)
Quartz and Sejnowski. The neural basis of cognitive development: a constructivist manifesto. Behav Brain Sci (1997) vol. 20 (4) pp. 537-56; discussion 556-96

Above you see an excellent summary table found in a seminal work by Quartz and Sejnowski. I’m reading this paper now, and aside from the die-hard representationalist instincts of the authors, it is an excellent overview of the development of neuroplasticity research and the relation of various forms of plasticity to learning and cognition. I find the above table fascinating simply because it demonstrates in one tidy arena the scope and temporal shape of brain development. You see for example, infamous studies in which the eyes of rats are sutured shut at birth alongside equally high-impact studies in which alterations in environmental complexity alter synaptic densities.

Overall, this is a list of studies in which the alteration of sensory motor input alters synaptic density and complexity in a dynamical fashion. I find it particularity interesting that the overall direction appears to be on in which increased complexity equals increased density. One stand out result is Valverde (1971) where an 20 day period of darkness is synaptically overcome when the mice are returned to a normal environment. Overall this table is a historically stunning account of the resilience of neural systems.

One big question though- why has it taken so long for plasticity to make its way into neurological acceptance?? Clearly the data was there… guess we needed fancy magnets to believe in it!

Cognitive Science in Pozna≈Ñ, Poland

I recently had the pleasure of being invited as a guest speaker for the annual Poznan Cognition Forum, a Polish graduate conference in the cognitive sciences. Before I summarize the academic aspects of my trip, I think it’s worth sharing my experience exploring Poznan. As this post is a bit long I will split into two parts, the first relating my general experiences in Poland and the second summarizing my talk.

Part 1: Exploring Poznań

IMG_2447

Before arriving in Poland, I did my best to educate myself with a brief trip to wikipedia. Although I knew that the country had once held an impressive empire, and suffered greatly in the two World Wars, I was shocked to learn that they had been under Russian Communism prior to 1980. I guess it says something about American education that I didn’t know this, and I was glad to enter the country slightly less ignorant than before. Overall, my trip was a lovely mixture of business and pleasure; my hosts were extremely gracious (more on them in a bit) and as the other talks were all in Polish, they were kind enough to show me around the city on my free time. Poznan is beautiful, a city rich in stunning architecture and cobble-stone city squares that left me breathless and curious to see more.

While it may have just been the abundant fog and my crash-course wikipedia history lesson, the best way I can sum my experience of Poznan is that she presents the viewer with an intriguing mixture of imperial and old wold grandeur, laced with a quaint yet quietly stern specter of the former Soviet presence. Something about the ghostly imperial streets and plain stone architecture gives one that feeling that Poland is not wholly a western nation. Probing deeper, I found Renaissance era castles and multicolored homes, interlaced with stunning baroque churches glittering with intricate gold adornments. It was first taste of a culture that struck me as both curiously and charmingly alien.

While I love Denmark, Danish architecture can be a bit minimal and homogenous, so it was refreshing to be in a country with a diverse mix of architectural styles and historical backgrounds. Completing the trip was my wonderful hosts, the organizers and attendees of the 5th annual Poznan Cognition Forum.

As astonishing as the mix of old world and modern imperialist cultures I found in Poznan, the group of dedicated young cognitive scientists seemed more impressive still. Here was a small group of perhaps 10 to 15 extremely dedicated, bright, and ambitious researchers who had taken up the charge of establishing one of Poland’s first and only cognitive science research centers. As they related IMG_2439their frustrations I could not help but think of my own early experiences trying to break into cognitive science and being told I was chasing a fools’ errand that could never result in gainful employment.

From what they told me, Polish research politics remain highly conservative, nationally isolated, and disciplinary in nature. Bartoz, a charming researcher who seemed an everyman of practical and academic solutions (of which many where needed from him during my short stay) related to me how himself and another dedicated researcher/organizer, Aga, had fought tooth and nail for the establishment of a cognitive science degree program that had required little more than cooperation between the philosophy and psychology departments at Poznan University which continued to be hostile and unsupportive of their endeavors.

The research community I found in Poznan did not reflect a group down on it’s luck- these bright young minds reminded me more of the Rebel Alliance before the battle of Endor than any remember-the-Alamo martyrs. Confident in their cause and self-sufficient in its’ needs- in some cases even going so far as to go around the administration of their university to secure funds and equipment for a state-of-the-art eye tracking research facility- these researchers seemed poised for success. Not only were they fully capable of dealing with these everyday issues, they were impressively contemporary in their mastery of cognitive science, demonstrating a familiarity with both phenomenological and empirical research that kept me on my toes throughout my stay. I can only hope to work with them again in the future, as they are both eager and fully capable of joining the global research community. If there is one thing Cognitive Science can’t have enough of, it’s the Poznan brand of genuine competence and sober passion.

Organizers!

Link to my Picasa Album of the trip:

Poznan Album