Saturday, December 31, 2011

2011 in review

In the spirit of Chris Guillebeau's Annual Review, I decided to take a few minutes this morning to review what worked well and what didn't 2011 and look forward to 2012.

Goals:

Last year I set three goals for 2011.  Here's how they fared.

FAIL: Work toward a travel moratorium for 2012.  This started with me responding to all requests with "I'm sorry, but I'm not traveling at all for work in 2012."  At some point that became untenable, and the floodgates opened.  At this point, I am still planning to travel less in 2012 than in 2011, but will still probably take 8-10 trips.

SUCCESS: Improve climbing skills well enough to lead climb. My climbing skills have improved enormously over the last year, and in the summer I began lead climbing at the rock gym, where I can now lead a number of routes in the 5.9 range.  I was not able to lead outside, mostly because the weather in December did not cooperate, but I plan to do so very soon.

SUCCESSNo new web projects. I only purchased one new domain name this year, and that was for a project that had been hatched in 2010.  We have instead focused heavily on our existing projects, particularly openfmri.org.

Here are my goals for 2012:

Improve my posture.  Some nagging neck and back issues this year have highlighted the need to improve my posture.  Who knows, I might even get some mental benefits from it as well.

Improve my code management.  In the last year I have started integrating source code management (using git) into my workflow (see my github repo for a tour of some of my adventures during the last year).  However, it still has not become a habit for me during everyday coding.

Exercise on every trip.  One of the reasons that I find travel so disruptive is that it interferes with my fitness routine.  I carry my yoga mat on nearly every trip, and this year I did a fairly good job of exercising while on the road, but I was not very consistent.  Next year I plan to make sure that I get some exercise on every trip, even if it's just some burpees and squats in the hotel room.

I hope it's not true that making these goals public will make them harder to achieve!

Stats

Countries visited: 7
Miles flown: 76,162
Talks given: 12
Papers published: 14
Grants funded: 2

Property crimes (committed against me, not by me): 2


Best meals:
1. Tasting menu at Congress
2. Lunch at Les Arcenuax, Marseille
3. Tie between Franklin BBQ and JMueller BBQ
4. Tasting menu at Uchi (the meal that sealed our transition to full-blown carnivores)

Tuesday, October 4, 2011

NYT Letter to the Editor: The uncut version

The NY Times has now printed our letter to the editor regarding the Lindstrom article.  However, the published version is an edited and shortened version of our original letter, which I am posting here for the record.


Dear Editor,
The Op-Ed “You Love Your iPhone, Literally” by Martin Lindstrom purports to show, using brain imaging, that our attachment to digital devices, reflects not addiction but instead the same kind of emotion that we feel for human loved ones. However, the evidence the author presents does not show this.  The region that he points to as being “associated with feelings of love and compassion” (the insular cortex) is a brain region that is active in as many as one third of all brain imaging studies.  Further, in studies of decision making the insula is more often associated with negative than positive emotions.  The kind of reasoning that Lindstrom uses is well known to be flawed, because there is rarely a one-to-one mapping between any brain region and a single mental state; insula activity could reflect one or more of several psychological processes. This same point was made by some of us regarding a similar Op-Ed piece in 2007.
We are disappointed that the Times has published extravagant claims based on scientific data that have not been subjected to the standard scientific review process, especially considering how often its pages exhort policy makers to pay more attention to peer-reviewed scientific evidence and disregard specious claims.
Sincerely,

Russell Poldrack, Ph.D., University of Texas at Austin
Geoffrey K Aguirre, M.D., Ph.D., University of Pennsylvania
Adam Aron, Ph.D., University of California at San Diego
Lisa Feldman Barrett, Ph.D., Northeastern University
Mark G. Baxter, Ph.D., Mount Sinai School of Medicine
Susan Bookheimer, Ph.D., University of California at Los Angeles
Colin Camerer, Ph.D., California Institute of Technology
McKell Carter, Ph.D., Duke University
Christopher Chabris, Ph.D., Union College
Molly Crockett, Ph.D., University of Zurich, Switzerland
Nathaniel Daw, Ph.D., New York University
Paul Downing, Ph.D., University of Bangor, Wales, UK
Russell Epstein, Ph.D., University of Pennsylvania
Michael Frank, Ph.D., Brown University
Janet Frick, Ph.D., University of Georgia
Paul Glimcher, Ph.D., New York University
Tom Hartley, Ph.D., University of York, UK
Benjamin Hayden, Ph.D., University of Rochester
Hauke R. Heekeren, M.D., Freie Universit├Ąt Berlin, Germany
Simon Hjerrild, M.D., University of Aarhus, Denmark
Scott Huettel, Ph.D., Duke University
Nancy Kanwisher, Ph.D., Massachusetts Institute of Technology
Brian Knutson, Ph.D., Stanford University
John Kubie, Ph.D., SUNY Downstate Medical Center
Michael V. Lombardo, Ph.D., University of Cambridge, UK
Ken Norman, Ph.D., Princeton University
Olivier Oullier, Ph.D., Aix-Marseille University, France
Steven Petersen, Ph.D., Washington University
Elizabeth Phelps, Ph.D., New York University
Rajeev Raizada, Ph.D., Cornell University
Antonio Rangel, Ph.D., California Institute of Technology
Peter B. Reiner, Ph.D., University of British Columbia, Canada
Gregory Samanez-Larkin, Ph.D., Vanderbilt University
Geoff Schoenbaum, M.D., Ph.D., University of Maryland
Daphna Shohamy, Ph.D., Columbia University
Jon Simons, Ph.D., University of Cambridge, UK
Peter Sokol-Hessner, Ph.D., California Institute of Technology
David Somers, Ph.D., Boston University
Damian Stanley, Ph.D., California Institute of Technology
John Van Horn, Ph.D., University of California at Los Angeles
Bradley Voytek, Ph.D., University of California, San Francisco
Anthony Wagner, PhD, Stanford University.
Daniel Willingham, Ph.D., University of Virginia
Tal Yarkoni, Ph.D., University of Colorado Boulder
Jeff Zacks, Ph.D., Washington University
Jamil Zaki, Ph.D., Harvard University

Monday, October 3, 2011

Signers of letter to the editor of the New York Times

A letter has been submitted to the editor of the NY Times regarding the outrageous Op-Ed piece by Martin Lindstrom.  (Once it is published I will add a link here.)  Because the NY Times will not allow a long list of signers on a letter, I am attaching here a list of all of the individuals who contributed to and signed the letter.  If you would like to add your name in support of the letter, please do so in the comments section.

Russell Poldrack, Ph.D., University of Texas at Austin
Geoffrey K Aguirre, M.D., Ph.D., University of Pennsylvania
Adam Aron, Ph.D., University of California at San Diego
Lisa Feldman Barrett, Ph.D., Northeastern University
Mark G. Baxter, Ph.D., Mount Sinai School of Medicine
Susan Bookheimer, Ph.D., University of California at Los Angeles
Colin Camerer, Ph.D., California Institute of Technology
McKell Carter, Ph.D., Duke University
Christopher Chabris, Ph.D., Union College
Molly Crockett, Ph.D., University of Zurich, Switzerland
Nathaniel Daw, Ph.D., New York University
Paul Downing, Ph.D., University of Bangor, Wales, UK
Russell Epstein, Ph.D., University of Pennsylvania
Michael Frank, Ph.D., Brown University
Janet Frick, Ph.D., University of Georgia
Paul Glimcher, Ph.D., New York University
Tom Hartley, Ph.D., University of York, UK
Benjamin Hayden, Ph.D., University of Rochester
Hauke R. Heekeren, M.D., Freie Universit├Ąt Berlin, Germany
Simon Hjerrild, M.D., University of Aarhus, Denmark
Scott Huettel, Ph.D., Duke University
Nancy Kanwisher, Ph.D., Massachusetts Institute of Technology
Brian Knutson, Ph.D., Stanford University
John Kubie, Ph.D., SUNY Downstate Medical Center
Michael V. Lombardo, Ph.D., University of Cambridge, UK
Ken Norman, Ph.D., Princeton University
Olivier Oullier, Ph.D., Aix-Marseille University, France
Steven Petersen, Ph.D., Washington University
Elizabeth Phelps, Ph.D., New York University
Rajeev Raizada, Ph.D., Cornell University
Antonio Rangel, Ph.D., California Institute of Technology
Peter B. Reiner, Ph.D., University of British Columbia, Canada
Gregory Samanez-Larkin, Ph.D., Vanderbilt University
Geoff Schoenbaum, M.D., Ph.D., University of Maryland
Daphna Shohamy, Ph.D., Columbia University
Jon Simons, Ph.D., University of Cambridge, UK
Peter Sokol-Hessner, Ph.D., California Institute of Technology
David Somers, Ph.D., Boston University
Damian Stanley, Ph.D., California Institute of Technology
John Van Horn, Ph.D., University of California at Los Angeles
Bradley Voytek, Ph.D., University of California, San Francisco
Anthony Wagner, PhD, Stanford University.
Daniel Willingham, Ph.D., University of Virginia
Tal Yarkoni, Ph.D., University of Colorado Boulder
Jeff Zacks, Ph.D., Washington University
Jamil Zaki, Ph.D., Harvard University

Saturday, October 1, 2011

NYT Op-Ed + fMRI = complete crap

Many of you may remember the controversy that arose a few years back when the NY Times published an Op-Ed titled "This is your brain on politics" by Marco Iacoboni and colleagues.  This steaming pile of shoddy reverse inferences inspired a group of us to write a letter to the editor, published online.  Well, the NYT editorial page is at it again, this time with a piece by self-proclaimed neuromarketer Martin Lindstrom, titled "You love your iPhone, literally" (h/t Raj Raizada for pointing me to it).  The argument of the article is that rather than our feelings about iphones reflecting something like an addiction driven by dopamine (which I have argued for in the past), our feelings about our digital devices instead reflect true love, based on fMRI:

But most striking of all was the flurry of activation in the insular cortex of the brain, which is associated with feelings of love and compassion. The subjects’ brains responded to the sound of their phones as they would respond to the presence or proximity of a girlfriend, boyfriend or family member.
In short, the subjects didn’t demonstrate the classic brain-based signs of addiction. Instead, they loved their iPhones.
Insular cortex may well be associated with feelings of love and compassion, but this hardly proves that we are in love with our iPhones.  In Tal Yarkoni's recent paper in Nature Methods, we found that the anterior insula was one of the most highly activated part of the brain, showing activation in nearly 1/3 of all imaging studies!  Further, the well-known studies of love by Helen Fisher and colleagues don't even show activation in the insula related to love, but instead in classic reward system areas.  So far as I can tell, this particular reverse inference was simply fabricated from whole cloth.  I would have hoped that the NY Times would have learned its lesson from the last episode.

Friday, July 1, 2011

My analysis of OHBM 2011 abstracts

As the past chair of the Organization for Human Brain Mapping (which just ended its 2011 meeting in Quebec City), I was tasked with giving the "Meeting Highlights" talk which traditionally closes the meeting.  It's a pretty daunting challenge to summarize an entire meeting with such little time for preparation, so I took the tack of doing lots of mining on the full text of the abstracts prior to the meeting.  My entire wrap-up talk is available here; below I present the main results of my text mining, along with some additional analyses that didn't make it into the talk.

Overall meeting stats:

Number of Abstracts 2230
Number of Unique Authors 7622
Mean # of abstracts/author 1.64 (max=33)
Mean # of authors/abstract 5.6 (max=41)

Authorship distribution:

The OHBM is known for being an international organization, and the authorship data confirm this.  In order to visualize the authorship data, I used the Google Maps API to identify the latitude/longitude for each affiliation in the authorship list. This was successful for more than 90% of the abstracts.  These latitude/longitude values were uploaded into Google Fusion Tables, from which I exported a KML file  (available here) which I then opened in Google Earth.  (That's a lot of Google!)

Using Google Earth I then created a tour that circled the globe, showing all of the author locations on a path from Quebec City to Beijing (location of the 2012 meeting).  Here is the video:



Each red pin represents the location of an author at the meeting.

Authorship networks:

Using the abstracts I created a coauthorship network and did some basic analyses on this network (using the Networkx toolbox in Python and the Network Workbench).  The code and an anonymized version of the graph (in graphml format) are available via github.  Here is an overall view of the network:


This shows one giant connected component with 4600 authors (60.3%), along with a large number of much smaller components (the second largest component had 103 authors).  Focusing in on the giant component, here is the spring-embedded visualization:



Here are the network statistics:

Clustering coefficient 0.88
Average degree 8.10
Average shortest path length (giant component only) 6.96
Maximum shortest path length 18
Modularity (giant component only) 0.92


Here is the degree distribution plotted in log space, with a degree distribution for a matched random graph for comparison:


The degree distribution has a long tail compared to the random network, which is what one would expect from this kind of network (for background on this kind of analysis, see Mark Newman's paper The structure of scientific collaboration networks).

Using PageRank centrality, I identified the 10 most central authors in this network (listed with number of abstracts and centrality value):
  1. Paul Thompson (33 abstracts: 0.002020)
  2. Vince Calhoun (21 abstracts: 0.001816)
  3. Arno Villringer (23 abstracts: 0.001756)
  4. Arthur Toga (30 abstracts: 0.001625)
  5. Yong He (19 abstracts: 0.001416)
  6. Peter Fox (26 abstracts: 0.001381)
  7. Michael Milham (24 abstracts: 0.001340)
  8. Alan Evans (16 abstracts: 0.001318)
  9. Robert Turner (23 abstracts: 0.001292)
  10. Daniel Margulies (13 abstracts: 0.001194)
Content analysis:


Using the full text from the articles, I created several tag clouds (using Wordle) to show different aspects of the content.  The first was created from the entire abstract text after filtering out standard stop words along with anatomical regions and author names.


The second was created using a count of all anatomical terms (from the PubBrain anatomical lexicon):


The third was created using a count of all of the terms in the Cognitive Atlas lexicon of mental concepts:


These tag clouds give a good overview of the major topics at the meeting.


If you have other ideas for mining of these data, let me know and I'll give it a try. I have also done topic modeling using latent Dirichlet allocation, and may get around to writing about that in the future.

Thursday, June 30, 2011

Recent Reads

Here are my thoughts about some books I have read recently.

Hits:

The Emperor of All Maladies: A Biography of Cancer:  An absolutely fascinating book.  It traces the history of cancer and its treatment, highlighting all of the ways in which medical science has gotten things wrong in the past and how cancer treatment has only recently evolved beyond blindly poisoning the body.  Not a lot of scientific content, but more than enough to keep me interested.  

Food and Western Disease: Staffan Lindenberg is a physician from Sweden who is best known for the Kitava Study.  This book is a systematic review of the evidence regarding dietary causes of western disease such as cancer, diabetes, and heart disease.  He's clearly an advocate for the paleo diet, but he seems pretty fair in saying when the evidence does or does not fit with that approach. Definitely worth reading.

The Queen of Fats: This is a relatively obscure book from a university press, but turned out to be a great read.  The writer is not a scientist but does a decent job of covering the science, while still making the story engaging and fun.  It has definitely changed how I think about food.

The Immortal Life of Henrietta Lacks: I found this book fairly engaging, though it was a bit too tilted towards the drama of the writer's journey versus the story itself.  What I found most interesting were the stories about how absolutely messed up the Lacks family was (e.g., the children were all partly deaf due to a combination of inbreeding and neurosyphilis).  However, I would have liked more scientific content.  I would definitely recommend this book as background for human researchers as it really highlights the reasons why we have such strict control over human research today.

Superbug: The Fatal Menace of MRSA:  I know that I am crazy for reading these kinds of books as they just make one paranoid about infections, but nonetheless I found it really engaging and interesting.  Not for the squeamish or hypochondriacal, however.

Do The Work:  This is a motivational book targeted largely at writers, but would be really useful for many researchers to read.  It discusses how we often get in our own way, and how to get around it.  It's definitely a different kind of book from the rest of these, but for anyone who is having trouble getting things done I would highly recommend it.

Misses:

The Information - A History, A Theory, A Flood:  This book is about the history of information theory, and thus will appeal to my geekier friends.  Gleick is a great writer, and it starts really strong and does a good job of explaining lots of concepts, but I thought that the end fell really flat.  I would recommend only if you are really seriously interested in the topic.

Bossypants:  I am generally a big Tina Fey fan and I really wanted to like this, but it just didn't work for me.  I made it about 1/3 of the way in before I gave up.

Everything is obvious: *once you know the answer:  I absolutely loved Duncan Watts' earlier book, Six Degrees,   so I was really excited to read this.  In addition, the topic is really fascinating and ripe for the picking.  However, I was really disappointed and barely made it through a couple of chapters.  The problem is that it's written for executives, and thus is peppered with dumbed-down examples without enough deep explanation.  I think it's a great example of how not to write a popular science book.

Sunday, April 10, 2011

why I cut the carbs

The last few months have seen a fairly major transformation in what I eat, with pretty amazing results.  For the last ~20 years my diet has been mostly vegetarian + seafood, and my weight has been very steady, between 160 and 170.  I have always been a major sugar fiend, with my college-age penchant for Skittles morphing into a significant chocolate habit in the last few years.  My exercise habits have always been hit-and-miss, until the last year when I became much more regular in my workouts, which at this point I am doing 6-7 times a week.  Despite this substantial increase in my exercise frequency, I didn't really see any changes in my body composition.  I felt better, but the fat around my belly just wouldn't go away.

My first step on the road to a new diet was my personal trainer's suggestion that I increase the protein in my diet, after I complained to her that all of my work in the gym was not showing results on my body. As I began to change my diet to include more protein, I also discovered Gary Taubes for the first time, and read Why We Get Fat followed by Good Calories, Bad Calories.  Taubes is a writer for Science magazine who has spent the last few years digging into the science of weight loss, and his books are pretty startling because they call into question nearly everything that we think we know about what is good for us.  In short, he argues persuasively that there is no scientific evidence for the common belief that saturated fat and dietary cholesterol are the causes of heart disease, and he also provides a clear physiological explanation for why carbohydrates are the thing that make us fat, as opposed to the "calories in, calories out" idea that most of us have (I certainly did).  In addition, he points out evidence that carbs not only make us fat, but also may contribute to other "diseases of civilization".  Most interestingly, he discusses work that I had not been aware of that links Alzheimer's disease to insulin, which is driven by carbohydrate intake.

The Taubes books really pushed me to rethink what I eat, and I decided to take the plunge and cut carbs from my diet as completely as possible.  I've been pretty successful at this, and the results have been pretty amazing.   I am down to 150 pounds since cutting carbs from my diet, which is pretty impressive given that my weight has never fluctuated more than about 5 pounds from my long-term average of 165, despite pretty radical changes in caloric intake across the years.  I can see the difference too; the fat around my belly is noticeably reduced, as well as in other places around my body.

Perhaps the biggest change for me was starting to eat meat.  I still don't eat much meat, and when I do I try to make sure that it was produced as naturally and ethically as possible, but nonetheless I am now eating meat several times a week (mostly bacon or proscuitto), as well as eating eggs almost every day.  I was very curious to see how this affected my cholesterol numbers when I went for my annual checkup this year, a few months into the new diet.  The results were pretty astounding:

Total cholesterol:  234 (2010) to 199 (2011)
LDL: 147 (2010) to 121 (2011)
HDL: 57 (2010) to 65 (2011)
Triglycerides: 148 (2010) to 64 (2011)

Obviously it's hard to know how much of this to attribute to diet and how much to other factors such as exercise, but these are the best numbers I've ever seen in my life, after years of being a vegetarian. I also don't put too much stock in these numbers; as Taubes points out in his books, the science connecting cholesterol levels to heart disease is pretty weak, except at the extremes.  However, my triglycerides, which are probably much more important, are clearly off-the-charts better after years of being right at the borderline of too high.

I'll write more soon about the interesting experience of deleting some seriously addictive foods from one's diet.

Saturday, January 1, 2011

Goals for the new year

Although I've never been a big fan of new year's resolutions, I do like to set some goals at the beginning of the year so that I have measureable objectives to strive for.  

My main goal for 2010 was to exercise at least 4 times a week.  That was difficult during the spring because I was traveling a ton, but since August I have done a pretty good job of exercising 5-6 times a week.  The main thing I have done to accomplish this is to make going to the gym a daily morning ritual.  It can be very hard to make myself go to the gym if I've not been doing it regularly, but once I'm in the habit then it doesn't really take much gumption to get myself there.

A second goal, somewhat harder to quantify, was "say no more often."  I apologize to those of you who might have borne the brunt of this goal, but I think I have been rather successful.  I said no to a number of talk invitations, skipped two conferences (SFN and MDRS), and have refused an increasingly proportion of review requests.  Then again, there were a lot of things I did not say no to, reflected in the fact that I flew more than 100,000 miles in 2010 (hello Platinum Status!)

For 2011 I am setting three new goals.  

Work toward a travel moratorium for 2012.  I have traveled a lot in the past few years, and 2011 will be no different.  I love traveling and have learned to deal with the stresses of air travel.  However, the physical toll of heavy travel can be substantial, because it makes it very hard to keep up my exercise routine and also makes it hard to stick to a healthy eating plan.  I will never be able to go a year without any travel, due to my various professional responsibilities.  However, the majority of my travel is elective, in the sense that I could say no without greatly harming my career.  During 2011, my default answer for any invitations to travel during 2012 will be "no".  

Improve climbing skills well enough to lead climb.  One big revelation for me in 2010 was the fun of rock climbing, which one of my friends has been kind enough to introduce me to over the last couple of months.  So far I have only done "top rope" climbing, where someone else (the "lead climber") first ascends the face and puts the rope in place from the top, and then I climb the same route.  By the end of the year I would like to be able to lead a route myself, which will require a combination of climbing skill and nerves (since one can fall much farther while lead climbing compared to top rope climbing).  

No new web projects.  Over the last few years my students and I have started a number of web projects.  Some of these, such as The Cognitive Atlas and PubBrain are fairly well established and get a decent bit of traffic, while others such as fmrimethods.org have languished.  In 2010 I started openfmri.org which is a project to support sharing of raw brain imaging data; this project requires a good bit of work because the data have to be organized and validated.  For 2011 I am placing a moratorium on new web projects, so that I can focus on the projects that I already have in place.