5-HTTLPR episode 17: The revenge of the neurocriticcritic

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I am sort of a neuropessimist believing that a large part of neuroscience results are more variable than we would like to think. I dont think that I am extremist like Why Most Published Research Findings Are False. I still need to understand its mathematical details and its critique.

The oldtimer 5-HTTLPR genetic polymorphism has long been hailed and then dethroned as associated with anxiety-related personality traits. Quite a number of meta-analyses have examined its effect on a range of variables and I recently listed some of these in tables for 5-HTTLPR meta-meta-analysis. The results are somewhat – hmmm – well – perhaps there is an effect on depression, perhaps only little effect or perhaps no effect. For the interaction between 5-HTTLPR and “stressful life events” on depression two 2009 meta-analyses (Munafo and some others) found no effect.

Anonymous neuroimaging blogger The Neurocritic had in 2009 a piece called Myth of the Depression Gene where he (probably not a she) with a certain amount of schadenfreude dethroned the optimistic original 2003 study of Caspi, Sugden, Moffit and all the others. Now yesterday neurocriticcritic nooffensebut pointed to a new meta-analysis published a few days ago, The serotonin transporter promoter variant (5-HTTLPR), stress, and depression meta-analysis revisited: evidence of genetic moderation, that claims a fair amount of effect from the 5-HTTLPR-stress interaction on depression.

Now I would say that you can’t trust the papers that say you can’t trust papers. But in the true spirit of neuropessimism I would say that you also shouldn’t trust that.

For you PubMed junkies: The next episode of 5-HTTLPR will come to a web-page near to you.


Secure multi-party computations in Python?

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I am not into cryptography, but I recently heard through Professor Lars Kai Hansen of secure multi-party computations, where multiple persons compute on numbers they do not directly reveal to each other, – only in encrypted form.

It turns out that Aarhus has done some research in that area and even released a Python package called VIFF (Virtual Ideal Functionality Framework).

The December 14th, 2009 1.0 release can be downloaded from their homepage. They provide a standard Python setup file:

python install --home=~/python/

The installation complained as it required the gmpy package which is in standard Ubuntu:

sudo aptitude install python-gmpy

With the package is example files in the ‘apps’ directory. They require the generation of configuration files where you specify hosts and ports for the ‘persons’ that need to communicate for secure computation. To keep it simple I stayed on localhost:

./ localhost:5000 localhost:5001 localhost:5002

In three different terminals you can then type (with the working directory being viff-1.0/apps):

./ player-1.ini 42

./ player-2.ini 3

./ player-3.ini 5

This example program will sum 42, 3 and 5. Each of the running Python programs then report the result:

Sum: {50}

The three values are private to each person (here each terminal) and the result is public. If you go in the middle of the Python program and write print str(x) thinking that you can reveal one of the private values (42, 3 or 5) you only get something like:

Share at 0x9751b4c current result: {805}

Close to pure magic.

Performance enhancement through TMS and TDCS

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Today I heard in the Danish Radio (“Danmarks Radio”) that British researcher had improved mathematical performance on subjects by sending electricity through the head. It is presently even on the front webpage of the “P3” channel with the headline “Is it ok to dope the brain?”.

Poor Thomas Z. Ramsøy, that I know, was dragged early out of bed by the radio to comment on the story. He is neuropsychologist, but I don’t think the story is in his line of research.

I got the impression that the research was performed with transcranial magnetic stimulation (TMS), – a technique where you apply a strong magnetic field just outside the head. Performance enhancement through TMS has been carried out before. A few years ago neuroscientist Daniela Balslev and her cos put TMS (or rather repetitive TMS – rTMS – if you are in the know) at the somatosensory hand area in the brain. You know the area “located at 3 cm posterior to the motor hotspot”. With that she was able to enhance the performance in the so-called mirror tracing task. This is a task where you trace lines on a piece of paper or computer screen, but through a mirror (actual or computer programmed). If you turn the computer mouse 180 degrees around you will see how difficult that task is.

Danish Radio doesn’t link to the original article they talked about as far as I can see. They should learn something from British Radio BBC in that aspect. But luckily Google News manages to find a reference. New Scientist writes Electrical brain stimulation improves math skills and references research by Roi Cohen Kadosh. He has done a TMS experiment, – but the mathematical performance fell. Actually the new research is reported to be performance enhancement with so-called transcranial direct current stimulation (TDCS), – a technique where you apply a small current through the brain.

The original article is called Modulating Neuronal Activity Produces Specific and Long-Lasting Changes in Numerical Competence. Danish science museum Experimentarium had an article a few days ago linking to that article.

2010-11-29: Minor correction

Hot or not or what: Data mining attractiveness

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From the media we hear that women are most attractive at 31. That fact is based on an “poll of 2,000 men and women, commissioned by the shopping channel QVC to celebrate its Beauty Month.” So this is a kind of science that is part of a media effort of a company. We also see such use of science in neuromarketing research. However, in this case the results are likely to be reasonably ok.

The web site Hot or Not has according to Wikipedia both been an inspiration for YouTube and Facebook. The site allows you to rate men and women based on their uploaded photo.

Back in 2009 I became aware of Hot or Not in a nerdish way: The computer programming book Programming Collective Intelligence uses the site as a real-life example for prediction based on annotation in the social web. Hot or Not has an API, so you can get some data from the site. You need an API key, and last time I checked you couldn’t obtain new keys, but I could use the one given in the book.

So I started to download data. You don’t get the individual ratings but the average rating for each person as well as a bit of demographics, e.g., the age. So there is really not so much you can do. The programming book try to predict the rating based on gender, age and location (US state).

I tried to see how the rating varied with age. I managed to make a plot of a sample of men and women from Hot or Not, and the result somewhat surprised me. I was expecting a decay in rating for women and men as a function of age, with around 31 years as a good candidate for maximum rating. However when I look on the ratings for women there is very little decay, in fact if you fit a second order polymonium you actually see a slight rise for older women. With unscrupulous extrapolation you would say that 100-year old women are maximum attractive. Men have the ‘correct’ decay with a highest rating somewhere around 30 or before. But there is considerably variance within year compared to the average between years.

One explanation for the effect seen among women is that only beautiful older ladies would “dare” to upload their image, while ugly young women are not afraid. There is also the possibility that we really cannot trust the average ratings reported to us by Hot or Not. I have got an account myself and uploaded an image. Presently I got a rating on 7.7 based on 206 people (the scale goes from 1 to 10). Hot or Not reports that I am “hotter than 74% of men on this site!”. When I compare 7.7 with the data I can download the percentage does not fit: Around 90% of males score higher than my 7.7. Yet another possibility is that the way I call the Hot or Not API does not give a fair sample of the people actually in the Hot or Not database.

Hot or Not data has been used in a few scientific reports, see, e.g., Economic principles motivating social attention in humans that made their own ratings and If I’m Not Hot, Are You Hot or Not? that has employees on the author list and thereby gained access to its unique data.

From the folklore of network analysis: The Erdos-Bacon number

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I have just discovered that I have an entry on IMDb through Director Dola Bonfis‘ documentary film Tankens Anatomi (The anatomy of thought). It is from 1997 but I do not recall seeing an entry for the film nor me on IMDb before. It almost makes it easy to compute my Bacon number. The Web-service The Oracle of Bacon allows you to type in name of two IMDb-listed people and it will then find the shortest path. However, I don’t seem to be present in The Oracle of Bacon database. Danish Entertainer, scientist and author Peter Lund Madsen also appears in the Tankens Anatomi movie, and he is present in the Oracle. Depending on the options set in The Oracle of Bacon it is possible to get to Kevin Bacon, although we need to go over, e.g., Mr Nice Guy which is just a recorded comedy show released on video. Mr Nice Guy features Trine Dyrholm who is a “proper” actress and from her it gets easy, e.g., by P.O.V. to Gareth Williams and Digging to China with Kevin Bacon. So it seems that I have a Bacon number of 4.

My combined Erdos-Bacon number then drops to 7.

In our research group we have relatively low Erdos numbers since our hub, Professor Lars Kai Hansen, wrote the concisely titled paper Neural Network Ensembles with Peter Salamon, – a researcher with an Erdos number of 1. The Hansen-Salamon paper from 1990 has become the most cited from our department (as far as I can determine). With Lars Kai I have written a large number of articles, e.g., Modeling of activation data in the BrainMapTM database: Detection of outliers.

Seven is still far from the five of Kiralee Hayashi, a former gymnastics champion, former scientist and present actress. According to her LinkedIn Profile she has worked at the Laboratory of Neuro Imaging (LONI), – a well-known neuroimaging research group. With noted neuroimaging researcher Paul Thompson she is on the author list together with big shot mathematician Shing-Tung Yau who has a Erdos number of 2, – according to Paul Thompson’s Wikipedia-cited Erdos number page. Their paper is Brain Surface Parameterization Using Riemann Surface Structure.

Now I have been trying to compute my Hayashi-Hayashi number. This must be 12 or less. Paul Thompson has a Hayashi-science number of one and through In vivo evidence for post-adolescent brain maturation in frontal and striatal regions Californian Terry Jernigan gets an Hayashi-science number of 2. (See also entry for the paper in the Brede Wiki). Terry is also in our Danish CIMBI brain project and with Jan Kalbitzer’s interesting neuroimaging seasonality paper Seasonal Changes in Brain Serotonin Transporter Binding in Short Serotonin Transporter Linked Polymorphic Region-Allele Carriers but Not in Long-Allele Homozygotes, where both Terry and I are in the author list, I will get a Hayashi-science number of just 3!

Allowing for the documentary/video trick and with Kiralee Hayashi and Trine Dyrholm in The Oracle of Bacon I get a Hayashi-film number of 5, and my Hayashi-Hayashi number then becomes 8.

What a small world.

(minor edit: 2012-10-16)


Brede Wiki and Brede Database 2009

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I have just drafted a section for the CIMBI 2009 annual report:

We have argued for a wiki approach to database information from published neuroimaging articles [1], and we now have implemented the Brede Wiki available from the Web site

The wiki is based on MediaWiki – the software that runs Wikipedia. With an extensive use of so-called MediaWiki templates information can be structured and easily extracted [2]. The content in the wiki is focused on neuroscience information: Text and data about neuroimaging studies, brain regions, topics, software, researchers, organizations, journals and events. The wiki makes extensive use of deep links to other neuroscience databases, enabling federation of content with other neuroinformatics databases. The Brede Wiki has almost 1,500 pages, e.g., describing 206 brain regions and 175 scientific papers. With the extracted data from the structured part of the Brede Wiki a small search interface has been constructed that allows for searching for nearby coordinates to a given query coordinate. The Brede Wiki also allows for upload of volume files in a standardized format. Thus it provides a uncomplicated means for sharing result volumes from neuroimaging statistical analyses.

Another project of the group – Brede Database – has now been included in the large scale American database federation effort ‘Neuroscience Information Framework‘. Furthermore some of the visualization efforts for the Brede Database was described in a recent article [3].

  1. Lost in localization: A solution with neuroinformatics 2.0? Finn Årup Nielsen, NeuroImage, 48:11-13, 2009
  2. Brede Wiki: Neuroscience data structured in a wiki, Finn Årup Nielsen, Proceedings of the Fourth Workshop on Semantic Wikis – The Semantic Wiki Web : 6th European Semantic Web Conference, Hersonissos, Crete, Greece, June 2009: Lange, Christoph
  3. Visualizing data mining results with the Brede tools, Finn Årup Nielsen, Frontiers in Neuroinformatics, 3:26, 2009.

The image is a figure from the CC-by Frontiers in Neuroinformatics article

23 year in coma and then in headlines.

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Rom Houben was thought to have been in coma for around 20 years but then Steven Laureys brain scanned him with positron emission tomography and found that he was minimally conscious. From a German news article it gets into English news and further even to the front page of a Danish tabloid. And the news media had citations from Rom himself: So he can communicate with complete sentences! That is something of a story.

I heard of this story and found that it already was on Wikipedia, where on Rom Houben’s page one could read a section called “controversy”. A video was linked from the Wikipedia page and it clearly showed Rom communicating via Facilitated Communication (FC) (p?? dansk: staveplade). Now FC has exceptionally low standing in the scientific community, and immediately that would call the whole story into question. I heard Steven Laureys in one scientific conference and he seemed to me to be an ok guy—not one that would start using FC. But this story could undermine his credibility. Anibal from Spain, that I follow on Twitter, pointed me to the an entry in Neurologica Blog where commentors were also very sceptical. But one—presumably Flemish speaking—commentor pointed to a recent Belgian news article where Steven Laureys had spoken. The commentor translated it to English, and according to this Steven Laureys says:

That (FC) is a debate that troubles me much more. I myself am sceptical, and that kind of facilitated communication still has a bad reputation, and rightly so. I’m not part of that, and have never suggested using it.

So it seems the news media made this story big by not being critical about the FC. And Wikipedia is more credible?