cpbotha.net » science

You have beautiful ize. [Weekly Head Voices #62]

cpbotha — Sat, 19 Nov 2011 21:29:09 +0000

I completely lack the genes that usually cause human males to have a thing for cars, but I do love Top Gear. This trailer for a fictional 60s detective show, made by Jeremy Clarkson, James May and Richard Hammond, encapsulates many of the reasons why:

Moustaches, guns, girls, cars and Hammond karate-chopping the porter at Playboy Club London for absolutely no reason whatsoever at 41 seconds can be nothing but 100% pure AWESOME.

It’s crazily busy at the moment, for a large part due to the extra load of having to teach and revamp, AT THE SAME TIME, the TU Delft’s postgraduate Data Visualization course. I’ve chucked out the written exam and the structured lab work, and exchanged it for paper reading, class discussion and four independent projects, inspired by positive experience with my Medical Visualization Ninja Training Course (third year in the running, Ninjas all over the place!), the postgraduate InfoVis course I gave at Stellenbosch and of course the teaching materials of esteemed colleagues at UBC, Harvard, Berkeley and Stanford. With a bit of luck, we will soon deliver a whole class of new-style DataVis Ninjas.

At a recent conference, I ran into an erudite half-British colleague from the far North, who in a few minutes almost managed to turn my world into rubble. You see, I’ve always proudly promoted the use of the -ise forms of certain words, such as visualise, realise, colonise and so forth, these being examples of British English. (Obviously, I adapt when American English is required.)

It turns out that, as is the case with life in general, it’s unfortunately not as simple as that.

It turns out that many of the -ise words are originally from the Greek or the Latin with “-ize” endings, and therefore the Oxford spelling prefers their use, although it accepts the “-ise” forms as well. On the other hand, the Cambridge University Press, as well as the mainstream media and most of the public in Britain and the former colonies, has a strong preference for the “-ise” forms. Certain other words like for example advertise, advise and surprise always take the “-ise” form in British English.

So now I’m faced with this conundrum. It would otherwise not have been such an issue, but the words “visualise” and “visualisation” come up quite often during my work day. Sticking to “-ise” is easier and still correct when in British English mode, but “-ize” for those few words of Greek and Latin origin could perhaps be considered more correct, and has the great advantage of allowing me to standardise on “visualize” as the canonical form of that important term. However, then I would run the risk of confusing the “-ize” and the true “-ise” words in Oxford English, potentially leading to painful embarrassment at the many cocktail parties that I frequent.

So you see, the Universe is just full of mysteries. Another mystery that has plagued humankind for decades, is what would happen if Stephen Hawking and Albert Einstein got involved in a rap battle. Well humankind, wonder no more:

Ok kids, thank you for tuning in again. Have a great week, I hope to see you again soon!

EuroVis 2011

cpbotha — Sun, 26 Jun 2011 11:25:00 +0000

I’ve written before about EuroVis, the most important European scientific conference on visualisation. In 2009, it took place in Berlin, in 2010 it was in Bordeaux, and, an a surprise non-twist of alliteration, the 2011 edition was held in Bergen, Norway. With 216 attendees and a practically perfect organization, this year’s edition has been described as the biggest and the best EuroVis ever. In a bid to save some time (I still owe you a mega-edition of the Weekly (actually Monthly) Head Voices), I’m going to give my biased account in bullet-list form:

On Tuesday evening, we were welcomed by the very charismatic vice mayor of Bergen in the Tårnsalen of the Lysverket building of the Bergen Art Museum. It seems the photo I took of the inside of the art deco tower, built in 1938, is quite a popular shot. The food was divine, thank you very much.

Art Deco tower from the inside in the Tårnsalen, Lysverket.

The next morning, during the conference opening, the following Bergen (rainiest city in Europe) joke was told: A visitor asks a local boy in exasperation “Does it rain like this all the time?” and the little boy answers “I don’t know, I’m only 12 years old!”.
The conference keynote was given by Scott McCloud, American cartoonist and comic theorist, on aspects of visual communication. This was most probably the best presentation I’ve ever had the privilege of experiencing. Besides brilliant oratorship, his slides are somehow more a visual stream of consciousness affair than discrete quanta of information. When I grow up, I’m going to present like that.

As per usual, I get to award the Weekly Head Voices Best Paper awards, and they go to the following papers:

A Shader Framework for Rapid Prototyping of GPU-Based Volume Rendering by Christian Rieder, Stephan Palmer, Florian Link and Horst K. Hahn. Rieder and his colleagues have constructed a full GPU-based volume rendering pipeline in MeVisLab of which the various shader based components are modifiable at runtime. This means that you can prototype your GPU-based volume rendering ideas in no time flat!
Curve Density Estimates by Ove Daae Lampe and Helwig Hauser. Back to basics and really important work on the effective visualisation of complex curves at any resolution, with smooth scaling between levels.
A Gradient-Based Comparison Measure for Visual Analysis of Multifield Data by Suthambhara Nagaraj, Vijay Natarajan and Ravi S. Nanjundiah. Another back-to-basics paper in which the authors show how to find the agreement between hundreds of scalar fields and visualise this agreement, thus enabling comparison.

The slightly less prestigious EuroVis 2011 Best Paper awards went to:

Uncertainty-Aware Exploration of Continuous Parameter Spaces Using Multivariate Prediction by Wolfgang Berger, Harald Piringer, Peter Filzmoser, Eduard Gröller. I was unfortunately in the other session, but was told by numerous colleagues that this was indeed an award-winning presentation as well.
A User Study of Visualization Effectiveness Using EEG and Cognitive Load by Erik Anderson, Kristin Potter, Laura Matzen, Jason Shepherd, Gilbert Preston, Claudio Silva. This was presented in the Evaluation session which I had the privilege of chairing. It is indeed a very compelling idea to measure the effectiveness of a visualisation through cognitive load and this paper documents the first very important steps in this direction.
A Gradient-Based Comparison Measure for Visual Analysis of Multifield Data by Suthambhara Nagaraj, Vijay Natarajan and Ravi S. Nanjundiah. This was also amongst the more prestigious WHV best paper award winners, see above!

The rest of the conference featured the following bullets:

During the social event on Thursday evening, Frits Post (my boss), was elevated to the rank of Eurographics Honorary Fellow, recognizing his service to and standing in the visualisation community. Including this newest addition, there are only five (5!) EG Honorary Fellows in the world today. I am very proud!
During the first session of the morning after the social event, I had the exquisite privilege of presenting the work of my Brazilian colleagues: Piecewise Laplacian-based Projection for Interactive Data Exploration and Organization by Fernando V. Paulovich, Danilo M. Eler, Jorge Poco, Charl P. Botha, Rosane Minghim, Luis G. Nonato. I really do like presenting at events like these, and it’s been a while. Do read and cite the paper, it documents a practical way of reducing any set of high-dimensional data points to the visual space, and enabling interaction with those points on the visual space!
The capstone of the conference was presented by the legendary Prof. E. Gröller, also known by the whole community as Meister. In typical style, the title of his talk was only announced during the talk itself. The title was The Haunted Swamps of Heuristics. In this philosophical and visionary contribution, it was argued that algorithms and parameters are too deeply intertwined to focus only on the former, but that it was more important to study, in detail, the exact behaviour of the latter. More broadly speaking, we need to accept the fact that there is a great deal of uncertainty also in the parameter spaces of our algorithms, but that this uncertainty can and should be dealt with correctly.

That thought-provoking capstone and this blog post will share the same concluding quote:

Doubt is not a pleasant condition, but certainty is absurd. — Voltaire / Gröller

I hope to see you in the comments below! You could also opt to click on my shiny new +1 button, or my slightly older but no less shiny retweet or facebook share buttons.

Schloss Dagstuhl: Computer Scientist Heaven

cpbotha — Sun, 19 Jun 2011 19:56:43 +0000

Somewhere in a remote but picturesque location in southern Germany, there’s a special castle called Schloss Dagstuhl. Every week, the castle fills up with a smallish group of Exceptionally Privileged Computer Scientists, who can only go there Because They Have Been Invited. Every week hosts a different field; In my case this was the Scientific Visualization seminar, one of the oldest participating groups. Everything has been setup just so to guarantee a perfect computer sciencey week for all guests. Because I’ve already been boring too many people with this story in person, I thought it prudent to write it up. Let’s hope it’s not a first (and second!) rule of Fight Club situation, in which case posting frequency over here might drop quite drastically.

Schloss Dagstuhl, picture courtesy of Wikipedia.

To begin with, the meals are exquisite, three times a day, every day. As we all know, the path to a computer scientist’s heart is through buying them new gadgets, but feeding them well is a great backup plan. Another very nice touch is the fact that seating is deliberately randomised, meaning that your introvert self is forced to sit at the table with a different group of guests during each lunch and dinner, in turn meaning that even if you try otherwise, you will probably get to have a good conversation with every one of the fifty attendees.

In the case of our seminar, the working day consists of presentations in blocks of three or four, followed by a longer block of discussion on all the preceding presentations, panel style. Attendees were all asked not just to give a standard scientific presentation, but to discuss open problems and future challenges in their respective sub-fields. I (and many others, judging by the aggregated post-meeting feedback) really enjoyed this format. The presentations made one think, and the discussion blocks were long enough to really get into the details. You can check out abstracts and slides on the seminar website.

After a full day of quite intensive discussion, there were breakout sessions during which four subgroups started working on the various chapters of a new Springer book that should appear sometime early in next year. The book will deal with multi-field, uncertainty, biomedical and scalable visualization, and it has the makings of being a keeper.

The other extremely important magic bit about this castle is the abundance of real coffee machines (ones that grind coffee beans for every cup), snack corners and, uhm, beer fridges. You can’t really go anywhere, as you’re in the middle of nowhere, so after dinner the conversations tend to continue till late in the night, conversant stamina enhanced by said coffee and beer facilities. Evil science plans were made, good old-fashioned deep conversations were had and the early next morning consequences were flatly ignored. I haven’t laughed quite so much in a long time, but that part of the programme prefers, and has the right, to remain completely silent.

If you ever get the invitation, don’t hesitate for a second to accept: You shall return an exhausted but terribly happy computer nerd.

On the importance of taking notes. [Weekly Head Voices #38]

cpbotha — Sat, 19 Feb 2011 22:39:52 +0000

Post summary: Part one is about friends graduating from Evil School, part two is rather short mentioning vague bits of good news and part three is 100% time management and productivity boosting goodness! Feel free to skip, skim or reorder!

One

On Thursday, February 10, 2011, my dear friend Mister Krekel graduated from Evil School after years of hard work and evil-doing, and will henceforth go through life as the formidable Doctor Krekel. Please do watch out.

Evil School. (Photo by the talented fpixel.wordpress.com.)

The joyous transition took place in the Evil School’s Academiegebouw in Leiden, and this time yours truly (I’m referring to me in a round-about fashion) even had the great honour of playing a part in the formal proceedings. If you’re curious as to what exactly this ritual constitutes, see this previous edition of the WHV on the graduation of another terribly evil colleague. I believe that the bunch of us now constitute a bona fide Axis of Evil. No, the evil jokes can unfortunately not stop yet.

The Party was held in a secret cafe nearby. You will notice that I’ve capitalised Party, as it was not your average run of the mill Evil School graduation affair, but a social event of note. Here in Holland, the PhD defence and graduation are a combined affair, and so the whole day is dedicated to just one person. It is actually very special: People take time off from work, sometimes even temporarily put aside their differences, and travel from all over to attend the festivities. It’s like a wedding, except that there’s only one of you. I can only recommend it very highly. At the Party, everyone had clearly read the memo, and they were there with that singular goal in mind: Celebrate the freshly minted Evil Doctor. Presents were given, speeches were held, photos were shown, beer was imbibed and, flying in the face of all advice concerning the mixing of alcohol, cameras and social networking, the best evil photographer in town, who’s coincidentally also in Evil School, took the most amazing photos that you should be able to see on Facebook if you’re one of the privileged few to belong to The Network, also known as The Friends of the Axis of Evil.

Two

On the good news front, you’ll see (or not) on the list of EuroVis 2011 conditional accepts, that a paper by cool colleagues from far away, to which I contributed a small part, has been conditionally accepted, and hence has a significant chance of being presented at said event in Bergen, Norway (May 31 to June 3). We also have plans to submit a poster (or two), so there’s an even more significant chance that I will make an appearance at this fantastic conference! We’re also cooking up various odds and ends that will hopefully crystallise sufficiently by the end of March to be submissible for VisWeek 2011. Cross yer fingers.

Three

Today’s backyard time management section is in fact more about planning than it is about notes. However, my Pro-Tips involve combining them in an easy to implement productivity booster. When people start out in research, one of the first bits of advice they get is keeping some kind of lab journal. I think this advice applies to more than just research: If you do any kind of independent or project work, jotting down your activities, thoughts and results during the day is useful in helping to structure your thought processes, and also very helpful when you have to backtrack a complex multi-day procedure. During my Ph.D., I filled a number of real cardboard-and-paper books with notes. More recently, I’ve started using Google Documents for the same purpose. Besides all the other advantages, having to document explicitly your work output keeps you productive and on your toes.

Pro Tip #1: Keep a lab journal, even if you don’t work in a lab.

I’ve mentioned before that my resolutions for 2011 included more concrete planning. This has manifested in a work-in-progress planning for the whole year, including milestones, awards won, and so forth, but much more practically, it has manifested in a little lab-journal-compatible trick. Every morning when I sit down to begin the day, I spend a few minutes thinking and then start the day’s journal entry by writing down, as concretely as possible, the tasks that I plan to complete by the end of the day. This also ensures that I spend effort on the important things, and not only on the urgent things. So, that brings us to:

Pro Tip #2: At the start of each day, write down in your lab journal exactly and concretely what you plan to accomplish by the end of that day.

These pro tips appear to be quite straight-forward, but together they help one to focus, and to keep tabs on one’s effective productivity. In other words, just being terribly busy the whole day gets you nothing; the trick is being terribly busy in all the right directions.

P.S.

Somebody is clearly pushing the boundaries of awesomeness… cowboys AND aliens!

Click here to view the embedded video.

The Future is Sick [Weekly Head Voices #36]

cpbotha — Sun, 23 Jan 2011 21:12:30 +0000

Post summary: Conference, VXLabs, SIP, boots, backyard philosophy on you the consumer, dramatic reading. Read on for more!

Just before the weekend I spent two days at the Dutch Bio-Medical Engineering Conference in Egmond aan Zee, in a ginormous seaside hotel. Probably because I attempted to keep up with the young ones during their nightly escapades, I’m currently dealing quite badly with a serious cold, which is why this is the first sick blog post of 2011. Besides all those germs, I also brought you this photo of said seaside right after sunset:

Sunset on the Egmond aan Zee beach. Gorgeous, innit? There's even a dude walking on the beach so that you can wax all pensive.

The conference was an energetic and motivating affair, at which yours truly even got to chair a session, during which I tried, in spite of not getting to bed all that early the night before, to Keep Things Extremely Punctual As Well As Mildly Entertaining. I succeeded in the former, you’ll have to ask the audience about the latter.

The absolute highlight, for me at least, was the capstone on Friday by Professor Richard Satava, a surgeon with an amazing vision of the future. Bordering on science fiction but for a large part backed by his own and other groups’ research, his superbly delivered presentation touched on surgical operating rooms completely staffed by robots (some elements remotely controlled by a surgeon), cell engineering, surgery robots that heal troops at the scene of the crime (hehe), genetic engineering, cloning and a healthy dash of trans-humanism. By the end the whole room was collectively straining at the leash to go and genetically upgrade anything and anyone they could find. With a room full of BME researchers, that’s more dangerous than it sounds. :)

Other note-worthy items of the past two weeks can be summarised in the following neat bullet list:

I’ve started a new blog, called VXLabs, for matters that are too nerdy even for this blog. If you’re interested, you can start by reading the HTC Desire Z (my lovely new smartphone) review I’ve recently gotten around to writing. If you’re nerdy enough, you might consider subscribing VXLabs as well!
There are far cheaper ways than Skype to call telephones around the world. With SIP software, such as SIPDroid on Android, you can use cheap SIP servers that even offer free calls to many destinations. See this page for a list of just the betamax (German VOIP company) providers and the free countries that they support.
I was approached by a company producing Ugg-like boots to review their boots, get a free pair in the process, and get a good deal for my readers. This is probably because I went on about those BEAUTIFUL Timberland boots in one of my previous posts. Although I was flattered that the gentleman in question thought my widely-read (haha) opinion would be good for his brand and he called this a fashion blog (!!), I declined, stating that my readership probably is more into Timberlands than Uggs. That’s true, readership? Right?!
Micro Backyard Philosophy: After one of those late nights refreshing my Twitter, Facebook, Google Reader and GMail for the Nth time, I got to thinking about how the internet sometimes turns us into 100% consumers, leaving no room for creativity. It’s insidious, because we believe that the internet will give us exactly what we crave if we just know how to search for it, and that it should do so with that next press on the refresh button, when in fact this is hardly ever the case, especially when that which you crave is in fact to create. Remember this the next time it’s getting late and you think Just One More Refresh. Don’t push that button. Sit back and think about what you really want to do.

That’s it boys and girls, thank you very much for reading this far! You go and have yourselves a fabulous and especially creative week. If you get lonely waiting for the next edition of the Weekly Head Voices, marvel at this dramatic reading of a bad user game review, creativity at its finest:

Click here to view the embedded video.

An Inside Job. [Weekly Head Voices #33]

An Inside Job. [Weekly Head Voices #33]

cpbotha — Sun, 21 Nov 2010 14:10:36 +0000

Hiatus: temporarily over.

My sleeping patterns are not quite what they used to be, mostly due to the latest manifestation of our little gene pool over here. Added to that, I’ve been really busy. Added to that, work has been throwing unnecessary curve-balls that have done their part in keeping me (pre)-occupied. In the end, a dash of perspective, several extremely wise friends and a generally sunny predisposition go a really long way, so here I am. :)

In this post, I’m going to touch upon the highlights of the past seven weeks (40 to 46) and I’m going to do so with bullets, seeing as I’m in a bullety-kind of mood.

I spent a week in Stellenbosch teaching Information Visualisation! Read all about it in this special blog post.
The week after that my mom came to visit us. She really has the best genes.
I met my new work laptop: A Dell Latitude E6410 with Core i5 M540 2.53GHz CPU, 4G ram, 500G HDD, NVidia NVS 3100m GPU with 512 MB video mem. It’s a 14″ latop (15.4″ is a completely useless format, flame me in the comments), but due to the materials used quite heavy. I like it!
Another one of our STW NIG research proposals has been granted. I conceived and developed this one together with colleagues from the LUMC Departments of Anatomy, of Surgery and of Orthopaedics. The title is High-definition Atlas-based surgical planning for Pelvic Surgery and we get to combine high-resolution human histology, mega-volume rendering, , biomechanical modelling and surgical simulation. With this grant we can appoint two more Ph.D. students (one in my group, one at the LUMC) for four years to work on this!!
The week after that I went to Salt Lake City (Utah, US and A) to attend the conference previously known as IEEE Visualization. It was AWESOME! (blog post half-written, will soon publish).
The week after that I had a really cool dream: I was playing high-speed catch with a bunch of people outside. The ball was randomly changing shape between rock, papers and scissors. If you wanted to catch it, you didn’t only have to be at the right place at the right time, but your hand also had to be in the right complementary configuration to catch the shape-shifting ball.
Now that we’re talking about dreams: I finally saw Inception and was completely blown away. It’s not about being complicated, it’s about being a well-told story and a fantastically filmed movie. What I positively adored, is the fact that Nolan doesn’t require much: He only needs you to believe that dreams can be shared, without giving away too many of the details of the mechanism, and then builds a marvellous story on that canvas. My absolute favourite scene was the waking up on the plane, just before the landing, almost at the end of the film. I loved the way in which the characters looked at each other, and the possible interpretations of their expressions.
On the topic of the Underworld gig in the Heineken Music Hall: I hope I have my voice back before my morning lecture tomorrow morning. Thank you Fantastic Friends!

That’s it kids. If you’ve come this far, you’re now mostly up to date. Please leave me a comment, it’s good for my serotonin! I hope you have a great week. To get you off to a good start, here’s a music video showing what an infectious idea could look like…

Click here to view the embedded video.

Teaching InfoVis in Stellenbosch

cpbotha — Sun, 21 Nov 2010 11:42:36 +0000

In week 40 (that’s Monday October 4 to Friday October 8 for those of you not so much into week numbers) I had the privilege of giving a week-long Information Visualisation course to a group of post-graduate students (a mix of B.A. Honours in either Socio-informatics or in Decision-making and Values Studies) at the Centre for KDD of the University of Stellenbosch in the building previously-known-as “The BJ”.

With this post, I want to summarise, extremely compactly, my impressions:

In spite of the odd publication at an InfoVis venue, and in spite of putting significant effort into broadening my horizons also into InfoVis, I’m strictly speaking still a Scientific Visualisation (SciVis) guy. In this context, developing and giving an InfoVis course was a fantastically educational experience. I aspire to be equally fluent in SciVis and InfoVis when I grow up.
I designed a course based on a mix of lecturing, paper reading and discussion and hands-on exercises. I can now highly recommend this combination. Next time I will put more effort into involving everyone more actively in the discussion. What also seemed to work well was the course website that students could add their work to during class.
I sourced almost all of my material from generous InfoVis colleagues, primarily Dr. Tamara Munzner, but also Dr. John Stasko, Prof.dr. Jarke van Wijk and Dr. Maneesh Agrawala. Thank you!
Having spent 7 years at the Stellenbosch Engineering Faculty (1500 guys all wearing t-shirts in jeans; furthermore, social skills are frowned upon) and the past 10 years at the TU Delft, a kind of Ultra-Engineering-Faculty, spending the week at The BJ interacting with socially adept and skilled communicators was a truly interesting experience.
I was otherwise also impressed with the level of cooperation between the students and their willingness to work hard (and long).
Laptop-use during lectures in a relatively small class: It’s an interesting phenomenon, having to deal with your own little communication backchannel. Banning laptop use is obviously not an option as there are too many possible advantages, but I’m not sure yet what a good solution would be towards making sure that the laptops are being used to augment learning.
Most students chose ProtoVis (from a list of 8 possibilities, and they were free to use anything else too) to implement their final mini-projects with. This was probably due to their previous web-programming experience, and also that ProtoVis requires more or less zero setup.

Conclusion: Much learned, hopefully the students did too. :) All in all a positive and energising experience!

An indecent proposal. [Weekly Head Voices #31]

cpbotha — Mon, 20 Sep 2010 20:03:58 +0000

Dear readers,

I would like to introduce you to my new friend:

Pretty Leifheit kitchen timer, ideal for the Pomodoro Technique. Also the first time I use the macro setting on my Canon. Doh.

It is old-fashioned and mechanical. It makes an extremely comforting ticking sound, and then after the 25 minutes of focus-time are over, starts ringing. The ticking is not too loud, and not too soft. The ringing is just the right length. You don’t take my word for it, as I’ve made you a short movie clip:

Click here to view the embedded video.

Comforting, no?

In spite of a number of deadlines having been successfully met, I’m still in the lamentable situation where every second counts, so I’m going back to bullet mode for the rest of this post:

The FNSF and I managed to finish that Indecent Research Proposal and submit it at 11:57 on Wedensday, 3 minutes before the Deadline for Indecent Proposals at the Dutch Science Foundation (NWO). We almost missed the deadline due to the extremely primitive web-submission system in use there. If you happen to be invited to review this proposal, please approve it. You Can Trust Us. :)
The real-time collaboration functionality in the new Google Docs was a life-saver during the writing of this proposal. Being able to see FNSF’s cursor move and edits happen in real-time was really great for coordinating. Now if they could only improve: 1) The styling possibilities (there are none at the moment, so you have to manually change typesetting if you don’t agree with their default style) and 2) The PDF export (it inserted page-breaks within tables and generally screwed up. Eventually I exported to MS Word, fixed typesetting and page-breaks there, then exported to PDF); then I would be happy.
On Friday I had one of the most hectic oral defences of my life. There’s a high probability I’ll have to try again in a year or two’s time. Or never. I’ll keep you posted. Or not.
Partly due to the events of Friday, but also to continuous general self-reflection (read: voices in my head that never sleep), I will gradually revise my publication strategy in the coming years. Bottom-line: I have to focus more on generalising until our applications start looking like pure theory. :)
I’m slowly learning how to say no. It’s hard, but at least there is some professional help available:

Click here to view the embedded video.

In a few weeks, I hope to have the time to write you a proper post. Until that glorious occasion, I’ll do my best to keep you up to date with these healthy and low-fat WHV light editions!

The Human Animal Post

cpbotha — Sun, 01 Aug 2010 21:26:15 +0000

(This post has a point. A very important point if I might say so myself and I’m even skipping the Weekly Head Voices because of it. Please read it, in sessions if you have to, from start to finish. It has a WHV Nerd Index of 0/5 and a Backyard Philosophy Index of 5/5. You can get back at me in the comments.)

It turns out that when any normal human being is faced with observations or evidence that oppose their already formed opinions, they tend to ignore or downplay the value of those observations. Conversely, any scrap of evidence that seems to confirm the opinion in question is considered to be good and trustworthy evidence. This is called confirmation bias: You and I both suffer from it, and it can be a dangerous phenomenon. Ideally, we would be able to judge the evidence and come to a reasonable decision, but this turns out to be exceptionally hard.

A photograph I recently took of a confirmation bias. Note that observations from below confirming preconceived ideas are favoured more than observations from above, resulting in the tell-tale yellow tinge and staircase edge at the bottom of the core.

Another interesting one is the planning fallacy: We are apparently hard-wired to underestimate the time we’ll need to complete some or other task. In other words, you always think you’ll need far less time to complete that project than you’ll end up using. Most of you have experienced this first-hand, or indirectly, when some huge IT or building project falls way behind schedule (and budget).

There is a whole list of such cognitive biases. As I’ve mentioned before, we’re basically walking jugs filled to the brim with misunderstandings, and mostly we’re unaware of it. Now you might think to yourself: But surely I’m better and more logical than the rest! I’m sorry to have to disappoint you, but you’re even biased about your biases. It’s called the bias blind spot, a meta-bias that means you’ll always estimate your own unbiasedness more highly than that of your neighbour.

I hope you didn’t nod off right there, because the next topic I’d like to touch on is that of sleep (please excuse the lame joke, I needed it for the continuity). Ever thought of exactly why you get sleepy at night? Or why your teenager (or teenage sibling, or yourself; substitute whatever’s more relevant) is not able to go to bed or wake up on time? Mostly we just go through the (sleep) motions without asking why or how. When you’re exposed to light in the morning, your eyes talk to your supra-chiasmatic nucleus (SCN), a cluster of brain-cells about the size of a grain of rice in your already small hypothalamus, which then, minute as it, starts raising your body temperature, releases the cortisol hormone (this gives you a boost) and stops the release of melatonin. When it gets dark, the SCN throws a switch which causes the pineal gland (itself just pea-sized) to start producing melatonin, another hormone, but one that makes you feel generally less alert and altogether sleepy, so you start thinking about that wonderfully fluffy and soft bed of yours, and it gets harder and harder to stay awake.

I find that really fascinating: There it is, the SCN, a rice grain sized clock that orchestrates the daily rhythm of your whole super-complex body! This helps us to explain to our toddlers why they should go to bed earlier: Because your melatonin is activated much earlier honey! (There’s no arguing with that, even when you’re 4 years old.) It also explains teenagers’ sleeping habits: Adolescent hormones and life-style seem to interfere with melatonin production, and so teenagers get their melatonin kick hours later than adults.

The hypothalamus consists of more interesting nuclei than just the SCN. The arcuate nucleus also lives there, and it’s one of the spots in your brain that produces dopamine. Dopamine rules your life. It plays an important role in just about every bit of your humanity that you care about: Motivation, punishment and reward, sleep, mood, attention, sexual gratification, learning, and so on. Dopamine is instrumental in drug addiction, and, perhaps unsurprisingly, also in ensuring that one human becomes completely and irrevocably obsessed with another when falling in love. Serotonin and norepinephrine are also involved, but dopamine is the one that makes you go completely crazy. Once you get past the crazies and you have the good fortune of finding yourself in a longer term relationship, guess what? Once again, there’s not really that much magic or even that much mystery: Oxytocin and vasopressin, two hormones that also act as neurotransmitters, help to ensure that you experience the warm-fuzzies when with your partner and hence facilitate the pair-bonding experience. Oxytocin also plays a crucial role in breastfeeding (our friend the hypothalamus notices sucking at the breast and kicks the oxytocin production into gear that gets the milk going to where it needs to be). Conveniently, it probably also plays a role in mother-infant bonding.

I could harp on for a long time about how exactly all of these (and many other) little tidbits determine your life, but by now, I hope that I’ve said enough and that you’re asking: What’s your point Vanessa?!.

My point is that you’re an animal. A cool kind of animal called the human animal, but an animal nonetheless. You’re a relatively complex machine, but a machine that can be studied and that can be understood. We humans have become incredibly skilled at picking apart the human machine. We have tools that can see which part of your brain is active during what activity, we even have tools to make the cells in your body glow in the dark when they’re being naughty. We still have much to figure out, but we know an astronomical amount more than we knew 50 years go. The points above are a microscopic example of recently acquired knowledge. Every day, the pile of Stuff We Know is growing more quickly, and the pile of Stuff We Don’t Know is shrinking more quickly. It’s a terribly exciting time to live in.

My actual point is: You’ve been given one of these human machines to drive. For life. You’ll be getting only this one, and you’ll be taking it to some strange places, even off-road at times. You’ll make a number of important decisions that deeply affect you and your machine and even the other machines around you.

Don’t you think that you should read the manual?

Weekly Head Voices #7: The Answer, a STAR is born, post-human YouTube

VCBM 2010 [Weekly Head Voices #26]

cpbotha — Thu, 08 Jul 2010 09:58:51 +0000

(This post is a slightly longer than average report detailing our trip to the EG VCBM 2010 conference. It’s of course super-entertaining, but if you still do wish to skim through it, I’ve bolded the per-paragraph themes. If you’re not sure what these danged conferences are about, see my recent EuroVis 2010 post for a general introduction.)

Last week, I accompanied Peter Schaafsma (he of the orbital fat mobility paper), Bastijn Vissers and André van Dixhoorn (they of the resting state fMRI brain connectivity paper) to Leipzig, where they had been selected to present their work at the second Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM).

Pretty VCBM logo.

Things got off to a great start when, as we were travelling there by speeding bullet (okay, it was just a brand-new rental Opel, but the Autobahn turns any car into a Speeding Bullet!), we managed to strike, at high speed, a high-quality German plastic bucket that had suddenly appeared right in the middle of the road. After a few more kilometres of noticing that our speeding bullet was not able to pass the very slowly accelerating bullet stage and was making strange disconcerting noises to boot (excuse the automotive pun), we stopped to investigate, noticing to our shock that the bucket, having been very badly burnt, Mustafa-style, was still lodged under the car.

After carefully dislodging the remaining half of the bucket, we were even more shocked to notice that the car was dripping concerning amounts of liquid more or less from the spot where the bucket had been stuck. Further on-site and online investigation by the crew brought to light the following observations: 1) The liquid was not hot, and so probably did not come from the engine. 2) The liquid was tasteless (don’t ask). 3) The air-conditioner had been running all the time, and certainly would have to get rid of water condensate from the cooled air. This latter observation was to us not immediately obvious, but now is, and hopefully to you as well: Automobile air-conditioners often get rid of condensed water through outlets under the car. Phew.

Our speeding bullet tore through the remaining 200 kilometres in record time, where my man Helmut from Vienna and these wonderful brain-boosters were waiting for us on the Nikolaikirchhof:

Leipzig's famous 1 litre brain boosters. Image deliberately deFaced. The arms in the photo might or might not belong to anyone that you know.

The conference kicked off the next morning bright and early with a brilliant keynote by Prof. Anders Ynnerman. This was related to the great talk he gave in Delft the week before, but even better, as, amongst other things, he had had the Virtual Autopsy multi-touch table shipped all the way to Leipzig to be able to demo live during his presentation. He even managed to undo the evil our projector in Delft had wrought on his laptop’s colour profiles and finally showed his visualisations in their full glory on the projector in the Mediencampus Villa Ida.

The second keynote, given by Dr Roland Bammer, focused on their work on eliminating motion artefacts in brain MRI, both by image post-processing but also, and this is the really cool bit, by mounting a special marker on the forehead of the subject that allows real-time 3D motion tracking and linked real-time low-level correction of the MRI acquisition process. They are currently working hard on getting their tech into users’ hands. Help them by bugging your local Radiology Department about this! :)

The multi-touch virtual autopsy table was available throughout the conference to try out. Two observations: 1. Sometimes the glass surface of the multitouch.fi table is harder to work with than the MS Surface's matt finish. 2. It's hard to use the table in environments with too much lighting.

The rest of the scientific program was perfectly varied, consisting of paper presentations, an invited talks session and a posters session, including a plenary fast-forward where each poster author was given three minutes to promote their work. What really shone throughout the two days, was the superb organisation in Leipzig: Thanks to Dr Alex Wiebel and colleagues, the conference was a text-book example of conference organisation, with each event occurring at exactly the right time, not a moment too soon or a moment too late. The Mediencampus Ida Villa was the ideal location for the conference, not in the least due to its air-conditioned auditorium shielding us from the more than 30 degrees Celsius outside temperatures. Another important manifestation of the superb organisation were the magical coffee breaks, always taking place exactly when you needed them, with copious amounts of cookies to boot!

Erik Pernod and Herve Delingette won the VCBM 2010 Best Paper award with their paper titled Interactive real time simulation of cardiac radio-frequency ablation, really great work combining elements of simulation, visualisation and a clear clinical application. The best paper committee had a relatively easy choice, as the reviews (3 to 4 per submission) were also unanimous about this paper’s ranking. As an added bonus, the work is available within the open-source SOFA framework.

My personal and completely biased Head Voices VCBM 2010 Best Talk Award however, goes to the invited talk by Marc Streit and Alexander Lex on Caleydo: Visual Analysis of Biomolecular Data. The presentation was an extremely entertaining show by two skilled speakers, striking just the right balance between focus and variety as they demonstrated several aspects of their Caleydo visual analysis software. At several points, for example the explicit visual linking of different heterogeneous data sources (paper here, youtube video here, see here for other publications.), I had the typical reaction to good scientific contributions: Now why didn’t I think of that?!

Three to four of the VCBM 2010 papers (this includes the best paper of course) will soon be selected to submit an extended version to the forthcoming special issue in the Computers and Graphics journal on Visual Computing for Biology and Medicine. Very importantly: Everyone is welcome to submit an aptly themed paper to this special issue! See the C&G special issue on VCBM call for papers for more information.

On a more personal note: This was the second VCBM workshop, with the first having been held in Delft in 2008, organised by yours truly. It was really great in Leipzig experiencing the growing community around this event and especially connecting with some of my favourite people. I’m greatly looking forward to future VCBM workshops, which makes it doubly cool that VCBM 2012 will be hosted by Prof. Anders Ynnerman in Linköping (Sweden) and that after that, it will become a yearly phenomenon.

Will you join us?