Tai-otoshi - free judo illustrations

Click the image to reach the illustration-library at Flickr, or you may cut and paste this URL: http://www.flickr.com/photos/hultstrom/sets/72157632298341948/
Image is free to use under the Creative commons - attribution - share-alike license.

At our judo club in Uppsala we have been looking over the graduation hand-outs that have been used for years. They are just lists of techniques with some illustrations. The illustrations are a mix of horrid old photocopies, illustrations stolen from different books, and some hastily drawn stick figures. There are two problems with this. First, they are mostly bad, and secondly they are either copyrighted or of uncertain copyright status. In an effort to fix this we went looking for creative commons or other freely available judo illustrations on the internets.

There are photographs for some techniques on wikimedia commons that are not terrible, there are even some illustrations, although mostly not so good. At judoinfo everything is copyrighted, and frankly the quality is not always what you would hope for. In the end we were not able to find more than a handful of usable images, which explains the quality of our present hand-outs as well as the quality online in general.

Since I clearly haven't got enough shit to do, we decided to create a set of illustrations and release them into the wild for the judo community to use and spread. All those books are great, and we all have them, but the children don't and they never will. So, here are (or will be) a collection of free to use illustrations of judo techniques. They are provided under the Creative commons - non-commercial, attribution, share-alike - license, which means that they are free to use for non-commercial purposes as long as they are properly attributed, and any derivative works are also shared freely under the same license.

Original tai-otoshi photograph. Copyright Michael Hultström 2012.

First out is Tai-otoshi, or body-drop. Mostly because that was one I had a good photograph of to use as template. Don't expect this to go quickly, but give us a year or two and there should be fair number of images to use. Quality-wise I will be aiming for proper vectorised line-art in the end, but that is even more work and will take even more time.

Edit: I have been convinced that the non-commercial license is too restrictive as it potentially limits uses I would like to allow. Thus, the illustrations are now re-licensed as attribution, share-alike.

Avoid boring people

Anna-Maria De Mars has some good advice for judo players that is equally applicable to science. What she is saying is, in short: Work harder than the competition, and work with people who are better than you are. Actually, the latter of these was originally advice for scientists from James D. Watson. He wrote a whole book on the subject:

Avoid boring people: Lessons from a life in science. 

Being a sucker for books I bought it immediately. So, thank you Anna-Maria for pointing it out to me (albeit indirectly). The best thing about it is the double-meaning title. Behind this is an autobiography, which is interesting in many ways, but today's subject is the Remembered Lessons at the end of each chapter. There is some very important survival advice there, like:

"Avoid fighting bigger boys or dogs."

 And some advice that will be good for your development no matter what you do:

"Seek out bright as opposed to popular friends." This is really what Anna-Maria was quoting although from a different article as: "Never be the smartest person in the room," which sounds better but not as good as the book-title.

Then, there is some advice for young scientists like:

"Choose a young thesis adviser" that I obviously think all bright young prospects should do now, but which I did not follow myself and do not think I should have.

Or, the more cumbersome:

"Extend yourself intellectually through courses that initially frighten you," which is really good advice, and, like for Watson himself, mostly means study more mathematics and statistics.

and

"Keep your intellectual curiosity much broader than your thesis objective." This is also one of my own goals, and a recurring suggestion for my students. To some degree it comes naturally to medical students, since they have to be able to handle a variety of patients. However, they (MDs) often have to be induced to read more widely from theoretical literature, while students with basic science degrees have to be motivated to read some clinical medicine as well (and everyone has to be forced and whipped to study more mathematics and statistics). 

The autobiographical part is also interesting. James Watson describes how he was very focused on forwarding his career, and not spending time on things (courses, projects, etc) that would not be of direct use for his research or advancement in science. Anyway, that was it for now. I am going to follow his advice to:

"Work on Sundays."

Wish for a responsive pocketable camera

Instead of working, which I should, I have been drawing another camera. I have been drawing space-ships, weapons, robots, and the occasional camera since forever. Mostly without any regard for cost, usability, or even feasibility. However, looking for a camera that fits my way of shooting have prompted a series of ever more detailed camera designs. I think it is getter rather close to what I would like to see, and although camera-makers are getting closer and closer in some regards other are yet to be fulfilled.

The basic design is a pocket-size, window-finder, all-manual camera. The body is all metal, possibly with some grip-friendly cover, and it should be weather-sealed. With weather sealed, I mean submergible. It should be small enough to fit comfortably in a normal trouser-pocket, or a largish shirt-pocket. There is a sharp-edged finger-grip and thumb-grip, which I think is especially important even in a small camera.

The sensor should be large, ideally full-frame 35mm, which balances field of view with depth of field. It should have in-body vibration reduction. The finder should be a frame-line hybrid view-finder with parallax correction. The primary focus-confirmation is by overlay of in-focus edges in the optical finder. The finder can be switched to all-digital for macro. 

The lens as envisioned is a fast non-interchangeable prime 35mm F/1.2 with a metal construction. Focus throw should be short, and the action smooth. Aperture is set on the barrel with click-stops as it is primarily a photography camera, potentially the aperture ring could be pulled out to engage a smooth aperture for filming. Both the focus and aperture rings can be set to auto. The aperture with only a slightly firmer detente, and the focus by pressing the mechanical AF-lock button. However, to get out of autofocus you just turn the focusing-barrel past a detente. There is no reason the lens couldn't be interchangeable, except that I would like to keep bulk to a minimum and lenses tend to keep accumulating if the possibility exists.

The top of the camera has mechanical dials for the other two main exposure settings: shutter speed and ISO. Both include positions for automatic settings, and the shutter-dial includes a T-setting for electronically variable speeds larger than one second, and a bulb-setting. If any exposure control is set to automatic, exposure compensation can be set with the thumb-wheel. Obviously, if you set all exposure-controls to automatic, you have automatic exposure. The small arrows light up to indicate over- or under exposure. On the top-panel there is an O-LED screen where the basic exposure info, including a histogram can be easily seen. In addition, the current focus-distance, photos remaining and battery can be seen. What is shown is obviously customisable. There is a button on each of the dials. Both have three-level shutter-release action. Both have LEDs on top. Finally there is the on-off switch, which is a mechanical breaker. If it is off, the camera is off, no more taking the battery out nonsense because of software malfunctions. If it is on it can go into a sleep-mode to save battery, but should take an image immediately if you press the shutter-release.

Now, the back panel is dominated by a high-resolution (think iPhone retina resolution) touch-screen. In addition, there is the thumb-wheel, two thumb-buttons and four buttons for the left hand. All buttons have LEDs so that they can indicate if a function is activated or not. All buttons and the thumb-wheel are customisable by way of a very easy touch interface. You could set  one to AF- or AE-lock, one to activate live-view, or have different buttons for single and multiple shot shutter-release. The touch-screen is used for organising images, setting up the button-based interface and can be used for composition, auto focus selection, exposure selection et cetera when shooting. It is obviously multi-touch so that it supports pinch-zoom and such. Even in live-view, and up to a scale where individual pixels can be seen so that critical focus can be easily achieved. Finally there is an additional button on the front. This and both thumb-buttons are three-level shutter-release type buttons, so that there are a potential total of five full-function shutter-release buttons.

One of the most irritating things is when you press a button by mistake, or touch the screen and something is changed or just hangs. Therefore there is a mechanical lock-switch. It can be set to lock everything, everything except the shutter-release, or any subset of buttons and touch-screen functions. 

There is no hot-shoe because there is no room, and it is a bit 20th-century. The camera has built-in radio sync that by software settings can control any and all radio sync devices. Sync-speed is very high because of the leaf-shutter lens. 

Basically it is a manual pocket-camera, where the interface can be configured to your shooting style and locked so that nothing is changed by mistake. Since all settings are electronic on the inside you can even set a button to be an emergency shutter-release that ignores even the mechanical settings and immediately takes a picture with some other settings. For example, let's say you are doing manual landscape work at base-ISO and f/16 at 1/30s using touch-screen focus. Resetting the camera to capture a moment would generally mean that you loose both your meticulous settings, and miss the moment. Using the preset emergency release set to take a photograph with f/8, at least 1/125s, and auto ISO,  you can always capture the moment. Or, conversely, if you are walking around doing street photography and suddenly find yourself wanting to take a macro, you could set another button to f/16, auto-focus, auto-ISO, 1/250s. You can even build profiles with different functions for different buttons that are changed all at once in the touch interface with just three actions: unlock, profiles, scroll and select profile.

Anyway, you get the idea. It is mechanical yet customisable.

Dogphotobooks

There are an insane number of pet pictures on the internet and there seems to be another book of puppies every other day, but when you like photography, books, and dogs you have to try to find something worthwhile. First in line is a thick thing that at a distance looks like any other book of puppies, but isn't. The Taschen published A thousand dogs is a thick (yes, Thick), soft-bound thing with 1000 (I assume) photographs of dogs.

However, instead of a collection of the 1000 currently cutest and cheapest pictures they could find they have collected a comprehensive historical selection of dog photographs. From 1839 and forward. The first are simple posed photographs made with some of the first cameras ever made, clearly showing the central role of dogs in our society across the years.

The book is divided into sections by years and includes some quite well-known photographers and photophraphs. The reproductions are quite good, at least matching the quality of the binding. It is a an interesting book both as a history of photography and for the wealth of images (of dogs), some of which are quite good.

Second out is the leading photographer of posed dogs, William Wegman. He has produced a number of books with his Weimaraner dogs. I picked the book Polaroids with pictures from an impressive 20x24in large-format camera. 

Some are more or less silly Weimaraners in clothes, but some are exquisitely posed humanesque dog photos. Let me just say that these are nor pictures you could make with boxers. No boxer I ever met would stand still matching paws with another boxer posing as it's shadow. At least not for long enough to make a large-format photograph.

Weimaraners, however, seem perfectly suited to the job. Some of the images are accompanied by short stories about how they were made and what Wegman was thinking or trying to create.  The book as such is a quite well-made soft-bound book of a size that is easy to handle. The reproductions are fine, and the dogs are cute.

Another book of posed dogs is Tim Flach's Dogs Gods. It is what we in Sweden call "praktverk", no expense has been spared. The binding is excellent, the format is non-standard. There are different high-quality photos on the binding and the dust-jacket. The reproductions are among the best available for large-production colour printing.

It is not quite as luscious, and not nearly as varied or complete as his book about horses Equus. Almost all photos are carefully posed and lit images. With only a few natural light - natural behaviour images sprinkled on top.

As with Equus there are some images that by their setting must have been taken in the wild but with lighting and posing that are nothing short of miraculous. Among dogphotobooks, this is the most equal of them all.

The nestor of dog-photography is Magnum's Elliot Erwitt. Elliot Erwitt's Dogs is a new collection of some of his most iconic dog photographs, as well as a number less well-known pictures. It includes a foreword in English, German, French, Spanish and Italian (as any proper book should). Elliot Erwitt represents the opposite of Wegman and Flach in that the book is all black and white, and while there are some studio shots the vast majority of photographs are of dogs doing what dogs do. They are ungroomed, sniffing each other, licking themselves or just taking a piss. If they are posed it is just the look-at-the-camera pose, or, they might be barked at. Something Erwitt is known for doing.

The book is a very nice folio hardback with excellent reproductions, although as is common with high quality black and white reproductions there is a bit of gloss differential. The book is too big to hand-hold but just right for opening in your lap while sitting in a leather armchair sipping a whisky.

Physiological illiteracy impedes progress in medicine!

A recent paper in PNAS has caused a bit of a ruckus discussion. The authors (Tim W. Fawcett and Andrew D. Higginson from U-Bristol) have compared citation rates with the number of equations in the text of papers, and found that more equations per page is associated with a lower number of citations in non-theoretical papers, but that there was no effect in theoretical papers. This carries over to all citations as well since the number of non-theoretical papers is much larger than the number of theoretical papers. They conclude that a higher density of equations leads to lower numbers of citations, and that this indicates a worse dissemination of the results to the wider scientific community. They go as far as using the title: "Heavy use of equations impedes communication among biologists."

This engendered a barrage of more or less agitated rebuttals with titles such as: "Do not throw equations out with the theory bathwater," "Mathematical illiteracy impedes progress in biology," "A suggestion on improving mathematically heavy papers," and "No evidence that equations cause impeded communication among biologists." Anyway, an alternative view is that theoretical papers (with lots of equations) are mostly cited in other theoretical papers, although this sounds obvious and would never have been published in PNAS.

I would wager that the same is true in all fields: Physiologists certainly cite other physiologists more often than they cite clinical scientists (and almost never cite mathematical biologists). It is further easy to extrapolate to the conclusion that detailed physiological data in a paper is associated with fewer citations in clinical medical journals. The obvious interpretation is that overzealous use of physiology in articles impairs dissemination of medical science, and that physiologists should use more common words and talk more about patient-survival and quality-of-life in the same way that mathematical biologists should relegate their equations to the appendix. The idea that they might be comparing apples to oranges (clearly a biological concept) is not even discussed in the paper, which makes the discussion a bit lopsided. More as if they were writing an opinion-piece than an article on empirical science.

First Floor

Finally some days off coming my way. Spent three days in Berlin at Hotel Palace, a really posh place. Morning and evening turn-down, including one-time slippers placed on a napkin (sic) by the bed. Nice spa, excellent breakfast, and the first-floor Guide Rouge star-restaurant: First Floor. No one would call it cheap, but very posh with polished wood-panelling, a total of eleven tables (whereof three were occupied on this Wednesday night), waited on by five waiters.

Some kind of olive-oil appetizer, very strange, but excellent.

Cracker with dill and some other stuff. Also an un-ordered appetizer that was excellent.

The six-course tasting menu with six selected wines was really good. As is common in these, posher, establishments, six-courses turned out to mean nine, and pralines for the coffee. 

Dove-filét with sauce, a light foam of something and some stuff on the side. Just brilliant.

Then, on Thursday, we went to another place with South-german food and wine. Very much simpler, although not in a bad way. A quite rustique atmosphere, small bare-wood tables and at least two booked sittings per night. They actually asked us to leave to be able to seat the next group. So, popular, and very good.

Friday morning I broke my two-day vacation streak with a meeting at the lab of a couple of my collaborators. After that we ate lunch at another rustique but Italian place, right under the rail-way. More brilliant food, I miss Berlin already.

Polar Obsession

Photobook review time! I just bought a new photobook: Edward Weston, Life Work offered as a special deal on The Online Photographer. It is the most expensive book I ever bought. No sorry, it is the most expensive non-work-related book I ever bought. Anyway, two days after the offer started the book sold out, now there are only some Special Edition books left.

However, I don't have the book as such yet, so this time it is Polar Obsession by Paul Nicklen. It is published by the National Geographic, and is absolutely stunning. Good format, slightly squat and not too large for having in one's knee. It is however to large for hand-holding. The binding and the paper quality are excellent and the reproductions are really nice.

There are a huge number of these amazing photographs accompanied by fascinating little stories. Like one about a female leopard seal that tried to feed him penguins. But don't read it here, listen to him tell the story himself:

This is really one of my best photobooks, and it wasn't even that expensive.

Hemodynamic Mechanisms of Acute Kidney Injury

Last week I was at an Acta Physiologica Symposium in Copenhagen. It was a scientific meeting jointly financed by the Scandinavian Physiological Society through the European journal Acta Physiologica, previously Acta Physiologica Scandinavica, and the German Science Council. As far as I have understood the first meeting they have ever financed outside of Germany.

From my perspective it was brilliant, there were at least six of my collaborators there and we got some time to discuss our future plans. Admittedly, not much time, but face-time is worth immensely much more than any number of mails and phone calls.

We were at the very worthy Royal Danish Academy of Science located in an old building right across from Tivoli in Copenhagen, just behind the city hall. It's from a time when there was money for science, and when that money wasn't unnecessarily spent on research. Marble, marble, marble, huge oil-paintings, relief-ceilings with paintings.

The actual meeting was about the hemodynamic mechanisms of acute kidney injury, which is a very current topic indeed. We are just about closing in on a time when we will be able to detect kidney injury already in the A&E, before the advent of renal failure with cessation of filtration. This means we will need to be able to distinguish different kinds of kidney diseases and will be able to follow treatment much more closely. What it means is that not only will we have to understand the early progression of kidney injury much better, we also need to find new, quick ways of defining it. It's going to be lots of fun. Look for the proceedings in the March or April issue of Acta Physiologica.

That third reviewer and the quality of your research

An interesting piece of meta-research has been circulating recently: Papers that have been refused and resubmitted receive more citations than papers that are accepted as is. This may appear counterintuitive or self-evident depending on your point of view.

It appears counterintuitive for non-scientists because it is easy to think that most of what gets refused is low-quality research. However, I would posit that authors are actually quite good at picking the right journal for their work, and get refused for other reasons than the over all scientific quality. This is where it seems self-evident. If authors are good at picking journals, then papers get refused because of insufficient supporting data. If, in addition, the quality is good this means that the reviewers find the results highly interesting. So interesting in fact that they would like more data to be really certain that the conclusions are correct.

This would certainly fit with the result of Calcagno and co-workers' findings that these previously refused articles are more highly cited. On top of that, a refusal generally includes reviewer comments and suggestions that pin-point the weaknesses of the work as seen from the outside. This often means that the authors will add even more data before resubmitting, and may then choose a higher impact journal as was indicated by the finding that the highest impact journals actually were more likely to accept articles that had been rejected elsewhere first.

There is of course still the possibility that the third reviewer is being an ass.

The Finish line

John Kovalic over at Dork Tower has some brilliant advice on his blog. As usual it is aimed at writers and artists, but equally usually, it is applicable in science.

There are only two things that are critical to your art.
Starting It and Finishing It.

- John Kovalic

There you are, I have nothing to add. I have some stuff to finish though. 

Analysis of genome-scale data

I thought I should do a post on strategies for handling genome-scale data from large experiments. Like many happy novices we rushed in and performed a couple of huge microarray experiments. Now we are trying to compare these against eachother and against strain-differences in in the form of SNPs. To say that this is not trivial is an understatement. In the end we have come up with a couple of strategies that might be useful to others as well. They might seem simple, but they will help you wade through your data, without getting stuck there for too long.

Don't look at untested data for anything but quality control. In most analysis programs it is very easy to just plot a gene by its intensity, either over all samples or by crude difference between group-averages. This is fun, and can give you some idea of what you are looking for. However, there are anything from 20k-30k genes in your dataset and you will not have time to look at all of them and make a reasoned decision. That means that if you pick genes this way you will indeed pick some hits, but not in a systematic way, and that leaves you open to errors. Either of picking a gene where the variation is too large, or that may only be the n+100th gene in your set and not the top one. The point is: You just don't know. The suggestion is to test your genes first, and then use the list of significantly differentially expressed genes to pick your top hits.

Consider doing a single comparison across several groups. If you have run a large experiment, with several groups (where several is anything from four to whatever). It is a chore to keep track of which genes were significant in which comparison, and even more to then pick a small number of genes to validate that are somehow representative across groups. So, try to pool your data by phenotype. If you have one group where something happens and lots of different controls. Just pool the controls and do a single comparison. That will give you just one list and make your selection process much easier.

When comparing experiments, use rankings. So, now you have a list, or several if pooling didn't make sense. Now you have to find your top candidates for validation. It is then helpful to use rankings. The easiest (and often quite accurate) way is to rank by average difference between groups (that would be your fold-change or log-ratio). If you have just one list, then you are done. If you have two, or several lists, then you can order your lists by rank-sum or rank-product. The rank-sum is a kind method that gives you some hits even if a gene is poorly-ranked (high number) in one of your groups. The rank product will pronounce those that are highly-ranked in all lists. Then you have the very particular rank-difference and rank-ratio. These may be very interesting if you have two experiments with wildly different phenotypes, but that you can not compare directly. If a gene is ranked in the top 10 in one experiment and 7815th in the other, it may be a very interesting gene and will then be ranked highly by the rank-difference or ratio.

Photographic necessities

Coming back to serious photography entails some additional expenses. Foremost being the latest version of Photoshop Lightroom, at the moment version 4. I spent quite some time testing raw-conversion and image database software some years ago. GIMP was fun but useless, not because it is impossible to do the stuff you want to do but because it is so complicated. Capture One was sleek and very nice, but head and shoulders above the rest was Lightroom, version 2 at that time. Subsequently I have also tested the combination of Adobe Camera Raw and Photoshop. Lightroom is based on Camera Raw so the difference shouldn't be that big, but it is. Lightroom is much more focused a on photographic workflow, while ACR and PS are supposed to be able to do everything from science to design.

Previously there were some things you had to go to Photoshop to do well, or at all. Keystone-correction was one of them. Now it is available under "Lens Correction" if you change from "Profile" to "Manual." I find it makes almost any picture look better, the background becomes less intrusive if it is rectilinear, and you just get the feeling of technical quality. For pictures such as the first one, it is absolutely necessary. Either you shoot it with perfect alignment, or you correct it. With sloping verticals it doesn't work at all. In the second it is not as important, but I think it improves the feeling that the image was made with precision.

For the last one it is maybe the most important. Either it is a snap-shot with some toys and a dog, or it is a well-aligned architectural photograph that uses the toys to lead into the image where the dog is. I find it makes all the difference. These are images that you would otherwise need a tripod and a tilt/shift capable camera for, and really quick too, if you wanted the boxer where she is.

So, how did I find this out? This is the second photographic necessity, I would argue, for all serious photographers. At least if you don't have an imp employee who does post-capture for you. You go to the Luminous-Landscape, click on "store" and buy their Lightroom 4 tutorial. With intro if you haven't used it before, without if you just haven't used version 4. It is the best instruction to be had for money. Well person-to-person teaching might reach the same level, but arguably not in the evening after the family has gone to bed, which is when I have time. Buying Lightroom without the tutorial is like buying a car without a key.

A walk in the park

Swedish national holiday, the government decided that Sweden should be more like other places and celebrate a national holiday. The Swedes are reluctant to say the least. It's fine to celebrate midsummer or Valborg (last of April), but you don't celebrate Sweden as a nation. However, you get a day off, so I went out with my new and Shiny™X100 for a stroll.

Not quite clear what it is supposed to be, but drawn by one or other of the kids in the neighbourhood with street-crayon. These kind of stylised, rectilinear things are perfectly corrected using "Enable Profile Corrections" in Lightroom 4. The slight barrel-distortion and vignetting disappears at the click of a button.

Poppy in front of lawn-chair. The macro capabilities of the X100 seem excellent. A thing that bothers me is the slow focus-update in macro mode. Another thing is that it seems quite difficult to achieve critical focus just where you want it. It may take a bit more practice is all.

Tagged utility-box. Critical focus is easy if the subject is flat, contrasty and in good light.

More macro, flower work.

Black and white is also fine.

River Fyris, more like a creek of mud. Still, it is pretty in black and white.

I found the X100 easy to work with. The finder is excellent, and the ability to switch to EVF for critical framing is brilliant. I still get lost in the variety of display and finder-options, but with any luck that will improve with experience. Most controls were easy to find, and usable even without moving your eye from the finder. It is annoying that the menu-system sucks so badly. Switching between manual and automatic ISO should be simpler. All options that you regularly use when shooting should be in the same place. Those would be ISO and auto-ISO, flash-compensation, external flash, ND-filter, Self-timer, and Dynamic range. The separate macro function should be done away with. As it is you have to use the macro mode from portrait range, and then you loose your window-finder and get an EVF that isn't fast enough for portrait work. You should be able to frame using the optical viewfinder even in the macro-range, no matter how inaccurate, it is still faster for capturing expressions.

Physically it is of a good size to walk around with. Certainly lighter and smaller than a Leica. Now I am using it with the filter adapter and lens-shade, half-case and strap. The lens-shade does make it too large for a jacket pocket, and the strap is too wide and too long, but apart from that I find it well made. The half-case fits perfectly, and provides just enough of an edge to grip it well with one hand. All told, I found it quick and easy to work with and quite intuitive, and the files are awesome.

X100 First Light

My X100, which arrived today, saw first light at 19:31:21. First I thought I would wait until night and shoot a star field, like a proper telescope. Especially tonight with a venusian solar crossing and all. However, I have weak character. Here's a picture of my foot.

X100 in the post

Saturday evening I buckled. I ordered the X100, and not just any X100 (no, not that X100 either, I have that already), I ordered the black limited edition Fujifilm FinePix X100. They say that many of the quirks that people complained about in the original reviews have been improved upon in the upgraded firmware, so that's good. Earlier you had to test stuff, now with the Internetz you can just read a ton of reviews.

The online photographer:
Fuji Finepix X100 Review by Ken Tanaka.
Shooting with a Fuji X100 by Robert Plotkin.

Luminous Landscape:
Fujifilm X100 On Test by Michael Reichmann.
Fujifilm X100 Follow-up Report by Michael Reichmann.

Reid Reviews (pay-site, but well worth it):
Fuji X100
Fuji X100 at the "Strolling Of The Heifers"
Fuji X100 New Firmware
Fuji X100 (Four Window-finder Cameras)

Zack Arias:
Fuji X100 :: Review

Steve Huff Photo:
Everything tagged X100

I have also had a touch and a feel. Both on the X100 and the NEX7. The NEX7 sits more like a small SLR in hand than I would have thought. You automatically grip the lens with a solid under-grip because otherwise it gets front-heavy, while the X100 have an excellent one-hand balance. Like a rangefinder, but lighter, much lighter. In my book that was 1 - 0 to the X100.

Then we have the finders. In my limited, in-store, testing I would say that the electronic part of the finders are about equally good. Keep in mind I couldn't test them both at once because I had to go to different stores. However, the window-finder in the X100 with digital overlay is possibly the best new idea in photography in ages. It's not as large and bright as a Leica finder, but it is not bad. That's 2 - 0 to the X100.

Then the NEX7 has a higher resolution, and a better sensor-score at base-ISO. So 2 - 1. But the X100 has a much better high-ISO performance, 3 - 1.

Finally the Black, limited edition X100 is just so much sexier than the NEX7, or the the silver X100 for that matter, or any non Leica M. That makes it 4 - 1.

It ships today.

Photographic restart

I have now spent more than half a year without a digital camera other than my iPhone. For this summer I find myself wanting to photograph again, there are weddings, 80th birthdays and road-trips a head, so I have been internet-shopping. Quite a number of exciting cameras have arrived. The digital Leica M iterations are a delight to work with, easy to use in manual, and relatively small. They are however very solid, and you get tired of them after walking around with them for a day. They are also very expensive unless you buy used, in which case I am back to the M8 I had before, M9s are still very expensive used seeing as they are the current model.

After seriously looking around for cameras that allow eye-level photography and are smaller than the Leica-M I am left with three cameras: Sony NEX7, which is class-leading in image quality at low ISO, 24 megapixel, interchangeable lens goodness in a small, really small package. In the micro four-thirds (MFT) class there is the very appealing Olympus OM-D. It is modelled on the old, film OM cameras, and going by the reviews one usable cameras out there. Finally there is the Fujifilm's X100 windowfinder camera, its like a Leica M only with a hybrid digital/opticalfinder and autofocus. Have a look at these excellent size comparisons: Front view, Top view.

Lens-wise there is only one good NEX lens: the Zeiss 24mm f/1.8, but it is getting such good reviews that it is a really appealing possibility. However, the NEX lenses (the Zeiss especially) are quite large for the miniscule body, so much so that when you attach them the camera isn't really pocketable any more. MFT has a number of nice lenses, including thinner, so called pancake lenses. Most of them get quite weak reviews though, especially the pancake-versions. There are two purpose-built Voigtländer MFT-lenses with huge apertures (which is good), but then they are huge, heavy lenses (bad), and the sharpness leaves something to be desired (worse). A good thing with NEX or MFT is that being interchangeable lens cameras with very short registers, they can take practically any lens ever made with an adapter. It is therefore tempting to get one of them to use with a Leica-M-mount adapter, which again turns out to make them quite a bit larger. On the other hand the Fujifilm X100 is not an interchangeable lens camera, but it does have a wonderful, sharp little f/2 lens with a 35mm effective field of view. However, everyone says manual focus on the X100 is horrendous so I would be forced to use automatic focus, which on the other hand is rumored to be quite good. The only way to know how usable and portable they really are is to test and compare the cameras in person before I possibly buy one. So, it is off to the camera shops for me.

More artistic advice for scientists

Photographer Chase Jarvis came up with the snappy-sounding advice: Create. Share. Sustain. And because original references are important: Originally formulated for the Art Director’s Club of Denver in The Consequences of Creativity.

Chase Jarvis believes that people create photographs in order to share them, and that there is a difference between personal work, and other work. So that, even if you are a professional photographer, most of what you do will be for money and not for the sake of art. This is the sustain part, if you are not a professional photographer maybe you sustain yourself by having a proper another job.

Create:

Coming up with new ideas, designing experiments to test them, and then to run those first experiments, when the method starts working and you get the first indication of whether you can reinforce or disprove your hypothesis. That's the essence of science, and that's where all the excitement lies.

Share:

Publishing is obviously the all-important sharing in science, but it being all-important also puts it firmly in the sustain-phase. Pleasing that third-reviewer, completing those control-groups and trying to fit three years of work into a 250-word abstract is not something you do for fun. The fun part of sharing, the part that actually lets you share your insights, get feedback and learn new stuff, is conferences.

That is where you can (not everyone does, but they could) present your really new data, and hint at ideas for the future and see how your thinking is received by the community. It sharpens your thinking, and brings the field forward. It will often reveal experiments that have already been done but not published, and might warn you off (or reinforce) some particularly difficult hypotheses.

Sustain:

Somewhere in each project's life it goes from being curiosity-driven to being driven by the need for completeness before publishing. Coincidentally this is where it often gets boring, which is why I put finishing up and publishing under the sustain phase. The other thing that is directly science-related that is part of sustaining is grant-writing, and grant-reporting. It is a bore and it takes a huge amount of time, but it is necessary to continue doing research.

Otherwise, sustaining often means teaching, supervising students and treating patients. If you are lucky, you find all of this exciting and entertaining as well, but even if you do, it is time off from research. However, just as in photography this is not only what often pays the bills, it is also a fountain of ideas for future research. Sometimes a question you can not answer may indeed be an unanswered question, and the problems that bother actual patients (or their physicians) keeps you founded in clinically relevant research.

So, there we are. Do some proper work, write some grants so that you can do research and go to conferences where you can drink beer share your findings, and get ideas for more research. Research that will have to wait until you have finished teaching for the semester, and aren't scheduled in the A&E every other night.

Advice from Neil Gaiman

Being a fan of Neil Gaiman's, like apparently everyone else on the planet, I watched his Commencement Address at the University of the Arts in Philadelphia, and I was once again struck by how similar worlds of art and science are. (I'm sorry, that should be Dr. Neil Gaiman.)

Anyway, the good doctor provides some good advice. First he notes that (or not first, but first of what I found particularly interesting) - that more and more art is produced on a freelance basis. That is you produce, and then you try to find buyers, or you put out an idea and find supporters so that you can produce. I think that is a very fitting description of an early science career, and in many ways even of the day-to-day work of established scientists. There are collaborations between scientists, there are grant-funded projects, and there are temporary academic positions, they all have in-common that you have to have a good idea (with some preliminary data), and you only get to continue if you do produce what you say you would. Or something equally awesome.

This above all other points has to be realised by anyone starting out in science, and by anyone in science who hasn't understood it yet: You are only what you bring to the table. The question is what to bring to the table. Neil's advice is simple: Produce good work, be easy to work with, and deliver on time. Pick any two. As he exemplifies if:

"People will put up with how unpleasant you are if your work is good, and you deliver it on time.

People will forgive the latness of your work if it is good, and they like you.

And, you don't have to be as good as everyone else if you are on time, and it's always a pleasure to hear from you."

 -Neil Gaiman

Sadly, this only goes for collaborators, and positions. Our backers in science have largely been dissociated from social interaction, which means that we only have two things to show them: How good our work is, and that it is delivered on time. Pick any two.

Now, if you aren't delivering at least two, you have a problem. It may be ok for a while if your work is really new and really good. However, if you're a chore to work with, your work is middling, and it isn't delivered on time, then you will notice that people aren't working with you any more. This is not because what you are working on isn't interesting. It's because we all hope to be doing this for the rest of our lives, and working with people who can't deliver, or are unpleasant to work with, just isn't worth it. An insight that fits well with the best advice Neil Gaiman ever got:

"You should enjoy it." 

-Stephen King

R-startup scripts

If there are some things you use all the time in R, you might not want to have to load them specifically every time. That is what ~/.Rprofile is for. As a start, have a look at R-bloggers: Customizing your .Rprofile and Customizing R: startup script. Then the question is what to put in your startup-script.

cat("Good morning Dr. Chandra.\n\n", sep = "") is an excellent choice.

As an alternative:
library(lubridate)
if (hour(Sys.time()) < 12)
  cat("\nGood morning Dr. Chandra!\n\n", sep = "")
if ((hour(Sys.time()) >= 12) & (hour(Sys.time()) < 18))
  cat("\nGood afternoon Dr. Chandra!\n\n", sep = "")
if (hour(Sys.time()) >= 18)
  cat("\nGood evening Dr. Chandra!\n\n", sep = "")
is more probable to be correct in a linguistic sense.

Then there are other important things. Like setting the language to English. For some reason R thinks I want it to speak German, even though nothing else on my system is in German. I have given up trying to find out how to fix it properly, so I use: Sys.setenv(LANG = "EN")

As they point out elsewhere though, you shouldn't put too many things in that you actually use for data analysis. That would make your code difficult to follow. It might be anyway, as mine is, but at least all libraries and such are loaded in the R-directory of the specific project. However, I do have a loading option for a .Rbasicfunctions.R:
if(file.exists("~/.Rbasicfunctions.R")){
    source("~/.RbasicFunctions.R")
    cat(".RbasicFunctions.R was loaded, providing the following functions:\n\n",sep="")
    print.functions()}

The actual file is empty though.

The center of the civilised world

That would be London. I am actually back in Uppsala now, but it was the center of the civilised world until Sunday. On the way home from the 22nd ESH meeting at ExCel I stopped at Paddington Station and went for a walk and some grub. Just as street or two away I found Micky's Fish & Chips, which I couldn't resist. To my great delight the fish was excellent, and the chips were chips. All told they just delayed my departure by fifteen minutes. I should have stayed longer, central London is much nicer than Heathrow Airport.

The ESH meeting was not bad either. I met many new friends and kicked off even more collaborations than at EB. I really must say that these meetings just keep getting better as I attend more of them (and have worked longer in the field). ESH suffers a bit from being too many clinicians. Some of the best work was relegated to posters in favour of rather bland clinical trials. That is not all bad, because then you really have time to discuss the data with the authors, and invite them out for a pint, which is actually the most important part of scientific meetings anyway.

The Big Day™

I have been waiting for this day for as long as I have ever waited for anything. In 2001, I and a group of my friends at the Gästrike-Hälsinge Nation (a student club/union in Uppsala) pooled our meagre resources, and bought one bottle of each of the five premier grand cru en primeur. That is, the three houses that produced the best wines in Medoc in 1855, Chateaux Haut-Brion, and Chateaux Mouton Rothschild that was elevated from 2'me Cru in 1973.

But first we had lunch, and to said lunch we had a collection of not-quite-as-illustrious 1999s. First out was Chateaux La Fleur-Petrus, the second-wine of Ch. Petrus (which was too expensive for us already 2001). Second was Ch. Pichon Longueville Comtesse de Lalande, then Cos D'Estournel, Ch. Ducru-Beaucaillou, and the odd-man-out Opus One.

As we always did in 2001, we voted for the best, and worst wine. The least smashing of the lunch-selection was the Ch. Pichon Longueville, and won did Opus One. It wasn't my choice, but it had a clear majority.

The main event, as you have already figured out, was the following wines:

Ch. Haut-Brion 1999
Ch. Margaux 1999
Ch. Lafite Rothschild 1999
Ch. Mouton Rothschild 1999
Ch. Latour 1999

Tasting this kind of mature (they have all reached their maturity-plateau) high-quality wines is very interesting because they change character so quickly when they are exposed to air. At first tasting, I tought Ch. Margeaux was going to be a clear winner. After some fifteen minutes I had changed my mind to Ch. Latour, but when it was time to vote the initally closed Ch. Lafite Rothschild had opened up and received my vote. I was wrong again, and Chateaux Margaux was voted best of the 1999 premier cru classé.

London - ESH-2012 - pre-report

For the first time in years I am back in London, and back in Love. It is just the most lovable city anywhere, and that is when it is windy and slight chill is in the air. They have promised rain. I couldn't say why I like London. Especially not why I feel different coming here, going through customs, riding the subway, and checking in to my hotel, than what I felt in San Diego, doing the same thing in better weather.

The ESH saw fit to award my abstract with a travel award this year. Very nice. Even more so considering they got me a suite less than fifty meters from the conference. Yes, a suite. First a small hallway with a side-board, then a massive bathroom, a sitting room with a kitchenette/bar (sadly unstocked), and finally a bedroom with a huge double-bed. There is a wide-screen TV both in the sittingroom and the bedroom. As usual, the only thing I care about is that there is free wifi, and there is.

Once I had installed myself I went out for braised mutton in gruel and a Guinness. Very English, and just what I was looking for after a week of margaritas and fajitas.

I pretty much missed the first day, but on the other hand it was mostly working groups and ESH-statements-in-the-form-of-seminars. Tomorrow til Sunday will be three crammed days of sessions. They run until 18:30 on Sunday so I probably have to miss the last one just to get to my flight home.

Traffic-analysis

It is always interesting to see what people find interesting. I use http://statcounter.com that provides a free tracking service for blogs with up to 1000 hits/month or something like that. In addition, google also keeps track of everyone ever visiting, but you have to pay to get at the good data. Going through my visitor logs for the last couple of months. There are some clear winners.

Using the OS X clipboard in R

Fillet of horse sous vide

Are to two most read. Then there are some that people arrive at after having used conspicuous google-searches.

Balls, great huge balls

But, rather gratifyingly, my very first post still receives some traffic. I guess there just isn't that much information on the Prevalence of hypertension in Norway to get.

When looking at visitors there are some regulars. You know who your are. Thanks for the traffic, it is good for my ego. Then there are some avid readers, what about reading 20 pages in a row as a visitor out of Aberdeen did the other day (no kidney research group there as far as I know, fmc corporation, I thought it was an ISP, but it seems to be a deep-sea oil-related business). Not the first time either. The only other hits like that are centered around one family member or other. I just hope I haven't developed a stalker.

Anyway, I suppose I should write more about practical problems in statistical programming, cooking strange meats, and eh… let's just say balls.

EB2012 - summary

The best chili and chocolate icecream I have tasted this side of the atlantic. Can't remember the name of the restaurant, but it was a hippish, italianish place on 5th avenue.

So, today is the second last day at Experimental Biology. It may be that I am a little late for the sessions this Tuesday morning. Yesterday was the renal-section dinner. I wouldn't call the party wild, but we managed to cram in a bit of warm-up, some post-dinner beer, and then we hit the margaritas. This being San Diego, the margaritas do not deny themselves. So, here I am blogging behind drawn curtains instead of attending the morning-sessions.

The conference has been quite a success even though I didn't present anything myself. Two of my students had posters. Posters that were gratifyingly well-attended. I established one new collaboration, and got invited to two labs to present our data. It is a special year for the American Physiological Society, 125 years since the establishment. Session-wise the meeting was excellent, although the renal- and the water and electrolyte-sections overlapped as always. I mean, who could be expected to choose between such interesting topics as "Angiotensin II and sympathetic nerve activity," "Novel signaling pathways in renal pathophysiology," and "Regulation of water and electrolyte-balance in diabetic nephropathy." It is impossible, and that is before even considering the programs of the other sections of the APS, or the other five societies that organise their own programs.

The exhibitions were, as they always are, full of wolves with bar-code scanners. I will probably be getting mail from them for years to come, but this year it might have been worth it. When I was looking at surgical instruments, as I am wont to do, I was looking at a double vascular clamp (a kind of holder for appoximating two vessels that you want to connect). These are generally quite expensive. This time, however, it turns out they had stopped producing the one I was looking at, and that I could have it for a smile and a song (almost).

Miniature vascular double-clamp with adjustable distance. Street value: $500, Today's price: $30. The two additional clamps was a bonus.

Now the cleaning lady wants to do my room. I shall valiantly go out into the sunshine and try to appear unfazed as the bright California sun sears my sensitive eyes, and the loud American noises pounds my fragile head. I might go for some more of that delicious chili and chocolat icecream.

Conference-season 2012

For conference-season this year I have two major meetings planned. I have done my share of extra time in the A&E during Easter to be able to go without using up my vacation. First, I am bringing two students to Experimental Biology in San Diego. Then, I am going to London for the 22nd annual meeting of the European Society of Hypertension where I have to present my data myself.

This year both societies are providing iPhone apps with the program: EB2012 and iESH2012. The Experimental Biology is actually available for Android as well. The EB-App works brilliantly, while the ESH-App shows nothing what so ever at the moment. The screen-captures in the app-store looks promising, so I understand it as if the App will be some kind of live-update thingy. That does not really help me now when I try to plan ahead.

Using the brilliant round-trip planner kayak.se I even managed to book a round-trip flight so that I do not have to go back to Sweden in-between or something equally stupid.

Having spent all my time in the A&E and helping put together the posters for EB, I am hopelessly behind in constructing my own poster. If I had had a talk it would have been much simpler. Then I could have kept preparing and changing it until the last minute, or at least the day before. Now I have to have time to print it before-hand.

So, maybe I should not sit here blogging. I will, however, try to report something from the meetings once I am there.

Beef-salad

One dish I have quite recently gotten to enjoy is salad. It is almost never done well at restaurants, and it is hard to do well in Scandinavia. It is getting better, but you can still only get really good, sun-ripened vegetables for a short period in the early autumn. Otherwise you have to buy your vegetables and let them lie for a week or so.

Now, the beef-salad is one of my favourites, you can do it with any meat, but prime, well-hung beef is just unbeatable. It is best served on plates, but you can equally well mix it in your salad-bowl and just put it on the table.

First you need some bitter lettuce. Today, I used ruccola, but finely-sliced endives are another brilliant choice. If you don't like it bitter, you are wrong may like it better with some baby-spinach. You can also add fresh herbs, for example basil. A less bitter choice may be a good idea if you are having wine, especially good red wine, to drink. The bitterness has a tendency to overpower the tannins and make the wine taste like juice.

Then you need ripe tomatoes. Best are the ones you watch fall and then use directly, but you can just buy your tomatoes and leave them to ripen on your counter for a couple of days and it will be almost as good. Watch out for really unripe tomatoes, they go powdery and soft before they get sweet and juicy.

I often use some peppers, red in this case, to get that crunchy feeling. Lately I have also started using Spanish pepper or mild jalapeno to get some extra sting. Olives are important, and they have to be good quality olives. There are any number of types, the green ones I used today were Greek Halkidiki olives.

I added an Italian air-dried ham, just because I could. Not Parma, but quite good anyway. There should always be cheese in a salad. I almost always use Parmigiano Reggiano, but Grana Padano is also good or Västerbotten, the only Swedish cheese worth its name.

Once you have built your salad, then you cook the beef. Rare to blue. Slice it, and spread it over the top of the salad. Finish off with a large-bodied olive oil and a liberal amount of Aceto Balsamico di Modena. Observe that I have never spent too much on a Balsamic Vinegar. They just keep getting better the more you spend.

Serve while the beef is still warm.

Opera, Baroque, and Vampire Weekend

I was never very fond of pop (not you Pop, pop the music). The lyrics always got in the way of the music, I thought (and often the music was not to my taste). Then Spotify happened. I promptly fleshed out my collection with new and exciting interpretations of Bach, Monteverdi, Telemann and Lully. It was glorious. Since it was free, I listened to some pop that my friends suggested. Most left little impression, but someone suggested Lily Allen, with the country classic: "Not Fair," and the equally brilliant: "Knock em out."

Let's just say that lyrics suddenly appeared in their proper focus. And then, someone else suggested Vampire Weekend. Their music can only be described as reminiscent of a British boy-band that went to the Caribbean, got high, and tried to remember public-school. Calling their music psychedelic will only put my life in bleak perspective for you, so I won't. Just listen to their piece: "Mansard roof", or "Oxford-comma."

Anyway, for as long as I had Spotify I did listen to some pop, and quite enjoyed it. Then I decided I didn't listen enough to warrant premium, and I can't abide adverts. In short, I stopped listening to stuff I didn't own. That was probably two years ago, or something.

So, -why this post? you ask.

Well, I should be producing a table and figure, basically statistics with bling, and I'm not highly motivated. The day before yesterday was a big funding dead-line in Sweden. Needless to say I worked the A&E two weeks straight before that, and had to do all the final writing in my spare time, that is, at night. Instead of preparing these data I have to do for some conference or other, I have spent the last hour, or so, listening to clever genre-twisting pop-music. Before I get back to my procrastinating ways, I'll leave you with a bit of modern music, a fugue on Telemann composed by Max Reger and played by Igor Levit.

National Kidney Conference, Bergen, Norway

I just attended the "National Kidney Conference" in Bergen. It was held in memory of Bjarne Iversen, my old mentor. Since the common denominator was that the presenters were old collaborators, the talks were very varied, or, you might say, the conference was a bit unfocused. Many did include a short presentation of how they had collaborated with Bjarne and tried to present data that in some way was connected to this, but equally many held their presentations as they would have at any other conference.

The highlights were Bill Arendshorst who talked about renal vascular function and Christos Chatziantoniou who talked about new markers and potential therapeutic targets in renal fibrosis. In addition Hans-Peter Marti presented data on markers of renal fibrosis on the genetic level. Personally, I had hoped for a wider attendance but I think the organizers wanted a more intimate meeting.

As with any meeting the important part was getting to meet some other experts in my field and discuss what we are and should be doing, and of course when and where we should meet next time to have a been and a chat. A bonus with invited lectures is that you get to aggregate your data and try to present them in a wider context. All-in-all a good meeting, although with a sad undertone as we remembered our mentor and friend who could not attend what was originally planned by him as a retirement seminar.