Micro Fluid Art

This started out as a fun way to display a new technique I developed to pattern proteins onto substrates. This technique allows for filling extremeley long microfluidic channels with solutions in a very facile manner.

I don’t remember ever doing a book review on this blog, and I figure it’s as good a time as any to start. To be honest, I was spurred on to do so by a less than favourable review of the The Yiddish Policemen’s Union by Michael Chabon that appeared in the Guardian. Well, it was pretty favourable, but I was annoyed by the reviewer’s insistence on an ‘almost fatal flaw’
To summarize briefly, TYPU deals with the creation of Sitka, a Jewish district in Alaska after the collapse of the new state of Israel in 1948. A temperory homeland, and one that is due to revert back to Alaskan control. In this setup, a murder is investigated by Police Detective Landsman, who takes to the case mainly out of a sense of outrage- since the murder was committed in his apartment block. The plot then proceeds to wind its way around Landsman’s ex-wife (who is now his commanding officer), Jewish tradition, political maneuvering, Jewish-Indian relations, chess obsessions etc etc.
The genre of the book lies, to my mind, fairly square within Alternate History, a subgenre of speculative fiction, which may explain why the Guardian reviewer had a hard time. It’s a detective story embedded in an alternate history. A close relative of this book is Len Deighton’s SS-GB, which deals with a murder enquiry within Nazi occupied Britain. It is obvious that TYPU is speculative fiction, especially because it follows most of the implicit rules of the genre. For example, there is little or no overt references to the historical differences. We begin to realize the true nature of the alternate history only through off hand comments, say like the destruction of Berlin by an atomic bomb, or the failure of the state of Israel. There is yiddish slang peppered all through the book, and most of the words you have to understand through context. And furthermore, there is (to my knowledge) new slang, a whole new vocabulary of this fantastic place. Once again this is consistent with Speculative fiction, where the ‘exposition’- a bulk of text explaining the setup- is now considered bad form. You begin to figure out the meaning of the words and the true nature of Sitka only by osmosis, and not by explicit instruction.
The book is, not surprisingly, very Jewish. Some familiarity with the tropes of Judaism is probably useful, but not essential . One reviewer claimed that it would be all but inaccessible to casual readers, but once again, people who read speculative fiction are used to being presented with a strange setup and having to make sense of it slowly. It’s almost a pre-requisite. Given this approach, I had very little problem ‘getting’ the book. Of course, I’m a bit pre-disposed to the book, since I did spend two years in Israel, and speculative fiction dominates my reading. Nevertheless, I think that despite the lack of clear hand holding, the book still delivers the goods. In fact, the book won the Nebula award for Best Novel, further cementing its ties with the speculative fiction genre.

My rating: Four stars (of David) from me.

Researchers re-create pre-Columbian sounds

Scientists were fascinated by the ghostly find: a human skeleton buried in an Aztec temple with a clay, skull-shaped whistle in each bony hand.

But no one blew into the noisemakers for nearly 15 years. When someone finally did, the shrill, windy screech made the spine tingle.

If death had a sound, this was it.

I have been using a Mac for around four years now, and the switch made it necessary for me to track down new software to replace my toolkit. I had grown accustomed to using a certain set of software in Windows, and the lack of Mac versions for most of them meant that I had to find equivalents. So I hereby present a list of essential Mac software that I have grown to be completely reliant on. The list is a collection of tools that I consider essential for someone in the sciences. And also, since I still haven’t upgraded to Leopard (10.5), I haven’t been able to check out the new cool ones (such as Macnification). I have left out the more obvious ones such as Word, Endnote, Excel and Powerpoint.
1. Quicksilver
Quicksilver is an application that is hard to describe but I’ll give it a shot. It is at its most basic level an application launcher, but due to its infinitely extensible nature, you can use it for a whole variety of tasks such as file handling etc. I’ll point to a few good tutorials, but what makes it essential is that it completely changes your computing experience. Instead of endless clicking and drilling down the Finder windows, you can get the file you want by simply typing the first few letters of the name. Also, since Quicksilver learns the files that you use more frequently, they tend to pop up in the list very quickly. It take a while to get the hang of it, but once you get used to it, you’ll wonder how you did without it. Some plugins that may be of special use are the dictionary plugin, the unit conversion plugin and the calculator plugin. These plugins lets you do these tasks right there in Quicksilver without the bother of having to launch separate applications. So if you’re in the middle of a paper and you want to do a quick calculation, you can do so without launching the default calculator. Very smooth.
2. Scrivener
Scrivener is an application that makes the writing easy. It’s basically designed to get a draft out, and then worry about the formatting later. You can arrange a single Scrivener file (which is basically a text file) into several sections that deal with different parts of the document. In this way you can just focus on writing and get the words out. It also has a brilliant FullScreen mode, where it blanks out the rest of your desktop and lets you focus on the text. I’m writing this in Scrivener, and the last three papers I wrote were in Scrivener. Scrivener also lets you paste in Endnote temporary citation, that are then converted into actual Endnote citations when you export to Word or some other word processor for formatting. Scrivener has a feature called ‘Typewriter scrolling’, which makes sure that the line you’re typing stays midway across the screen. Other word processors scroll so that you end up always looking at the bottom of the screen. You can set a word count target and this lets you know how much more you have to write, which is especially useful for stuff like Abstracts and Grant proposals, which have strict word counts. In Scrivener, you can also import pdf or image files into a ‘Research’ section, which makes it ideal for referring to other papers or even graphs while you’re writing the paper.
3. Papers
Papers is a new program that drastically changes the way people normally deal with pdf files. Even the most organized of scientists have problems organizing their library and Papers solves this problem most elegantly. It’s a sort of iTunes for pdfs. You can import your pdf collection directly into papers, and then spend a bit of time getting it in order. There’s a bit of initial time investment with your old pdf files, but Papers makes it easy by using the Match feature. You select a pdf file in Papers, click on Match , and you can search for metadata (such as author, journal etc etc) through a variety of repositories such as JSTOR, Google Scholar and Web of Science. New papers are easier since you can download them directly to Papers, and since new articles have better metadata (such as DOI), it’s easy to deal with. Integrating Papers into your paper writing workflow (with respect to Endnote) is a bit tricky, but even without this, Papers is a godsend for the harried reference herder.
4. GraphPad Prism and JMP
GraphPad Prism is my first choice for exploratory data analysis. You paste the data from excel, it spits out a graph, and you have some idea of what the data looks like. Things like normality testing and simple tests such as t-tests and ANOVAs are a breeze; the software speaks English instead of spitting out interminable tables (E.g. Is the variable normally distributed? Yes). The graphs it produces are very much configurable, and very easy to use. There are a few types of analysis that Prism doesn’t do such as multiple regression, and for these and other more detailed analysis I then use JMP. JMP is hard to get the hang of at first, but if you persist, it becomes easier all the time. I now use JMP for any analysis that Prism doesn’t do, and the graphs that JMP produce are pretty decent as well.
5. Graph Sketcher
I still haven’t found a good dedicated graphing program, and I’ve tried a few. Deltagraph is downright annoying and the free ones that I found were quite mystifying. If I can’t tell immediately how to use the program, then it probably will prove to be more annoying as time goes on. But I did find this really cool software that draws blank graphs. I reckon Graphsketcher is very useful when you need to draw graphs of models, i.e. when you need to illustrate a hypothesis. It might be a bit of overkill to use a program meant only to draw blank graphs, but I have come to believe that it’s much better to have a small simple program that does one thing very well, than to use a big program that does many things but not so well.
6. Inkscape and Lineform
Occasionally you need to draw the setup of an experiment or to illustrate part of your paper with a line diagram. I have been dabbling with the opensource Inkscape (which needs X11 installed) and while it looks very competent and reliable, I still found it quite a bit annoying. Recently I downloaded the Demo version of Lineform and tried recreating a figure that I had just finished labouring over in Inkscape, and I found that it took a fraction of the time to do so. Lineform has recently won an Apple Design Award, which means that now everybody knows it’s good. I think I will get this program, and I foresee that it will become an integral part of my toolkit, and with luck replacing Powerpoint for poster making.
7. ImageJ
Images are all the rage and chances are you will use images as part of your data in some form or the other. I take photographs of spiders and webs and measure the photograph in the comfort of the lab rather than do a whole heap of measurements in the field. ImageJ is free, comes with a million plugins and macros that make image measurements a breeze. I’ve only recently started realizing the full extent of this application’s capabilities, so I can’t say very much but I am beginning to become a big fan. You can even import avi files and there are plugins that aim to do object tracking.
8. Skim
Skim is an alternative to Preview and Acrobat reader for reading pdf files. You can annotate and read fullscreen, but I guess it’s a matter of personal preference. If you’re happy with preview, I guess there’s really no need to switch to Skim. But it’s worth a look. Skim loads much faster than Acrobat reader, and has more options than Preview.
9. Carbon Copy Cloner
CCC is a highly configurable data backup software that make the job of backups a breeze. I use Carbon Copy Cloner, mainly because you can choose which folders to backup, and because it does incremental backups which means that if backs up only the files that have changed and new files. It’s a matter of seconds if you back up regularly.
10. Newsfire (Free)
Now that journals are starting to get the hang of this here interwebs, many of them are now offering their table of contents as a feed. So if you get your hands on good feed reader such as Newsfire, you can subscribe to the journals and saves you the trouble of checking whether the next issue is out, since Newsfire automatically checks the site for you. It also prevents you from having to get the table of content information in your email…but I guess that’s also a matter of personal preference. I think TOC feeds are ideal to keep abreast of the latest issues.

I have been interested in mystical experiences for a long time. Growing up in India, surrounded by religion, and especially religions that make ‘enlightenment’ a core of any person’s sense of spirituality, it is hard to avoid hearing about the mystical experience. Buddhism and Hinduism deal with the transcendence of ego, or sense of self and a merging or unification with the, for lack of a better word, the Universe. The land is littered with sages and seers who are honoured because they have crossed from the mundane everyday life into one that where the person is described as one that is one with the Universe.
I had always assumed that the only way one could achieve this state of being was through the practice of religious/ spiritual techniques. In Hinduism, Buddhism and even Taoism, the goal is to free yourself of earthly cares by realizing the self’s infinite nature by a series of devices such as koans and meditation. In Hindu mythology, sages often communed with the gods after performing a range of austerities that would often go on for hundreds of years. This can be considered as the ‘religious route’ to mysticism. I believe that once a person has had a mystical experience, he/she usually tries to make sense of it in terms of the pre-existing religious worldview that the person grew up with. Therefore a Christian mystic would have visions of angels, whereas the Hindu mystic would be visited by his or her own gods.
However mystical experiences are common all over the world. I read a book called Supernatural, written by Graham Hancock, in which he makes the case that all the world’s religions, as well as the religious thoughts of early civilizations had their roots in consciousness altering substances such as psychoactive drugs. I don’t believe he was the first to propose this; it is merely the first book about this phenomenon that I have read. This can be considered as the ‘psychoactive route’ to mysticism. The best example of this that I can find to show that psychoactive substances can lead to a mystical experience is that of Alan Watts. Alan Watts has been a great inspiration to me. His book, called ‘The Book’, is a delightful introduction to eastern thought for the western reader. It is weird that despite having been born in India, I still needed a westerner’s account to get me to appreciate eastern thinking properly. In one of his essays, Watts describes the use of psychoactive substances to train the mind to access the mystical state. He reported that after a while, he no longer needed the aid of the psychoactive substance in order to do so. Of course, there are thousands of tribes and cultures that incorporate the use of such substances into their spiritual landscape. Some examples include the use of Ayahuasca in Brazilian shaman ceremonies, and peyote in Mexican culture. I once visited a couple of museums devoted to pre-columbian art and I noticed several ‘smoking’ pipes used by the shamans of the pre-columbian cultures in order to induce the spiritual experience. However, like Alan Watts, I believe that these substances help only when the person using them is already of a religious/spiritual frame of mind.
The third route to mysticism is more uncertain. Eckhart Tolle, who’s book ‘The power of now’ basically deals with the attainment of transcendence, describes how he was undergoing a really rough stage in his life - depression, thoughts of suicide, desperation- and suddenly underwent a massive epiphany that led him to an understanding of an other state of consciousness. This can be considered as the ‘brain crunch route’ to the mystical experience. I suspect that this route is the result of a massive ‘rewiring’ of the brain, a result of extreme stress in some cases, and a spontaneous switch in others. I think that this route is fairly common, but if the person is religious, then the experience becomes subsumed within the framework of the person’s existing religion. Simply from his writings, I now think that the author Richard Bach went through something like this. He started out writing stories of planes and flying (eg: Biplane), and starting with ‘One’, ended up writing more and more mysticism influenced books. The best example, however, comes from the incredible story of the brain scientist Jill Taylor. In this talk, which is a must see, she describes how she went through a stroke caused by a hemorrhage in her brain. She says that since the left and the right hemispheres operate differently, the closing down of the left hemisphere freed her to experience consciousness through the right hemisphere, and by her description (and her assertion) sounds like every other description of the mystical experience I’ve ever read.
Many authors who talk about the mystical experience, or indeed just about spirituality, emphasize the potentially destructive nature of mental chatter. Mental chatter is the ongoing dialogue we have with ourselves all the time. Mental chatter apparently helps us to ‘edit’ the world, so that we don’t get overwhelmed by all the sensory input. While we benefit from the editing of the Universe, we also tend to get caught up in it, in a manner similar to the way we consider a photograph without considering the landscape that it represents. By forgetting that we are indeed editing the world, we become more and more reliant on the mental chatter to explain the Universe to us. According to Jill Taylor, it is the left hemisphere of the brain that is responsible for this editing, while the right hemisphere is responsible for the actual acquisition of experiences. Jill says that since her left hemisphere was affected by the stroke, she was in a totally silent brain for the first time in her life, and this led her to experience the universe with the right hemisphere, which is all about the present, free of editing. The sense of now, the present, free of constraints, free of any boundary between self and other- the essence of a mystical experience.

Spider WebWatch: A citizen scientist initiative in North America
Spider WebWatch is a biodiversity monitoring effort for biologists, naturalists, educators and students. From more than 4,400 species of spiders in North America, 9 were chosen as eight-legged ambassadors.

Should you by chance find yourself in Melbourne, a fair city that rests along the southern side of the southern continent, you will be at once taken by the feeling that you have entered a foreign country. You have barely stepped off the train at the Station and even before your gait sheds the rolling movement of the train, you step onto the surreal heart of this city. And the heart is not one you expect after all your wanderings in Australia, it is a space totally devoted to a stance away from the normal. The square is not a square, it is a jagged irregularly lit space lined by equally angular buildings, all glowing this way and that in the cold wintry night. The rain that falls intermittently is cold as well, but you will scarcely feel it, dear traveler, as you wander around the square with a jaw threatening to drop in anticipation of further wonders. Here, for example, is the debris of a celebration, with only a giant and serene Buddha bathed in the light of an enormous screen relaying a popular entertainment. Here, for example, is the nerve centre of that most excellent of broadcasting services, and seeing the familiar blue and white logo makes you nostalgic for a time that is yet to come, a time when you realize that you are no longer in Australia. Words sidle across buildings, lights dangle between buildings, and there in the distance you can make out a spire reaching for the sky.
As you wander among the alleyways and the bylanes and the little connections between the streets, you notice throngs of people gathered together, huddling in barely lit cafes on chairs thrust onto the streets. You get the feeling, as you walk past the people, and as you peer into the various shops selling exquisite paper, or clothes or coffee or even books, that there is at least one city in this land that knows how to be a city. And the walls themselves bustle with the efforts of hundreds of artists who seek to claim a tiny bit of the wall, knowing full well that this claim shall soon fade to another’s hand. Some find a little more permanence than others, their work protected by a perspex sheet, but even this is mocked in this impermanent world.
A multitude of languages beguile your ear here, dear traveler, and even though you might be schooled in many, there are still several here that elude your grasp. And as you walk along the road, you will soon encounter the trams trundling along anachronistically, electricity arcing from the wires. And if you forego the road for the trams, you will soon realize that an entire series of lessons in etiquette await you. There are wonders here, in buildings that house ancient manuscripts that gleam in the light, in secret museums devoted to the capturing of light or to stones that capture the light, and in eccentric shops that are crammed with scientific curiosities -from miniature engines that work with the heat from light to insects and spiders fossilized in resin blocks.
And then, dear traveler, as your feet weary and you yearn for respite, you may well be surprised to stumble upon a restaurant that serves you food from your homeland, and in the manner that you only have memories of, and then, as you watch the city unfurl before you as you drink a fine coffee, you realize that you have always known Melbourne. You only had to see it to be sure it existed.

Some photos from a recent visit to Melbourne

European Spider of the Year 2008

Link

This first little fungus, a mold called Nomuraea atypicola, is not dangerous to you or I, but as you can see, it is a mortal enemy of spiders. It’s not just growing on the spider, like a bad case of athlete’s foot. No, it has consumed it from the inside, and it is now making a kajillion pinkish spores on the cadaver. Kind of like that old movie, Invasion of the Body Snatchers. This spider is thoroughly dead.