What happens when the probably brighter reflective or refractive light of the microscopic slide supersedes the fleeting light of the fluorophore that we use to render the microscopic subject? We take autofluorescence as artifact. As interference. As noise. As the cause of an unwilling suspension of the gaze.
What, then, constitutes the "real" in the dialectic played out in and on the visible of the slide? The effects, it would appear, of photosensitive dye. And so it is that the real gets rewritten as the effects on an injection. As the short-lived effects of a glowing dye.
So there's an attraction here. The potential of an induced autofluorescence. A xenographic encoding on the surface of the slide. An inscription prior to seeing. And a willing redirection of the gaze.
What happens when the light of the microscopic slide becomes the subject of the microscopic slide? We then take autofluorescence as subject. As carrier. As the deliverer of some foreign message.
What's interesting here is the idea of the long-standing physical attributes of glass acting as a type of inhibitor, or limiter, over what it is that glass lets us see in the first place. When we inscribe the surface of the slide to encourage this type of internal glow we cut a channel through our own field of sight.
Sunday, December 28, 2008
Thursday, December 18, 2008
The Accessible Aquarium
We should keep our eye on this experimental music department at Georgia Tech.
Sunday, November 30, 2008
Triptychs and triplets.
Place holder for follow up on tonight's discussion about Francis Bacon, his triptychs, the triplet nature of codons, your Cedar allergy, medieval spies, the possibility of para-immunity, parasites, the possibility of expanding on the triplet nature of codons, the wobble position, the number 20, and the fact that the ribosome does wild and wonderful things like frameshifting and shunting, so art is not that far off the mark. More soon.
Meanwhile, in perusing some Bacon triptychs, I found a common theme in many of them that the first two heads are oriented in the same direction with the third facing the other two. Thus it seems that the Bacon triptychs, like codon triplets, also have a wobble position. Three examples below.
Meanwhile, in perusing some Bacon triptychs, I found a common theme in many of them that the first two heads are oriented in the same direction with the third facing the other two. Thus it seems that the Bacon triptychs, like codon triplets, also have a wobble position. Three examples below.
Tuesday, November 25, 2008
Julius F. Jezek Prize
Saturday, November 8, 2008
Boy who "sees" with sound.
Blind Boy That Sees Using Sounds Like Dolphins -
Also from my friend. Thought this one is especially pertinent considering our Austin conversation about dolphin linguistics.
Device for visualizing sound.
Shapes Using Sound Effects - video powered by Metacafe
A friend of mine at the Cavendish shared this after visiting the blog.
Hearing heat motion.
Thoughts on Schrodinger's first lecture in What is Life?
Schrodinger begins his exploration into Life with the question of why our bodies are so big compared to an atom. He cites a common frustration among those of us that study the very small, which is that our human senses are insensitive to them. This, as we discussed in August, necessitates that our observations be indirect. He presents an argument as to why it must be this way by explaining the statistical thermodynamic principle that the ordered phenomena we observe (e.g. paramagnetism and diffusion) result from the averaged behavior of independent atoms. These atoms are influenced by thermal fluctuations (he calls them “heat motion”), each other, as well as the force being tested, such as a magnetic field. Therefore, when observed as an ensemble, particles in a magnetic field align with the field. However, if your level of sensitivity was on a single particle scale, the pattern would seem confusing and chaotic. Our senses are thus tuned to relay to our brains, averages. Thus, a paradox that he highlights is that in the process of achieving the level of complexity required to comprehend the concept of a single atom, a human being has lost the ability to sense a single atom.
The perpetuum mobile project thus, strives to restore to us, through the aid of machines, a level of sensitivity that only our most distant unicellular biological relatives still possess: the ability to “hear” heat motion.
Schrodinger begins his exploration into Life with the question of why our bodies are so big compared to an atom. He cites a common frustration among those of us that study the very small, which is that our human senses are insensitive to them. This, as we discussed in August, necessitates that our observations be indirect. He presents an argument as to why it must be this way by explaining the statistical thermodynamic principle that the ordered phenomena we observe (e.g. paramagnetism and diffusion) result from the averaged behavior of independent atoms. These atoms are influenced by thermal fluctuations (he calls them “heat motion”), each other, as well as the force being tested, such as a magnetic field. Therefore, when observed as an ensemble, particles in a magnetic field align with the field. However, if your level of sensitivity was on a single particle scale, the pattern would seem confusing and chaotic. Our senses are thus tuned to relay to our brains, averages. Thus, a paradox that he highlights is that in the process of achieving the level of complexity required to comprehend the concept of a single atom, a human being has lost the ability to sense a single atom.
The perpetuum mobile project thus, strives to restore to us, through the aid of machines, a level of sensitivity that only our most distant unicellular biological relatives still possess: the ability to “hear” heat motion.
Sunday, November 2, 2008
Wednesday, October 22, 2008
Tuesday, October 14, 2008
Friday, September 26, 2008
Reflections
Just got back from the engraver's this morning to look at the final assembly of the pieces I'm sending off to the Chelsea Art Museum for next week's opening of the Notations21 show there. And it's remarkable going back through the process the engraver and I have collectively engineered over the last couple of months to project notation directly into glass.
Dozens and dozens of industrial engraving processes. There are processes for engraving on glass, on metal, on wood, and on every type of stone. There are processes for engraving on concrete and brick and even asphalt. Different types of laser, acid, UV- and photo-reactive film all make an appearance, depending on the detail of the work, whether the product is to be seen indoors or out, the thickness of the engraving target, and the depth and coloration of the resulting incisions in the body of the piece.
The glass panels we've put together for the show in Chelsea are 13 x 19" and engraved with several thousand individual vectors taken from the parts of the score to Reiko's flute piece that we premiered earlier this year in Berlin. The postscript sourcefiles drive a laser powered by the three different highly excitable gases. The laser etches directly into a sticky green film which adheres to the obverse side of each panel. The dots, flags, noteheads, stafflines and other symbols the laser cuts through the film open spaces in the mask and leave the gestalt collection of symbols in the piece open and exposed for the next step in the process, which is treatment with fine, 220-grit sand blown at 90 PSI directly at the back of each panel. Demasking follows -- always done only by hand -- and takes several hours. The entire piece is then washed in an acetone bath and rubbed with a dry cloth.
What results are whitened, calligraphic bits of score code showing back-to-front through completely transparent media.
Backgrounding becomes important. Hold each panel up to black and the symbols pop. Next to white, they evanesce.
There's an ambiguity to all this. Glass makes both the agent and the object of the the traditional microscope, in, respectively, the lens and the slide. What other materials becomes both agent and object of a type of seeing?
And then glass traps whatever may be its contents in equal measure to the degree in which it lets pass our view.
Slides? What do molecular biologists use in place or slides?
Dozens and dozens of industrial engraving processes. There are processes for engraving on glass, on metal, on wood, and on every type of stone. There are processes for engraving on concrete and brick and even asphalt. Different types of laser, acid, UV- and photo-reactive film all make an appearance, depending on the detail of the work, whether the product is to be seen indoors or out, the thickness of the engraving target, and the depth and coloration of the resulting incisions in the body of the piece.
The glass panels we've put together for the show in Chelsea are 13 x 19" and engraved with several thousand individual vectors taken from the parts of the score to Reiko's flute piece that we premiered earlier this year in Berlin. The postscript sourcefiles drive a laser powered by the three different highly excitable gases. The laser etches directly into a sticky green film which adheres to the obverse side of each panel. The dots, flags, noteheads, stafflines and other symbols the laser cuts through the film open spaces in the mask and leave the gestalt collection of symbols in the piece open and exposed for the next step in the process, which is treatment with fine, 220-grit sand blown at 90 PSI directly at the back of each panel. Demasking follows -- always done only by hand -- and takes several hours. The entire piece is then washed in an acetone bath and rubbed with a dry cloth.
What results are whitened, calligraphic bits of score code showing back-to-front through completely transparent media.
Backgrounding becomes important. Hold each panel up to black and the symbols pop. Next to white, they evanesce.
There's an ambiguity to all this. Glass makes both the agent and the object of the the traditional microscope, in, respectively, the lens and the slide. What other materials becomes both agent and object of a type of seeing?
And then glass traps whatever may be its contents in equal measure to the degree in which it lets pass our view.
Slides? What do molecular biologists use in place or slides?
Sunday, September 21, 2008
Beckett in Berio
Mahler. Symphony no. 2, movement III (of V), 1888 - 94.
Marked "In ruhig fliessender Bewegung":
Berio. Sinfonia, movement III (of V), 1968 - 69.
Marked "In ruhig fliessender Bewegung":
"... this represents at least a thousand words I wasn't counting on ..."
Marked "In ruhig fliessender Bewegung":
Berio. Sinfonia, movement III (of V), 1968 - 69.
Marked "In ruhig fliessender Bewegung":
"... this represents at least a thousand words I wasn't counting on ..."
Tuesday, September 16, 2008
Beckett on Biology
My uncle reminded me of the opening lines of The Unnamable this morning. It made me think of you and enzymes and embryonic cell fate decisions:
Where now? Who now? When now? Unquestioning. I, say I. Unbelieving. Questions, hypotheses, call them that. Keep going, going on, call that going, call that on.
Where now? Who now? When now? Unquestioning. I, say I. Unbelieving. Questions, hypotheses, call them that. Keep going, going on, call that going, call that on.
Thursday, September 11, 2008
A decentered biology
So we talk and I have to update image after image and image to keep up. Whatever ideas I have about the mechanics of the passing of secret messages break under the weight of your epigenetics.
DNA is still the repository; check. RNA still transient? Um, kinda. But these 'maternal effect' factors? This stuff that hangs out in the cortex ... who the hell cares about the cortex? I couldn't ante up a damn thing about the cortex. The nucleus is where all the information lives, right? And information equals control, and control is what manages change, and development is change, and so the nucleus is center stage for development ...
Or maybe not.
The cell divides and somewhere by 8 or 16 or something daughter cells differentiation sets in. Something is inside, something is outside. And nowhere in any of the stuff they shoved down our throats in school was there any clue of a reason as to why differentiation actually happened: the daughter cells all have the same DNA, right?
But what if precisely that stuff that's hanging out in the cortex can actually play a role? What if the stuff that's hanging out in the cortex isn't distributed evenly around a too-smooth sphere but actually has a COMPLEX PATTERN -- or maybe better a complex SERIES OF PATTERNS -- to its distribution. And what if the patterning inherent in the distribution of the magic stuff of the cortex matters precisely because the different daughter cells grab different parts of the cortical information as they cleave?
More head blowing up. Because what happens is that the intolerably round, intolerably centered model of the perfect egg dissolves: we can't answer the question of fundamental differentiation when there's too much symmetry, that is, when we think according to too perfect a model. The tyranny of the sphere. What's needed is precisely asymmetry in an amount enough to decenter the model. Enter the edge of the cell as the source and keep of just the asymmetry we need. And we start to explain why we get a head over here but a tail over there.
If this is right -- if magic stuff living in the remote edges of the cell acts as type of control over the all-important information in the central repository that is DNA -- then what we have is a decentered biology. A molecular biology that yields up the secrets of its center in its first 60 years and opens its edges only now.
RNA as the winged messenger. How else to explain how the stuff at the edges -- in the form of these maternal effect factors -- can actually effect control? Stuff, in the form of (m)RNA has to visit the factors present in the cortex. And so a new image: a visit there and back again as critical to development. This is the image of the pilgrimage.
Put it together and the centered repository part of the model sticks around. But the model augments centralization with control from the periphery. All by means of developmental pilgrimage upon developmental pilgrimage.
As you get closer and closer to the image of the epigenome I see colors. Literally. A dusting of green and sapphire specks, scattered rainbow colors in the shadows of the cell, patterned to control, to help, to develop, to break a tyranny of too much symmetry.
DNA is still the repository; check. RNA still transient? Um, kinda. But these 'maternal effect' factors? This stuff that hangs out in the cortex ... who the hell cares about the cortex? I couldn't ante up a damn thing about the cortex. The nucleus is where all the information lives, right? And information equals control, and control is what manages change, and development is change, and so the nucleus is center stage for development ...
Or maybe not.
The cell divides and somewhere by 8 or 16 or something daughter cells differentiation sets in. Something is inside, something is outside. And nowhere in any of the stuff they shoved down our throats in school was there any clue of a reason as to why differentiation actually happened: the daughter cells all have the same DNA, right?
But what if precisely that stuff that's hanging out in the cortex can actually play a role? What if the stuff that's hanging out in the cortex isn't distributed evenly around a too-smooth sphere but actually has a COMPLEX PATTERN -- or maybe better a complex SERIES OF PATTERNS -- to its distribution. And what if the patterning inherent in the distribution of the magic stuff of the cortex matters precisely because the different daughter cells grab different parts of the cortical information as they cleave?
More head blowing up. Because what happens is that the intolerably round, intolerably centered model of the perfect egg dissolves: we can't answer the question of fundamental differentiation when there's too much symmetry, that is, when we think according to too perfect a model. The tyranny of the sphere. What's needed is precisely asymmetry in an amount enough to decenter the model. Enter the edge of the cell as the source and keep of just the asymmetry we need. And we start to explain why we get a head over here but a tail over there.
If this is right -- if magic stuff living in the remote edges of the cell acts as type of control over the all-important information in the central repository that is DNA -- then what we have is a decentered biology. A molecular biology that yields up the secrets of its center in its first 60 years and opens its edges only now.
RNA as the winged messenger. How else to explain how the stuff at the edges -- in the form of these maternal effect factors -- can actually effect control? Stuff, in the form of (m)RNA has to visit the factors present in the cortex. And so a new image: a visit there and back again as critical to development. This is the image of the pilgrimage.
Put it together and the centered repository part of the model sticks around. But the model augments centralization with control from the periphery. All by means of developmental pilgrimage upon developmental pilgrimage.
As you get closer and closer to the image of the epigenome I see colors. Literally. A dusting of green and sapphire specks, scattered rainbow colors in the shadows of the cell, patterned to control, to help, to develop, to break a tyranny of too much symmetry.
Wednesday, August 20, 2008
Constructive : Synthesis
It’s interesting you mention Finnish because it is in the Ural-Altaic language group along with my first language, Turkish. I say first, and should probably also say last.
Tuesday, on a balcony overlooking the Golden Horn, I was told the story of a Parisian philosopher, who wrote most of his works in French, was also fluent in German, and who eventually could only communicate in French, then German, and then finally in Romanian (the language of his childhood) as he progressed through the stages of Alzheimer’s. This makes sense given the fMRI studies showing that the cluster of neurons associated with one’s native language is spatially distinct from that of languages learned later in life.
And right there a question arises — do you guys feel yourselves visualizing the abstract or the concrete?
The short answer is the concrete. Which is why I chose noumena over phenomena.
The longer answer is that we like to think we are studying the actual object (in this case the ribosome) however, it is true that in fact we are studying the phenomenon, the appearance of this object to our senses (which in the case of smFRET is our sight). The phenomenon we are observing may directly report on the ribosome, or may be an artifact of the system. This is a question that Scott fields a lot during lectures on his work. Perhaps he will have more to say.
More so, sounds like in plenty of cases we're only going to be able to visualize the (indirect) effects these structures generate on their immediate environment and on other local structures with which they interact ... rather than, say, (direct) observation of the structures themselves.
Yes, our senses evolved to directly observe food and predators and mates. Objects typically (except perhaps if you consider a virus to be a predator) larger than the cell. Therefore, all observation on a subcellular scale is indirect in the sense that we require tools to mediate the observation.
So, yes, we are model guided from beginning to end. And that is one of the goals of this project: to push the boundaries of biological observation. To add a new sense to the toolbox. We have well-established indirect methods of seeing things smaller than light. I’m hoping through this collaboration we can also start to hear things smaller than light.
So that's where the friction — the constructive friction — will lie. In the language of research (and questions about research) rubbing up against the language of composition (and questions about composition) as the work progresses.
Yes, and before friction comes contact. The earliest enzymology lesson I learned was that in order to react, two objects first must bind. Corpora non agunt nisi ligata. In fact, one of the principle functions of an enzyme is to accelerate the process of bringing objects together. Thus by extension, it is not surprising that it is an enzyme, the ribosome, that is bringing us together for (I would argue rather than friction) a constructive reaction, a synthesis.
Tuesday, on a balcony overlooking the Golden Horn, I was told the story of a Parisian philosopher, who wrote most of his works in French, was also fluent in German, and who eventually could only communicate in French, then German, and then finally in Romanian (the language of his childhood) as he progressed through the stages of Alzheimer’s. This makes sense given the fMRI studies showing that the cluster of neurons associated with one’s native language is spatially distinct from that of languages learned later in life.
And right there a question arises — do you guys feel yourselves visualizing the abstract or the concrete?
The short answer is the concrete. Which is why I chose noumena over phenomena.
The longer answer is that we like to think we are studying the actual object (in this case the ribosome) however, it is true that in fact we are studying the phenomenon, the appearance of this object to our senses (which in the case of smFRET is our sight). The phenomenon we are observing may directly report on the ribosome, or may be an artifact of the system. This is a question that Scott fields a lot during lectures on his work. Perhaps he will have more to say.
More so, sounds like in plenty of cases we're only going to be able to visualize the (indirect) effects these structures generate on their immediate environment and on other local structures with which they interact ... rather than, say, (direct) observation of the structures themselves.
Yes, our senses evolved to directly observe food and predators and mates. Objects typically (except perhaps if you consider a virus to be a predator) larger than the cell. Therefore, all observation on a subcellular scale is indirect in the sense that we require tools to mediate the observation.
So, yes, we are model guided from beginning to end. And that is one of the goals of this project: to push the boundaries of biological observation. To add a new sense to the toolbox. We have well-established indirect methods of seeing things smaller than light. I’m hoping through this collaboration we can also start to hear things smaller than light.
So that's where the friction — the constructive friction — will lie. In the language of research (and questions about research) rubbing up against the language of composition (and questions about composition) as the work progresses.
Yes, and before friction comes contact. The earliest enzymology lesson I learned was that in order to react, two objects first must bind. Corpora non agunt nisi ligata. In fact, one of the principle functions of an enzyme is to accelerate the process of bringing objects together. Thus by extension, it is not surprising that it is an enzyme, the ribosome, that is bringing us together for (I would argue rather than friction) a constructive reaction, a synthesis.
Five senses
Five senses, indeed. We only see and hear according to some model. And seeing things in the existence of which we're not yet prepared to accept is a feat. Maybe a reason that moving things in and out of different media can open things we didn't know we're there ...
Been working the last couple of weeks to get music engraved on glass ... something happens when indications for performance jump the page set themselves up to be looked through ...
That's a part of the flute, violin & piano trio from February. The glass guy brought the proof by this morning ... glass on black becomes a mirror ... with embedded code. The real work is running as a series of eight engravings and will show at the Chelsea Gallery in New York in October ... so everyone else can see notation hovering somewhere it usually doesn't ...
Been working the last couple of weeks to get music engraved on glass ... something happens when indications for performance jump the page set themselves up to be looked through ...
That's a part of the flute, violin & piano trio from February. The glass guy brought the proof by this morning ... glass on black becomes a mirror ... with embedded code. The real work is running as a series of eight engravings and will show at the Chelsea Gallery in New York in October ... so everyone else can see notation hovering somewhere it usually doesn't ...
Tuesday, August 19, 2008
Dinner reflections
"Per" as a prefix is great, btw. I think the people who study these things label one of the profusion of noun cases in Finnish the "perlative" for things set on some path through a place, a time, or some other thing.
I was in San Diego last week and this weekend working with friends. I'm back now, and I'm thinking about your voicemail. So how'd it go? How was dinner?
Some stuff and some hopes come to mind. We're smashing molecular biology & music together and so we can expect what we might call fruitful model friction, right? You guys have different practices devoted entirely to aspects of visualizing stuff at levels much much smaller than the cell. And right there a question arises — do you guys feel yourselves visualizing the abstract or the concrete? The abstract / concrete thing is probably a false dichotomy under any circumstances ... and it seems especially problematized by the whole premise of molecular visualization ... especially at the level that Scott is pushing it ... and at the level you're pushing at Cambridge, right? Whatever these ribosomal (sub)structures turn out to actually "be" the visualization is always going to be some type of superabstraction. More so, sounds like in plenty of cases we're only going to be able to visualize the (indirect) effects these structures generate on their immediate environment and on other local structures with which they interact ... rather than, say, (direct) observation of the structures themselves. So, fine. One of the implications of proceeding that way is that the visualization is model-governed from beginning to end. Which means that whatever model(s) we can invoke from the way that we think about music — the development and dissolution of musical structures, the perception or reception of those structures by people, or how structure vanishes when we think musically in different ways — carry at least the possibility of friction with whatever models it is that drive the work of visualization in the lab. Which is what we can point to by 'model friction'.
Related thought: language matters in this work. We've got the blog, some trips and possibilities to meet for a reason, and we're opening up times and places to exchange language in the process. So posit for a minute that language use for each of us depends on some graph of whole, fractured or composite concepts that interconnect all over the place in our thinking, and also when we write to each other, and talk. Stuff connects in different ways and the words and syntactic patterns we pick out and avoid when we look at each other's work — sketches, result sets, pics, soundfiles, whatever — probably trigger things for us even before they mean things for us. Which probably comes out to mean that we can sure as hell expect something to tremor or to shake in our thinking when you let a molecular biologist in to critique to the construction and development of the sounds in music as the piece progresses and when you let a composer feed back and react to data of actual results as research progresses.
We carry whatever models it is we have with us as our most powerful tools in the form of learned connections — neural, numeric, sonic, maybe literary. And we communicate whatever it that we carry through our language ... and also the sound and image we embed in and around that language.
So that's where the friction — the constructive friction — will lie. In the language of research (and questions about research) rubbing up against the language of composition (and questions about composition) as the work progresses.
So tell me about dinner ... and whether 'visualization' became a keyword at the table. And then I'll tell you what's frictive in the sketches I'm working on now.
I was in San Diego last week and this weekend working with friends. I'm back now, and I'm thinking about your voicemail. So how'd it go? How was dinner?
Some stuff and some hopes come to mind. We're smashing molecular biology & music together and so we can expect what we might call fruitful model friction, right? You guys have different practices devoted entirely to aspects of visualizing stuff at levels much much smaller than the cell. And right there a question arises — do you guys feel yourselves visualizing the abstract or the concrete? The abstract / concrete thing is probably a false dichotomy under any circumstances ... and it seems especially problematized by the whole premise of molecular visualization ... especially at the level that Scott is pushing it ... and at the level you're pushing at Cambridge, right? Whatever these ribosomal (sub)structures turn out to actually "be" the visualization is always going to be some type of superabstraction. More so, sounds like in plenty of cases we're only going to be able to visualize the (indirect) effects these structures generate on their immediate environment and on other local structures with which they interact ... rather than, say, (direct) observation of the structures themselves. So, fine. One of the implications of proceeding that way is that the visualization is model-governed from beginning to end. Which means that whatever model(s) we can invoke from the way that we think about music — the development and dissolution of musical structures, the perception or reception of those structures by people, or how structure vanishes when we think musically in different ways — carry at least the possibility of friction with whatever models it is that drive the work of visualization in the lab. Which is what we can point to by 'model friction'.
Related thought: language matters in this work. We've got the blog, some trips and possibilities to meet for a reason, and we're opening up times and places to exchange language in the process. So posit for a minute that language use for each of us depends on some graph of whole, fractured or composite concepts that interconnect all over the place in our thinking, and also when we write to each other, and talk. Stuff connects in different ways and the words and syntactic patterns we pick out and avoid when we look at each other's work — sketches, result sets, pics, soundfiles, whatever — probably trigger things for us even before they mean things for us. Which probably comes out to mean that we can sure as hell expect something to tremor or to shake in our thinking when you let a molecular biologist in to critique to the construction and development of the sounds in music as the piece progresses and when you let a composer feed back and react to data of actual results as research progresses.
We carry whatever models it is we have with us as our most powerful tools in the form of learned connections — neural, numeric, sonic, maybe literary. And we communicate whatever it that we carry through our language ... and also the sound and image we embed in and around that language.
So that's where the friction — the constructive friction — will lie. In the language of research (and questions about research) rubbing up against the language of composition (and questions about composition) as the work progresses.
So tell me about dinner ... and whether 'visualization' became a keyword at the table. And then I'll tell you what's frictive in the sketches I'm working on now.
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