On the relations of biomedical and astronomical imaging

Michelle Borkin's talk at TEDxBoston is here.

Excellent collaboration across the fields, tied together through the structures of image.

Running / Machine

"I'm not a human. I'm a piece of machinery. I don't need to feel a thing. Just forge on ahead. I repeat this like a mantra. A literal, mechanical repetition. And I try hard to reduce the perceptible world to the narrowest parameters. All I can see is the ground three yards ahead, nothing beyond. My whole world consists of the ground three yards ahead. No need to think beyond that. The sky and wind, the grass, the cows munching the grass, the spectators, cheers, lake, novels, reality, the past, memory -- these mean nothing to me. Just getting me past the next three yards -- this was my tiny reason for living as a human. No, I'm sorry -- as a machine."

From Haruki Murakami's What I Talk About When I Talk About Running. Proving the machine metaphors may still be sometimes deeply meaningful. The short book is Murakami's monograph on marathons and the work of training for them.

Crystals, Fabrics, and Fields (3)

In Haraway's review of the work of Joseph Needham:

"The use of the fiber and tissue metaphor amply expresses Needham's mature conception of the resolution of the field-particle dichotomy in biological field theory ... Fields invited the introduction of topographical models and reasoning. For example, Needham described, a kind of qualitative mathematical model of an amphibian neurula ... Needham believed that fields were distinguished from simple geographic regions of the embryo by three criteria: any given point within the field force had to possess a given quality, a given direction, and a given intensity. Fields were judged in terms of instability and successive equilibrium positions." [124-5]

Haraway's observations here matter because they make us reconsider what portion of our thinking is metaphorical and what is nonmetaphorical or other-than-metaphorical in some way. It makes perfect sense to reason topographically with continuously varying quantities of different values present in certain areas of the cell once you have decided to model parts of the cell as fields. But would such reasoning arise in the absence of a comparable metaphor?

Further:

"Explanation implies a picture, and analogy is a vehicle for connecting the internal subjective perception of the structure of a phenomenon with the public function of theory building." [106]

In Haraway's review of the work of Paul Weiss:

"After observing the intact lamella, Weiss and Ferris took electron microscopic pictures of reconstruction of the membrane after wounding. The sequence of events was easily determined: Epidermal cells first migrated over and covered the wound. Fairly uniform fibers of small size (less than 200 Å) spread in the space between the underside of the epidermis and the subjacent fibroblasts. These small fibers were oriented at random. Then, proceeding from the epidermal face downward, a "wave of organization" spread over the fiber mass, straightening and orienting its elements. The fibers became packed in the characteristic layered structure and enlarged until they were about 500 Å in diameter ... Weiss was profoundly impressed with orthogonal tissue organization and its genesis. He frequently drew from the work in lectures and general speculative articles ... The "weaving of threads into fabrics, such as we find in living tissue" seemed to necessitate the judgment that "some sort of 'macro-crystallinity' [was] a basic property of living systems"." [170]

Can the liquid crystal bridge atomistic physics and the orders of biological organization? The idea of a 'wave or organization' spread over some part of the cell is striking or even eerie. And yet researchers observe this sort of thing all the time. But why?

Haraway's conclusion to Crystals, Fabrics, and Fields joins the organicism of Harrison, Needham and Weiss in both image and world view:

"For Harrison the limb field is like a liquid crystal and unlike a jigsaw puzzle. for Needham the embryo is like history interpreted from a Marxist viewpoint and unlike an automobile with gear sifts. For Weiss butterfly behavior is like a random search and self-correcting device and unlike a deterministic stimulus-response machine. Such a catalog could be continued indefinitely, but the basic point is that organicists, even granting their internal differences, share central perceptions on the level of images and language." [205]

Crystals, Fabics, and Fields (2)

Haraway's dissertation was first published in 1976 by Yale; the reprint now available from North Atlantic Books dates from 2004. Haraway divides the work into six chapters, the middle three of which detail selections of the work of Ross Harrison, Joseph Needham and Paul Weiss. All three biologists are now identified as organicists and part of Haraway's work in the book is to illustrate the largely visual metaphors that each researcher used to transcend the mechanist-vitalist divide.

The answer in Harrison's case would appear to rest largely on the notion of a biological field active in the cell during growth and development. Haraway found the image of the field important enough for the book's title and first glosses the metaphor in her discussion of Harrison:

"Area boundaries overlap, and tissue of an intermediate region is organized into one organ or another as a function of the center whose influence predominates. Such systems came to called fields, but it is not a word used by Harrison in that context until the late 1930s. As Waddington cautioned later, the term field should convey more than a geographical meaning; he suggested a term such as area or district when one does not intend to refer to the complex of processes involved in organ formation ... Harrison's discussion of structures and processes involved in axis determination of the limb and ear is an analysis of the nature of a field and constitutes one of the first and most basic of such studies. Harrison did not use the word field very often and especially not as a deliberate theoretical concept as Weiss would have done; but nonetheless, it was his fundamental work that first gave concrete content to the organicist notion." [80]

As to Harrison's understanding of how fields might operate, the answer would appear to involve an appeal to liquid crystals:

"Some kind of paracrystalline organization, specific for a type of cytoplasm, would underlie form relations and form changes -- morphology and morphogenesis. Progressive orientation of protoplasmic elements (restriction of degrees of freedom) could account for polarity and symmetry, without any need to postulate the cell as a homogeneous system. Crystal organization in organisms was itself an example of an intermediate level of organization, joining processes of organic and inorganic nature. And perhaps most significantly, Harrison's use of crystal analogies allowed him to bypass assumptions of the mosaic-mechanistic theories of development about part-whole relations and to account for the existence of equipotential systems without turning to either entelechies or classical machines." [93]

Crystals and liquid crystals appear and reappear throughout the book. Their mention here in reference to Harrison's understanding of the operation of development fields stands out as the identification of an intermediate level of organization between the atomism of molecular biology and the whole organism of an earlier vitalism or the later organicism.

What of the edges of things?

Harrison apparently wasn't much of an attention-seeker when it came to his own work, but the following would seem to have been downright prophetic of the coming work in epigenetics:

"Birefringent material was seen in Harrison's material, especially at cell membranes. Harrison noted that their work was preliminary and should be followed up systematically. "Especially should the cell boundaries be examined thoroughly, for it is there, perhaps more than anywhere else in the cell, that we may expect to find the seat of directive forces" ... A glance at current journals in cell and developmental biology reveals the appropriateness of the admonition to study cell membrane systems in relation to form problems." [82]

Material regarding Needham and Weiss to follow in later posts.

Crystals, Fabrics, and Fields (1)

Donna Haraway is perhaps best known as the critical theorist behind the cyborg manifesto. Haraway wrote the manifesto during the Reagan years. In it she made the case for, among very other things, an intelligently hybridized understanding of the feminine.

Haraway has since moved on to work on the species boundary and an exploration of the relationships that obtain between dogs and their human cohorts. What I think is much less well known is that Haraway's work Crystals, Fabrics, and Fields from the 1970s is something of a gold mine of images and explanations for why the life sciences model certain key concepts as they do.

From Scott Gilbert's forward to the new printing of the book:

"... I would contend that one of the most important precepts in her most recent pamphlet -- namely that "'the relation' is the smallest possible unit of analysis" -- can be traced directly to the embryological science analyzed in this 1976 volume. No matter what else Donna's philosophy might be -- Marxist, feminist, affectionate, ironic, cyborgian, anthropocanine -- it is thoroughly and uncompromisingly epigenetic."

And further:

"What does that mean? Epigenesis is an embryological concept that celebrates interaction, change, emergence, and the reciprocal relationship between the whole and its component parts. Epigenesis states that the identity of any particular cell is not preordained, but that this particular fate arises through the interactions between the cell and its neighbors ... Epigenesis tells us that 'being' never is anything except the processes of 'becoming' ..."

Breath, body, words (#2)

The vocabulary of anatomy features unexpected synonyms. The word 'alveolus' is Latin for a small cavity or indentation. The anatomy of the body features many such cavities. So it is perhaps unsurprising that anatomists pull the word into service in two different ways. First in the description of the hundreds of millions of tiny sacs of blood contained in the lungs. Second in the description of the 32 or so sockets in the gums that hold the teeth. These are, respectively, the pulmonary alveoli and the dental alveoli.

A sketch from the text.

Spherical cavities of the lungs, the pulmonary alveoli measure in microns and number in the hundreds of millions. Sheathed in epithelia and a coating of capillaries, it is along the membranes of these tiny spaces that both the breath and blood must pass. The dental alveoli are the sockets of the teeth; in adults, they number just thirty-two. Gomphoses are fibrous joints that move almost not at all and through which both rows of teeth bind to the sockets that contain them. Absent some singular moment of violence — a sudden fall, a blow to the face — the alveoli of the teeth stand fixed for a lifetime in their task. Small cavities interior to the lungs, small cavities in which to house the teeth. Small cavities connected the each to the other in only the passing of the breath.

The last sentence focuses on the breath. The last sentence imagines the breath as a type of invisible tissue that connects the many millions of alveoli in the lungs with the far fewer alveoli in the gums.

The pulmonary alveoli and the dental alveoli share nothing much in common except a name. But when thinking deeply into the structure of the body, it is possible to imagine these different things — these different classes of cavity — as connecting not only in name but in body.

Body, breath, words (#1)

I'm in the process of finishing a short article that's taken a long time to write. As a topic for the article I chose to write about my experience engineering a collection of sounds for use on the flute. Most of the work I describe in the article took place in 2004, 2005 and 2006 while I was writing Ćáry. The piece is a bass flute solo written for Carin Levine and the piece is composed almost entirely of these sounds.

The sounds I engineered at the time were sounds of the vocal apparatus — sounds you make with the throat, the tongue, the hard and soft palate, the ridge of the gums, the lips and so on. (These sounds might stand in contrast to, for example, those you make by tapping, stroking or rubbing the instrument with a feather, a pencil or a wooden rod, sounds that might be inherently percussive and that are, for a number of reasons, marshaled into service on the piano and the strings much more frequently than with the winds.) Even though a good many of these sounds that I was working with at the time of the piece are extremely close to many of the sounds important in the production of speech, I hesitate to use the word 'phonetic' to describe them, probably because the word would seem to invoke a whole systematic and analytic manner of thought that was absent from the way I was working on the piece as a whole.

The sounds are still with me. I draw a greater or lesser number of them into service depending on the needs of whatever piece I'm currently working. Mon Seul Désir binds the four instruments in the quartet permanently together to create a series of different color areas that are everywhere composite — that are everywhere the result of a working-together of the instruments, rather than a standing-alone of the instruments — thus calling for far fewer of these sounds; on the other hand, Lidércfény works in an intensely horizontal way with each of the instruments in the trio shining separately, thereby allowing for or even demanding a greater number of these sounds.

A very specific set of sensations internal to the body arose when I was working on those sounds. And because those same sensations continue to appear each time I further develop the sounds and the music in which the sounds are deployed, it is precisely these sensations that form the basis of the chapter I'm now finishing up. Writing about the felt sensation of the body — what parts of the body are active in the production of sound, what parts of the body resonate in sympathy in the production of sound, how the body relates to the felt and heard perception of sound, and so on — has turned out to be surprisingly rewarding, surprisingly difficult and surprisingly poetic. Words come only very slowly when fishing around for a description of what happens in motion through time. And a kind of composite sensation of color and touch would seem to be always just around the corner.

An example.

Consider body of the flutist and the instrument together in motion. Arms raised, flute upright and turned in, mouthpiece resting against the lower lip, muscles of the face alternately drawn tight or left slack. Breath passes up out of the lungs, through the throat, over the length of the tongue, past the hard palate, past the alveolar ridge, past the gums. Lips are engaged and spread. Breath spills forward from the mouth and rushes over and into the instrument itself. Tendons tense and tendons release as fingers work in coordination with silvered keys and with the mechanism in which the keys are set. Shoulders move forward towards the center of a phrase and then draw imperceptibly back, in response to which the chest cavity tightens and then opens again. The in-motion body of the flutist and the instrument are a special machine. In the operation of this machine the breath is transformed and acquires its color. The color is blue and the quality is that of a cold-flowing flame.

It's something of an effort to figure out how this sort of description and the images and felt sensation that generate it fit together with the more usual description of technical materials and so on that usually accompany words written post facto about the construction of a piece. And I suppose that it's somewhere in the middle of a process of fitting things together that I now find myself in finishing the article up.

Dead or Alive

This article was in the NY Times today:

"Many examples of mulchy, redolent, unmistakably organic art are on display in a new exhibit called “Dead or Alive,” at the Museum of Arts and Design in New York. The museum recently hosted a round-table luncheon in which scientists and artists addressed the hardy evergreen issue of how much the arts and sciences had in common and where they differed. The basic conclusion: both enterprises are important, difficult, creative, driven by insatiable curiosity and a desire to solve problems, but artists are allowed to make stuff up and scientists really shouldn’t."

Resonating Light

A recent mailing from the Rubin Museum of Art opened with a quote from Robert Schumann in a letter to his wife that "Music is nothing but resonating light."

Accordingly, this will be the theme of an up coming music series at the museum.

Of The Wind Dying Down

This evening at the New York Public Library, George Prochnik was interviewed about his book, In Pursuit of Silence: Listening for Meaning in a World of Noise.

The dialog was rich with discussion points applicable to p mobile.

Some snapshots for future research and elaboration:

We must find a copy of the BBC recording of the two minutes of silence that were observed for the first Armistice day. It is a notable recording of silence because there is a lot of noise. There is likely a copy of the recording in the British Library sound archives, but I am wondering if as a Harvard student you might have access to it through inter-library loans. Signal to noise is a recurring theme in our dialog. I am curious how you will respond to the recording. I think it would be brilliant if we were to transition from the audience sitting in the dark to the Armistice day recording before the musicians take the stage. In fact, it could also be quite interesting, since it is your working plan to compose a number of individual pieces, to have them interspersed with historic and/or otherwise interesting recordings of subtly noise-infused recordings of silence. As a study of signal to noise.

Prochnik writes: Let's hold a moment of silence in memory of silence.

He also explained that the drafters of the US Constitution had the road outside Independence Hall covered in soil so that their thoughts and deliberations would not be interrupted with traffic noise.

Speaking of hamsters: he explained that research has shown that humans find soothing the sound of water running over small, irregularly shaped boulders. In contrast, the sound of water running over metal brings to mind an unpleasant association with drainage. I wondered if anyone has ever written a score for the sound of water hitting objects and called that a percussion piece.

The concept of sound as a stimulant was discussed.

I learned that the equivalent of applause in the deaf community is to hold your hands in the air and shake them. I also learned that it is pretty spectacular to have a room of people hold their hands up and shake them, as this was the prescribed method for applauding at the event. I have never liked applause. Neither the tactile sensation nor the aural. From now on, I might just raise my hands and shake them whenever I approve.

Prochnik also described the "mystical silence of the hunt," underscoring the importance of silence to stalking and catching prey.

One thought that struck me during his description of urban "pocket parks" like Paley Park in midtown Manhattan was how relatively easy it is to create absolute darkness compared to absolute silence. For complete darkness, I can simply close and tape the frame of the closet door. Complete silence would be a much more high tech undertaking, and then I would still likely be left with the sound of blood rushing through my ears or the pseudo-sound of my thoughts. This is something we should explore further.

The cherry on the Prochnik sundae was a short lecture on tactile sound sensation by biologist Sheila Patek, a pioneer in crustacean communication. Before Patek's work, it was believed that crustaceans were deaf, but she realized that they hear through small vibration sensitive hairs covering their bodies. The highlight of the evening was hearing a chorus of California spiny lobsters. More on this in a separate entry when I have time to research more.

Finally, I learned that deep in the etymology of the word "silence" is the phrase "the wind dying down." There is a melancholy beauty in that image. Of the wind dying down. It brought to mind a memory of Texas in late spring. Vaporized tar mirages on the highway horizon. Track and field practice. Wind drying sweat on my sunburned checks and high ponytail. In that moment, the only sound I can remember is the rush of the wind. And then the wind dying down.

That box of hamsters? Percussion instrument.

I spent today working in the Aldrich reading room of Harvard's Paine Hall as Trevor darted in and out between classes. I attended his first seminar of the day: Chris Hasty's musical critique and theory class, which was populated with a few of the composers I met on Saturday plus music theoreticians and musicologists. The discussion turned on the idea of cross-disciplinary collaborations, and the thought that we have inherited a common intellectual heritage, which is both enriching and encumbering at the same time. We come together to explore our differences, and yet a strong binding thread and starting point is often common ground and the exploration of common problems. As a biologist, I can find fault with a deterministic view of the gene as a simple string of chemicals reproducibly encoding the same molecular output the same way that Trevor can argue that music is not just the structure set down in a score. Dr. Hasty cited and recommended the work of Susan Oyama for further exploration of this specific question. By extension, the dialectic of genetic/epigenetic control of the cell is a philosophical parallel to score/interpretation in musical performance. Which is a better comparison, perhaps, than the hardware/software analogy often used.

On the subject of intellectual tradition, we discussed the limitations that academic writing currently imposes on thought across the art-science spectrum. One classmate commented that in the humanities it is frowned upon to be "goal oriented" in an approach to a problem or to state subjective truths: "musicologists feel torn between the desire to say something and the fear of doing so." Biological statements of truth are bolstered by objective, quantifiable, and reproducible observations. However, perhaps influenced by decades of government grant proposals and the need for tangible demonstrations of "returns on investment", biologists often have to present a hypothesis driven linear approach to an only incremental point of progress. Most statements are goal oriented and lack the "whimsy" that is better tolerated in the humanities. And yet some of the most interesting and important discoveries in biology have been predicated on whimsy.

Most notably, perhaps, Francis Crick's formulation of the Adapter and Wobble hypotheses. From Crick's What Mad Pursuit:

"The main idea was that it was very difficult to consider how DNA or RNA, in any conceivable form, could provide a direct template for the side-chains of the twenty standard amino acids. What any structure was likely to have was a specific pattern of atomic groups that could form hydrogen bonds. I therefore proposed a theory in which there were twenty adaptors (one for each amino acid), together with twenty special enzymes. Each enzyme would join one particular amino acid to its own special adaptor. This combination would then diffuse to the RNA template. An adaptor molecule could fit in only those places on the nucleic acid template where it could form the necessary hydrogen bonds to hold it in place. Sitting there, it would have carried its amino acid to just the right place where it was needed."

On the subject of structural constraints in communication, Trevor feels that the limitations to describing time-related events such as music are not stylistic but rather perhaps a fundamental limitation of language itself. Time is not a visual object. Do we even have the linguistic tools to describe certain aural experiences?

Perhaps not. And in that case, what is the solution (or in a humanities paper, perhaps I would say "alternative")? To borrow methods for describing space/time from physics perhaps? To become more graphical, create new symbols?

Taken much further, this becomes a full circle. Starting with music and, in an attempt to describe it, transforming it into a non-transferable and non-intuitive set of visual symbols: words, graphs, charts, pictures. The same types of data representation I am arguing would be more easily communicated through music and sound.

In the end, it struck me that the musicologist or theorist suffers from the same dilemma, in trying to describe and communicate to others about music, that the composer does in struggling to bring it to life through performance. What tools can I use? Do I use a cello, but test the boundaries of the cello like in Kristian Ireland's piece on Saturday? Or do I make a new instrument all together?

That box of hamsters on the stage? Percussion instrument.

Goblin of a tongue

I'm in the last days of finishing up an article about the types of materials that I've developed for the flute in each of my pieces since about 2004. And the writing has proven rewarding in an unexpected way: I've become much more aware of feelings centered strongly within the body as I've chipped away at my own understanding of what it is that goes into the breath, the fingers, the muscles of the face, and on and on in the production of many of these sounds. An excerpt:

The tongue extends forward in the space of the mouth. Apical tip in contact with the ridge of the gums, the blade becomes imperceptibly taut and the muscle takes on the function of a lock, sealing the vocal tract and blocking the expulsion of air from the lungs. In this small fraction of a second the tongue transitions from lax to ready, waiting, as it were, at attention, pressed up and into the alveolar ridge, fixed just between the hard palate and the upper row of teeth. A goblin of a tongue --- imbued with a magic agency --- might wonder at this. Pink skeletal muscle. Arbiter of bitter, sweet, sour, savory and salt. But confined to darkness and unable to see. Would such a tongue wonder at the boundaries of its world? At its root buried past the the glossopalatine arch? At the hardness of the gums against which it presses?

The language has wound up as a mix of the partially poetic and the partially exploratory, in all cases centered on direct sensation of the body, or of parts of the body. And this has been, for me, something of a revelation.

Lidércfény

Congratulations to Trevor for the East Coast premier of Lidércfény and his debut concert as a doctoral student at Harvard. And compliments to Joshua Modney, Elizabeth Janzen, and Steve Beck of the Talea Ensemble for a breathtaking performance.

With both of us back on the same continent, Perpetuum mobile is gaining momentum. I traveled up through the blizzard from New York City to observe Trevor in his academic habitat and learn about the preparation that goes into a contemporary music performance.

Upon arriving, I parked with my luggage quietly in the back of Harvard's Paine Auditorium to observe my first music rehearsal. Rehearsal is spelled with the word "hear", which had not occurred to me before. I jotted a couple of first impressions down on the DNA mismatch repair article I had been reading on the train: for one, the musicians spoke to and interacted with each other much more than with the composer. Trevor was a humbled observer rather than the proactive "maestro" that I was expecting. This dynamic was reiterated with other composer/musician pairs in the dress rehearsal the next day. It was clear that a lot more power resides in the virtuoso talents that perform the music than my biases had programmed me to expect. The musician-composer dialectic seems a balanced symbiosis, truly each party dependent on the other. I was also struck by the remarkable level of focus and intensity both Trevor and the musicians had while on stage. After the rehearsal, I got a chance to interact with the musicians. I am grateful to Elizabeth Janzen, who took the time to show me the mark ups on her score. She explained that color coding and notation helps her act on instinct during the performance rather than having to remember or process all the levels of complexity embedded in the piece.




Afterward, I got the opportunity to speak to one of Trevor's instructors, Prof. Christopher Hasty, who kindly agreed to let me audit his critical theory class while I am here this week. He shares our interest in exploring the question of how to achieve true interdisciplinary collaboration. What are the barriers that prevent a scientist from musical expression? Or a composer from using, as a creative point of departure, aspects of the natural world that are beyond the scale of human senses.

Trevor and I agreed that a central goal of our project is to expand access, 1) for scientists to communicate through sound, which is a fundamentally more intuitive and finely tuned sense for comprehending small frequency fluctuations and differences than the eye and 2) for composers to draw inspiration from the natural world that is currently only accessible through high tech or cryptic intermediaries such as microscopes or genomic sequences.

Do these barriers exist for a good reason? If not, how do we start to dismantle them?

The flight of the bumblebee, post-genomic redux.

Minimalism? Discuss.

Question posed to P, forwarded to Trevor:

Science and music together reminds me of John Adams or Phillip Glass (whose stuff I love). Unfortunately, he's a horrible podium speaker who can't really articulate what he's trying to acheive in his compositions, but they are wonderfully complex, especially the symphonies (not so much the operas). They make for good background music for writing. Is your work of a minimalist structure? Would you call it chamber music?

Trevor response:

The style and texture of the music that we will together be building may, in many ways, work and move in ways that are *exactly opposite* to the masterworks of Glass, Reich and their followers working in the New York scene today. Glass's pieces are a pleasure to have on while writing: he departs from (and returns to) repetition as the embodying texture of his music, hence, perhaps, the comfort of writing in the presence of the music. In our case we will be looking through real data from real science at the bench with what we might describe as a hyperattentive eye for *disparity of patterns*; that is, our research together finds both patterns and *different types of* patterns to be a virtue. The resulting music hopes to project a weave of these patterns, one after the other, with gaps in between, and frequently on top of each other all at once. In some sense maybe this sort of work looks at the patterns of Glass, Reich and the minimalist masters and asks "what of a simultaneous, nonsensical understanding of *all these* patterns at once, and even more?"

P back to Trevor:

Beautifully elaborated as always. And exactly the dichotomy between bulk steady state enzymology versus non-equilibrium single molecule enzymology. Glass would be the former, an averaged pattern that is intuitive and sensical. In our work there may be a crowd, but of juxtaposed individuals.

Coda back from Trevor:

*bing!*

that would be it, precisely.

Omnivolution

Transcript of a recent email discussion. On the heels of an afternoon discussion in the Modern that carried over to an evening in Korea town.

Aaron Lee highlighted a viewpoint published recently in the New Scientist:

"Over the aeons of evolutionary time, the interaction of these multiple constraints has produced many viable phenotypes, all compatible with survival and reproduction. Crucially, however, the evolutionary process in such cases is not driven by a struggle for survival and/or for reproduction. Pigs don't have wings, but that's not because winged pigs once lost out to wingless ones. And it's not because the pigs that lacked wings were more fertile than the pigs that had them. There never were any winged pigs because there's no place on pigs for the wings to go. This isn't environmental filtering, it's just physiological and developmental mechanics."

This hit a chord with Trevor and me, who have been lamenting the intellectual laziness of academic biologists and popular science writers, alike, who use the theory of evolution as a mindlessly applied coda and rationalization for everything from behavior to flower petals.

Trevor's reply:

LOVE IT. OMG LOVE IT.

Why, I hear you ask? Because the public discourse so desperately needs effective narratives in biology that point to something *other than* evolution as cause.

You know, normal people never got over teleology. Student of Aristotle: "Why does an acorn fall to the ground?" Aristotle: "Because of its inner potential, its arete. The acorn *wants to* fall towards the ground." Weird, yes. But notice, especially in biology: "Why does the heart beat?" "To pump blood."

Really?

Really to pump blood?

Whatever else is going on, the heart beats in response to nervous impulse originating from multiple other sites in the body. But then this is frustrating: turtles, all the way down.

SO INSTEAD, the New York Times, among others, have decided that the answer to literally every question in science reporting -- especially reporting on issues in biology -- is due to evolution, by which they mean (and understand) only selection pressure, to the exclusion of all the other factors of macroevolution that could matter. Why does the heart beat? Because a beating heart was *evolutionarily advantageous*. (It works even better if an already-formed image of humans hunting or mating can be pulled into the picture because popular discussion of evolution always everywhere takes place against a silent cartoon backdrop at the level of the Flintstones: well, you see, long quadraceps meant that man was able to run faster to kill prey, and that's why their evolutionary adapted; or if not for running, then to hunt down women and pass on his genes.)

Grrr.

First, it's a danger to understand evolution as a (19th-century) narrative of individuals. Evolution doesn't care about the narrativity (or not) of individuals; it cares about the sum genetic material lodged in *POPULATIONS*.

Second, the reason a lot of shit exists in the world is because a lot of shit is possible to *grow from patterns* ... patterns that, in probably most cases, haven't ever been the subject of selection pressures. The difference between a 2-, 3- or 4-chambered heart probably has, indeed, been the target of millions of years of selection pressure. But finding of every result in neurobiology (or dietary genetics, or human locomotion, and on and on) shouldn't always everywhere -- and unreflectingly -- be assumed the result of selection pressure.

* * *

Which is why I like the quote above.

:)

And mine:

Aaron, as you can see, you touched upon one of Trevor and my "pet topics." My favorite part of the article is when they broke from the scholarly tone to be angry:

"However, the internal evidence to back this imperialistic selectionism strikes us as very thin. Its credibility depends largely on the reflected glamour of natural selection which biology proper is said to legitimise. Accordingly, if natural selection disappears from biology, its offshoots in other fields seem likely to disappear as well. This is an outcome much to be desired since, more often than not, these offshoots have proved to be not just post hoc but ad hoc, crude, reductionist, scientistic rather than scientific, shamelessly self-congratulatory, and so wanting in detail that they are bound to accommodate the data, however that data may turn out. So it really does matter whether natural selection is true."

---

Having said that, I have to take a step back and be critical of the authors. Of most significance: Darwin was the first to point out the limitations and potential pitfalls of his theories. So, I tend to be annoyed with the Darwin deists as much as I am with his detractors. Like with all good religions: NO ONE ACTUALLY READS DARWIN. At least not anymore. That is why I have made a habit of working my way slowly through his writings.

I prepared a lecture for my colleagues in Cambridge on this topic and also on why Lamarck wasn't as silly as BIO 101 course books make him out to be. In fact, Darwin had read and respected many of Lamarck's original thoughts on evolution, namely soft inheritance: that heritable changes can occur during the lifetime of an organism, not just during the transition for organism to organism. It isn't as simple as giraffes and tall trees, but it is still compelling and an important part of the puzzle for understanding inheritance and evolution. The plan can change mid-stream, and that can be inherited.

Visual

This was amazing. And made me think we should be open to incorporating a visual component to the performance of our project. Building perhaps on the idea of single molecule data (the actual on/off blinkings of the FRETing fluorophores) and the fluorescent score. Other images that come to mind, the perpetual motion of sperm plus egg to cleavage divisions to fetus adult then full circle with sperm and egg. Though the latter should not be too literal, but rather a template.

Local rules, global patterns

Let's discuss more about emergent behavior,

"The system would use local rules between interacting agents to create higher-level behavior well suited to its environment."

RNA = RAM

Aaron noticed this blog. It is oversimplified, but a great comparison of genetics concepts to computational ones. I thought it would give us something to contemplate at the end of the month.

Dichotic listening 2

Alan Cruttendon writes, in his book-length treatment of the prosody in language, Intonation, published 1997 by Cambridge University Press, the following:

"While the links between intonation and punctuation apply, of course, only to literate societies, the links between intonation and gesture are of an altogether more primitive sort. That intonation is a unique part of language is clearly demonstrated from experiments in dichotic listening. In this sort of experimentation similar auditory material is fed to the two ears and the listener shows a preference for the material presented to one ear. For language generally, for tone in tone languages, and even for consonant-vowel nonsense syllables, an advantage is shown for the right ear, which involves the left hemisphere of the brain; whereas a left ear (right hemisphere) advantage is shown for intonation, along with music and general environmental noises. So it is not surprising that in a large majority of cases of acquired language disorders, and even in cases of severe phonological or grammatical disorder, intonation is unaffected. In those few cases in which intonation is affected, patients may well have gestural problems as well. This suggests a close connection between intonation and gesture." [177]

Dichotic listening?

What about the listening of sound refracted through the hundred tiny lenses of the eye of the fly? What becomes of listening passed through the compound eye that, per force, must reassemble its contents in the form of a mosaic? Through the pincers of a dichotomy we come only to the doorstep of gesture, and of shape.

Dichotic listening 1

It was in August that I listened to Steve Takasugi's Der Fliegenpapier the first time. The piece flickers back and forth between German and English readings of Robert Musil's text of the same name, working in, about and through a carefully assembled (and then reassembled) milieu of words, parts of words and sounds.

Musil's text is a page a half long, maybe two. A full reading takes the narrator, composer and poet Wieland Hoban, only part of what becomes a six-minute piece. Wieland is German / English bilingual and reads both versions of the text.

German Fliegenpapier is English flypaper and there's a sense in which the inter- and admixture to which Takasugi subjects Wieland's spoken-word recordings creates a type of linguistic stickiness: parts, and sometimes only parts, of language inhere such that the affect of language reception changes during the course of the piece. Moments of clarity, instants of pulverization, stretches of such complete and unexpected linguistic hybridization such that — at intervals — the historic development from Old High Gothic into the present unravels.

Dozens of cuts between languages, between texts, in the first seconds of the piece. Announcement — or pronouncement — of title. Der Fliegenpapier / The Flypaper ... Pronouncement that sets into motion the uneasy relationship between the spoken word and the three or four different sense of text active about the work: Why pronouncement? Why here? Any number of European art songs from any number of centuries treat the entirety of some text. But never, whether at beginning or end, the pronouncement of title. A strange reading-aloud.

Sounds, images and bodies multiply. And so some months ago I became another something hovering about Musil's texts, and Takasugi's piece. And now comes the opportunity to shape words into the form of a listened pathway through this constellation.

I'll put some bits of writing here. And I'll start with with an idea of dichotic listening.

What parts of the word, the syllable, or the parts of the syllable, shine through a thousand cuts? It depends on the nature of the cuts and the nature of the reading. And in Wieland's careful treatment we perceive the spoken contour of the phrase. We hear where sentences begin and end amid cuts back and forth between languages, and between text. Form — in the up-and-down shaping of the sentence — at the level of the midground becomes perceptible through a flurry of cuts at the level of the foreground.

It is Alan Cruttendon who will suggest to us a dichotic listening as we assemble instead a fragmented listening. And it is from him that I'll quote in the next post.

Autofluorescence as artifact

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.

The Accessible Aquarium

We should keep our eye on this experimental music department at Georgia Tech.

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.

Julius F. Jezek Prize

Trevor, congratulations on your prize for Sekka! I'm still looking forward to hearing how your lecture in Cork, Ireland was received.

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.

More stones for our soup.

"a dusting of green and sapphire specks"

Biological Harmony

Erwin Schrödinger

What is life?

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?

the source of energy driving biological motions

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 ..."

Pervertebrate Paramecium

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.

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.

Mouvement perpetuel I

The first of Poulenc's three mouvements perpetuels.



Unaccompanied piano.

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.

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 ...

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.