Shannon Info, Jung-Paul Synchro, digital holographic DNA cosmology stuffing

Is preparing food for my nerdrons: Claude Shannon's Information Theory and DNA sequencing as fresh news that seems to me a hopeful avenue for some cutting edge research: 
"What they prove is that there is a channel capacity that defines a maximum rate of information flow during the process of sequencing. " It gives the maximum number of DNA base pairs that can be resolved per read, by any assembly algorithm, without regard to computational limitations," they say."http://www.technologyreview.com/blog/arxiv/27689/
it's a long wynding story, if you wanna' likkle primer, watch this short video about Claude Shannon. I see this being useful as providing a framework (Shannon's infomation theory) for thinking about human DNA RNA synthesis, and calculating better--more efficiently--so as to speed up the emerging DNA based medicine and therapy. It could be useful for every single aspect of human biological medicine, and at the same time, makes an explicit link between 'digital bits' and 'the biological 'binary' aspects of biology. '
So, to continue on this tip, and explain myself a little, it's been my hunch over the last 3 or so years that the 'holographic principle' co-founded by Dutch Nobel prized physicist: 'Gerard t'hooft' and 'information theory' as developed by Claude Shannon, underly a somewhat hermetic 'unified theory'. The above link to DNA sequencing, and the following link to 'cosmological' BIT Theory, if you like, are examples for the seriousness of this pretty 'far out' idea that, in some sense, the whole universe seems contained within each atom! or you could say a 'Digital' Universe, or better yet Multi-verse. As above, a new 'Digital' DNA information theory, and below:
"Hogan’s noise arises if space is made of chunks. Blocks. Bits. Hogan’s noise would imply that the universe is digital."http://www.scientificamerican.com/article.cfm?id=is-space-digital
 p.s Physicist Jack Sarfatti has proposed similar idea's that include Shannon's maxim's, and a neurological-cosmological ratio. I picked up on these ideas via Dr Robert Anton Wilson, who I suspect picked up some of these ideas from Jack, Saul Paul Sirag, David Bohm and others from the now legendary Bay Area based 'Physics Consciousness Research Group' that he attended.

--Steve Fly



Atom and Archetype: The Pauli/Jung Letters, 1932-1958 Edited by C. A. Meier


Atom and Archetype:
The Pauli/Jung Letters, 1932-1958
Edited by C. A. Meier
With a new preface by Beverley Zabriskie
Translated by David Roscoe


In his physics, Pauli sought a unified field. But his personal life was one of fragmentation and dissociation. Within one year, his mother poisoned herself in reaction to his father's involvement in an affair, and Pauli plunged into a brief marriage with a cabaret performer. At thirty, he turned to Jung for help.

Jung, in his 1935 lectures at the Tavistock, offered the following example of dreams effecting change:
I had a case, a university man, a very one-sided intellectual. His unconscious had become troubled and activated; so it projected itself into other men who appeared to be his enemies, and he felt terribly lonely because everybody seemed to be against him. Then he began to drink in order to forget his troubles, but he got exceedingly irritable and in these moods he began to quarrel with other men. . . and once he was thrown out of a restaurant and got beaten up.16
Jung saw that "he was chock-full of archaic material, and I said to myself: 'Now I am going to make an interesting experiment to get that material absolutely pure, without any influence from myself, and therefore I won't touch it.'" He referred Pauli to Dr. Erna Rosenbaum, "who was then just a beginner . . . I was absolutely sure she would not tamper." Pauli applied the same passionate brilliance to his unconscious as to his physics. In a five-month Jungian analysis, Pauli recorded and spontaneously illustrated hundreds of his dreams. "He even invented active imagination for himself He worked out the problem of the perpetuum mobile, not in a crazy way but in a symbolic way. He worked on all the problems which medieval philosophy was so keen on."17 For three months, "he was doing the work all by himself, . . . for about two months, he had a number of interviews with me . . . I did not have to explain much." Jung believed Pauli "became a perfectly normal and reasonable person. He did not drink any more, he became completely adapted and in every respect normal . . . He had a new center of interest." Jung had thirteen hundred of Pauli's dreams as the basis for his research into alchemical symbolism in a modern psyche. "At the end of the year I am going to publish a selection from his first four hundred dreams, where I show the development of one motif only."18
The physicist F. David Peat believes Jung's assessment of Pauli's state after his termination with Dr. Rosenbaum was too positive. Pauli's new "reasonableness" didn't last, and later he again drank excessively.
While Pauli's work aimed toward a "psychophysical monism," his intense inner tensions seemed to manifest physically in the so-called Pauli Effect, when his mere presence caused laboratory equipment to explode or fall apart.19 His internal "monotheism" and his sharp critical acumen and tongue earned him the titles "scourge of God," "the whip of God," and "the terrible Pauli." Even in the midst of personal disarray, Pauli kept his stance as a scientist of such rigor that he was called "the conscience of physics." Asked whether he thought a particular physics paper was wrong, he replied that was too kind--the paper was "not even wrong."20 Heisenberg's account of a 1927 conversation reveals that, in his youth, Pauli was concerned about the distinctions between knowledge and faith.21 Heisenberg saw that behind Pauli's
outward display of criticism and skepticism lay concealed a deep philosophical interest, even in those dark areas of reality or the human soul which elude the grasp of reason. And while the power of fascination emanating from Pauli's analyses of physical problems was due in some measure to the clarity of his formulations, the rest was derived from a constant contact with the field of the creative and spiritual processes for which no rational formulation as yet exists.22 For Pauli, the creativity of science included considerations of the psyche. In science, he subscribed to the quantum uncertainty theory that the position and presence of the observer changes the perception and reality of what is observed. To that thesis--that one cannot measure the wave and the particle at the same time--he added a psychological dimension, observing that insofar as the scientist must opt to know "which aspect of nature we want to make visible . . . we simultaneously make a sacrifice, . . . [a] coupling of choice and sacrifice."23 Pauli demonstrated the value of intuition to science's empiricism. As Weinberg recounted,
physicists in the early 1930'swere worried about an apparent violation of the law of conservation of energy when a radioactive nucleus undergoes the process known as beta decay. In 1932 Wolfgang, . . . Pauli proposed the existence of a convenient particle he called the neutrino, in order to account for the energy that was observed to be lost in this process. The elusive neutrino was eventually discovered experimentally over two decades later. Proposing the existence of something that has not yet been observed is a risky business, but it sometimes works.24
In a metaphysical leap, Pauli referred as well to "forms belonging to the unconscious region of the human soul" and stated that "the relation between a sense perception and Idea remains a consequence of the fact that both the soul and what is known in perception are subject to an order objectively conceived."25 He acknowledged that he had realized in a dream that the quantum-mechanical conception of nature lacked the second dimension, which he found provided by the archetypes of the unconscious.
It seems, however, that he could not find his way to the uncertainty, the "choice and sacrifice" that allows for reparation within analysis. While Pauli knew "that a truly unified view must include the feeling function, since without feeling there is no meaning or value in life, and no proper acknowledgment of the phenomenon of synchronicity," M.-L. von Franz said that he later sought only a "philosophical discussion of dreams":
He wrote to me . . . [and] made it clear that he did not want analysis; there was to be no payment. I saw that he was in despair, so I said we could try. The difficulties began when I asked him for the associations which referred to physics. He said, "Do you think I'm going to give you unpaid lessons in physics?" . . . He wanted something, but he didn't want to commit himself. He was split.26
Van Erkelens speculates that Pauli would have had to submit to a transference and to a deeper Eros than "his inner urge to develop a unified view of matter and spirit." For whatever reasons, von Franz and Pauli were not able to achieve the relational bond that holds and contains explosive emotional material and so allows surrender to one's unconscious and to a suffered analytic relationship.
Jung and Pauli corresponded and later met, not for analysis but for a comparison of ideas--Pauli pursuing Jung's synchronicity thesis and Jung fostering Pauli's understanding of the archetypal and collective factors in the psyche. Through their contact, William James's two fields, to which both Jung and Bohr had been attracted, come together again. Von Franz writes that the
notion of complementarity introduced by Niels Bohr to provide a better explanation for the paradoxical relationship between waves and particles in nuclear physics can also be applied to the relationship of conscious and unconscious states of a psychic content. This fact was discovered by Jung, but it was particularly elaborated by Wolfgang Pauli.27


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Shannon's Mathematical Theory of Communication Applied to DNA Sequencing

If we could have James Joyce and Robert Anton Wilson in the mix we might get close to something very really close to 'the tale of the tribe'. With a focus on RAW's book 'Coincidance' in which he defines DNA based information theory through a Joycean measure of the redundancy of information, poetry as information, political speeches as low. love, fly.


Shannon's Mathematical Theory of Communication Applied to DNA Sequencing

Nobody knows which sequencing technology is fastest because there has never been a fair way to compare the rate at which they extract information from DNA. Until now.
kfc 04/02/2012

One of the great unsung heroes of 20th-century science is Claude Shannon, an engineer at the famous Bell Laboratories during its heyday in the mid-20th century. Shannon's most enduring contribution to science is information theory, which underpins all digital communication.
In a famous paper dating from the late 1940s, Shannon set out the fundamental problem of communication: to reproduce, at one point in space, a message that has been created at another. The message is first encoded in some way, transmitted, and then decoded.

Shannon's showed that a message can always be reproduced at another point in space with arbitrary precision provided noise is below some threshold level. He went on to work out how much information could be sent in this way, a property known as the capacity of this information channel.

Shannon's ideas have been applied widely to all forms of information transmission with much success. One particularly interesting avenue has been the application of information theory to biology--the idea that life itself is the transmission of information from one generation to the next.

That type of thinking is ongoing, revolutionary, and still in its early stages. There's much to come.
Today, we look at an interesting corollary in the area of biological information transmission. Abolfazl Motahari and pals at the University of California, Berkeley, use Shannon's approach to examine how rapidly information can be extracted from DNA using the process of shotgun sequencing.

The problem here is to determine the sequence of nucleotides (A, G, C, and T) in a genome. That's time-consuming because genomes tend to be long--for instance, the human genome consists of some 3 billion nucleotides or base pairs. This would take forever to sequence in series.
So the shotgun approach involves cutting the genome into random pieces, consisting of between 100 and 1,000 base pairs, and sequencing them in parallel. The information is then glued back together in silico by a so-called reassembly algorithm.

Of course, there's no way of knowing how to reassemble the information from a single "read" of the genome. So in the shotgun approach, this process is repeated many times. Because each read divides up the genome in a different way, pieces inevitably overlap with segments from a previous run. These areas of overlap make it possible to reassemble the entire genome, like a jigsaw puzzle.

That smells like a classic problem of information theory, and indeed various people have thought about in this way. However, Motahari and co go a step further by restating it more or less exactly as an analogue of Shannon's famous approach.

They say the problem of genome sequencing is essentially of reproducing a message written in DNA, in a digital electronic format. In this approach, the original message is in DNA, it is encoded for transmission by the process of reading, and then it is decoded by a reassembly algorithm to produce an electronic version.

What they prove is that there is a channel capacity that defines a maximum rate of information flow during the process of sequencing. "It gives the maximum number of DNA base pairs that can be resolved per read, by any assembly algorithm, without regard to computational limitations," they say.

That is a significant result for anybody interested in sequencing genomes. An important question is how quickly any particular sequencing technology can do its job and whether it is faster or slower than other approaches.

That's not possible to work out at the moment because many of the algorithms used for assembly are designed for specific technologies and approaches to reading. Motohari and co say there are at least 20 different reassembly algorithms, for example. "This makes it difficult to compare different algorithms," they say.

Consequently, nobody really knows which is quickest or even which has the potential to be quickest.

The new work changes this. For the first time, it should be possible to work how close a given sequencing technology gets to the theoretical limit.

That could well force a clear-out-dead-wood from this area and stimulate a period of rapid innovation in sequencing technology.

Ref: arxiv.org/abs/1203.6233: Information Theory of DNA Sequencing


Japanese Masterpieces From The Museum of Fine Arts in Boston travel to Tokyo

Japanese Masterpieces From The Museum of Fine Arts in Boston travel to Tokyo

Orson Welles' fans push for commemorative U.S. stamp in time for centennial celebration

Orson Welles' fans push for commemorative U.S. stamp in time for centennial celebration

Published: Sunday, March 11, 2012, 8:11 PM     Updated: Sunday, March 11, 2012, 8:12 PM
With the approach of the 100th anniversary of the birth of the late Orson Welles, Woodstock, Illinois, where the actor-director spent his formative years is leading the call for a U.S. postage stamp to honor the maverick filmmaker.
Woodstock Celebrates, is planning events in May 2014, marking the 80th anniversary of the Todd Theatre Festival during which Welles made his directorial debut, and in May 2015 to mark the 100th anniversary of his birth.
Woodstock Celebrates and Wellesnet, a Welles resource website, are petitioning the U.S. Postal Service to issue a stamp in 2015 honoring the Orson Welles centenary. They argue that Woodstock is the proper locale for the first day issuance.
Woodstock Celebrates hopes the stamp drive and anniversary celebrations will attract Welles enthusiasts from around the United States and perhaps the globe, according to Kathleen Spaltro of Woodstock Celebrates.
“We want to reconnect Woodstock with two remarkable people in its history, Orson Welles and Roger Hill, an extraordinary educator at Todd School, who understood how to nourish creativity and foster love of learning,” Spaltro said.
At the Todd School for Boys, from 1926 to 1931, Welles met Hill, his mentor and lifelong friend. Asked as a middle-aged man who was the most important influence on his creativity, Welles replied, “Roger Hill. I think about him every day.”
Welles returned to Woodstock throughout the 1930s and 1940s – in particular for the theater festival at the Woodstock Opera House in 1934 that he organized and Hill, then headmaster, funded. There, Welles made his debut as a professional director, and he made his first venture into film in Woodstock with the 16mm short “The Hearts of Age.” In addition, Hill and Welles published the book“Everybody’s Shakespeare” in Woodstock that year.
Initial plans call for several Welles scholars to talk about his early life and career on the 80th anniversary of the 1934 Todd Theatre Festival (Tentative guests currently scheduled to speak include Joseph McBride, Jonathan Rosenbaum, Michael Dawson and Wellesnet's Lawrence French).
In May 2015, Woodstock Celebrates will throw a 100th birthday party for the late actor-director-writer. Related, concurrent events may include library and/or county historical society exhibits, screenings of Welles-related films, sales by vendors of radio and movie memorabilia, and a re-enactment of the historic 1938 radio broadcast of “The War of the Worlds.”
The issuance of a Welles commemorative postage stamp celebrating the 100th anniversary of his birth would complement Woodstock’s birthday party, organizers said.
Welles' image appeared on a U.S. stamp in 1999 in a scene from his landmark film "Citizen Kane." The 1941 film is regarded as the finest movie produced in Hollywood.
Stamp proposals must be submitted to the Citizens’ Stamp Advisory Committee in writing. Proposals made by e-mail will not receive a response. Subjects should be submitted at least three years in advance of the proposed date of issue to allow sufficient time for consideration and for design and production.

Stamp proposals should be submitted  to:
Citizens’ Stamp Advisory Committee
c/o Stamp Development
U.S. Postal Service
475 L’Enfant Plaza SW, Room 3300
Washington, DC 20260-3501

Orson Welles's lost Heart of Darkness screenplay performed for the first time

Orson Welles's lost Heart of Darkness screenplay performed for the first time

Orson Welles’s audacious adaptation of Conrad's 'Heart of Darkness’ has never been performed - until now.

A fictional poster for Orson Welles's Heart of Darkness by Fiona Banner Photo: Fiona Banner and La Boca
It was the one that got away. Heart of Darkness was meant to have been Orson Welles’s first film: a monumentally ambitious, technically innovative adaptation with which he hoped to shake up the industry.
Hollywood took one look at it – and baulked. Written in the late Thirties, Welles’s 174-page reimagining of Joseph Conrad’s 1899 novella was considered too expensive, too challenging, and the theme of lust for power made the moguls uneasy. So he abandoned the project and embarked on Plan B, a little film called Citizen Kane.
Rejected by RKO’s sceptical president, George Schaefer, and bound up in rights issues with the Welles estate since his death, the Heart of Darkness script has never once been performed – until now.
On Saturday afternoon (31 March), a one-off production is being staged by the Turner Prize nominated artist Fiona Banner and live-streamed around the world from the most apt setting imaginable: a riverboat installation modelled on the Roi des Belges, the vessel Conrad captained on his journey up the Congo in 1890. Scottish actor Brian Cox will play - as Welles intended - both Marlow, the narrator-protagonist, and Captain Kurtz, the despotic ivory trader he seeks.
Over the entire event hang titanic spectres of hubris and defeat – both Welles’s own and those described in the story. This is what fascinated Banner. “It seemed to embody so much failure to me,” she says. “Or so much disappointment – the disappointment at the heart of Conrad’s story, the hopes and aspirations of all of us, and how they co-exist with impossibility. I think disappointment’s underrated, and such a rich part of life.
“Also the myth of the hero is so powerful in that tale. If you superimpose the heroic figure of Welles, he and Kurtz, and, in a way, all of the great Conrad characters sort of mingle together into one.”
Banner’s three-way obsession with Welles, Conrad and Heart of Darkness came out of an earlier project, The Nam, in which she confronted Hollywood’s mythologising of the Vietnam War. Francis Ford Coppola’s Apocalypse Now, the most famous Heart of Darkness adaptation, is a movie with its own parallel set of myths, a grandiose near-failure. Time and again, it seems, the strange power of Conrad’s text – “the dark cloud of genius”, as Banner puts it – has tempted film-makers up river and run them aground.
“The reasons Welles didn’t get [the film made] are interesting,” adds Banner. “When he started writing it, fascism wasn’t such a big story in Hollywood, but by the time he finished it, in 1939, it must have been something of a hot potato. That was probably the main reason it didn’t get made. The more I’ve looked into it, the more I’ve realised how close he is to the stuff in Europe, and not just in the obvious ways of giving all these company men that Marlow meets German names. It’s central to the tale.”
The political subtext of Welles’s script can’t have been the only thing that made Schaefer and his underlings quiver with uncertainty. The screenplay begins with an on-camera “screen test” in which he asks the audience to assume the role of a caged canary. There’s another prologue, utterly unrelated to Conrad, that places the viewer in an electric chair. All this is by way of establishing a radically new grammar of film-making, in which the camera’s eye is the same as our own. Welles visualises Marlow’s voyage as an implicating, first-person journey of discovery.
“I’ve never seen a script that dedicates so much space to camera,” says Banner. “You feel that if this film had been made, Hollywood might have been a different place.”
There’s no doubt that Welles’s innovations were ahead of their time: eight years after he had the idea, the you-are-the-camera gimmick was used in a Hollywood production – Robert Montgomery’s noir adaptation of Raymond Chandler’s Lady in the Lake (1947). The sense that Welles was pushing at the boundaries of what was possible within the studio system, but still failing to get most of his ideas off the ground, is precisely what makes his career such an endless source of fascination.
“He didn’t fulfil his potential – he ended up making frozen peas adverts and stuff,” Banner says. “But all through his life he’d go off and make these extraordinary things. He’d fund them himself, and some of them were never shown.”
The variety of techniques flaunted in the script pose mind-spinning challenges for Banner and her cameraman, Hugo Glendinning, whose images will be beamed down live across the internet. She’s guarding the exact details of how the production will work, practically speaking, but the aims are clear. “It will appear as if Cox is talking to himself, so this idea of duality, of one man’s vision challenging his intellectual condition, will be evident in the performance.
“Plus, Cox has the aura of a lead guy, but he doesn’t do many leads. So I like the idea of his being a kind of triple lead here – he’s channelling Welles, he’s channelling the allure of Kurtz and the almost moderate Marlow.”
It could make for a backward-looking exercise, an archaeological game with old-hat material, were it not for the curious relevance of Conrad’s work – and Welles’s – to what Banner calls “systems of control” that have lingered in their wake. “It does feel like a relevant text for today,” says Banner. “It’s about greed and lust for power. If you want to look globally, the tragedy is that the situation in the Congo is really no better now than it was then.”
Heart of Darkness will be streamed live from 5.30pm tomorrow online at aroomforlondon.co.uk and in the Purcell Room, London SE1