## 20100930

### In Honor Of

We bought the sky, the greatest ticket the universe had to offer. 100,000 of the best and brightest Terra had to offer. Brave pioneers who sacrificed everything for a chance to make it on new planet, free from the troubles of home. They said we were fools; there was no way to build something that big, that the cryosystems would never work, that our ship would break. They said we were traitors; Earth needed our skills, the resources that went into our ship came out of the mouths of the starving. But we were heroes, out on the grand question for evolution. Some of us died before the work was completed, their children carried on. When the time came, we took the shuttles to geosynchronous orbit, started the fusion Orion/pulse drive, sealed up the cyrochambers, and slept. We dreamed of green fields and blue skies.

A stranger opened the cyrochamber door. “Welcome to Eredani Prime. Please present your papers for inspection?” Not an alien, not a pioneer, just the children of those who had take waited for the technology of interstellar colonization to become accessible to the masses. They had brought everything we hated about home with them. We closed the cyrochamber, turned our ship towards the outer darkness, and engaged the main drive.

Fuck physics, and fuck FTL.

## 20100928

### The Rightful Place of Science Policy

This previous post on the goals of neuroscience (and the ensuing flamewar) got me thinking. What is it that I am trying to do?

I'll freely admit it, I am not a scientist. I don't generate testable hypothesis, knowledge about the natural universe, or anythng that can be nailed down with a reasonable degree of certainty. Why then should I be trusted (and publicly funded?). As science policy expert, I believe that I provide a unique skillset and viewpoint for decision-making in the 21st century.

Science policy has two research thrusts: guiding the development of the natural sciences through funding mechanism and other incentives, and understanding and responding to the effects of science and technology on our society. Science does not exist in a vacuum, every it of knowledge or technological artifact has associated social processes, what Sheila Jasanoff calls 'co-production.' The ultimate goal of science policy is to combine the two research thrusts into a means of steering society by favoring certain research paths. Though this seems at anti-democratic, elitist, or even Orwellian, it is the state of the world. We are always making choices vis a vis science policy, even relinquishment or defunding counts as a choice. The work of the science policy professional is to make good choices, in a full understanding of the technosocial context in which they are made, and as broad of public participation as possible.

The origins of science policy as a discipline can be traced back to WW2, where America rapidly mobilized its scientists and engineers to produce war-winning weapons: the proximity fuse, operations research, and the atomic bomb. Vannevar Bush's Office of Scientific Research and Development organized thousands of scientists to turn knowledge towards military ends, but despite its spectacular success, it could only be tempory. Bush ruled in a climate of secrecy and military necessity which justified any decision. The war forced people to work together, and Bush was a managerial genius. The conditions of the OSRD could not be replicated indefinitely, and so Bush moved to create a civilian successor to the OSRD for basic research, the National Science Foundation, and pressed for more scientific expert participation at the highest echelons of government.

Within the decade, spurred on by sputnik terror, Federal science funding had become a permanent part of the political landscape. Dozens of agencies, from the Department of Defense to the National Institutes of Health, funded basic and applied science. Corporate labs served as epicenters of invention in Silicon Valley and along Route 128. But while this era brought forth wonders, science remained a servant only of those wealthy enough to directly support it; the military and high tech. The vast majority of America's scientific output languished in academia. In 1980, Congress fundamentally reorganized science policy with Bayh-Dole Act, which allowed patents for the products of federally funded research. Now, scientists did not need to choose between the public and private sectors, their work could be universally applied. The Federal government took on the role of a basic driver of innovation.

At the same time, citizens became more aware of the role of science and technology in constituting their world. The environmental and anti-nuclear movements exposed people to the hazards of modern technology, while making science itself an object of contention. Neo-luddite responses to computerization, suburbanization, and militarization further mobilized ordinary people and academics to seriously consider the state of science, technology, and society.

We stand now poised at the edge of a great transformation. Convergent technologies in nano, biological, information, and cognitive realms propose to alter and redefine human beings. A combination of population growth and industrialization has placed the planetary ecosystem and resource supply under near critical stress. In this delicate scenario, we can no longer trust to the blind forces of the market to make the best decisions, or leave it entirely in the hermetic hands of a self-selecting technological elite.

Science policy is therefore about making good decisions. It is about a set of intellectual tools that allow you to analyze issues and expose critical elements, consequences, and constituencies in political decisions involving human beings and scientific knowledge. I do not believe that science policy experts should have a preeminent role at the table, that's just as bad as turning decision-making over to politicians, or bankers, or generals, or engineers. Instead, we try and get as many people at the table as possible, as many views to ensure that science is working towards socially desirable ends, that people are not being unjustly excluded, and that there is a full and fair engagement with the future.

The deterministic loop between advances in science, deployment of new technologies, changes in society, and new socially supported science to advance certain ends is an exaggeration. It is impossible to predict the future. But we can give people the tools to make the best decisions they can.

## 20100926

### Paper Review : Neural Plasticity and Consciousness

For neuroscientists, treating "The Hard Problem of Consciousness" outside of bar-room speculation is a risky career move. This is why we have true doctors of philosophy, and why the philosophy paper "Neural Plasticity and Consciousness" by Susan Hurley and Alva Noë is a good thing. Hurley and Noë's thesis relates to some recent activity on WeAlone [1,2, maybe 3] , so I will attempt to summarize the article in a language that makes most sense to me.

First Hurley and Noë note that the "hard problem of consciousness" is equivalent to what they call an "absolute gap", i.e. "why should we assume that neural activity is solely responsible for conscious perception at all ?". My interpretation is that Hurley and Noë say "we can't, this is a leap of faith", and for the purposes of the paper accept as an axiom that neural activity corresponds to perception. The meat of the paper then, discusses why some neural activity should take on a particular quality, like seeing, and other neural activity should take on a distinct quality, like hearing.

Lately, I've been throwing around the term "neural topology" and "manifold structure" in an embarrassingly non-rigorous manner. I'd like to say "the topology of qualia acquires the topology of stimuli via learning of the intrinsic statistical structure of the stimuli, and in a sense, the stimulus stimulus model constitutes the nature of qualia", but this is vague. Hurley and Noë express, I believe, a similar sentiment clearly and without abusing terms from mathematics :
It is argued that the different characteristics of input activity from specific sources (visual vs. auditory) generate not just representational structure specific to that source but also source-specific sensory and perceptual qualities.
That is to say, when the brain learns the topology of stimuli ( possibly in union with the topology of motor outputs as they modify stimuli ), the brain acquires the qualia corresponding to said stimuli.

Earlier we talked about the possibility of defining an algebraic structure representing the shape of information coded in the brain. The take-away point was that it might be possible to rigorously say "these two areas have effectively the same abstract structure, since you can relate them by some structure preserving relationship". The Hurley and Noë paper provides anecdotes which suggest that, when two physically distinct neural circuits have the same abstract structure (topology), then the subjective experience (qualia) are also the same. Specifically, they discuss experiments in which blind patients were able to acquire visual qualia through a tactile stimulation device that translates camera images into stimulation of the skin.
After a period of adaptation (as short as a few minutes), subjects report perceptual experiences that are distinctively non-tactile and quasi-visual. … However, Bach-y-Rita emphasizes that the transition to quasi-visual perception depends on the subject’s exercising active control of the camera. … Perceivers can acquire and use practical knowledge of the common laws of sensorimotor contingency that vision and TVSS-perception share. For example, as you move around an object, hidden portions of its surface come into tactile-visual view, just as they would if you were seeing them."
This experiment suggests that giving a system a new topology induces qualia of that topology, and that learning the new topology does not necessarily require expensive and lengthly re-wiring. That camera control was necessary for inducing visual qualia from tactile stimulation suggests that the structure of visual stimuli and the experience of seeing must necessarily incorporate how our actions : movement of the eyes and head, and translation in space, alter the content of visual stimuli. Thus, when we talk about the "topology" of a stimulus, we must also incorporate how our actions change the stimulus (how our motor operators transform the stimulus space).

Hurley and Noë cover a number of other interesting anecdotes, including what happens when the brain fails to adapt its structure to reality, and pointing out that, in a left-right reversal of vision, reversing the interpretation of visual data is topologically equivalent to reversing the coordinates of motor output and proprioception, such that many different possible explanations of neural adaptation may be topologically equivalent.

So, I really do feel like, if we can make this notion of "neural topology*" more rigorous, we will have a satisfying answer to the portion of "the hard problem" that is amenable to scientific and mathematical investigations.

*neural topology : the idea that, in high dimensional sensory spaces, the distribution of probable stimuli occupy a reduced subset of said high dimensional space, and that one can move about this subset in a differentiable manner to transition smoothly between probable stimuli. This is a vague notion. It is related to "statistical structure" and "manifold", although I should note that we don't have enough information to say that the space of probably sensory-motor states is actually a manifold.

## 20100924

### Cynicism and Its Discontents

I was reading this Times opinion piece, about the supreme court, recent decisions, the idea of standing to sue, etc., and which touches on some issues we have been discussing recently.

I have always kind of liked discussing legal issues, but I also don't really have any legal background to speak of, other than what I've learned from my Dad. I'm familiar with some of the really historically important ones, and some of the history surrounding the court, but I never took that supreme court class at Caltech or anything like that.

There's a lot of sort of high level, abstract stuff about how the law should be interpretted that I think is kind of gibberish. It always seems to piss people off when I say this, but I really don't understand what this "living document" theory is. This idea that a document means anything besides what the person who wrote it thought that it meant, or what the people who signed it mutually agreed that it meant, that it is some how "informed", as these post modernists like to say, by subsequent historical or cultural developments, strikes me as completely insane. I don't want to dwell on the point, and I suppose that different people might have different views on how drastic this new information may be, but obviously the text of the document doesn't change, and if the meaning somehow still changes nebulously while the text remains fixed, then the meaning of the document is now defined in someway that is completely inaccessible to any person, who only has access to the document. So any, alternative notion of meaning suggested by this living document idea is inaccessable to us as humans, inaccessible to the layperson, and thus utterly useless to talk or think about and should be abandoned. I understand if you want judges to have their ear to the ground, attuned to society and cultural developments, but to be honest, culture is not something we can form a consensus on -- different people interpret culture differently.

What I was more interested in discussing is that, the commenters in this piece were extremely cynical about the whole thing. Take #12, Jimmy from NJ:

"I used to care about the Supreme Court when I was a kid in law school---well, a little anyway. But these days, I couldn't care less. Why? Because watching both sides--liberal and conservative--engage in absurd, utterly risible result-oriented analyses was enough to put me off the whole thing. The idea that any of these justices actually believes in any of the interpretive philosophies unto which they ostensibly cleave is pure fantasy. There is no real intellectual debate in the Court. These are political actors making self-serving political decisions to benefit the interest groups who helped put them on the court. It's as simple as that."

I mean I've heard the more typical shrill partisan whining (#9, merits of his argument aside):

"I have no doubts that a Court that can find that a cross is not a Christian symbol, nor that a Justice (Scalia) who finds that women do not have inherent rights in the Constitution, can deal with a trivial matter like standing with ease."

But I'm kind of curious how many students of Biffpolitik view the court as a whole as a fundamentally intellectual, disinterested body, or like Jimmy, think they are obviously just a bunch of posers. Having not really scrutinized a Supreme court decision, is the level of argument really a step up from think tank policy debate? Or is it just more esoteric.

yay the beatles

## 20100922

### Cybersabotaging Iran's Nuclear Program

Cyberwarfare is nothing new. People in the know have been tracking hacking attempts and viruses for decades. Markus Hess broke into computers for the KGB in the late 80s, while the Morris worm brought down the internet entirely in 1988. But what's new is that an incredibly sophisticated worm (4 0day exploits, and a P2P communication system) has been infiltrated into specific pieces of hardware, Siemens Programmable Logic Controllers, for unknown ends.

"When Stuxnet finally identifies its target, it makes changes to a piece of Siemens code called Organizational Block 35. This Siemens component monitors critical factory operations -- things that need a response within 100 milliseconds. By messing with Operational Block 35, Stuxnet could easily cause a refinery's centrifuge to malfunction, but it could be used to hit other targets too," Byres said. "The only thing I can say is that it is something designed to go bang," he said.

Most of the computers infected are in Iran, and Siemens controllers are used to run U-235 separating centrifuges. Depending on the sophistication of the attack, Iran's nuclear program could be significantly set back, or if the finished uranium undetectably contaminated, even deemed a failure.

This could be the first strategic cyberattack on a specific target, as opposed to tactical network disruption to break through air defenses. But while cyberwarfare is less deadly than kinetic warfare, the entry of sophisticated groups (not going to point fingers at states yet), putting disruptive software on large computer networks is a bad deal. There's too little accountability, and too much of an incentive to try and disrupt the economy of a rival. Sum over the world, and soon nothing much will work correctly due to ultra-sophisticated hacks.

## 20100921

### Neuroscience, Manifolds

This has been bothering me fore some time, and rather than go through and read the literature I'm just going to dump speculation here.

It seems like it should be possible to derive a general theory for embedding cortical maps. At its simplest, I am referring the to the problem of embedding manifolds with arbitrary topology into the surface of the brain. I understand that "low distortion embeddings" of high dimensional spaces are reasonably well studied, and I think in some instances it might be as simple as naïvely applying mathematical notions of "low distortion embedding" to embedding of manifolds in cortex.

( Side note : in an earlier conversation with Beck, it was noted that, if your space is high dimensional, and your points few, arbitrary embedding is about as good as the optimal low distortion embedding. I think there definitely are high dimensional spaces that only need to encode a relatively sparse set of points that are pretty much randomly organized. Olfactory bulb may be an example : 1000 dimensional vector space, and most attempts to make some sort of map on the surface of the olfactory bulb have failed. However, this could simply mean that high dimensional spaces never embed with low distortion, so random embeddings are getting close to optimal, but optimal is still bad. )

Anyway, places where you typically want to think about low distortion embeddings : primary sensory areas are somewhat obvious, and retinotopic, somatotopic, and tonotopic maps are well studied.

So, what I'm talking about here is more interesting than say, the problem of embedding a spherical globe into a two dimensional map. Visual and somatosensory data have an obvious manifold structure because they are coming from manifold sensory organs. However, the information carried in these sensory streams has a more complex structure, and we ultimately see organization in cortex that reflects this structure.

Lets use the visual system for an example. First, visual information is coming in from the retina, which is to first approximation a hemispherical sheet. Ignore foveal magnification, and just say that this sheet basically ends up being squished, stretched, and flattened onto most primary and secondary visual processing areas. The shape changes, but neighborhoods are preserved.

But, theres also all this natural structure in the information coming from the retina. First of all, you've got brightness, yellow-blue opponancy, and red-green opponancy, so that's three channels effectively forming our familiar three dimensional color space. I'm not sure the brain actually does anything particularly fancy with color information, actually, but basically whats coming into the brain is already this kind of function from a disc to three dimensional color space f:ℝ²→ℝ³.

The really interesting thing about embedding visual space in cortex happens when you start trying to extract low level features. Forget about color for now, its confusing. For now, lets just assume that these low level features are oriented edges. We have to represent a function from the visual field ℝ² (or maybe ℂ would do, or ℝ⁺×𝕋, you know, something two dimensional) to the circle group (apparently called 𝕋). I'm being vague here: something that looks like ℝ²→𝕋.

If you've made it this far and aren't enraged by my bastardized notation, you might have noticed that I'm dropping a component from this visual-orientation space, which is the salience of an oriented edge. The brain represents this as firing rate, but theres no immediately obvious reason why salience should be the component that gets represented in firing rate, and not, say, orientation. Its obvious that firing rate would not work for representing location in the visual field, since it's quite common to have two points in the visual field contain bars of the same orientation, but its impossible for one point in the visual field to contain two bars of the same orientation but different salience.

Incoming visual information on oriented edges takes on the form f:ℝ²→(ℝ⁺×𝕋), so we end up needed to embed a space shaped like ℝ²×(ℝ⁺×𝕋) into cortex, which can be represented simply as a function from a manifold sheet (cortex) to a positive* scalar firing rate** f:ℝ²→ℝ⁺. I'm not sure how to state this formally, but it seems natural that when embedding f:ℝ²→(ℝ⁺×𝕋) in f:ℝ²→ℝ⁺ the ℝ²×𝕋 (orientation) information is going to have to get flattened into ℝ², preferably with minimal distortion.

There is no uniquely optimal way to choose this embedding***. This is evidenced by the fact that orientation selective patches end up forming bands in some animals, and neat little hexagonal "hypercolumns" in others, and sometimes even a mixture of both [citation needed]. The problem is complicated, of course, by the fact that orientation maps aren't the only thing being embedded in the primary visual cortex. In realty, the space you are trying to embed still contains color information, and rather than oriented edges you have this over-complete space of temporally modulated Gabor wavelets****, all of which still needs to get squished into f:ℝ²→ℝ⁺. Oh, also there are two eyes that need to fit into one cortex, hence the ocular dominance columns.

Naïve models of so called "orientation column" formation consider simply the problem of embedding ℝ²×𝕋 in ℝ². These models can reproduce some of the orientation maps we see, but are unsatisfactory. Whenever I run simulations (code lost, hearsay) of this phenomena, I get disorganized columns that eventually converge to stripes if I let the simulation sit long enough. We do see this in some animals, but in many species orientation preference has a crystalline hexagonal packing. At some point in the past, this was thought to indicate a regular periodic organization of cortex. We now know***** that this structure is due simply to the learning rules and the act of embedding ℝ²×𝕋 in ℝ².

Ok, yeah, I'm out of ideas here. I guess I'll leave off with : I'm not sure if anyone has tried to model embedding the space of complex cell receptive fields into ℝ², or tried to construct a nice story about why the space might be embedded as we observe. I'm also not sure if anyone has successfully reasoned about how significantly more complex spaces might end up embedded in cortex. I think in areas like IT, which is supposed to respond to specific objects, the reaction is "well, the space of possible objects is so ridiculously complex theres no way you could flatten it reasonably, so its probably just all mashed in there". Perhaps there are spaces with intermediate complexity that we can look at, perhaps interesting spaces over in parietal lobe that partially represent both visual and motor spaces.

I... guess I'll go try to read more papers.

*its actually non-negative but ℝ∖ℝ⁻ wasn't as stylish. can we just exclude 0 due to "spontaneous spiking" ?

**many simplifications. First of all, I'm not sure we can prove its even firing rate and not something like spike timing that neurons are using to code, second of all neurons have receptive fields that depend on the modulation of a stimulus in time. So, time is another dimension here that I have no idea how to treat formally ( if you can call this nonsense formal ).

***I guess

****I'd say its not completely clear that V1 complex cells _are_ temporally modulated gabor wavelets, but rather that they seem to more or less resemble such wavelets, so we just stopped right there and declared the problem solved.

*****by "we now know" I mean "i assume, I'll look for a reference later"

## 20100920

### Project, preliminary

Keegan and I are working on a new project. It should look something like this. We have the electrical stuff worked out, but may need some assistance with the mechanical aspects. The basic idea is to make a conveyor belt of phosphorescent fabric, then write things on it using a bar of ultraviolet LEDs.

/>

## 20100919

### "Nothing dates the past like impressions of the future"

Was oscillating online, came across this, with an interesting quotation:

"Nothing dates the past like its impressions of the future."

Debatable?

I think certainly nothing speaks of an era like its dreams, and dreams do become dated.

When it comes to tech speculations its certainly easy to misinterpret an era as being optimistic -- yes Sci Fi writers loved rocket cars and space ships, but to call the 60s and 70s an optimistic era I think is a bit misleading. Of course there are dystopian sci fi futures as well... my impression of much of Sci Fi is that it was not so much about making accurate predictions as suggesting interesting possibilities, with a goal of commenting on society.

Getting a little off topic... forget about dreams, can we focus on impressions of the future?

For instance I'm not really aware of any impressions of the future that anyone had, in Ancient Rome, even in the 1800s? What did Cicero think the world would be like in the year 1000? Did anyone in the pre-industrial age foresee the industrial revolution?

Getting back to the claim, itself, are there reasons we should think it should really be true? Its easy to see why impressions of the future would age quite badly, and obviously, to observers with knowledge of the future. And its hard to think of any other subject that they should have many ideas on, but a person from our time would surely have different ideas about.

Yet, if you just ask the simple question, "How should I know a person / thing from the past when I encounter it?", its not clear that my obvious first step is to try to determine what ideas they carry about what the future will be like. Generally I would expect such a person or thing to be immediately recognizable because of stylistic elements -- perhaps style is wrapped up in this question as well though. The sleek, the modern, the cutting edge, all this is related to the future.

Is this true? Does fashion really have to do with our ideas of the future? To be honest when I put on a T-shirt and a pair of jeans and go to class, I don't really feel like I'm "dressing for the future", even though I guess I am.

My instinct is that, the fashions, the design ideology, the style of an era speaks most about how that era believes they will solve the great problems. Modernism, modernist buildings particularly, of a grand, uniform design, with a utilitarian focus... speaks of a dispassionate, unified approach to science and all problems great and small, with which one may suppose all our problems may be subdued before us. When I throw on a T-shirt, I'm still solving a problem, however small... in some sense, the now pervasive "casual work environment" which has come to pervade the 90s and 2000s, I think speaks quite highly of our society -- on a typical day, I do not expect I will have to negotiate with an extremely powerful superior, or for any other reason need to curry favor with someone by dressing formally. My work place is substantially more egalitarian than that. I don't wear a watch either -- but no one wears a watch anymore except someone trying to look professional. Watches are dated -- it is clearly expedient to look at any of the hundreds of computers which will surround you throughout your work day. They are the trappings of the wealthy from a few decades ago, and while they will probably percolate down through society for a few decades to come, for all intents and purposes they are now as quaint as the pocket watch, and the "upper class" will rid themselves of them not so long from now.

I'm not really making a very strong argument that fashion reflects the ideology of an era -- at least when it comes to personal fashion, I'm only really able to argue that it reflects the technology of the era which is kind of obvious. I'm also pretty fashion illiterate, maybe there's much better arguments to be made, and maybe I should be looking at fashion statements by entertainers, rock bands, high profile people etc. the fashionistas.

I would also suspect that you can come up with lots of counter examples -- in the case of traditions, when they are kept alive they aren't seen as dated, even though they are still sort of relics of the past. Very few traditions and religions actively hold impressions of the future, I assume because, things like this have to keep it short and simple or the extra cruft won't be passed along. The book of Revelations is one of the few major examples of predictions of the future that I am aware of... but this aspect of Christianity at least doesn't seem to be the part that makes it most "dated". In my mind, the fixation on rituals, the lighting of candles, the latin, the peculiar dress and language, the frequently gothic or baroque taste of churches, these are the things that one immediately recognizes as dated.

Well, we've wandered around for a bit. What's the verdict? Is there some truth here, does "nothing date the past like impressions of the future"? Or is it just a zippy one liner in a magazine?

## 20100918

### Subjective

At some point I should attempt to articulate the questions that motivate me to do neuroscience. Presently, questions take the form of "what would it even mean for neuroscience to succeed?". We don't know. Another phrasing : "what form do you expect the answers from neuroscience to take?".

What would it mean for us to say we understood consciousness? We are looking for both a functional duplication, as well as a satisfying philosophical explanation. The "hard problem" of consciousness is not a problem from science, it is philosophy. For me, personally, statements like "existence of information is equivalent to experience of information" and "consciousness is a mathematical entity" assuage my doubt and scratch th surface of the hard problem, but these are more religious statements than scientific.

I think, fundamentally, what we want is a mathematical story. We want that story to say that there is something elegantly simple about consciousness, that we are some sort of standard algorithm that happens to have been implemented in neurons. Such a theory ( or is it philosophy ? ) in union with the minute details of the wiring of our impulses and emotions, can satisfactorily explain consciousness.

WeAlone editors* and readers : what would it mean for your respective fields to succeed ? Is this even a fair question to ask ? In general, is there a cohesive underlying goal that holds fields together, or are most fields loosely connected pursuits of very specific, very obscure problems, with no overarching goal ? Does society implicitly assume certain grand goals when funding and conducting scientific research : immortality, wealth, equality, space colonization, machine consciousness, or are we forced to concede that "science marches on blindly, without regard to the real welfare of the human race or to any other standard, obedient only to the psychological needs of the scientists and of the government officials and corporation executives who provide the funds for research."**

*editors feel free to respond with primary posts, since a lot of your post-length statements get buried in comment threads
**[quote from the undeniably insane Theodore Kaczynski's "Industrial Society and its Future" (I guess terrorists have intellectual property rights too?)]

## 20100916

### Biff demands content. Content shall be generated

The prosecution responsible for the recent nation wide injunction against embryonic stem cell research has written this article, in their defense. A fellow neuroscience graduate student described it "one of the least factual arguments I have ever read". Many of the comments ( explaining why Mr. Bowmen is bad at science ), are insightful. I don't need to duplicate why Matt Bowman is oh so very wrong here, but it reduces one word : "epigenetics". Adult derived stem cells aren't going to replace embryonic lines any time soon.

--- [[ meta ]] ---

Beck has noted that we seem to have degenerated into commenting on events that happen in the news. This is fairly accurate. The truth is that few blogs sustain themselves with daily updates of original content. The ones that do are called news, webcomics, and the weather report. Blogs with large readership scrape the internet, post, link, maybe sometimes even analyze or comment. Who wants to spend all day looking for funny videos of rats staring at each other just to keep readers fed with a constant stream of novelty? We do not need to be such a blog. We have few readers, and therefore can post whatever the hell we want. I think we can even swear in posts without upsetting people.

Beck has noted that he feels bad about posting raw research on WeAlone. I say this is nonsense, all of us are in graduate school now, and most of what we have to say is going to take the form of raw research for the foreseeable future.

Here, I'll start : what do you think the most natural generalization of principle component analysis (PCA) to finite fields ( like bit vectors ) is ? In an offline discussion, Beck and I decided that the notion of "vector of maximum entropy" makes more sense than "vector of maximum variance", when your vectors have elements from a finite field. So, we think its possible to define a PCA like operation for distributions of vectors with elements from a finite field using entropy instead of variance. However, we have no indication that this is even remotely useful.

## 20100913

### Cultural Enclosure

In the late 18th century, English society underwent a major structural change: the enclosure of the commons. The enclosure movement effectively destroyed ancient patterns of rural life, as wealthy land-owners used legal clout to turn peasant farmers into landless laborers. Something similar is happening here and now; an attempt by powerful media companies to enclose our common cultural heritage inside a fence of copyright law.

Copyright is one of the few specific powers enumerated in the American constitution. “The Congress shall have the power To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries.” Copyright was initially established at 14 years, with a 14 year renewal, but the term has been lengthed repeatedly, with the Sonny Bono Copyright Term Extension Act bringing the duration to life of the author plus seventy years, or 120 years for corporate authors. At the same time, the scope of copyright has expanded from maps and direct copies of literary works to all forms of media, adaptations, and translations.

The stated rational is that extending copyright benefits creators, and while it does, this grand cultural enclosure has inflicted grievous harm on our cultural vitality. It walls off immense tracts of our shared heritage, fights against technological architecture, and has raised high barriers to entry. At the current rate, any work created after 1923 will remain in copyright effectively forever, even if it has become completely out of print and of only limited utility to anyone. Bringing old works into the open is very difficult, because there is now registry of copyright owners, and prospective publishers must prepare for surprise lawsuits. For a devote of old culture this is a crime.

On a computer, there is no difference between the act of reading and the act of copying. Software controls are required to prevent copying, strictly making our digital tools less useful. As a simple example, Adobe's restrictions on use mean that I can't easily highlight and annotate academic papers. So much paperless office, or a searchable, linked database of articles I've read, and for the protection of who's rights? The penalties for violating copyright are entirely excessive. The putative fines associated with a typical pirated music library are an order of magnitude larger than the gross revenue of the entire music industry.

But most significantly of all, no cultural artiface exists in a vacuum, and internet culture especially is a mash-up, a juxaposition and collage of objects in a new context, whether it be youtube videos or fan fiction. I can't deny the quality of a lot of internet culture is terrible, but it is sandbox tomorrow's artists play in. As it stands, monetizing internet culture is basically impossible, and working in the medium exposes you to those putative copyright violation penalties. There are ways around this, through fair use and getting permission, but that's expensive in terms of time and lawyer's fees. Copyright has become a barrier to commerce and creative expression.

What can we do? We can slap the Creative Commons license on everything, but that's a crude patch. Copyright law should be rewritten to recognize that not all works of art are equal. If you want a copyright, you should be forced to pay a nominal fee for it. The term should be short, and extensions easy, but rising in cost with the term and value of the copyright. Lobby your Congress-drones, support open media, and prepare for the infopocalypse.

((With thanks to Lawrence Lessig and his book Free Culture))

## 20100911

### The Hazards of Ze Goggles

Kenna - Hell Bent (Official Music Video). Watch more top selected videos about: Kenna

Long term effects of ze goggles have not been adequately studied. Possible side-effects may include persistent visual artefacts, vocabulary reduction to "whoa", "dude", and "groovadelic", and loss of your human essence. Pregnant and nursing mothers should avoid use of ze goggles. Use in moderation. Protect your vital bodily fluids.

### Nature

Yes, it has come to this : the prestigious scientific journal Nature mentions, by name, Limbaugh, Fox News, Glenn Beck and Sarah Palin, as concrete threats to the American scientific complex, and hence threats to the future prosperity of this country.

I almost don't want to weigh in on this ( all sides have committed errors ), but the fact that one of the most prestigious scientific journals is listing enemies by name clearly signifies at least one thing : the relationship between science and society is deteriorating.

Some time in the past, I'm told, Americans respected science. It let us end WWII brutally and concisely, and got us to the moon before the Soviets. What is different today, that the public no longer respects scientific evidence for making informed policy decisions ?

It also seems to me that complaints about liberal bias in science have a very simple solution. If you think science is too liberal, get off your political stage, get a doctorate from a reputable research institute, and do some quality peer reviewed science of your own. Science doesn't really care that much about your politics. One of my more excellent mentors, who taught me about the Fourier transform and various image processing algorithms, was politically conservative. This was absolutely no barrier to his ongoing stem cell research. So, my more conservative friends, rather than complaining about the inherent liberal bias in science, why don't you come on over and learn some rigorous scientific reason and help us out.

p.s. : the comments on that Nature opinion piece get, predictably, a little crazy. "La République n'a pas besoin de savants, uniquement d'équité" .. oh dear, has it really come to this again ?

## 20100910

### Quran Burning

Its hard to avoid discussing the planned Quran Burning. I saw something about how there had been riots in Afghanistan in anticipation of this, and Petraeus thinks it could endanger lives of troops.

Of course I don't think quran burning should be prohibited on national security grounds, but it would seem that, there should be someway to imprison the pastor for inciting riots. This usually how it works in the states, right? If someone is shouting at a thronging crowd, on the verge of inciting violence, they can be arrested immediately -- and even if, the police simply believe there is likelihood for there to be a riot in the next week or so because of a massive anarchist gathering, they can just throw all the well known anarchist leaders in prison "for their protection" for that week... I'm not going to try to say that's right, but it is the situation I believe.

Question: If the Florida pastor is intentionally starting riots in Afghanistan outside of military bases, can his freedom of speech be impinged on the grounds that he presents a "clear and present danger" to national security? Just because the crowd he is inciting to violence is not right in front of him, it is in Afghanistan, the internet connects them instantly, so it makes no difference, right?

It seems that it would be much better to arrest him tomorrow so that the Quran burning does not take place on 9/11, even if it ultimately happens a week later.

If the above grounds do not work in your mind, is it still not much better to have a massive counter protest poised directly on site, threatening to riot in the states, which would then surely justify his being jailed? I guess I don't know if there are enough youth groups that care about this in the states, and I guess I kind of doubt it but who knows, it doesn't need to be a dramatically large portion of the population to have a significant counter protest.

## 20100909

Hey guys, graduate school started, and I won't have nearly as much time to pick apart court rulings and speculate on the future of society. However, WeAlone content will continue to be generated at a regular basis using Markov random text models, which I assure you will make exactly as much sense as my usual ravings. This reminds me, I need to bug editor Keegan to release instructions or at least some vague description of his Markov random religious text screen saver.

Social complexity and transitive inference in humans and animals in the world of the living room and dining room with a view to share videos with friends and family. Fractal organization of the human body and the mind of the reader from Adobe's website at www mobilechoiceuk com English Additional information on your Dell Laptop Deals Laptops & Minis View All 0 comments are shown first if best seller information is available. Future studies should examine the effects of the drug in the treatment of the subject areas below and select the most appropriate way to deal with the problem of the invariant Laplacian of the electron beam.

Hallucinations and delusions are esteemed for their own use and not for the faint of heart or the brain stem and spinal cord injury in the rat brain. Psychedelics dissociatives and the other is a new and improved version of the Macromedia Flash Player to view this video in a new window. Introspection and self catering holiday accommodation in the heart of the city of New York City Area Directory of All Stores International Sites & Affiliates Forum & Resources for Teachers and Students at the University of California at Berkeley and the University of California at Santa Barbara and Ventura Counties and SW San Bernardino County Sun Forum Rules & Guidelines for posting on the calendar are also available for shipping.

Dissociated thought processes of the present invention is to provide a login for access if already a patient. Concerned Citizens of Ridgeview Drive and the driver of the vehicle are not covered by the Act of Union in Evolving Political Landscapes. Genetic manipulation of the data and information provided by merchants and third parties in limited circumstances set forth in this Agreement shall be governed by English.

Lateral view in the direction of the arrow represents the wind speed and direction of travel of each individual. Society can not be held responsible for any loss or damage resulting from any business conducted with any company listed. The government has also been shown to be a member of the International Criminal Police Organization and Management Theory Division of Cardiology.

These results suggest that the two are not the only one who can not afford to pay for the shipping. Data are representative of the entire world. The authors would like to thank all of you who have not been able to find a way to get a good deal of the day and night to make sure that the following conditions are met and the application of the law of the land is situated in the heart of the beautiful.

## 20100903

### America's New Ruling Class

America's New Ruling Class

As promised, we return to America's Ruling Class, Obsolete Nation-States, and Consensus for an exploration into the new ruling class.

America's current ruling class finds itself rightfully discredited. It has failed to generate wealth for the masses, has failed to improve our security, has failed to articulate a vision for the future, and instead of doing anything about it, spends its time in endless incestual recriminations, accusations, and empty promises to “fix Washington.”

Well, it's about time we give up on the traditional power-elite. The American Spectator suggests a rise of the Country Class, rooted in good old-fashioned Judeo-Christian morality and frontier individualism. This is bullshit. Christianity is too riven by culture-war anti-gay discrimination and hypocrisy to present itself as a moral basis for society. The frontier is a lie, and as oil prices rise, the great exurbs will become endless howling wastelands of people too poor to move.

Instead, energy is going to flow inwards, into the city centers. Power is associated with knowledge, the ability to manipulate technical systems, and the ability to motivate people, not linkages to the old and wealthy. With networks, everybody knows somebody who knows somebody, and if you are unique, your skills will be found.

This does not mean that the old power structure is going away; it's far too entrenched for that. But it'll be a joke, something to be manipulated with smart media, and blitzkrieg dadaist marketing campaigns. Money isn't going away, but it's something to be spent, not horded. Cashless economies of favors and goods-in-kind mediated through semi-AI agents and craigslist will help the new America dodge the taxman, the rulers will be the ones who make the system work, enforcing trust, and making proper connections between interested parties.

The future leaders of the world are urban, urbane, and not worried about the battle of the past. The decrepit towers of power, the Federal government, the mainstream media, multinational corporations, are the raw material of their ambitions, inert mass ready to be sculpted into the monuments of the future.

## 20100902

### Drop Day Octahedron

I was digging through the archives and I found some documentation for the CCFL Octahedron project from Drop Day that was never published. We don't have photos of the build process, just a text description and the source code, as well as pictures of the finished project in action. This should be good for inspiration and perhaps source code for a similar project, if not total duplication.

Physical construction

Each edge of the octahedron structure is a 2-foot piece of wooden dowel rod. A hole is drilled perpendicular to each rod at each end. The rods at each vertex are held together with a double loop of fishing wire through these holes. Rods and wire are spraypainted black.

The lights are cold cathode flourescent bulbs, as sold for lighting computer cases. A pair of bulbs are attached to the outside of each edge with cable ties. Each pair is powered through an inverter attached to the inside of the edge. I've left some spare bulbs in the elevator closet in alley 3. A pair of bulbs together with inverter can be purchased online for about \$8.

A power cable runs from each inverter to a common vertex where they are bundled together and exit through one side. Each of the twelve cables is dual-conductor 18-gauge (?) speaker wire. One end terminates in a connector accepted by the inverter; the other is permanently soldered to the control board.

The control board is powered through a long three-conductor ribbon cable terminating in a Molex 8981 male connector, which will interface with a standard ATX computer power supply. (To make an ATX power supply turn on without a motherboard present, one must connect the ~PS_ON signal on the motherboard connector, normally green, to ground.)

Electronics

The control board is built around an ATtiny2313 processor, two CD4094BC 8-bit shift registers, and three ULN2068 quad-channel Darlington switch arrays. The processor is clocked by an external 16 MHz crystal. The fuse extended and high bytes are left at factory default. The fuse low byte is programmed to 0xFF: no prescalar, no clock output, external crystal, slow start-up. The shift registers are cascaded to act as a single 16-bit serial-in, parallel-out register. The processor has three outputs to the shift register: Data (pin PB3), Clock (pin PB2), and Latch (pin PB4). A single bit is loaded by setting Data high or low, setting Clock high for 4 processor cycles (250 ns), then bringing Clock low again. This is repeated 16 times, once per bit of a 16-bit word, with the least-significant bit first. After all 16 bits are loaded, the Latch pin is strobed high for 4 cycles, at which point the shift registers will present the 16 bits on their output pins.

12 of these 16 bits are wired to inputs of the Darlington switch arrays. When a switch-array input is at logic high, the corresponding output will sink current to ground, illuminating the corresponding lights. The unused bits of the shift register are (from LSB = 0) bits 6, 7, B, and F.

The power supply to the control board consists of ground, +5 V, and +12 V. The 12 V supply is wired directly to the positive side of each inverter's DC input. The negative side of each inverter's input sinks through a Darlington switch. When all bulbs are on, the system will draw about 5 amps on the 12 V line. It has an inline fuse holder loaded with a 10 amp fuse. The 5 V line is used for powering the logic chips only and should draw minimal current.

.. you see how much effort I'm putting here : screen shot of the monospace text figure

hdr2 is used to program the processor via a standard AVR programmer, such as the AVR ISP mkII. From top to bottom as oriented above, the pins are:

MOSI, MISO, SCK, VCC, ~RESET, GND

hdr1 is currently unused but is connected to the circuit. From top to bottom:

VCC, GND, not connected, PD4, PD5

This could be used to communicate with another board via a 2-wire serial protocol.

The push buttons will short PB5 or PB6 to ground when pressed. The switch will short PD6. Neither is used by the current software.

Software

See code at the end of this post. The software implements a few modes and switches between them. It includes a very simplistic random number generator (which is not random at all because the seed is hard-coded).

Bugs and quirks

Sometimes, especially when starting, the system will go into a bad state such as freezing or strobing synchronously in an unappealing fashion. I seem to have fixed this by adding another filtering capacitor on the 12 V rail, but the problem may return.

Sometimes after switching off the ATX power supply it will not turn back on for a number of minutes. Perhaps a large resistor between power and ground would fix this problem by acting as a stabilization load.

Many aspects of the circuit, such as the use of shift registers, an external crystal, and extra buttons and switches, are historical or arbitrary. Where the speaker wire meets the board it can short against unintended pins of the ULN2068 in ways that are not visually obvious. This can result in all four channels on that chip turning on when only one is activated in software.

You can pulse-width modulate a light channel in software, but it will not dim the light. Instead, it will light up part of the tube from one end, which looks cool and is probably very bad for the bulb.

Replacing the control board

The control board is a crufty prototype and it may be desired to replace it with something nicer: either a better-produced custom board or a totally off-the-shelf controller. Essentially all that is required is to switch on and off with some reasonable speed the sinking of ~ 500 mA current on each of 12 channels. This could be accomplished with any number of devices: Darlington pairs, power FETs, solid-state relays, etc. Optical isolation of the control signal may improve robustness. Many microcontrollers can provide the 12 I/O pins directly, so external shift registers are unnecessary.

Software

Here is the source code associated with the Octahedron. First, build-and-upload.sh, the bash commands used to compile and upload the program to the AVR.

#!/bin/sh -e

# build with avr-gcc suite
avr-g++ -o octahedron.bin -mmcu=attiny2313 -Wall -Winline -save-temps -fverbose-asm -Os octahedron.cpp
avr-size octahedron.bin
avr-objcopy -j .text -j .data -O ihex octahedron.bin octahedron.hex

# upload using AVR ISP mkII
avrdude -p t2313 -P usb -c avrispmkII -U flash:w:octahedron.hex


This is the straight up AVR C++. You'll need an in system programmer to upload it.


#define F_CPU  16000000L

#include <stdint.h>
#include <avr/io.h>
#include <avr/interrupt.h>
#include <avr/pgmspace.h>
#include <util/delay.h>

typedef uint8_t byte;

// a shitty "random" number generator
uint16_t xrand() __attribute__ ((noinline));
uint16_t xrand() {
static uint16_t y = 3;
y ^= (y << 13);
y ^= (y >> 9);
return y ^= (y << 7);
}

// delay by an amount known at runtime
void delay_ms(uint16_t ms) {
while (ms-- > 0) _delay_ms(1);
}

// Define pins for the shift registers
#define SREG_PORT PORTB
#define SREG_DDR  DDRB
#define SREG_LCH  (1 << 4)  // latch, high to set
#define SREG_DAT  (1 << 3)  // data
#define SREG_CLK  (1 << 2)  // clock on rising edge

// Define pins for the buttons and switch
#define UI_PORT     PORTB
#define UI_DDR      DDRB
#define UI_PIN      PINB
#define UI_BTN_A (1 << 6)
#define UI_BTN_B (1 << 5)

#define UI_BTN_A_DOWN (!(UI_PIN & UI_BTN_A))
#define UI_BTN_B_DOWN (!(UI_PIN & UI_BTN_B))

#define UI_SW_PORT PORTD
#define UI_SW_DDR  DDRD
#define UI_SW_PIN  PIND
#define UI_SW   (1 << 6)
#define UI_SW_EN   (DARK_PIN & DARK_SW)

// Init the shift registers
inline void sreg_init() {
SREG_DDR |= (SREG_LCH | SREG_DAT | SREG_CLK);
}

// Optional delay when setting pins for the
// shift registers.
// At 5V they will handle at least 12 MHz.
inline void sreg_delay() {
asm volatile ("nop");
asm volatile ("nop");
asm volatile ("nop");
asm volatile ("nop");
}

// Shift a bit into the shift registers.
void sreg_shift_bit(bool x) {
if (x)
SREG_PORT |=  SREG_DAT;
else
SREG_PORT &= ~SREG_DAT;

sreg_delay();
SREG_PORT |=  SREG_CLK;
sreg_delay();
SREG_PORT &= ~SREG_CLK;
}

// A full shift-register write.
// Shift 16 bits, then latch.
void sreg_write(uint16_t x) {
for (byte i=0; i<16; i++) {
sreg_shift_bit(x & 1);
x >>= 1;
}

sreg_delay();
SREG_PORT |=  SREG_LCH;
sreg_delay();
SREG_PORT &= ~SREG_LCH;
}

// The bits corresponding to wired-up channels are:
// FEDC BA98 7654 3210
//  XXX  XXX   XX XXXX
// This function maps 12 contig. bits onto these.
uint16_t lights_to_channels(uint16_t x) {
return  (x & 0x003F)          // 0000 0011 1111
| ((x & 0x01C0) << 2)    // 0001 1100 0000
| ((x & 0x0E00) << 3);   // 1110 0000 0000
}

// Set which lights are on according to a 12-bit value.
uint16_t lights = 0;
void set_lights(uint16_t new_lights) {
static uint16_t state = 0;
lights = new_lights;
uint16_t new_state = lights_to_channels(lights);

//if (new_state == state) return;

for (byte i=0; i<16; i++) {
_delay_us(500);
}

state = new_state;
}

/*
inline void ui_init() {
// pull up both buttons and the switch
UI_DDR  &= ~(UI_BTN_A | UI_BTN_B);
UI_PORT |=  (UI_BTN_A | UI_BTN_B);

UI_SW_DDR  &= ~UI_SW;
UI_SW_PORT |=  UI_SW;
}

inline void ui_debounce() {
_delay_ms(50);
}
*/

#define L_R1 0x400
#define L_G1 0x002
#define L_B1 0x004

#define L_R2 0x008
#define L_G2 0x040
#define L_B2 0x010

#define L_R3 0x100
#define L_G3 0x020
#define L_B3 0x080

#define L_R4 0x001
#define L_G4 0x200
#define L_B4 0x800

/// RGBRBGGBRGRB
/// BRGR BGGB RBGR
/// 0101 0000 1001 = 0x509
/// 0010 0110 0010 = 0x262
/// 1000 1001 0100 = 0x894

#define ALL_R (L_R1 | L_R2 | L_R3 | L_R4)
#define ALL_G (L_G1 | L_G2 | L_G3 | L_G4)
#define ALL_B (L_B1 | L_B2 | L_B3 | L_B4)

#define ALL_LIGHTS (ALL_R | ALL_B | ALL_G)

const uint16_t tris[8] PROGMEM = {
L_R2 | L_G2 | L_B2,
L_R1 | L_G3 | L_B2,
L_R3 | L_G3 | L_B3,
L_R4 | L_G2 | L_B3,
L_R3 | L_G1 | L_B4,
L_R4 | L_G4 | L_B4,
L_R2 | L_G4 | L_B1,
L_R1 | L_G1 | L_B1
};

const uint16_t squares[3] PROGMEM = {
ALL_R, ALL_G, ALL_B
};

/// modes

return (1 << (xrand() % 12));
}

void noise_fast() {
uint16_t len = 300 + (xrand() % 300);
for (uint16_t t = 0; t < len; t++) {
_delay_ms(60);
}
}

while (lights != 0) {
_delay_ms(1);
}
}

while (lights != ALL_LIGHTS) {
_delay_ms(1);
}
}

void updown_fast() {
uint16_t len = 20 + (xrand() % 20);
for (uint16_t t = 0; t < len; t++) {
}
}

void rgb() {
uint16_t len = 150 + (xrand() % 100);
for (uint16_t t = 0; t < len; t++) {
for (byte i=0; i<3; i++) {
_delay_ms(120);
}
}
}

void tri_rand() {
uint16_t len = 300 + (xrand() % 700);
for (uint16_t t = 0; t < len; t++) {
_delay_ms(60);
}
}

/* causes reset?
void tri_strobe() {
uint16_t len = 100 + (xrand() % 300);
for (uint16_t t = 0; t < len; t++) {
_delay_ms(30);
set_lights(0);
delay_ms(xrand() % 200);
}
}
*/

/*
void test() {
for (byte i=0; i<12; i++) {
set_lights(1 << i);
delay_ms(1000);
}
set_lights(0);
delay_ms(5000);
}*/

int main() {

sreg_init();
//ui_init();

set_lights(0);

for (;;) {
rgb();
updown_fast();
rgb();
noise_fast();
rgb();
tri_rand();
}

}


## 20100901

### Welcome to the Future : Weaponized Sound

I'm not talking about the LRAD*, this is far more interesting. Thingiverse user neurothing ( or should I say Brown University neuroscientist Seth S. Horowitz ) lists among his interests "creating neurosensory algorithms for weapons class sound". In addition to the implied military applications, it seems he can use a mysterious sound algorithm to modulate emotion, attention, and state of mind. He has started a company called neuropop to commercialize these effects :

Our proprietary Neurosensory Algorithm (NSA) technology can be used to modify virtually any sound or music to activate specific parts of the listener’s brain to encourage sleep, reduce stress, enhance attention, or create specific mood-states. We are currently developing health and wellness, entertainment, and gaming products.
Finally, I feel like I'm living in the future. I am, of course, reminded of BLIT. Neuropop claims uses such as meditation, altering state of mind, enhancing effectiveness of advertisements, and providing music for movies and video-games better tuned to manipulate the listener. You can even test out some of the simpler effects on their website. If you guessed that binaural beats have something to do with this, you're right, but they also use a diversity of other techniques, not all of which appear to be published, to achieve much more than binaural beats are capable of. Having not (yet) experienced their auditory stimuli, I can't verify that their technique works. However, having seen what a couple of colored flashing LEDs can do to my visual cortex, I'd wager their effects are real. The big question, then, is weather or not Professor Horowitz was joking about the "weapons class sound".

*Having witnessed the LRAD in deployment I should note that some young folk these days are immune to it, due to a decade or more of loud rock concerts. However, if your hearing happens to be intact this machine will quickly induce the accumulated damage of a decade of loud rock concerts (hyperbole), which is painful. I imagine ultimate military or riot control applications of Horowitz's sound algorithms might be piped through something such as the LRAD, but perhaps could induce confusion at a less damaging decibel level.