Tuesday, December 30, 2008

Finished door panel prototype

Actually I spent most of the day working on a paper with Andy but there's no cool picture for that. Afterwards I finished the door panel prototype. I think they look pretty good but they were a real pain in the ass. I'd like to do it all over the house but I think I'll wait until I have access to a large mill.

Monday, December 29, 2008

Old media to new media conversion rate? Negligible

I was curious as to what the conversion rate might be from old media such as Science Magazine to new media like this blog so I tracked the hits of this blog during the publication of the Science article about me last week. The answer? Anemic. On the day of the release, only 90 visits to this blog and most of those came from HackerNews because my friend Jim posted it there. Granted, that's a lot more than the background of near zero, but compared to times when my website Mine-Control has been mentioned in obscure blogs, it's nothing. For example, an obscure Spanish art/video site once linked to Mine-Contol and I ended up with a $1000 monthly bill on bandwidth after tens of thousands of hits. A single tag on a social bookmarking site like digg usually generates thousands of hits. So, despite the fact that lots of people read Science, the conversion rate is apparently low. Of course, this is a single biased sample and it might just be that nobody cared enough about that article, but I suspect that it wasn't that much different in interest than any of the much higher converting blog entries I've been on the receiving end of before. So, thinking of advertising in old media and hoping for a lot of resulting web hits? -- maybe not a great idea.

Thursday, December 25, 2008

More back seat wall progess

Christmas day progress on the back wall. I built a temporary mold with bricks and leveled out the top surface in preparation for the seat course.

Wednesday, December 24, 2008

Back seat wall progress

Today I made good progress on the back seat wall on a perfect 60 degree day. It isn't doesn't require any creative thought as the pattern is regular over the whole length so it's an almost meditative task that requires nearly zero brain power.

Tuesday, December 23, 2008

Diffusively coupled oscillators

Having previously seen the effects that oscillators near 180 degree phase-boundaries run faster, I conducted the experiment of isolating two oscillators and varying the diffusive constant between them (thanks John). This first graph shows the time trace of the two diffusively-coupled oscillators started 180 degrees out of phase. Note how both amplitude and wavelength are different early-on compared to later when the two have synchronized. The next graph shows the peak frequency of the first phase (before phase lock) as a function of diffusion.

I know this is a well-known phenomena and is the basis of reaction diffusion systems so I started hunting for references. First google hit was: PRL 96 054101 - Daido and Nakanishi - Diffusion Induced Inhomogeneity in Globally Coupled Oscillators. They show various facets of a similar system without regard to spatial dynamics (like this experiment). They refernce Erik's father's (A T Winfree) book The Geometry of Biological Time which looks like a must read. They also reference an interesting sounding book: Synchronization - A Universal Concept in Nonlinear Sciences which looks like another must read and the UT library has an online copy!

Monday, December 22, 2008

Feature size varies to the 1/2 power in diffusive latches

I extended yesterday's bi-stable diffusive latach over a larger diffusive range. It was roughly linear over a 0 to 1 domain. It is proportional to the 1/2 power over a larger range. I took Edward's advice and plotted it with error bars and just ignored the deviation information. Here is the sampling over 30 trials with differing random small initial conditions with 1 SD error bars.

Sunday, December 21, 2008

Latch with diffusion

Feature size changes with diffusion ... more diffusion, bigger features.

Today I played around with how the diffusion coefficient effects the formation of pattern in the simple latch case. This is an array of bi-stable switches with uninitialized starting conditions (i.e. a little bit of noise). The feature size varies directly with the diffusion. The graph shows that the mean feature size (blue, multiple trials) rises fairly linearly with diffusion as does the variance (standard deviation plotted in red, same trials). There's probably a sexier way to make this plot with error bars or something, I'll think about that.

Friday, December 19, 2008

Science article

The journal Science wrote an article about me (free registration req.) released in this week's edition. It's not bad -- at least it gets all the facts right which, evidenced by numerous previous experiences, is a real accomplishment in journalism, kudos to the author Mitch Leslie. The article is a "Curious Character" kind of story which is a relief as I feared that it would be a "Man loses legs, runs marathon" story. Unfortunately it has only a touch of what I hoped for which was a "Want to get into science from the outside? You can! This guy did" story.

I get asked about my odd non-academic entry into the world science all the time. And I very much hope that my example demonstrates that if you dream of playing the ultimate-nerd-sport of pure science research then just do it. Not only is it possible to enter the so-called ivory towers from the outside but it was easier than I ever imagined. My outsider’s knowledge base was both sufficient and valuable. When I got into science I thought it would take a long time before I could contribute anything. I was pleased to quickly realize that I wildly underestimated what my contributions would be.

My entry story boils down to this. I went down to UT, talked to a graduate adviser who gave me the party-line ("first get a GED, then get an undergraduate degree, then ... "). As I left that adviser's office, discouraged, I asked for a name of a professor who might be into certain subjects and he mentioned Edward Marcotte's name. I took Edward to lunch and we became instant friends because we share a huge enthusiasm for all things nerdy. After hours of geeking-out together he asked: "So what do you want to do?" and I said, "I don't know, just hang out and learn stuff." "Cool," he replied, "there's a desk. Meetings are on Fridays".

That's really all there was to it. I started hanging out in his lab and everybody seemed to assume I was a postdoc. Before long I had met several other professors and within weeks I was working on more projects than I will be able to finish in my lifetime. It wasn’t long before people were making job offers. While this episode might be a rare event based on the meeting of two like minds, I think it says something about the refreshingly open culture of science. Don't get me wrong, academic science is a human endeavor with human feelings of territorialism, etc., but in comparison to many other fields, it deserves credit as being fairly open-minded and meritocratous. After all, science is the ultimate nerd pursuit -- and nerds as a stereotype value technical achievement over prestige (not all, but many). Still, contrast it to walking into the similarly nerdy engineering department of a major corporation, say Boeing or GM, and telling someone that you just wanted to "hang out". Even if you found a friend in the company it wouldn't be long before a higher-up manager would suspect you as being a corporate spy and want you to either join the company or get out while threatening your friend with NDA violations.

Part of the openness of academics lies in the simple fact that a University is not a chartered feudal hierarchy but rather a coalition of independent lords with a governing body. (I suspect this is not so much an analogy as it is that the actual history of English academics is modeled after the post-Magna Carta arrangement of free, independent lords under royal patronage). Thus, a tenured professor or "principal investigator" (PI) such as Edward runs his lab however he sees fit -- constrained only by safety, morality, and money. That said, there are standard working procedures: undergraduates become graduate students become doctors become post-docs become professors. So, while it is very abnormal for an outsider like me to just show up out of nowhere, the system is refreshingly tolerant to such an entry.

When writing this story, the author, Mitch, called my friend Professor John Davis of the EE Department. John told me that Mitch asked: “So should we be looking for more Zacks or is he totally unique.” I said to John, “I hope you replied that there are lots more Zacks in the world!” John fell silent. “Oh no!” I exclaimed. I mean, just among my own friends I’ve already gotten three people to come into the system in ways somewhat analogous to my own entry. Thomas -- game programmer now working on molecular simulators for two labs. Mark -- game programmer and self-taught organic chemist working in another lab. Steve -- playwright turned biotech entrepreneur about to employed by the Center for Systems and Synthetic Biology. I mean, if 3 of my small circle of friends are inspired to get into science in just 5 years then there must be tens of thousands of other outsider-nerds waiting to be recruited! It’s a vast would-be nerd conspiracy! The only thing I hoped for out of this article is for those people to be inspired to action if they so choose to be and I'm not too sure that came across.

I’ve made this argument about my entry and non-uniqueness to several “insider” friends and I keep getting the same response: “But Zack, you’re so smart”. I find this response psychologically interesting. I can’t help but think that my insider friends find it easier to explain me as a freak of nature than it is for them to admit that all the expense and work they went through to get into their positions could be so easily bypassed. Of course, they well know that I studied just as hard as them to get where I am. I wasn’t born knowing things anymore than they were. But there is a difference in our paths -- I never did even one second of work I didn’t want to do while many of my grad student friends frequently (and somewhat hyperbolically) complain of being treated like slaves. So, yes, I’m smart; but I’m no smarter than my PI friends such as Edward, John, or Andy.

Indeed, Edward and I form an almost perfect experiment and control. Edward and I are freakishly similar. We are both high-functioning mildly autistic. We have eerily similar responses to many stimuli and have very similar temperaments. We both hate being told what to do. The only really significant difference in our skills is that I have dyslexia and he has whatever the opposite of that would be called (“superlexia”?). He can read 20 papers in the time it takes me to read 1. We both went to bad public high-schools although his was slightly better than mine. Had my school been a little bit better or his a little bit worse, we could easily have ended up on the other one’s trajectory. What’s different about Edward and me is mostly the path we took, not our natures. And it is why we work so well together – because we have different points of view but backed with the same intelligence and enthusiasm.

People (such as my own family) often frame my story as success “despite” dropping out of school. I find this highly prejudiced. Nobody ever seems to consider that I succeeded “because” I dropped out of school. It seems to me that our society treats school as a kind of magical elixir – a cure to whatever ails ‘ya. Poor and disadvantaged? School! Rich and spoiled? School! Curious? School! Bored? School! Let me clear -- the universal access to school is one of the greatest and most important accomplishments of our civilization. I am not dismissing the wonderful contribution of formal education to the world. That said, school is not a cure all. It is not the perfect path for everyone’s journey. To make my case, let me point out some of the advantages of my path.

First, my natural temperament is to resist doing anything I’m told to do. My mother claims I’ve been like this since I was born and that parenting me was an exercise in making me believe that things in need of doing were my idea. So getting out of school took away all of this unnecessary friction. (One can argue that I should have “just gotten over” that stubborn streak and I’d counter that if school cures whatever ails ‘ya then why didn’t it “fix” that?)

Second, by entering the workforce at 17, I started saving money very early and the compound interest on that savings is significant. While my friends went into debt to educate themselves (some are still paying those debts), I was being *paid* to educate myself. At 38 I’m in a much better financial position than my friends who went through school and that affords a lot more options such as, but not limited to, hanging out in labs, making artwork, and building pretty houses.

Third, I arguably have a superior education -- after all, I had a student to teacher ratio of one to one! While they sat in big anonymous classes I sat on the porches and couches of those same professors’ homes. All my teachers were my friends; they didn’t teach me because it was part of an institutional compact, but rather because that’s what friends do -- they hang out, they share ideas, the older ones impart knowledge to the younger while the younger impart enthusiasm to the older. That bond of friendship is much stronger than the one between a professor and a student and thus the two-way street of care and respect that is the magic of education is consequently more robust when spontaneous and voluntary.

Fourth, I never did anything I didn’t want to do. I never did someone else’s dirty work. I didn’t take any retrospectively useless classes. I didn’t worry about my grades. I didn’t suck up to any professors. I didn’t have to prove myself to arbitrary gatekeepers. I wasn’t told what to learn and more importantly I wasn’t told what not to learn. Someone once told me that I “owned” my knowledge while others seemed to “borrow” it and while I think that is overstating it, the degree to which there is truth in that statement is a result of constructing the learning path myself.

Fifth, I ended up with a broad knowledge base. My knowledge in any one field is certainly shallower than any of my friend’s knowledge in their respective fields, but I have a passing knowledge of a lot more fields. Grad school is very narrowly focused and consequently it seems to me that it is as much about indoctrination as it is about education.

The world needs lots of people that have deep penetrating knowledge of their subjects. The world also needs people who have broad but consequently more shallow views of many subjects so that they can help to bridge subjects. The educational system produces many of the first type but few, if any, of the second. Indeed, this gets me back to my thesis: I think my utility, my success, is *because* I didn’t go to school not despite it. Outsider opinions are necessary and valuable; they, ipso facto, don’t come from inside the system.

Tuesday, December 16, 2008

Artwork videos

Finally got around to updating the videos of some recent art pieces. All my videos are indexed off of mine-control.com -- the new ones are birthday, resonator, dragonfly, diffusion, and elevator goblins.

Sunday, December 14, 2008

Acid washing and starting of back wall

This morning I made the first acid wash of the planter. The acid is pretty nasty to work with. I'm probably overly-paranoid, but I get dressed in a full acid apron, face shield, and gloves. The acid wash makes it look so much better, so despite what a pain it is, it's really quite fun to see the final product emerge. It usually takes two passes to get it really clean with a power wash after each acid application. Unfortunately I don't have a power washer at the moment so I'm just going to leave it like this for a while until my room mate Aaron brings his from Houston.

Meanwhile, I also finished up the brick apron adjacent to the driveway which is where I park garbage cans on garbage days, a small detail but worth it.

Then I started on the back seat wall. First I stacked up dry bricks to work out the pattern and then starting on the first few courses until I ran out of mortar for the day. That small section is about 2 hours of work once you include mixing, cleanup, etc.

Saturday, December 13, 2008

Planter brickwork completed

I finished the brickwork on the planter this morning. All that's left is acid washing, filling with dirt, and planting. I think it took me something on the order of 40-60 hours over about 3-4 months -- but that's a guess, I don't keep track.

Friday, December 12, 2008


Today I worked on updating an old project of mine "fretview" that is used by Rick Russell's Lab to do analysis for single molecule kinetics. We had recently improved the capture program to permit pixel binning, but the analysis code did not yet take this into account with the result that it tended to incorrectly sub-sample binned pixels resulting in rounding errors when coordinates were mapped from side to side.

Wednesday, December 10, 2008

Pattern formation phase experiments

Today I played around with trying to understand where the patterns come from in simple oscillators. In the following picture, the center region is exactly 180 phase shifted relative to the outside (circular "boundaries" as always). Note the cool reconnection events about 1/3 and 2/3 the way up from the bottom (t=0).

The interesting thing here is that the boundaries begin to oscillator faster than the surrounding regions. The center goes through 6 cycles in the time it takes the boundary to go through 7. At 7 edge-cycles versus 6 center-cycles there's a disconnection event where the two regions become disjoint and then reconnect one cycle later. These discontinuities are where interesting patterns emerge.

Why should it be that the boundary oscillates faster than the center? This is a bit counter-intuitive. Imagine two oscillators sitting next to each other and diffusing some of their energy into each other. Consider the moment when the first oscillator is at its maximum value and the second is at its minimum. At this moment the first oscillator is dumping a lot of its material into its neighbor. In other words, right when the second should be at its minimum value it is instead being "pullled forward" by the incoming flux. Conversely, by dumping flux into its neighbor, the first never quite makes it to maximum value and thus sort of short-cuts it way to the downward part of the cycle. Half a wavelength later the reverse is true. Thus, both oscillators act to pull the other one ahead and thus they both run a little faster as their amplitudes are reduced.

As noted before, work on coupled oscillators is as old as Huygens 1665 paper. Here's a more recent synthetic biological investigation from Garcia-Ojalvo, Elowitz, and Strogatz. What I haven't found yet (probably because I haven't looked hard yet) is a paper showing the spatial dynamics of such coupled oscillators as demonstrated here.

So what happens when the two regions are not started exactly 180 out of phase? Yet another interesting instability forms. Here's the same thing at 170 degrees:

This time the boundary between the two regions begins to wobble around as the two sides compete for control of the boundary space. This instability also creates interesting disconnection / reconnection events around 7 cycles. And what if we symmetry break the size of the two areas? Here's 180 degree separation with the center region being a bit smaller than the outer:

Now you see the unstable edge oscillation like above case after the perturbations travel all the way around and end up interacting with the center during the second reconnect event. Clearly such patterns are all reminiscent of diffraction scattering and other sorts of complicated spatial pattern-forming phenomena where waves are bouncing around inside of closed spaces -- I find all such phenomena hard to intuit and these examples are no different. Where things get fun IMHO is to see how noise plus such simple oscillators generates interesting formations as the ones I posted a few days ago.

Several people have asked me what is the relationship is between these simulations I'm showing here and cellular automata? I argue that these systems are analog, memoryless versions of CAs. While CAs are very logically simple, they aren't nearly as hardware simple as the systems I'm working on here. For example, Wolfram's lovely illustration of all 256 binary 1D CA rules are simple rules, but their implementation presupposes both memory and an a priori defined lattice that includes left/right differentiation. However, as Wolfram points out on page 424 of NKS, the symmetric 1D rules do generate interesting short-term random patterns when initialzied with random state so these are a good binary model for the analog systems pre-supposed here.

Meanwhile, my friend Erik Winfree's lab has very cleverly built DNA crystaline structures that have do define a lattice and thus can implement the Turing comple rules at molecular scales. But on the scale of complexity, I'd argue that these amorphous analog systems are "simpler" in the sense that I can more easily imagine them evolving from interacting amplifiers that would have independent precursor functionality and without imposing a lattice. Erik might disagree, but anyway, it's this idea of evolving-interacting-amplifiers that I'm going work on as I continue this.

Tuesday, December 9, 2008

Pattern formation sanity check

I ran a test where I changed the spatial resolution of the ring oscillator system (changing the number of spatial buckets while also changing the capacitance and conductance variables accordingly) to make sure that the pattern formation is not an artifact of the integration technique. These images show a 32, 64, and 128 bucket integration in each. It is clear that the spatial resolution matters in the sense that you can see a few small changes (features look temporally sharper, not just spatially), but I don't think that the pattern formation is an artifact. As always, thanks to JHD for help in working out the right parameter transformation -- which he knows like the back of his hand because its equivilent to a transmission line / heat equation.

Saturday, December 6, 2008

Planter progress

A little progress on the top of the planter this morning.

Friday, December 5, 2008

More AC experiments

I'm starting to have fun exploring the possibilities of this AC simulator. Above are spatially stable patterns using a bi-stable latch and small random initial conditions (approximating the noisy conditions of uninitialized amps). In the first picture, there is no diffusion so each parcel of space commits to one of the two states randomly. In the second picture, with diffusion, larger areas that by chance share a state tend to recruit their neighbors into that state. But, all of this recruitment must happen early because the gain on the latches eventually wins at which point there's no changing anyone's state (like an election). Thus, by dialing the ratio of diffusion to latch gain, you can choose the mean size of the features which is a cool phenotype all by itself. For example, imagine that this was a self-organized filter -- that one parameter could allow the construction of different kinds of mechanical particle filters.

In this picture I've stated to combine features. The left and center are two independent ring-oscillators with noisy initial conditions which create these interesting patterns as I've shown previously. (Although I'm still not positive they aren't artifacts, I'm starting to get a theory about how they form, and I'm going to be testing those ideas with controlled experiments tomorrow.) On the right is product of the two in oscillators which results in interesting spatio-temporal patterns. Like the latches above, these patterns are uncontrollable in all but gross properties because the pattern's position is the result of what amounts to "fossilized noise". In other words, the asymmetries at t=0 are amplified/converted into patterns at later time. That said, the form of the patterns is inspirational -- it hints at what is possible in potentially more information-rich initial conditions. For example, I now have an inkling how to partition space into integer sub-divisions (like fingers on a hand) without explicitly putting them there -- I'll be trying that soon.

Wednesday, December 3, 2008

Oscillator + Diffusion + Noise = Pattern

(Ring-oscillator with diffusion; x-axis: space, y-axis: time )

After an incredible multi-day pain-in-the ass getting Matlab installed, I'm able to start to explore some of the amorphous computations possible with this toy model I've been playing with. (Previous results came from running Matlab over X which was painfully slow). The above image is a simple ring-oscillator with diffusion and initialized with small random values. The random initial values seem likely in a molecular implementation whereby the inputs to the molecular amplifiers were un-initialized and therefore small stochastic deviations would dominate.

I know that simple processes can produce complicated structures as Wolfram is wont to repeat, but it's still astonishing when you see it. I mean, this thing has no clock, no memory, no boundaries, no initial conditions (just background noise) and a very simple oscillator; it doesn't get much simpler than that. I think the result is kind of beautiful, sinuous, like a tree made of waves. Maybe I'll do my next door panel like this.

All that said, I'm not positive that the patterns aren't an artifact of the integrator. Since I partition space up uniformly, it might be a result of that. I need to run a test where I reduce the spatial step and proportionately reduce the concentrations but my code isn't set up for that yet.