Wednesday, February 27, 2013

Wanderers 2013.2.27

I showed up late, driving from Apachecon, where I much enjoyed the reception.

The Technology Association of Oregon delivered a message of welcome to open source people in general.  The Apache community is somewhat esoteric within the movement, and has built itself around http, httpd, https and related services.

You could link Apache through CERN in that way, to the W3.  Citrix (of Cloudstack) was a big sponsor.  Some readers may remember HP's high profile around OpenStack from OSCON.  The cloud is a place to be these days, whereas in older cartoons it was a sometimes satirical view of Heaven (Harps Inc.).

Doug McCarty had the rare privilege of serving as astronomer in residence at a very remote lodge in Namibia, where the darkness factor is 10+ (there's actually a scale known to astronomers).  Astrophysical phenomena are astoundingly clear, if your vision is 20-20 or better (as corrected).  They have a great eyepiece waiting.

The feel of the place is also amazing.

Whereas this particular lodge has a high luxury quotient, more like a cruise ship in adventure travel circuits, you may pay a lot less renting a camper-on-wheels (motorized) and buzzing about a bit.  However in a certified dark patch, such as near this lodge, you'd not be welcome with high beam headlights, or any lights.

People living there use red or focus them tightly.

Doug had a nice slice of nickel-iron meteor from the region, one of the bigger impact zones.  The Negev desert makes meteors easier to see.

Ecotourism was again the theme, reminding me of Lynne's talk.  She was there with two dogs.

Dick Pugh gets a lot of credit for promoting Namibia as a STEM stop, a place to earn credit towards your career in the field, as a mineralogist or perhaps craftsman like Glenn, a Wanderers co-host.

Our venue was packed, people sitting on up the stairs.  Great to have a large cast now and then.  I started proposing anti-talks when we wanted to thin it out.  "My weekend exploring I-205" maybe?

I've got a full work week going.  For me, Apachecon means listening head down with my face immersed in light from a laptop computer, the Mac Air.  At geek conferences, that's completely OK i.e. it's not considered rude to stare at your screen while a technical talk gets delivered.  We multi-task.  We're geeks.

So what I'm really doing is teaching Python.

But then I also transport items around (such as the director himself and his accoutrements), given Open Bastion is based at the Hilton.

Good seeing Patrick there, and Nancy, a conference producer with her crew, used to working with Holden Web.


Friday, February 22, 2013

Naked Lunch (movie review)

Steve was actually a friend of a friend of William Burroughs, the friend being Ian Sommerville.  Neither of us had ever seen it, and Christine, a Wanderer knew it was good, that we would like it, and volunteered to scrounge it up.

I'm quite glad to have seen this, in part because of the big dot connect with eXistenZ by the same director.  All that icky gooey bug stuff actually went somewhere.  Archy (friend of Mehitabel) move over.

Watching in 2013, the typewriter itself has become exotic.  The scene of the "typing bar" (or coffee shop) is an eerie anticipatory sketch of today's coffee shop in Portland.

I'm not a big Burroughs reader.  I think back to The Discipline of Doing Easy, which is obscure.  So what here is parody, and what is gentle fun?  I get the movie version, without yet reading the book.

Speaking of fun, my thanks to John Driscoll for having me by Systems Science today, as a guest speaker.  I have this fun roller coaster of a slide show that, while not Burroughs-like maybe, is still literary and somewhat fluent.  A mix of Python and MAD Magazine.

Note to self:  introduce OSCON peer reviewers to David Feinstein's work with ISEF.  Some additional layers of display to help us plan the tracks... we were lunching at Thai Baan near PSU, after we joined SysSci students for beers.

That was too much fun for a Friday I'm afraid.  Saturday will be on the clock again.  Nice to set when I work, if not the total hours.

Saturday, February 16, 2013

Surgery on the Blue House

:: demolition ::
 :: new beams in 2013 ::

Saturday, February 09, 2013

Bacteria Ain't Dumb

Bacteria Ain't Stupid

Dr. James Shapiro regaled us with stories tonight, of the picture biology has painted in the last 40 years, which, to read press accounts, has yet to be unveiled.  These aren't secrets though, just technical results that require some added vocabulary.  We were outside of the standard 4000 words or whatever English speakers tend to get by on.

The short of it is:  cells don't just change (morph) because hit by random cosmic rays, with natural selection then weeding out the losers.  There's no time to be that stupid and cells are not.  They form alliances, as symbiants, as parasites, as lethal adversaries or whatever, and they exchange DNA / RNA.  They seem to share information.

We went through some of the history.  Barbara McCormick's research is key.  Cells have lots of feedback loops and respond to stresses by moving DNA around.  Those sequences are not read-only, but read-write, and there's lots being encoded based on what's happening or what gets in.  Since Lynn Margulis we've started to get it:  once independent life forms have swallowed one another.  Today's mitochondria and chloroplasts where at one time bacteria in the wild.

The microbiology also seems to show that once X swallows Y, a redivision of labor occurs, with X taking on perhaps more of Y's responsibilities.  The eukaryotes have their own special ways of doing things etc.

If you think of cells as both cognisant and sentient, you'll have access to more of the English grammar needed to map the circuitry a little.  Fear of anthropomorphism is misplaced.  It's an intelligent mapping of an articulated part of language to something complex.  Letting British novelists describe intra-cellular relations using the the tropes and conventions of their trade might actually make for better cell biology, when it comes to conveying the nuances within our gray matter.  Make it more of an opera, and you'll get it.  It's Machiavellian all the way down.

It's when cells get starved that they really go crazy.  Being unsuccessful, or "insulted" as Terry put it during the Heathman dinner afterwards, is a primary stimulus.  As they said in est at the graduation, it's being losers that reactivates us, as humans (vs. the angels).  That's when we / they innovate, duplicating whole sequences (making backups) so as to be able to perform tricks of the trade on a copy.  How does it all work in real time?  We don't know that yet.  Lots more science is needed.

The problem with a lot of scientists, biologists etc. is they're victims of the die-out of "vitalism" versus "mechanism" in the great debates of the recent past.  The vitalists didn't have modern microbiology to draw from, to state their case.  The feedback mechanisms were hypothesized in a crude manner, the human imagination applying a rude sketch to nature's true face.  Now, a century and a half later, with more of that face revealed, the vitalist metaphors are more appealing, and what is language above metaphor, analogy?  Nature is alive, we know that, or do we wish Machine World as our only description.  It's more a decision about language than about Nature, as she is what she is.

My role at the church was outside security at first, a role I'm well used to playing.  In this case all that meant was directing ticket holders to one door, ticket buyers to another.  I had help.  I was wearing a thermal shirt under my coat and tie.  I had a large coffee from McDonald's (cardboard with plastic lid).  Certainly it was my privilege to welcome guests, not in any way an onerous duty.

Dr. Shapiro was right to pitch his talk where he did, as a science lecture that didn't try to dumb it down too much.  He knew he might have some real peers scattered in the audience, eager to suck down what they could.  His talk was high bandwidth in that the slides said a lot too, to those more versed in reading that kind of diagram.  Yet he was able to hold the attention of those just starting to get their feet wet.

It's not that we want to be superstitious about cells.  It's more that we want to not "misunderestimate them" (he cited George Bush for that one).  When challenged, bacteria respond like "knowing machines" that have had millions or billions or years to learn their tricks.  They're like transformers.  They don't just wait for mesons from heaven to throw the right switches in the face of adversity.  They're a lot smarter (more optimized for exaptation) than that.  As human beings with science, that gives a sense of where / how we might innovate, but also tells us more about what we're up against.

Dr. Shapiro said he'd given only two pieces of advice to the medical community:  wash your hands between each visit, and don't give them antibiotics unless it's really to save a life.  The latter advice is not just altruism.  Antibiotics wipe out a lot of friendly bacteria and if there's any surgery in this picture (say within six months), you'd have been way better off with your allies intact.  You kill part of yourself in other words (not unlike chemo then, in some ways).

The Q&A was all over the map, about cancer, about autism, about any given professional community's resistance to new ideas (memes -- microbiology in language).  Steve Holden and I slipped out just before the last question (he'd been ushering too) and headed over to the Heathman.  A very talented female vocalist was on the piano, with accompaniment, in the downstairs gathering.  We convened at the mezzanine level, per usual.  The wine and fish were excellent, as we've come to expect from this world class hotel.  I was grateful to have this privilege and gratified to see all this updating of world views happening.  Portlanders are staying in the loop at least.

My question during the Q&A after dinner was to cite the Pfizer guy's talk and ask if he felt walled out or otherwise denied access to what big pharma might be finding, behind closed doors.  The Pfizer guy was saying research was stagnating because playing it close to the vest, hoping to cash in big time with a few puzzle pieces, was not working out.  Researchers needed to put their cards on the table, for the good of everyone.  The liberal arts view.

Dr. Shapiro replied that he'd some time ago made the decision he couldn't afford that kind of profit-oriented seclusion for himself.  He felt the open source community (openly published science) was producing a flood of new findings, while being secretive was just shooting oneself in the foot.  As a geek, I could appreciate that analysis.

I used the "maxi taxi" for this one, finding less expensive parking than last lecture.  The crisp cold night air was welcome.  Mostly I'd been holed up indoors all day.

Sunday, February 03, 2013

Tosca (opera review)


I had mistakenly assumed that, with a name like Puccini, the guy would know Rome like the back of his hand, maybe own his own Pinocchio factory (like Giapetto) and sell puppets at Piazza Navona at Christmas time.  Nope, turns out he went to Rome precisely to research the script, get the landmarks right.  Apparently the old libretto had Angelitto or whatever his name was swimming across the Tiber river to seek sanctuary in St. Peter's.  But as we all know, these two institutions (Castel Sant Angelo and St. Peters) share the same bank of that river.  The original author was fine with taking dramatic liberties, but Puccini wanted more realism than that.  The opera was going through a phase:  "verisimo" they called it, or verisimilitude.  The music was becoming more like a soundtrack.

I've been putting on my Teilhard de Chardin goggles from time to time and looking at history with that benefit of hindsight.  Sure, the explosion in logic made little sense at the turn of the last century.  What were they thinking?  Their rationality hardly improved and politics stayed as dumb as ever, so what was that all about?  Looking back, the computer languages were being born.  Lineages were getting started.  Turing fed into Von Neumann with channels back to player pianos and other hole-punch controlled devices.  Ada, Hopper...  It all makes so much sense in retrospect.  Like evolution creating the eye.

Likewise one can see the stage as prototypical of the "big screen" we'd be getting later (Plato's Cave version 3), which is still pushing the envelope at 48 frames per second of little Hobbits running around in IMAX 3D.  That's what we're up to by the time of this writing.

Back in Puccini's day, we didn't have film yet, but we had something very like IMAX 3D, namely The Opera.  And the singing took (still takes) real athletic capability.  Not just anyone could belt it out like that without slipping.  In any case, artists had what amounts to a big screen, and they had a sound track to think about.  So there were lots of things to try, lots of niches to carve out.  Theater evolved in parallel.  Then we had "musicals" (not opera, but operatic).

Looking back, Puccini was an early film director and verisimo was a move to ground more in the nitty gritty of the time, any time.  Yes, a genre, but an anticipatory one.

They say Puccini went to great lengths to get to tone of St. Peter's bell right.

Yes, it's been a long time.  When I was young and thin and more like a fish, clambering around on that Trevi Fountain guy with my friends (we didn't steal the coins tourists were throwing, and we were tolerated as colorful youth, boys at play never mind we might be expats) I used to get "dragged to the opera" quite often by my culture-loving parents.  I was getting some of the best of the best back then, but didn't really realize it.  Now I'm back, as a gray.  I blended right in too, though I also saw quite a few kids, along for the ride with mom or more likely grandmom or dad.

What I need to sort out is the back story.  What was the Vatican doing vis-a-vis Napoleon and why was the escapee being pursued?  What was the painter's view of Napolean's wins or losses?  And what was Scarpia the secret police chief of again?  Of what exactly?  Was that the Vatican's secret police or what?  I'll have to do some more homework eventually, fit those puzzle pieces together.  After Super Bowl:  OK, Wikipedia clears it all up, complicated story, all the worse because Napoli (Naples), ruling Rome at the time of the play (set in 1800) is not named for Napoleon (Neo Polis = New City).  Speaking of which, good to hear Civitavechia mentioned.  That was Etruscan you know.

And that was my Superbowl Sunday folks.  Doesn't sound like I'll be doing any comments on the commercials, per previous years (I sometimes scan them for geometry).  I did write about the cuboctahedron on Math Future though.

Oh well.  Opera is cool too, not just kicking (and throwing) some ball around.

I hear the power went out in the stadium.  That's pretty interesting.  Tell us more.