Extended Phenotype

Open Letter to Democrats Who Threaten a Boycott Vote in November

Fellow Democrats:

I'm increasingly disturbed by reports (or perhaps merely polls) that some Democrats will "boycott" the general election, or even vote for John McCain, if their preferred candidate doesn't win the Democratic nomination.

After nearly 8 long years of the Bush White House, scandals and wars and torture, after the twisting of the meaning of "executive power" and constitutional rights, after the trashing of America's image to its allies and the world....after all of that, are you seriously ready to vote for "a third Bush term with a different face" simply because your favored candidate ends up not getting the nomination?

If you can really look at the last 8 years, and still decide to throw your vote away or vote for McCain in order to protest not getting your favorite nominee, then shame on you.

As I've said previously, both here and to many friends, I'm supporting Barack Obama. Perhaps not surprising, given my demographics. But as I've also said, I will happily vote for either Hillary or Barack in the general election. We're in the middle of a particularly protracted and hard-fought primary battle. And the reason why it's hard-fought and protracted is that -- surprisingly -- the Democrats actually fielded two viable candidates this time!

We need to recall that the number of viable candidates for President we typically field is somewhere between ZERO and one. If we're damned lucky it's been one per election. In my whole lifetime, it's often it's been closer to zero.

So two strong candidates is an embarrassment of riches, and we ought to stop the incendiary language and threats of boycotts. First of all, there's another six long months for all of us Democrats, regardless of who we support now, to really get to know John McCain and our chosen nominee, whomever it turns out to be. And are you really going to say, right now, that you're willing to irretrievably throw your vote to McCain, before you know what we're all going to find out once the general election campaign begins in earnest?

Frankly I don't buy it. I think you'll reconsider once the difficulty of this primary season fades into the "swift-boating" and right-wing media blitz to come. I think you'll come home to the party and support our chosen candidate, whomever it turns out to be. And yes, I know it's difficult to read my references to "whomever" it turns out to be and not think that I'm simply gloating over Obama's perceived chances of victory. But I really mean it -- whomever our nominee is, has my support, and my vote.

And if some of you choose to make good on your threat and abandon our nominee -- then I ask of you one simple thing. Look back at the last 8 years, in detail. Look at the run-up to Iraq, at Abu Ghraib, at Guantanamo Bay, at the torture memos, the attitude to constitutional rights, the Supreme Court nominees, at Valerie Plame and the politicization of intelligence, at the secret energy committee we still don't know much about....look at the last 8 years as a whole, and know for certain that if you make good on your threat then you're voting for more of the same, and that when it gets even worse because of all the precedents set by the Bush Administration, that you have only yourself to blame.

But I don't think you'll throw your vote away. I think that no matter what happens in the primaries, Democrats on both sides of the nomination fight cannot, and will not, look at the last 8 years and decide to -- in effect -- vote for more of the same.

That's why I think it's going to work out, why the party will remain unified, and why we'll all rally around whichever candidate soon emerges as the nominee. I hope I'm right.

The Perfect Manhattan and Other Adventures

It's been a good (if odd) weekend up here on the island, with snow on Friday and Saturday (though nothing like the convergence zone N. of Seattle where my brother lives), and brilliant sunshine (though cold weather) today. I've been working on dissertation stuff this weekend, honing my topic after a bit of a breakthrough last month, and trying to deal with domestic stuff (bills, learning how to maintain/flush/ignore the new septic system, finding a list of tile places to visit in Seattle for my upcoming bathroom remodel).

But I also went to the first farmer's market of the season, and bought some great stuff. Tonight I'm going to make a roast chicken (currently brining its little juices out in the garage fridge), served with sauteed baby chard from Nootka Rose farm on Waldron Island, and I'm chilling out and reading some Rorty with Rebecca's radishes from Blue Moon Farm on Waldron as well, along with several olive mixes, my homemade pickled vegetables, and the Perfect Manhattan.  And by the way, Rebecca's radishes are some of the best I've ever had -- I've never described a radish as sweet and juicy, but these are just dripping with internal juice but still with a good bite.  Dipped into sea salt they're incredible.

I'll get to the Manhattan later. First, I have to remember to recommend Vessel in Seattle. I'd hemmed and hawed about going in since it always seemed to be packed, but Madden and I hit the joint on a Monday night last week and immediately went nutty about the selection of rare, interesting, hard-to-find, and homemade items. They make their own bitters! The bartender responded to our boyish enthusiasm by immediately making us taste all the homemade bitters and herbal tinctures, and furthered the process of getting us thoroughly drunk which I'd begun by making Manhattans at the apartment and then having rose champagne and Charmes-Chambertin at Campagne. I recommend proceeding to Vessel at once and asking for anything made with their house-made bitters. Oh, and try the two vodkas from Sub Rosa in Oregon: saffron and tarragon. Madden preferred the saffron and I preferred the tarragon but both were stellar. Not sure they're available up here commercially yet but I'll find some.

Yesterday I ran across a bag of key limes at the store, just normal supermarket stuff, and thought, "I should do preserved key limes, like preserved lemons." Madden is making preserved lemon marmalade on the new menu at Steps, and all three of my favorite olive mixes at PFI involve preserved lemons, so the idea of soaking citrus in salt for three weeks is pretty much in my wheelhouse. So I have a big jar of cross-cut key limes soaking in strong brine with bay leaves and black peppercorns. Sometime in early May I'll figure out a use for these guys....

But the original point of the post was to say that I'd finally perfected the Manhattan, at least from my standpoint. Long, long ago I worked hard on Martini making; in fact, that's pretty much all I remember about my master's degree. To this day, I keep a shaker and two glasses in the freezer, since thorough chilling of everything involved keeps the gin (yes, Martinis are made of GIN) from watering down when it hits the ice in the shaker (and a strict 5:1 ratio with good Noilly Prat vermouth or better should be observed).

But I digress. The perfect Manhattan turns out to involve replacing 1/3 or 1/4 of the sweet vermouth (again, Noilly Prat is my favorite, the Italians don't make good vermouth, at least that we see over here) with a good dark Amaro. Amaros are Italian herbal bitters, the most common of which is Fernet Branca in the States. Fernet is a bit too dark and medicinal for this application, but you can do 1/5th Fernet for the same effect and keep more of the vermouth.

The absolute best Amaro for this job (and for drinking straight) is the Amaro Santa Maria al Monte, which comes into the Seattle area in miniscule quantities that you have to fight restaurants for. It's gorgeous, herbal, complexly flavored stuff, and it gives the Manhattan a bit of an edge but nothing medicinal. In bars in Seattle, the lighter Amaro Nonino is more popular as a Manhattan addition but I think it's too sweetly similar to the vermouth to be much use.

Well, it's almost time to roast a chicken. More later.

Recent Research

I just returned today from the annual meeting of the Society for American Archaeology in Vancouver, B.C.  I presented a paper (in poster form) about some recent work bridging the gap between formal models of cultural transmission (i.e., social learning and imitation between individuals) on social network graphs, and measures of cultural behavior that are observable in discrete traits (e.g., archaeological artifact classes).  A corrected PDF version of the poster is available here

Download madsen-lipo-bentley-saa2008-poster.pdf

and will be published soon along with our entire poster session as an issue of the online Journal of Evolutionary and Historical Sciences.  I'll talk more about this soon, but this week is incredibly busy and I wanted to get at least one link up for the paper before I forget.

Recent Food and Wine

I'm slammed at the moment getting ready for an academic conference in a few weeks, so I haven't had time to much lately outside work and research.  But I did manage on Friday to take the afternoon off, and go to lunch with a regular group of friends at Nell's.  The group as a whole has met for 20 years, and I participate when I can (which isn't nearly as often as I'd like).  Phil cooks us lunch and we have the restaurant to ourselves. 

Yesterday was "Great 1980's Wines" as a theme, and the group dug reasonably deep and came up with some good stuff.  My 1988 Raveneau Vaillons Chablis to start was slightly oxidized and we've all had better bottles; you win some and lose some.  Highlights were the 1980 Jaboulet La Chapelle, which was mellow, pretty, but with some spice and weight left, the 1988 La Chapelle (superb), and a slightly advanced bottle of the 1989 Aldo Conterno Barolo Cicala (absolutely superb, despite being a little mature for its age). 

Probably the wines of the day for me were the 1982 Montrose Bordeaux, of which I still had a bit left and am sipping on while I write this a day later.  Incredible -- beautiful Bordeaux nose, but lacking the brutality and tannins of the 1970 and 1990 Montrose, the latter of which probably won't be ready to drink in my lifetime. 

Tonight I'm having dinner (paella!) with another group of friends, and I'm bringing some old Spanish wines to go with the dinner, and a special appetizer.  I don't have the bottles in front of me here, but there are two 1976 Riojas, and a 1970 Marques de Riscal Rioja.  I'm planning to finish things off with a 1910 Solera Pedro Ximinez sherry -- a bunch of it hit the market some years back at very reasonable prices.

But the exciting thing for me will be an appetizer -- a small slab of thinly sliced Jamon Iberico "reserva" -- the fabled pinnacle of serrano hams, aged 24 months and only recently imported into the United States.  I'll let you google for the going rate on a whole leg of Jamon Iberico, but let's just say that you can fly to Europe and eat it cheaper, probably.  I have 4 precious ounces of the stuff, and I'm looking forward to sharing it with folks (and saving a little slice for Madden at Steps) tonight.

Then it's back up the island to hunker down for a few days and bang out some simulation results.  I'm doing most of my numerical work on Amazon EC2 clusters these days, so I don't have to worry about where I am or whether I have computers available, which is sweet.  I'll post more after the old Riojas and the Jamon Iberico...

A Re-Updated Personal History of Personal Computing

Back in 2003 on my "previous" blog, and in early 2005 on this blog, I updated a long-standing essay I'd called "A Personal History of Personal Computing." My first and second blogs are long gone in the transition away from Radio Userland to Typepad, but I think it's time to reprint and update that essay (a second time). Moore's law is one way to look at the history of personal computing. Another is the history of companies that have come and gone, making personal computers and software. Still another is a personal view. This story is about my own personal computing history -- the machines, what I did with them, what software I thought was important. I omit computers that I didn't really have control over, such as University mainframes and Unix servers, and I also omit the vast array of servers and computers I administered at RealNetworks, Internap, Network Clarity, and computers I used at Microsoft and now GridNetworks.

By my count, I've purchased 21 computers in my life, and of course used and worked with hundreds, if not thousands more (managing a Systems Engineering group will do that for you). 

The story starts in the late 1970's, shortly after personal computers came about and before IBM changed things forever.... 

Back in 2003 on my "previous" blog, and in early 2005 on this blog, I updated a long-standing essay I'd called "A Personal History of Personal Computing." My first and second blogs are long gone in the transition away from Radio Userland to Typepad, but I think it's time to reprint and update that essay (a second time). Moore's law is one way to look at the history of personal computing. Another is the history of companies that have come and gone, making personal computers and software. Still another is a personal view. This story is about my own personal computing history -- the machines, what I did with them, what software I thought was important. I omit computers that I didn't really have control over, such as University mainframes and Unix servers, and I also omit the vast array of servers and computers I administered at RealNetworks, Internap, Network Clarity, and computers I used at Microsoft and now GridNetworks.

By my count, I've purchased 21 computers in my life, and of course used and worked with hundreds, if not thousands more (managing a Systems Engineering group will do that for you). 

The story starts in the late 1970's, shortly after personal computers came about and before IBM changed things forever.... 

Deval Patrick, Political Speech, and Barack Obama

When juxtaposed to her slowly deflating campaign chances, the Clinton campaign's attacks on Barack Obama for incorporating language used by his friend Deval Patrick makes perfect sense.  Democrats have a long history of responding to dicey primary prospects by firing torpedoes at one another.  Michael Dukakis successfully derailed Joe Biden's 1988 campaign with accusations of plagiarism in a speech.  Clinton appears to be attempting a duplication of that feat. 

And it truly would, and should, be a "feat" to derail a popular political campaign with this particular attack.  Because "plagiarism" requires a higher bar than has been demonstrated here.  Sure, Obama did a riff, nearly word for word, from a speech of Deval Patrick's.  As Deval Patrick has done, with speech language, from Obama even earlier.  As Biden did to Neil Kinnock.  As politicians have done from time immemorial.  As Patrick himself did, to the Founding Fathers and Martin Luther King.  For in none of these cases, did the politician in question start by claiming that any of these words were actually their own.  "Plagiarism" implies that such a claim has been made, and that the claimant is lying.  It implies that the speaking or writing is occurring in a context within one will be judged, and possibly rewarded, for being the actual author of a speech or some writing.

No such claim is occurring in most (if not all) political speech.  And the criteria we use for electing leaders doesn't specify that their words must be their own.  This isn't a final exam, and our country isn't high school.  We don't have a "plagiarism policy" in the Constitution, and candidates aren't disqualified from office if they can't "show their work" and demonstrate that they -- and only they -- wrote the words they deliver to us in stump speeches and debates. 

Clearly, on the other side of this coin, we voters often do want to assure ourselves that our chosen candidate can "pull their own weight" and isn't an intellectually empty shell.  As, for example, some recent political leaders we could mention, but won't.  Barack Obama has cleared this hurdle quite well enough in my mind, and apparently in the minds of an increasing fraction of primary voters. 

So I sincerely hope that Democratic voters in Ohio and Texas view the current flap over Deval Patrick's speech for what it is:  a last-ditch effort by Senator Clinton to revive a campaign on the decline.  No further confirmation of her unsuitability as our nominee is needed than the sight of her striving to emulate Michael Dukakis in campaign victories -- his "plagiarism" fueled defeat of Joe Biden.   Do we really want a Democratic nominee who takes Dukakis as their  example? 

Why I'm Caucusing for Obama

I've been mostly silent here on the subject of politics for awhile. There are any number of reasons for this, mostly practical -- time, and other priorities. But at least part of my reticence comes from a feeling, in retrospect, like I've been holding my breath in anticipation. Not necessarily over the Democrats' chances this year; I think they're good (but definitely not a lock, now that McCain is the defacto nominee).

I've been holding my breath, I think, hoping that the "practicalities of winning" don't overwhelm this election far too early. Ever since a mostly-unknown Barack Obama stood up in Boston at the 2004 Democratic National Convention and delivered the most stunning political speech of my lifetime (I'm too young for JFK), there's been the possibility of idealism this time around.

Politics, at least in my adulthood, has been a grim, pragmatic affair, split by dry-as-dust tinkering in the boiler room of the Great Society welfare state for Democrats, and rigid adherence to a set of litmus tests among Republicans aimed at enforcing ideological purity on tax cuts, guns, and abortion. Politics has been thoroughly computerized, mapped, analyzed like baseball box scores and run by experts on polling, advertising, demographics, and mass fundraising. In other words, it's a gigantic commercial ecosystem, and both sides increasingly treat it that way.

Obama has seemed, since his declaration became all but inevitable last year, like our generation's best hope for short-circuiting the wiring of the increasingly robotic Body Politic, and perhaps -- even if in small ways -- re-envisioning the rules of the game. Perhaps even re-imagining them in ways which cross-cut, and thus defuse, the power of our current definitions of "red" and "blue."

Naturally, Obama's relative youth has laid him open, on both sides of the aisle, to those who wonder about his toughness, his experience, his ability to win. Once the primary campaigning got seriously underway, moreover, it has seemed like Obama hasn't lived up to his 2004 performance. Early debates showed him quiet, almost deferential, and he left us underwhelmed. Polls showed Clinton with an early and massive lead, and one had to wonder, as recently as the holidays, whether it truly was the case that Obama needed more time and experience before running. A series of fairly lackluster press events and appearances have done little to change that impression.

I have to admit that despite never wanting anyone else as nominee, I have fallen prey to all of these species of doubt and skepticism, and probably a few others.

No longer. I don't know whether Obama will make it and become our nominee, but I think it's very possible. Nothing magical has happened, except for one thing: he's made it thus far, all the way through Super Tuesday, and his momentum does seem to be building.

But the uphill climb is seeming more and more like a social movement, and less like a political campaign. Obama's message of change is largely in the eye of the beholder, but it resonates precisely because much of the voter base today has only experienced the type of politics I described above. We want something more. We're all slightly cynical about the ability of politics and government to change anything for the better; some of us are much more than slightly cynical. In part, our generation's growing flirtation with libertarian economics and even politics stems from this disillusionment with government.

Some of that disillusionment is quite proper; we are the inheritors of a New Deal and Great Society that turned out to have noble goals but often methods that were flawed, either in the short or long terms. We are also the inheritors of the social world created when the Supreme Court short-circuited a slowly developing social consensus, as they did with Roe v. Wade, and handed a minority of the nation a rallying cry that would drive judicial nomination and set much of the political landscape for a generation.

That landscape now seems frozen and unalterable. Acquiescence in, and intimate knowledge of, this landscape, is now the mark of a "serious" politician or staffer. An entire industry of political staffers, pollsters, lobbyists, advisors, and of course politicians have a vested interest in that landscape, since knowledge of it is crucial to their employability or electability.

Obama may or may not be serious about changing that landscape, and even if he is successful in beating the odds and securing the nomination, as well as winning the general election, he may only succeed in making small alterations. But the chance -- just the chance -- that we may see something other than the politics of "culture war," or the politics of "triangulation" -- both manifestations of a politics of cynicism -- during our lifetime, makes it well worth supporting his campaign.

We deserve something more from our collective efforts at self-government, and although we might not get it during the next President's term, a social movement starts somewhere, somehow. Social changes always start out as small, seemingly fragile things, laughed at by the "grownups" who know "how the world works" and label anything but the status quo as "impractical" or simply sheer nonsense. In retrospect, of course, social changes always seem inevitable, when observed through the lens of history, growing seemingly logically out of preceding conditions given our knowledge of the outcome.

In the hazy middle, when those who laughed or ignored it in its early stages are caught short, and forced by the size of the crowds or vote counts to wonder whether a movement or change should be taken seriously, is the crucial moment. The moment when growth could feed on itself, or fizzle out. A moment when a little extra support and encouragement could make all the difference to whether a social movement succeeds in changing the way we think, and act.

That's why I'm supporting Barack Obama, with a vote on my primary ballot, at the caucuses tomorrow, with donations, and hopefully on November's ballot. And it's why I hope you will as well.

My new Macbook Air arrived!

OK. I'm going to gush a bit. Whatever its faults, and however often Apple displays a contempt for customers (and believe me, anytime I want something outside the narrow box they sell, I've experienced it), sometimes they connect with the pitch and hit it straight out of the park.

It's a simple thing these days to do just-in-time manufacturing and shipping from China, and I wasn't expecting my Macbook Air until Feb. 12. But Apple pulled the shipping date in by a week, and was going to deliver it on Feb. 6th. I was thrilled.

It arrived this morning. Sure, it's not that complex, but boy, do they know how to make a tech geek happy. The packaging is gorgeous -- a coworker said it reminded him of a Tiffany's box. Even the Apple skeptics in the office -- the dyed-in-the-wool, live-in-Redmond-even-though-they-don't-work-at-Microsoft types, were drooling just a little bit. When they thought I wasn't looking. They know who they are, and today I can see that their snide comments about Apple and the Cult of Steve are just envy wrapped in sarcasm.

Then you unpack it, and the Air feels both lighter and more substantial than you expect. The screen is terrific, the keyboard very nice, and the overall experience is exactly what I hoped a subnotebook from Apple would be. Even the "Remote CD/DVD" thing works perfectly for installing software -- although I bought an external Superdrive, mostly because the remote thing doesn't work well for playing DVD's due to the copy protection schemes.

I'm sure after a couple of days or a week of using the machine daily I'll have the usual list of gripes, wishes, etc. But not today. Today I'm sitting on the sofa, having loaded LaTeX, Office 2008, and a few other essentials, and just enjoying that "first day" experience.

Wow. Bravo Apple.

Screen sharing in OS X Leopard

I have to say, lately I've been using screen sharing in Leopard a great deal, to work more flexibly around the house. This isn't much of a concern in Seattle, since my apartment is small enough that I rarely have to move my laptop at all, but at home on the island, I often find myself wanting to work from the living room or by the windows, but not wanting to interrupt some long process I've got running over wired ethernet. So I leave my machine where it is, and use a different machine to work from downstairs via screen sharing. No more copying files around, worrying about having every application on every computer, synchronization issues, etc.

Of course, I used to use VNC for this in a limited fashion prior to Leopard, but the way Apple has integrated this into the Finder networking list and with account security is very nice.

And, when my Macbook Air arrives in February, I can really move around, but without worrying whether I can do "heavy" work given the smaller hard drive and memory footprint, since the Air can be just a light "terminal" for a larger machine.

I know, not problems that most people have, but it's a nice feature of Leopard that I'm coming to really appreciate.

Sunday Night Windstorm, and What I'm Doing and Studying

I just came in from standing on the deck, under clear skies, a partial moon, and the most amazing windstorm. The moon made visible the big waves crashing on the rocks below me, and the whitecaps out in the channel. It's been blowing hard all day, without cease, and I'm happy to be inside with a wood stove and food on the stove. A brief respite at home before another stretch at the office. I haven't quite figured out the optimal amount of time to spend down in Seattle, but I'm pretty sure it's shorter than I've been spending as things heat up at work. Seeing friends and doing things in Seattle is great, but I miss the island. The slow process of meeting people and "becoming a local" has all but stopped as I commute back and forth.

I haven't written much here since late December, but only because life has reached a fever pitch again, and the brief times I have free away from a full schedule need to be devoted to research and my dissertation, not idle contemplation for my website. But we're in the thick swamp of an election season, unseasonably early of course, and I haven't written anything about the candidates, the primaries, the debates, as I did for much of 2004. I can't promise to get back to regular posting before Super Tuesday, but I hope to soon thereafter. Or as soon as I can get my two projects more firmly underway (one paper, one poster) for the SAA (Society for American Archaeology) meetings in late March in Vancouver. Both are co-authored with Alex Bentley and Carl Lipo, and we're working on the statistical consequences of expressing formal models of cultural transmission within realistic social networks.

For those unfamiliar with cultural transmission, this is the observation that humans are not born with a hard-coded set of cultural behaviors (in the sense of genetically transmitted) but learn, over the course of child development and throughout life, ways of behaving and believing and thinking through interaction with others in our social groups. In a formal sense, cultural transmission is modeled mathematically through analogues of haploid population genetics models (Wright-Fisher and Moran processes), replicator dynamics and allied models from evolutionary game theory, and the contact and voter models in the study of "interacting particle systems" or spatial stochastic processes by probability theorists and statistical physicists. An open question, whose likely answer is "yes," is that these methods of modeling cultural learning and transmission are formally equivalent, given appropriate variations of population structure and the focus on deterministic versus stochastic models. But more of that in future posts, hopefully.

Basically, I'm working with some collaborators studying models of social learning and communication, for predictive ensemble or spatial statistical "signatures" in cultural data which are mapped spatially and dated temporally. A "signature" would be a unique pattern of statistical properties which tells us how a given population was structured (in terms of social networks) given the results of how cultural information flowed within the population, and came to be reflected in material objects or artifacts. An example would be a model in which we learn about, and adopt, preferences for songs and music from our social network of friends, but in an unbiased fashion -- we occasionally adopt the preferences of a colleague or associate. What statistical properties does this local process of imitation have, when projected into a "global" perspective -- statistical patterns within a population, spatial patterns in kinds of data we can map and chart?

Of course, we all know that the model I just described is pretty simplistic. Nobody "just copies" their friends, let alone doing so without any filters, biases, and on a strict "coin flip" or probabilistic basis. But it turns out it sure can look that way when you aggregate the results of many people imitating, choosing, learning, and adopting ideas. So this kind of model is a good "null hypothesis" for a simplistic kind of cultural communication -- anything more realistic will have to depart from this simple random model in striking, hopefully unique ways.

Being able to find unique, predictive patterns from more complex models of cultural learning and communication is possible, but not guaranteed -- it is easily possible (maybe even likely) that several different kinds of social situations could lead to the same overall patterns at a local, regional, or even global level. We call this problem "equifinality" -- the data we have are insufficient to distinguish between several possible processes, so given our models and data, each process is "equally likely" to have caused the observed pattern.

This type of research is what I've been engaged in for a long time -- at least since 1995, with conference papers, publications, and Carl Lipo's dissertation research covering some of the results. Now I'm extending our previous work and learning a lot of math, probability, and population genetics in the process. It's fascinating stuff, but in addition to the job at GridNetworks the work keeps me pretty busy.

This is all by way of explanation for my longish absences from writing something here. I hope to remedy that, as I said, but there's some serious work between now and then.