Tuesday, September 18, 2012

Mittens insults his own base!

There is a rich and delicious irony in the news story that broke late Monday afternoon, 17 September, and which was covered extensively tonight major network news hours. Romney describes a group of voters to a group of investors and, by extension political supporters. The scene, according to David Corn of Mother Jones, was a private a fundraising party with lots of booze and sex playmates. Those who take more from the government than they pay, said Romney, are not his concern. They will vote for Barack Obama under any circumstances. This inane charge breaks entirely new ground in political naiveté. Unbeknownst to mittens, he was actually describing where most of his votes actually come from!!! According to quite readily accessible demographic figures, It insults precisely those voting blocks most likely to vote for Romney himself. If these voting blocks only could hear what he said about them, might change their minds about for whom they are going to vote. The only demographic in which Romney holds a lead are those over 65 - those "entitled" to medicaid and medicare. Those who pay little or no income tax are those in red states! Ah what a glorious turn of events! When your enemy is making a savage mistake, don't interrupt - Napoleon.

Friday, March 30, 2012

Administration defense of the Affordable Care Act

As a former enthusiast for Barack Obama’s 2008 campaign and as someone approaching most political questions from the far left, I register here my dismay at the case prepared by Mr. Verrilli and Mr Kneedler to support the Affordable Health Care Act. Good friends who are accomplished lawyers tell me that the SG and ASG are indeed among the best of the nations lawyers. I am also not a lawyer. Nonetheless, it is clear to me from what was presented on the media I’ve seen that both the SG and the ASG were unconvinced of the constitutional foundation of the ACA. Their argument failed even to convince me of its constitutionality.

Ironically, the unconstitutional part of the law is actually a conservative republican idea that the president was forced, against his better judgment, to admit because he began negotiations by taking most reforms worth achieving off the table before any negotiations took place in Congress. The defense given repeatedly by the Administration is that the ACA does many good things. Perhaps that is true. However, if as seems likely, the five conservative justices declare the individual mandate unconstitutional, then we are left with a skeleton from which most of the good things in the bill have been removed.

I don’t know why the arguments presented by the Administration were not better prepared. I suspect it is a combination of factors, including the sense that the ACA itself is deeply flawed together with the national inattention of the President for the detail necessary to ensure that the Act will be declared constitutional, which led to a pathological combination of overconfidence and insecurity. At least that is what came across. How else could the Republicans find so easy a path to ridicule the Administrations presentation (ie., the clinking of glass and repeated “excuse me” from Verrilli). The SG’s closing remarks were typical flimsy liberal argument so pastiched by right-wingers over the years. Nowhere was there evidence that the Administration understood that the right wing plays hardball. No mention of the underlying constitutional issue. In short, it failed even to convince me that the law really is constitutional. It is difficult for me to imagine a worse argument, or to think of the SG and the ASG as anything but rookies. I am deeply embarrassed and shamed.

Thursday, January 19, 2012

venture/vulture capitalism

There was an especially helpful discussion of this issue on PBS last night where Judy Woodruff interviewed Josh Kosman and Stewart Kohl. Kohl is head of a Canadian Venture Capital group that has an much more respectable record than that of Bain Capital. Kosman is one of the most articulate and well-informed critics of venture capitalism that I have heard on the topic.

http://www.pbs.org/newshour/bb/business/jan-june12/privateequity_01-18.html

One aspect of venture capital that is especially troubling to me is those cases, exemplified by Mitt Romney's Bain Capital, in which the debt incurred by Bain to purchase a company - usually one that is not in need of any help, but is unable to defend against the hostile takeover - is then vested somehow in the company itself, so that the purchaser (Bain Capital) can basically swallow up the assets of the healthy company, often including the pension plans of the workers at the purchased company, leaving that company to pay off the debt incurred when Bain Capital purchased them. Statistically speaking, many of these companies go bankrupt, while the venture capital group reaps multimillion dollar profits.

In my view, this practice should be highly illegal. However, it is not. It is, rather, venal, hypocritical, and devastating to the jobs and pension plans of the employees of the company taken over.

I cannot believe that anyone in his right mind can think of such an odious vulture as Mitt Romney in positive terms. The prospect of his ascending to power is abjectly horrifying.

Monday, October 3, 2011

video

Some years ago, I made a dance that celebrated the molecular choreography of three transducing NTPases. These are molecules, also known technically as "motors", that make things happen in the cell. They all use a fuel called adenosine triphosphate (ATP). Having misplaced the relevant files several times, I decided to post it here, with these notes.

Thoughts about the NTP Celebration Suite – Cincinnati July 2002


Discussing myself over the years with colleagues and friends, I’ve describe myself as an eclectic, pragmatic, Platonist – I have worked in a wide variety of areas, from biological electron transport to the origin of life, mechanistic enzymology, statistics in experimental design and screening (phase diagram analysis), the crystallographic phase problem, bioinformatics, and allostery. Each time I’ve changed into a different area, I’ve had to re-define myself, learning new things. It’s been a pretty good run, all things considered. Although I’ve embraced many different techniques for pragmatic reasons, however, I feel inwardly committed to one ideal form or another, and consequently am fascinated with models. I question data first, when they conflict with models I’ve invested in. For that, I consider myself a Platonist as opposed to an Aristotelian.

I read in Aaron Klug’s biography from the Nobel pages that his wife is a modern dance enthusiast. I hope it does no injustice to Aaron to reflect on his role in shaping these aspects of my professional life. I was in Cambridge barely long enough to learn where the lifts and centrifuges were. Yet, Aaron and Roger Kornberg both proved to be major intellectual role models, to whom I return in my mind surprisingly frequently for spiritual renovation. So, I am deeply grateful that Aaron was generous enough to share his lab with me for that brief, but very formative year.

Interpreting Molecular Choreography

The dance, NTP Celebration Suite, is an interpretive piece drawing inspiration from the three-state behavior of molecular motors. I want to share some of the history of this dance. I learned late in life that I derive a deep joy from dance. When I was in secondary school (grade 7-8) I enjoyed ballroom dancing (in those days, I tolerated it better than my friends!). At one point, I had the opportunity to perform in a recital as the partner of one of the instructor’s serious dance students. It was truly a lovely experience, and I seemed to have done pretty well, because the instructor came to me afterward and told me I should consider studying dance.

The Research Triangle has a major cultural resource in the American Dance Festival, ADF, located on the Duke Campus in Durham each spring and summer drawing the best modern dance companies from around the US and the world. I re-discovered dance in the mid 1990s, after we saw Pilobolus, a marvelous company with musical grace, gravity-defying choreography, a sense of humor, and a very full sense of what the human body can and cannot do! We have had season’s tickets ever since. Some years later, I decided to volunteer at ADF, and have been a docent for their summer school tours ever since. The classes are every bit as exciting for me as the professional performances.


Being ACA Past President


So it was natural that I thought of dance on my first terror-stricken moments after I was elected President of the American Crystallographic Association and thus would have to present a Past President’s address at an annual banquet three years later. The ACA Past President’s address is a wonderful tradition, and the previous ones I had witnessed had a very intimidating variety of creativity and intelligence! I began to talk about what I might do with Bill Duax (Past President of the IUCr), whose wife and daughter are both dancers. I told others, thinking that if I told enough people, I would HAVE to do make good on my plan.

In Memoriam Pierre Morell

An especially poignant moment came at our departmental Christmas party six months before the banquet when I would have to perform. I was talking about the idea to friends, and one of them, a neurochemist named Pierre Morell, got excited and volunteered to invest in the project and help me hire a choreographer! Sadly this colleague very soon fell ill with a brain tumor and died within four months. So the dance will always have that personal memory.

The suite of three dances (myosin, kinesin, and F1 ATPase) did not spring fully blown. I actually had worked out much earlier a crude version of the ATPase segment after a Gordon Conference at which Andrew Leslie presented the F1 crystal structure. That structure was a tremendous stroke of luck for Andrew: three successive states analogous to those it had taken me a decade to solve for tryptophanyl-tRNA synthetase – Open, Pre-transition state, and Products – were present in the same crystal structure, owing to the cyclic symmetry of the ATPase. Three in one go! I was quite envious of people like Andrew and Ivan Rayment, because I recognized the enchantment of free-energy transduction, but had not had (or made) the same opportunities they had had. Yet, the F1 ATPase was indeed a wondrous and very beautiful structure, both intellectually and esthetically. By celebrating it with a dance, I found a way to “own” it in my own way, without taking anything from those who had solved the structure and my envy dissipated.

A Choreographer!

Anyhow, chance brought Joy Javits into my path. The daughter of a wonderful Republican Senator from New York, Jacob Javits, and recognizably his kin, Joy is a choreographer who enjoys working with eccentric academics. She had worked before with a maths professor I knew pretty well, and was a perfect match for this project. We worked out something of a contract, and went to work, with roughly eight weeks to go. I described the ATPase structure and what it meant functionally to her and showed her a schematic video of the ATPase as well as Ron Milligan’s molecular videos of kinesin and myosin, and she started to work with me. Joy has a wonderful imagination, and she quickly seized what it was I wanted to capture about the three-state behavior of transducing NTPases. I got really excited when I selected the music and found that I could synch it with the videos. We decided that it would be a multi-media performance.

A Clog

When Joy found I had selected a Doc Watson rag for the ATPase segment, she immediately suggested a clog. Clogging is a dynamic folk dancing technique native to North Carolina. I had tried and failed several times previously to learn to clog. Joy took me in hand and carefully worked through the various steps, and soon I found myself doing it! She also suggested a simple two-step to go with the Myles Davis Blues accompaniment to the kinesin segment. The lament from Talk to Her by Alberto Iglesias for the myosin segment was the first one I selected. It matches Ron Milligan’s video just right, and was perhaps my favorite choice in the end. I had great fun editing the soundtrack and video to synchronize them. Little by little things fell into place.

Chicago Art Institute: Dress Rehearsal

I went to Chicago a couple of days before the ACA meeting in Cincinnati to give a lecture to the ACA summer course, and stopped in to visit with my daughter, Emily, then at the Chicago Institute of the Arts. Emily had a recital for an improvisation course that day, and I was privileged to watch it. Afterward, over snacks, I got to talking with the instructors and students, and it came out that I was working on the dance. We also spontaneously realized that I had yet to perform the entire suite in one go. So I got out my laptop and had the chance to do dress rehearsals for two different audiences in a small room where the sound quality from the laptop was pretty good. Their enthusiasm was an incredible tonic!

In the end, the performance went over very well. It was accompanied by a short, non-science reminiscence, not included in the video. There was a photographer but no video camera (I had kept the whole thing so secret that this was impossible to arrange without spilling beans). It was glorious fun for me, and I think others enjoyed it.

A common theme in all three parts of the suite is that my arms represent the three successive states – ligand-free, ATP, ADP plus Pi – encountered during a single cycle of ATP hydrolysis (or synthesis in the case of the F1 ATPase. There is an introductory phase showing these three states for the kinesin and F1 segments, whereas the myosin segment begins with the ligand free (attached, rigor) state and proceeds without explanation. There is no footwork to speak of in the myosin segment, whereas there are steps associated with the other two.


Credits


The video was shot by Alex Tropsha, a colleague in Bioinformatics here at UNC, at a reprise I did for the Triangle Biophysics Symposium in 2004. It is not professional, but then, neither am I!

Thursday, March 12, 2009

Don't Sleep, there are snakes - a review

I just finished reading a remarkable book by Dan Everett, entitled Don’t Sleep, there are Snakes. The title is an admonition given frequently by the Amazonian Pirahã to visitors, expressing the fact that the Pirahã sleep very little and only for short periods, because it toughens them and keeps them prepared for dangerous wild animals. The author, an evangelical and linguist, spent about a decade living with the Pirahã over the past thirty years. He first went to their home on the Maici tributary of the Amazon river, to learn their language, Pirahã, sufficiently to translate the New Testament. (The Maici river is a tributary of the Madeira River, which in turn is a tributary of the Amazon. The River of Doubt, renamed the Roosevelt River after Teddy Roosevelt navigated it from the source to the Madeira is also a tributary of the two rivers, which lie to the south of the Amazon.

Everett belonged to an evangelical sect that believes that the Bible is the word of God, and that it therefore is sufficient to translate into a native language for the people speaking that language to read it for themselves. Thus, this particular brand of evangelical missionary work expressly forbids proselytizing and has produced a significant body of work on endangered languages. Everett is an academic, now Chair of Languages, Literature, and Cultures at Illinois State University. He has studied in Noam Chomsky’s linguistic department at MIT and extensively at Campinas State University in Brazil, where he got his PhD.

The book is the saga of his encounter with the Pirahã language and culture, and documents the transformative effect that it had on him. In effect, the missionary became converted, and he now embraces the Pirahã culture, has acknowledged his nontheism, lost his marriage and family, and is evidently a happier man for having taken the odyssey. The narrative is at turns exciting adventure, light-hearted comedy.

Because the Pirahã language exhibits quite unusual formalities, the book is also a penetrating intellectual transformation of some significant consequence. The language lacks a number of basic properties which, according to Chomsky are innate and essential to all human languages. Most notable of these is recursionary grammar. The Pirahã use only simple declarative sentences of just a few words, never combining sentences into more complex thoughts, which are always conveyed instead by multiple simple sentences. This makes it sound as if the people and their culture are deceptively simple. The simplicity is amplified by the almost non-existence of words for family relationships, color, or number. Although there are a very large number of verb forms, these make only rudimentary reference to relative time.

The Pirahã cannot interpret two-dimensional photographs, and even have difficulty recognizing photos of people they know. The book is blessed with an outstanding series of brilliant portraits by Martin Schoeller, and which appeared in the New Yorker, along with a fascinating article by John Colapinto, which I read several years ago when it first appeared. The lack of ability to abstract from two to three dimensional representation, together with the dominance of what Everett refers to as the “immediacy of experience” principle (IEP) comprise a fascinating cultural portrait that raises many significant questions about cognition and the interrelationships between language and culture. The Pirahã actively oppose anything for which there is not a first-hand eyewitness account, and yet they appear often to witness “spirits” as a community.

Ample evidence quoted in the book that the Pirahã respond to their world in a far healthier fashion than do most contemporary societies. A team of cognition specialists from MIT concluded that they are significantly happier than other cultures (with the possible exception of the Danes!).

The book is written in a sweet, gentle, and compassionate style, with a wry sense of humor, informed significantly by the Pirahã directness. One anecdote jumped out above all others. Toward the end of the book, Everett is discussing the origins of his “conversion”, where he realizes that the Pirahã values are actually more comfortable for him than his own Christian beliefs. Apparently, he frequently entertained the Pirahã in his home for coffee. On one such occasion, as he poured a cup for his best friend some time after he became integrated into the society, he relates this:

‘As he took the cup from me, Kohoi said, “Ko Xoogiái ti gi xahoaisoogabagai” (Hey Dan, I want to talk to you). He continued “The Pirahã know tha tyou left your family and your own land to come here and live with us. We know that you do this to tell us about Jesus. You want us to live like Americans. But the Pirahã do not want to live like Americans. We like to drink, We like more than one woman. We don’t want Jesus. But we like you. You can stay with us. But we don’t want to hear any more about Jesus, OK?”’

Thursday, February 19, 2009

Yales's Grave Robbers

The news this morning brought up the lawsuit of the Apache nation against the Yale University Skull and Bones Society, seeking the return of Geronimo's remains, which they claim were stolen in about 1919 in desecraton of the holy burial grounds.

This news strikes remarkably close to me. One of the Bonesmen involved in the
desecration of Geronimo's burial ground is supposed to have been Winter Mead, class of 1919 and a fellow Bonesman with my grandfather and who I knew as a very young boy as "Uncle Winter". The story of the grave robbing and desecration is told in some detail by Gary Trudeau over the course of several
recurring episodes of Doonesbury. I'm near certain that it is true. It has been the source of
considerable shame for some time, because of my grandfather's implicit involvement with the perpetrators.

This sorry history came very close to the surface not long ago when Mary Casoose, an Apache woman of considerable distinction and who had lived with my family for a year on an exchange program, came to South Hadley for four days' visit with my family for my father's funeral. Dad had received the grandfather's clock, given by Bonesmen to each other as wedding presents, on his father's death. Inside, together with a glass beer mug in the shape of a skull, there was a small leather booklet with photographs
and signatures of the Yale Bones class of 1919. Among the signatures I read while, seated in the living room next to Mary was Winter Mead. I felt proud that Dad had in his own small way and perhaps unknowingly, done penance for his father's friend's sins by becoming a friend and mentor to Mary, who has become the tribal leader of her community in Arizona.

It is both appropriate and my fervent hope that the Apache plaintifs win the case and that:

a) the proceeding brings considerable daylight to the case and to the society and

b) the judge imposes hefty punitive damages that significantly impact the obscene wealth of the society.

Wednesday, February 27, 2008

Why I do not support Barack Obama

I just sent this reply to a request from the Obama campaign for a contribution.

I have no intention of joining those who have contributed, to Barack Obama. I have found no evidence in Obama's campaign to justify the enthusiasm of his supporters. I think they are largely being duped by a smooth, but fraudulent campaign. I want to tell you all why.

There was an extraordinary opportunity the night of the last debate to compare a true statement of issues with the totally phoney one promulgated by the MSNBC debate. Democracy Now aired the entire speech of Noam Chomsky to a group in Massachusetts. His topic was the fact that the entire issue of the illegal aggression in Iraq had been submerged by the media and the candidates in total submission to the will of the junior bush administration. His address was truthful, calm, comprehensive, filled with irony and entirely correct about the past half century of US history, linking Vietnam and Iraq in pretty much every respect.

On the other hand, the debate was appalling. Not a single issue was addressed with candor or honesty, or with any attempt whatsoever to bring wisdom to the American electorate. Instead, both candidates tiptoed around what might otherwise have become substantive discussions. For example, "Isn't the real source of insurgency in Iraq, the presence of illegal occupying troops?" Evidence presented by Chomsky from very reliable and essentially unanimous sources around the world made a convincing case that the real reason for the insurgency in Iraq is that the US has illegally ravaged and plundered it for the benefit of a tiny and wealthy minority. This question was, of course not raised by either of the moderators, who are nothing but stooges for the administration. Neither of the candidates made the slightest effort to change the trajectory of the debate. Nor will the eventual candidate ever attempt to change the trajectory of future debates with John McCain.

NOT A DIMES WORTH OF DIFFERENCE!

Given Chomsky's position, and the sickening pablum of the debates, I have decided that in all honesty there really is not a dimes worth of difference between any of the three remaining Republican candidates, two of whom are still running for the democratic nomination. My friends turn apoplectic when I mention the possibility of not supporting the Democratic nominee. That's too bad. I am not going to vote for anybody who hides the truth from me this way, with his/her silence on the really important issues.

What is extraordinary here is that 84% of the US population believe the aggression in Iraq is illegal and immoral. Nevertheless, the democratic candidate, whoever it is, will never approach that percentage of the votes. Partly because many Americans do not vote, but also because the democractic party has abdicated its natural role. However, an even more important reason is that neither candidate has the courage to state what is obvious to a vast majority: the entire vocabulary associated with US foreign policy is fraudulent. This is not a war we have in iraq, it is an illegal occupation. One that has taken the lives of 1.5 million Iraqis and sent another 2.5 million of the most highly gifted and skilled into exile.

OBAMA's FREE RIDE WITH THE PRESS

Lanny Davis was interviewed on Morning Joe this morning. I know Lanny well from our days as undergraduates. He is working for Mme Clinton. As much as I loath Senator Clinton for her votes in the Senate regarding the authorization and funding for fraudulent and illegal activities in the Middle East, I have to agree with Lanny that Barack Obama has essentially been given a free ride by the press. Obama voted precisely the same as Clinton on all issues relating to the war, except for the Kyl-Lieberman resolution, and Obama was awol when that vote was taken. He hides this artfully, but this does not serve the public well. Obama lies to the American people when he pretends to be anti-war.

Neither Democratic candidate is willing to acknowledge or point out the the surge is a fraud. That it is not working. That the principal reason that violence has declined is that ethnic cleansing is essentially been allowed to go almost to completion. I am ashamed that no candidate besides Dennis Kucinich ever had either the wisdom or the courage to say so. Quite frankly, I do not believe that either candidate will be able to withdraw even 25% of the forces now in Iraq. Why? because neither has ever even used the appropriate vocabulary to describe what is happening there. Every time a candidate extols the wonderful things our military forces are doing to "protect" us, it makes me quail. These are largely mercenary forces, brainwashed to commit atrocities. My heart goes out to them, especially to the bereaved and maimed, but I am neither proud of them, nor do I "support them", nor do I think that they are doing anything but damage to US interests in the region. You cannot praise the military, perpetuating the pernicious myth that they are "defending democracy" and then hope to be credible about ending the engagement!

CAN DEMOCRACY STILL WORK?

I don't know. What is important is to discuss NOW how to make democracy work, rather than to wait until November and lose the chance to change our trajectory. Now, democracy doesn't work. The fact that the eventual democratic nominee will have a fight on its hands is symptomatic of the fact that they are not articulating what >80% of the population wishes they would do. Enough are willing to BELIEVE that such things are articulated, that when subjected to the ritual casting of votes, someone will be elected. In fact nothing of the sort it is true. None of the important issues is being discussed at all! Without forceful interjection into the process, no serious issue in the campaign will ever get a decent airing, and things will simply NOT CHANGE.

I feel that the only reasonable response to this situation is to do my part to force discussion of the issues, in this case by refusing forcefully to perpetuate the myth of democracy.