Monday, November 4, 2013

Introducing you to the bad boyfriend...

There was a lovely little piece by Barbara Moran in the New York Times over the weekend about what it's like to study organic chemistry. It gets so much exactly right about how students experience the course and why it's worth taking, even if you never "use" the material again. I give a speech on the first day of every Orgo I class about that includes a bit about why medical schools might require the course. Here's that speech, from a different point of view:

But the rules have many, many exceptions, which students find maddening. The same molecule will behave differently in acid or base, in dark or sunlight, in heat or cold, or if you sprinkle magic orgo dust on it and turn around three times. You can’t memorize all the possible answers — you have to rely on intuition, generalizing from specific examples. This skill, far more than the details of every reaction, may actually be useful for medicine.
“It seems a lot like diagnosis,” said Logan McCarty, Harvard’s director of physical sciences education, who taught the second semester. “That cognitive skill — inductive generalization from specific cases to something you’ve never seen before — that’s something you learn in orgo.”
Moran also does a great job of describing the sheer amount of time and constant practice learning organic chemistry takes.

This takes a huge amount of time, for me 20 to 30 hours a week. The class turned me into a bore, a sleep-deprived, orgo-obsessed grind who saw the shapes of molecules in every sidewalk crack and snack cracker. My study partners and I called orgo the “bad boyfriend,” because it stole so much time from our personal lives. As in, “I just blew off Thanksgiving dinner to hang out with the bad boyfriend.” Once, my 3-year-old clung to my leg as I tried to leave for class. “Mama, don’t go!” he cried. “No more chemistry!” Sorry, little buddy. Bad boyfriend’s calling.

Wednesday, March 26, 2008

The drumbeat...

There's been more publicly expressed (at least on the op-ed page of the New York Times) worry in the past couple of days that (a) Hillary Clinton is willing to "burn the village to save it" and (b) an Obama presidency would have to struggle to get support from the party machinery, or at least the party machinery that's aligned with the Clintons. I've expressed both those worries before, and really don't know what do to with them except be filled with dread, which doesn't seem very productive. 

The offending columns are from David Brooks yesterday and Maureen Dowd today

Update: Two more columnists chime in with the same message today. Nick Kristof compares Clinton (actually he says "the Clintons", showing his bias) to Ralph Nader. Ouch. Gail Collins adds, with an analogy to a bizarre sounding old kids TV show, that there's little in Clinton's history that suggests she won't push on until the end, whenever that may be. 

Dread, fear and loathing, my three buddies...

Tuesday, March 18, 2008

An interesting connection

Just something that caught my attention, that I wanted to share. An article in the New York Times magazine this week about the Democratic election noted that Obama seems to win states that either have smaller minority populations or where the Democratic electorate is largely African-American, but loses in states that are most racially mixed.
The assumption has always been that a black candidate should perform worse among white voters in states with less racial diversity because those voters are supposedly less enlightened. In fact, the reverse has been true for Obama: in the overwhelmingly white states of Wisconsin and Vermont, for instance, he carried 54 and 60 percent of the white voters respectively, according to exit polls, while in New Jersey he won 31 percent and in Tennessee he won 26 percent.
What this suggests, perhaps, is that living in close proximity to other races — sharing industries and schools and sports arenas — actually makes Americans less sanguine about racial harmony rather than more so. The growing counties an hour’s drive from Cleveland and St. Louis are filled with white voters whose parents fled the industrial cities of their youth before a wave of African-Americans and for whom social friction and economic competition, especially in an age of declining opportunity, are as much a part of daily life as traffic and mortgage payments. As Erica Goode wrote in these pages last year, Robert Putnam and other sociologists have, in fact, found that people living in more diverse areas evince less trust for others — no matter what their race. Maybe it shouldn’t surprise us that while white Democrats in rural states are apparently willing to accept the notion of a racially transcendent candidate, those living in the shadow of postindustrial atrophy seem to have a harder time detaching from enduring stereotypes, and they may be less optimistic that the country as a whole would actually elect a black candidate.
I was reminded of this paper in Science (subscription or access from subscribing campus required) that came out in September from May Lim, Richard Metzler, and Yaneer Bar-Yam, a group of "complex systems" scientists at Brandeis and M.I.T. They decided to treat the basis of ethnic violence as a type separation problem.
Here, we focus on an aspect of spatial population structure that has been neglected so far; we analyze the global pattern of violence and propose that many instances are consistent with the natural dynamics of type separation (1518), a form of pattern formation (19) also seen in physical or chemical phase separation. Violence arises due to the structure of boundaries between groups rather than as a result of inherent conflicts between the groups themselves. In this approach, diverse social and economic causal factors trigger violence when the spatial population structure creates a propensity to conflict, so that spatial heterogeneity itself is predictive of local violence....The dynamics of this model assume that individuals preferentially move to areas where more individuals of the same type reside (14). The resulting dynamics lead to progressively larger patches ("islands" or "peninsulas") of each type.
Then they go on to figure out, or rather, to propose where violence will occur.
To model violence, we assume that highly mixed regions do not engage in violence, and neither do well-segregated groups, an intuitive hypothesis with empirical support (7). The analysis is applicable to communal violence and not to criminal activity or interstate warfare. In highly mixed regions, groups of the same type are not large enough to develop strong collective identities, or to identify public spaces as associated with one or another cultural group. They are neither imposed upon nor impose upon other groups, and are not perceived as a threat to the cultural values or social/political self-determination of other groups. Partial separation with poorly defined boundaries fosters conflict. Violence arises when groups are of a size that they are able to impose cultural norms on public spaces, but where there are still intermittent violations of these rules due to the overlap of cultural domains. When groups are larger than the critical size, they typically form self-sufficient entities that enjoy local sovereignty. Hence, we expect violence to arise when groups of a certain characteristic size are formed, and not when groups are much smaller or larger than this size.
A bunch of mathematical modeling follows. Then they apply their model to census data from Yugoslavia from the early 1990s, before the start of the violence that broke the country apart and compared the results to news reports of where violence had occurred. To use their understated scientific language, "overlaying the locations of reported and predicted violence...demonstrates a significant ability of our simple model to identify regions of reported violence." They did the same analysis with Indian census data from 2001, looking at religious groups. Again, their model was able to predict where conflicts had occurred with a high degree of accuracy.

So, maybe we shouldn't be surprised about Obama's troubles in the "big states", which have racial distributions described well by the phrase "partial separation with poorly defined boundaries".

Monday, March 17, 2008

Politics, ugh

So, for a couple of weeks, I've been wanting to write something about the Democratic race (it's hard to call something that feels like it's not going anywhere a "race", but there it is), but I'm having trouble coming up with anything coherent. My gut reaction is "this has got to stop". I think this was put most succinctly in an article about Clinton in the New Yorker by Ryan Lizza.
It is tempting to say that the Clinton campaign’s plan is to burn the village in order to save it—that Hillary Clinton believes that Democrats, hypnotized by Obama, are making a historic mistake from which only she can rescue them. And it is tempting to add that this means the political destruction of the man who is still most likely to be the Democratic nominee.
It is tempting to say that, and sort of terrifying to think it. Lizza goes on to argue that maybe Obama will be the stronger candidate for it. I've had friends tell me that Obama stands a good chance of being "Dukasis-ized" by the Republicans in the fall, and that if he can't come up with a response to that treatment now, he'll be such a weak candidate that it won't matter. Maybe that's true, but if it means that fear-mongering still works, we're screwed anyway.

Roger Cohen, editor of the International Herald Tribune, has been writing columns in the New York Times for the past few months. His writing can be awfully fragmented, but he has some good insights. This column, about Kofi Annan's success is mediating a power-sharing agreement in Kenya, made me think about what it means to have "foreign policy experience".
My colleague Jeffrey Gettleman, who has chronicled the Kenyan crisis with immense authority, speaks of ''Annan Zen.'' Annan needed that imperturbability. The atmosphere between the Kenyan president, Mwai Kibaki, who had been declared the narrow winner of a demonstrably rigged election, and Raila Odinga, the opposition leader who felt robbed, was ''very icy,'' Annan said.
Kibaki's team kept saying, ''We won it fair and square,'' as Odinga's countered, ''You stole it fair and square.'' Kibaki, a Kikuyu, talked of ''accommodating'' the opposition; Odinga, a Luo, bridled. If pushed, he would form ''an alternative government.''

''It took a while to convince them that there was no way either side could run the country without the other, that it was a perfect political gridlock,'' Annan told me.

He got a German official to explain grand coalitions. He got Jakaya Kikwete, the Tanzanian leader, to talk about how presidents and prime ministers work together. He was helped by President George W. Bush declaring during his recent African visit that ''there ought to be a power sharing agreement.''

Kibaki's foreign minister retorted that Kenya would not be ''given conditions by foreign states'' — the old anti-imperialist thing. But this was international intervention of another kind. The pressure cornered Kibaki. He ceded, empowering Odinga as a prime minister with authority anchored by constitutional change.

''When we talk of intervention, people think of the military,'' Annan said. ''But under R2P [the global ''responsibility to protect'' citizens in states whose own governments prove unable to do so], force is a last resort. Political and diplomatic intervention is the first mechanism. And I think we've seen a successful example of its application.''

Some will quibble over technicalities, but Kenya kindled the somnolent spirit of R2P. We've also seen American might in subtler guise: listening better, applying soft power. That's another reason what happened in Nairobi matters so much.
"Imperturbability", "listening better, applying soft power" - these don't, to me anyway, describe the sort of foreign policy experience that McCain and Clinton are talking about, but their the sorts of things that we'll need to fix the mess that we've gotten ourselves into.

A memory comes back to me of watching Charlie Rose on PBS a couple of days after September 11, 2001. The basic premise of the show was "we should ask the Israelis how to deal with this, they have lots of experience". I couldn't help shouting at the TV ,"And look where it's got them!" It seems to me we've followed that advice. Look where it's got us.

Cohen makes no secret of his preferences in the Democratic primary. In another column with a reasonably insightful premise "Tribalism here, and there", he compares tribes in Kenya to the American tribes
...the black vote, and the Latino vote, and the women-over-50 vote, and the Volvo-driving liberal-intellectual vote, and the white blue-collar vote, and the urban vote, and the rural vote, and the under-30s vote - sub-groups with shared social, cultural, linguistic or other traits and interests.
Others have made this point, and fortunately it's mostly rhetorical. So far, no machete wielding enforcers have been spotted in the U.S. Cohen's real emphasis is on getting beyond tribes, in both countries.
An American generation under 45 has glimpsed an interconnected world beyond race and tribe. They know its attainment will be elusive but, after a bitter season, they feel summoned by what Lincoln called "the better angels of our nature." And, speaking of experience, they know Lincoln came to the presidency with all of two years in Congress behind him, and a failed Senate campaign.

Looking out from Kenya, where he mediated an end to the tribal violence, Kofi Annan, the former United Nations secretary general, told me: "I think an Obama presidency would be inspirational, an incredible development in the world."
Not a bad endorsement, though I bet you could use it to "Dukakis-ize" someone, if you were so inclined.

Saturday, March 15, 2008

Is this a good idea?

The other night as I was going to bed, I was reading Chemical & Engineering News, the weekly publication that everyone who is a member of the American Chemical Society automatically gets, hoping that it would put me to sleep. I came across an article that woke me up instead. The focus of the article was on biotech companies that are for the most part "virtual". What this means is that they outsource almost all of the physical work, while maintaining the underlying intellectual property. The particular company featured is scaling up production of an anti-radiation poisoning drug that would be sold to the military. Their drug is a protein, a fragment of the bacterial protein flagelin, which is involved in bacterial mobility. In human cells, this protein fragment will interfere with the action of NF-kB, a signaling molecule that is plays a role in apoptosis, or cell suicide.

When cells are exposed to high levels of radiation, the apoptotic pathway kicks in, essentially sacrificing the cell. What this drug would do is block cell suicide. One of the scientists involves claims "If you prevent it for 10 days or so, cells will restore themselves naturally to their original state, even when exposed to lethal doses of radiation". Maybe I'm missing something here, but I'm pretty sure that the "natural state" would involve cells with DNA that is severely mutated, the kinds of cells that are prone to become cancerous tumors.

So a soldier, exposed to a normally lethal dose of radiation, injects himself with this drug for ten days and survives, only to face a high probability of suffering from a variety of cancers for the rest of his (probably short) life. Why is this a good idea?

Sunday, February 24, 2008

It changes your life

Slate's been posting these terrific videos of Alex Chadwick setting up a card table with a sign that says "Interviews 50¢". People come up and talk to him.

This one is the most striking I've seen. I remember how many random people told me when my wife was pregnant with our first child. "It changes your life." I had no idea what they meant. The depth of the sympathy I have for this man is one way it's changed me.

Wednesday, February 20, 2008

Corruption in Kenya - Old news

This past week a judge in San Francisco tried to shut down Wikileaks, a website that publishes leaked government documents. One of the documents on the site is a report, known in Kenya as the "Githongo Report" that outlines the extent to which ex-President Moi used his position to extract money from the country. The report is sort of old news, but I wasn't aware of it. What's more, I didn't realize that it had been suppressed by the very person who commissioned it, current President Mwai Kibaki, of electoral fraud fame.

Apparently Moi and Kibaki became close political allies. According to the Wikileaks site:

Ex-President Moi, a corrupt, brutal, discredited former dictator, has somehow again become a key player in political life in Kenya - so much, that he is now an essential pillar in current President Kibaki's re-election campaign. His massive financial resources are expected to be used to buy Kibaki popular support particularly in the populous Rift Valley region, which voted almost to the man against Kibaki in the last election, and in November 2005 during a constitutional referendum. The leaker thinks the re-emergence of President Moi is scandalous and must be stopped.
What's clear is that money and power had a lot more to do starting the current violence in Kenya than did tribe. (Moi is Kalenjin, one of the tribes that's attacked, and been attacked, by Kibaki's Kikuyu tribe.) It's tragic that once corrupt leaders let the tribalism genie out of the bottle, there's no putting it back.

Update: Nicholas Kristof wrote a powerful column in today's NY Times that's good evidence of how far out of control things have gotten.

About Me

I'm a biochemist at a small college.