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.

Sunday, February 17, 2008

"Like disposable people"

Last weekend I got the wrong paper. We usually get the Sunday New York Times, but our local metro paper came instead. One syndicated article struck me hard. A reporter for the Los Angeles Times decided last year to report on every homicide that occurred in LA county.

I wanted readers to see all the killings -- roughly 1,000 violent deaths each year, mostly of young Latinos and, most disproportionately, of young black men. The Web offered what the paper did not: unlimited space.

So the Homicide Report, as it was called, began with the simplest of journalistic missions: exposing a painful, largely unseen problem. The first list of homicide victims, published slightly more than a year ago, contained the names of 17 people. Eight were Latino. Six were black. Two were of Cambodian descent -- killed in a double homicide. None was white. Most were in their 20s.
And so it went. The list is frighteningly long, and the number of the really young is startling. I'm ashamed to say that most of what I know about the world that many of these murders come from is gleaned and extrapolated from the HBO show The Wire, but that's enough to have made me cringe in horror and recognition when I saw the list and read one person's comment "Almost like they're disposable people."

Saturday, February 16, 2008

Biofuels and global warming

A couple of papers got published online in Science last week that gave me pause, and that I think everyone should know about them. The basic message of both papers is that even though biofuels are theoretically carbon neutral (carbon taken in from the atmosphere when the plants are growing is then released when they're burned), converting land for the production of biofuels leads to such a huge release of stored CO2 that the overall effect is to increase the amount of greenhouse gases in the atmosphere. The papers are here and here. An interview with one of the authors is the first bit of this podcast. A very nice set of interviews on NPR's Science Friday, including a discussion of alternative ways of producing biofuels, is here.

Worries about Obama

So, after the caucus in my state, a bunch of Obama stickers appeared on cars in the faculty parking lot. The students had been all over him for a long time, but we needed him to win the state by a huge margin to come out of the closet.

The other consequence is that there's been a lot in the press lately that brings up worries about an Obama presidency. Some of these have provoked thought. So, here are some thoughts.

Trouble from detractors. Paul Krugman wrote a column more than a week ago comparing the beginning of a potential Obama presidency to the beginning of the Clinton presidency in 1992, when, in Krugman's telling, attacks from Republicans over anything from the staffing of the White House travel office to the childcare arrangements of potential appointees seriously hampered the effectiveness of the new administration. Krugman's point is that Obama's apparent inablity to play hardball would make him vulnerable to similar attacks. Maybe. I feel like Obama done a pretty good job dealing with the Clintons' attacks during the campaign so far. His "aw shucks" appeal to the moral high ground has the effect of making his attackers look bad in a way that the hyper-defensive Clinton style didn't.

But Krugman's column brought up a different worry for me. My recollection of the early Clinton years is of a time when he had to struggle with not only attacking Republicans, but the Democratic leadership in Congress, which had been there a long time and which seemed to resent his "skipping over" of the party hierarchy. To my mind (and I'm not a historian or a political scientist), it was this infighting among the Democrats that opened the door for Newt Gingrich, the Republican congressional majority, and the attack machine Krugman warns of. This is the scenario that I worry might play out again in an Obama presidency, especially after the close primary contests. If he can't bring the Clinton supporters and the mainline Democratic establishment around to support him, then the broad coalition he hopes to form falls apart not becuse he can't reach across the aisle but because he's lost people who should be natural supporters. There's a lot of talk about the Democrats pulling together before the general election. I worry about them staying together afterwards.

Troble with supporters. David Brooks wrote a masterful column last Sunday about why Obama pulled in more educated, higher income people, while Clinton got lower income, more working class voters. It comes down to marketing. Obama hits the same "aspirational" place as Starbucks and Whole Foods, taking the mundane into big ideas, new ways of doing things. Clinton's supporters want the basics at an affordable price. They shop at Safeway.
I felt completely pegged by this analysis. Besides that, I felt a little worried about the depth of support. When I'm feeling poor, I make my own coffee. (Okay, so it's shade grown, fair-trade beans from the local independent version of Starbucks, but still...) What happens to Obama's support when times get rough for the majority?

Check out this (semi-serious?) piece about how he's "so last week".

Finally, there's the cult of personality thing. There's a lot that's been made of this. I'm quite sure that there's a there there. I've seen enough in his books, in his speeches before he was officially a presidential candidate, and in that old New Yorker piece to be convinced that he's a serious thinker who'd be able to take in enough information and advice to make good decisions (and who'd stay firmly rooted in the "reality-based" world). But there's something to the fretting about the rockstar like appearances, about the bizarre "Yes We Can" video, about the way that message can be misread as just "vote for me". There's part of me that worries it'll go to his head too much. I don't think so, but I'd love it if he'd just give me a little of that thoughtful, earnest, junior senator from Illinois act that I fell for in the first place every once in awhile.

Update: Here's a piece from Slate (and CNN) political analyst John Dickerson with similar concerns.

Wednesday, February 13, 2008

Academic Honesty

About two weeks ago, Freeman Hrabowski came to our campus to give a series of talks. Dr. Hrabowski (I don't usually call Ph.D.s Dr., but he mentioned several times that students call him "Doc" so...) is the president of the University of Maryland, Baltimore County, which is best known (at least in the crowd I run in) for the Meyerhoff Scholars program, which has achieved a fantastic success rate in producing minority, especially African-American, research scientists, not only among the scholars but throughout the university, and has provided a model that many in the country are trying to emulate. 

The main reason for Dr. Hrabowski's visit was to deliver a convocation address (audio and video available here) that marked the beginning of Black History Month. It was an fantastic talk, that left few dry eyes, but it wasn't the most important part of his visit, at least for me. The previous day he delivered a talk at our Learning and Teaching Center to a group of mostly faculty on "Diversity in the Sciences: Creating Climates of Success" and then later in the day had a conversation with mostly students (though I and a few other faculty were there) on more or less the same topic. Both of these conversations were, as a colleague puts it, "focused, blunt and intense" but also amazingly funny and comfortable. I had a feeling of being in the presence of someone who tells the truth - the truth that you already know in a fuzzy way, but either haven't had the guts to say or haven't been able to put together in a way that would convince anyone. 

The take-home lessons for me were all about honesty. 

• You can't solve a problem if you don't state the problem. The retention rate for African-American students at liberal arts colleges in general, and ours in particular, is worse than for majority students. Retention in science majors for under-represented minority students (African-Americans, Hispanics, Native Americans, some Asians) is worse than for majority students. Hrabowski told the story of encouraging some prospective students who'd been admitted to Harvard that they should come to UMBC instead. When asked by someone at Harvard why he would do such a thing, he said "I want those students to become scientists. If they went to your place, they'd end up as lawyers." Talking in generalities about "climate" or about how the statistics of small numbers makes these patterns harder to follow avoids stating the problems, and can make them harder to solve.

• In general, people are more comfortable around others who share similar backgrounds, at least at first. Dr. Hrabowski said this again and again. His point, or at least the point I took, is that labeling as racism the frustrating slights that minority students commonly experience - being the last to find a partner when the professor says to break up into groups, the initial awkwardness that can turn into long term awkwardness in interacting with professors, the difficulty in joining study groups - isn't helpful. These are very real problems, but they come from carelessness and a mostly unconscious desire to stay in one's comfort zone, not from maliciousness. Solving them should involve creating awareness and situations in which students interact with each other in ways that force them out of that zone. 
It also means that pointing out the slights when they occur can be the most effective way to fight them. Dr. Hrabowski told a story of getting his first exam back in graduate school, where he studied math. The professor had written "You did surprisingly well." Hrabowski approached him afterwards and asked "Why the adverb?" That was all it took. The professor hadn't even thought about the impact when he wrote the comment, and never would have realized if Hrabowski hadn't pointed it out. Doing so took courage and confidence, but also trust - trust that the professor was a well-meaning, if slightly clueless (aren't we all!) educator, not an ogre.

• Preparation matters in the math and science. The example Dr. Hrabowski used was long division. It's just not possible to do long division if your multiplication and subtraction skills aren't well honed. That kind of cumulative accumulation of skills is taken for granted in college science and math courses. Students are expected to be comfortable with algebra and with basic skills in the sciences when they arrive. Upper level courses depend on concepts from lower level courses. This seems fairly obvious, but the consequences can be devastating for students who come into college science classes without a few crucial skills that their classmates got in high school. It makes it extremely difficult to continue in the major successfully without doing well in the intro courses. Hrabowski encourages students to retake intro courses if they didn't get an A or a B, something that's against the rules at our institution. He discourages students from taking multiple science courses simultaneously during their first year, so they can focus on getting the crucial material in one class at a time. He's fine with students taking more than four years to graduate, if that's what it takes to do well in the classes that they do take. 
Implementing these suggestions, though, takes honesty. It takes both students and advisors who will figure out where the gaps are in a students background, and do what needs to be done to fill them. It takes an understanding that these gaps have nothing to do with intelligence or ability. It takes changing or working around rules that were make when the college had a more homogeneous student population. All of those things are hard. 

• Students need to talk to each other about how they're doing. There was a marvelous moment when Hrabowski asked students who was excelling in their science classes. Embarrassed silence. Students at our place simply don't speak to each other about their grades. They'll say things like "that went pretty well" about a test, or "things are okay" but they won't go through an exam with a classmate or a group and figure out how to do the problems they missed. (I often worry that students won't even do this on their own.) This is a great way to put cement on the gaps in knowledge. Of course it's hard to show a classmate that a test that didn't go well. But hiding it away, saying that everything is "okay", or joining the "organic chem is kicking my butt" group on Facebook isn't a productive way forward. 

• Above all, it's important to treat students as individuals. To learn their strengths. Not to make assumptions. It's too easy to fall into the trap of talking about "these students", to make generalizations. To be too careful about what is said. That can be as problematic, as dishonest, as doing nothing at all.

Thursday, January 31, 2008

Update on Kenya. Worse news every day.

Another friend of mine who is still in touch with friends in Kenya sent along a report today, this one from Eldoret, a town in the Rift Valley that's had a lot of violence. He writes:

As Wasike describes it, towns throughout significant swaths of Kenya are barely recognizable. Most shops have been looted and few businesses remain open (and those that are open barely have any wares to sell). Many businesses and homes have been set ablaze and are either now in ashes or smoldering. Crops have been razed, livestock slaughtered, and as the press has covered, people murdered (roughly 800, to date). Transportation is virtually at a stand-still. The latter has repercussions throughout East and Central Africa as Kenya is the main artery connecting the entire region to its ports in Mombasa.

Wasike talks about the politically organized gangs of machete-wielding young men looking for people from "opposing" tribes to intimidate, injure or kill. For better or worse, those targets are dwindling as most people living as a minority tribe have vacated back to their tribal strong-holds. I'm not sure what the international press is reporting, but my friend is hearing a statistic of about 1/2 million such internally displaced persons.

At the moment there are still basic utilities in the towns and cities. But there is concern that things could take a drastic turn for the worse if that situation changes. Most significantly, people are looking to the current talks in Ethiopia, mediated by the UN and African Union, as the last best chance to quickly end the chaos and restore order. However, people are simultaneously worried that more political assassinations (there have been 2 in the past 48 hours) would more-or-less permanently derail such progress and put a stop to any meaningful political dialog.

I asked Wasike what people imagine might happen if these talks fail. He said that the most-discussed solution is that the Kenyan army would come in to restore order and impose a timeline for another election, once things have calmed down. However, he acknowledged that it's not clear if the army is unified enough to withstand the pressure of soldiers to side with their ethnic brethren. (Soldiers would be under tremendous pressure from their tribal members not to point their rifles at them, for example.) To date I have not read anything about such a military solution in the international press.

In spite of all that has transpired and the highly uncertain future he and his fellow Kenyans are facing, Wasike manages to comport himself with a tremendous sense of hope and optimism, and amazingly, manages to inject levity into our conversations.

But maybe the current situation in Kenya can most simply be conveyed by this. Wasike, a 42 year-old father of three and self-acknowledged non-religious person, has begun saying prayers and has asked others to offer their prayers for him and his fellow Kenyans.

I'm praying.

Sunday, January 27, 2008

Coming out for a candidate

A disclosure. I fell for Barack Obama pretty early. I first read about him in the New Yorker in May of 2004, when he was running for Senate. (For those who, like me, have received "The Complete New Yorker" on DVD - a much appreciated but sadly underused Christmas gift - it's the May 31st issue, page 32.) I'm the son of an immigrant father and an American mother. I'm someone who tends to buy into grandiose, if vaguely defined and sort of naive, ideas about how the greatest thing about the U.S. is the fact that we're a nation of immigrants. I'm a sucker for "give me your tired, your poor, your huddled masses, yearning to breath free". I'm also a sucker for the idea of being able to find a common humanity in everyone, regardless of background, something that struck the reporter, William Finnegan, who wrote the New Yorker piece, about Obama's Senate campaign then and strikes me about his presidential campaign now. (I'm looking over the New Yorker article now for a particular quote that will make my point, but there are too many. The article's a better advertisement for Obama than his campaign website is.)

So, I didn't have far to fall. Obama's father was even from a part of Kenya very close to where I served. Then came the speech at the Democratic convention in 2004, which made me cry. When podcasts came to iTunes, one of the first I subscribed to was his, which was great - sensible, hopeful, modest, direct. (It hasn't been updated since he declared for president.) His Iowa speech choked me up, as did the New Hampshire speech.

I don't know if making some chemistry professor cry for the possibility of what his country could do right (and out of sadness for what it's done wrong) is a sufficient qualification for the presidency, but it's enough for me for now.

Wednesday, January 23, 2008

Undergraduate research

Over the past week or so, I've been up and down about a major component of my job - having undergraduates participate in my research.

The project that I spend most of my research energy on involves understanding how a particular enzyme recognizes its macromolecular substrate, a transfer RNA, rather than any of the similar molecules present in the cell. The methods that I use to gain this understanding are fairly traditional for biochemists. I make guesses about which parts of the enzyme or parts of the tRNA are involved in specific interactions. I use the tools of recombinant DNA technology to mutate or remove those parts, and then I find out whether or not the enzyme can still recognize the tRNA. If it doesn't, my guess was right, if it does, the guess was wrong. In principle, these changes are simple to make and to test, but the process can be tedious and many of the reagents we use are expensive. The quantities of material we work with are also very small. A milligram of enzyme or tRNA is considered "tons". Like most biochemists, I've accumulated a freezer full of very small test tubes, each containing a couple of drops of water in which some precious DNA or RNA or protein is dissolved. These tubes are labeled with codes that are for the most part cryptic to anyone who hasn't worked in my lab.

Undergraduates who work in my lab are part of the big project. They make and test the mutant tRNAs or proteins, and in many cases design new mutants. This is the usual way it's done in chemistry labs at small colleges - students are a central part of the professor's major research project. Some of my colleagues in other departments, for example mathematicians or theoretical physicists, can design separate projects for students while maintaining their own primary projects. That model is far harder to implement with hands on projects that require expensive reagents and access to a relatively small number of instruments.

Okay, enough background. Here's how the last week has gone.

Stage 1: Undergraduate research stinks!

Much of my current sabbatical leave has been spent getting things to work in the lab that did not work for my research students over the course of the last couple of summers. For the most part (knock on wood!) that's now done. Two things have been frustrating about this process. One is that some of the major problems have been due to simple mislabeling - tubes that were labeled as containing one piece of DNA or RNA, in fact contained something that was similar enough, but not what I wanted. The lesson for the future is simple enough - Trust but verify.

The second frustration is more fundamental and troubling. I'm simply more able to troubleshoot technical problems in the lab when I'm doing the work with my own hands. Having a student tell me what she did or show me a picture of a gel or a set of results simply doesn't engage my ability to walk through the experiment and figure out what could have gone wrong as much as doing it myself does. While there are certainly ways to work on this, which would be good for both the students and for moving the research forward, it's hard not to think that everything would be easier if I just did all the experiments myself.

Stage 2: It's good for them, even if it stinks for you.

Sandra Laursen, a chemist who has become an expert on science education, visited our campus this week and gave a talk about work she's been involved in exploring the benefits to students of undergraduate research. The take home lessons for me were that what students gain most from doing research has nothing to do with whether or not the project moves forward. What they gain is an understanding of their temperament, their ability to deal with failure and frustration, and a sense of what it feels like to be a scientist. In other words, they gain confidence from being treated like colleagues, which is really what they are. All of this I knew, of course, but the reminder came at an appropriate time.

Stage 3: God, do I ever love to work with undergraduates on my research!

This week I've been talking to (You can call it interviewing if you'd like.) students who are applying for summer research positions. I've talked to at least 12 and will have at most 3 or 4 positions this summer. Choosing will be so difficult. Some of these kids have had research experience elsewhere already and would come up to speed in the lab very quickly. Others are just so wonderfully earnest. But mostly, it's just a thrill to talk about science with these students. And not just some vague, out there, Science with a capital S, but my science, the questions that I've been obsessed with for years, the cool little details that made me choose the project in the first place.

What I get out of the deal then, isn't at all a set of worker bees who turn my ideas into results. That part I could probably do better on my own. What I get out of the deal is a group of people who share my passion for the problem, who can remind me, mostly just by listening and asking questions and getting excited themselves, why doing science - not just studying science, but doing it - is so much fun.

Cute? More like dorky....

Several ex--students sent this to me.
Me, I think it's cute. Maybe that makes me dorky...

Monday, January 21, 2008


Last night I read this article in the New York Times about the continuing violence.

I was a Peace Corps volunteer in Kenya from 1989-1991. Around the time that I was leaving, one party rule, then under Daniel arap Moi, was being seriously challenged, perhaps for the first time since independence. Moi's response was to claim that Kenyans in particular and Africans in general weren't ready for multi-party rule, that tribal allegiances were too strong, and that parties would end up aligning themselves on tribal lines. A series of violent raids, probably orchestrated or supported by Moi's government, suddenly occurred in the Rift Valley, mainly Kalenjin (Moi's tribe) and Maasai attacking Kikuyu. Moi pointed to these raids as evidence that the country needed his despotic rule to hold it together.

The Times article indicates that much of the recent post-election violence is similarly well organized, though this time not by the government, but by "local tribal chiefs" with possible involvement of the opposition.

Today I received an email from a fellow returned volunteer, forwarding a message from a friend in Kenya that must be making the rounds. It's a list of "10 REASONS WHY I LOVE KENYA", including
• I am sure Kenya must be the only country in the world where 95,000 votes are realized in constituencies with only 70,000 registered voters.


• Kenya is surely a country with a transport network that is simply unpredictable and just can't be explained. Sample this – results from Wajir, Funyula, Budalangi, Isiolo, and Lodwar [all remote spots in the semi-desert north of the country] take a just day to reach KICC Nairobi, yet results from Kiambaa (just past Muthaiga-Kiambu [just outside Nairobi]) take more than three consecutive days being transported to Nairobi.

So I'm torn. The election was probably stolen in a vicious and somewhat obvious way. (At least have butterfly ballots!) The way in which the police and army have put down post-election protests has been brutal. See this video if you can stomach it. Yet at least some of the anti-Kibaki opposition consists of organized killers, the same people who worked against democracy and multi-party government in the first place. It feels like Moi's prophesy of tribal divisions came true, which makes me sick to my stomach.


Since I'm feeling like I need a spot to put my stuff, and since buying a bigger house isn't really an option, here we are.

I think I saw George Carlin's take on stuff when I was in high school. I found this version on YouTube.

It's stuck with me. Enjoy, whoever you are.

About Me

I'm a biochemist at a small college.