Tuesday, September 23, 2008

A bit of perspective

There's something of a financial crisis playing out in the US at the moment. Forecasts of doom and gloom are pretty common right, with phrases such that this is the "worst since the Great Depression" floating around.

At the moment, we're hearing about the horrific crashes on Wall Street, with record breaking losses.

Taken completely out of context.

The absolute value of losses are indeed record levels. This is because the Dow Jones is worth one heck of a lot more than it used to be. At the moment, the Dow Jones Industrial Average is around 11,000, which is around what it was back in 2000. In 1990, it was less than 3,000.

The market has been sliding for the past year. As of the moment I'm writing this, the Dow Jones Industrial Average is down just under 17% for the year to date, and somewhere around 21-22% for the past year. Obviously, this is not a good thing.

On the other hand, on October 19th, 1987, the Dow Jones lost approximately 22.7%. On one day. It took 2 years to recover. Do you think that might be more recent than the Great Depression?

Keep in mind that percentage changes are a lot more meaningful than absolute value changes.

Saturday, August 23, 2008

Attribution of malice

I read this opinion piece in Slate today which bothers the heck out of me. The article really is summed up by its headline: "Racism is the only reason Obama might lose"

Now, don't get me wrong: I do recognize that racism is problem Obama will have to deal with. There will undoubtedly be people who will note vote for him based simply on the color of his skin. There will also be people who will vote for him simply based on the color of his skin, but I think, on the whole, it will be more of a harm to him than a bonus. After all, the majority of black people are registered as Democrats anyway, so there are probably more anti-black racist Democrats and Independents not voting for him than there are racist Independents and Republicans voting for him, even if you assume different percentages of each type within their respective categories.

My problem with the sentiment about this stems mainly from the elevation of one piece of information about the candidate above everything else. Take the paragraph:

"Many have discoursed on what an Obama victory could mean for America. We would finally be able to see our legacy of slavery, segregation, and racism in the rearview mirror. Our kids would grow up thinking of prejudice as a nonfactor in their lives. The rest of the world would embrace a less fearful and more open post-post-9/11 America. But does it not follow that an Obama defeat would signify the opposite? If Obama loses, our children will grow up thinking of equal opportunity as a myth. His defeat would say that when handed a perfect opportunity to put the worst part of our history behind us, we chose not to. In this event, the world's judgment will be severe and inescapable: The United States had its day but, in the end, couldn't put its own self-interest ahead of its crazy irrationality over race."

That is an argument that voters should vote for Obama specifically because he is black, and electing a black President would be good for reasons historical, international, and inspirational. It leaves aside everything else about the candidate: economic policy, Supreme Court legacy, foreign policy, education policy, health policy, everything. There is a word for making a decision solely on the basis of race. It's not a word you want applied to you.

This sort of thinking pervades much of the rest of the piece as well. For instance, the line: "Or he is an 'elitist' who cannot understand ordinary (read: white) people because he isn't one of them.". No. He is considered an elitist because he's an intellectual who went to very good schools and has essentially only held jobs in public service. Charges of elitism are incredibly common in American politics, and have the ability to stick to basically anyone who isn't either a populist or has had substantial military experience. This is why so many politicians attempt to get folksy during the primary season; the meme of George W. Bush being the candidate you'd want to have a beer with, and who you could talk with (despite him being at least as much of a blue blood as Kerry was) was part of why he got elected. I highly doubt the majority of people who think Obama is an elitist mean that he doesn't understand white people; I think most of them think he doesn't understand what it's like to worry about whether his home is going to be foreclosed, or whether he'd be able to scrape together enough money to send his children to a public in-state college. I'm not saying they're right, but it's an entirely different concern.

This is actually very similar to how I felt about Lieberman when he was a vice presidential candidate and stated that the only reason people would vote against him would be anti-semitism. Actually, I was much more annoyed at Lieberman, as he himself stated this, and Obama's not the one making this argument, so Lieberman takes much more of the blame. Conceptually, though, the bigger of a deal someone makes about a characteristic that isn't directly relevant to job performance, the less likely I become to support that person. It's a problem of priorities.

For this election, I haven't decided between Obama and McCain. Neither of them have the executive experience (governor, business executive, president of a non-profit, etc) that I would like to see of a President. Obama's a very charismatic man who has the ability to change a lot of things, but I worry that the vague meme of "change" might be applied to things which don't need to and shouldn't be changed. I oppose a number of the policies both candidates are proposing (both of them on the war and on gay marriage, Obama on health care and affirmative action, McCain on abortion and energy policy [actually, both on energy, but McCain's worse]). Most likely, I'll end up figuring out which of these I think will have the longest-running implications on the Supreme Court and make my decisions on that. But I hate the implication that if I choose McCain, it's because I'm a racist. And, further, I think it's this pervading attitude that is a large part of why the polls are inaccurate about Obama. Yes, some people will say they're voting for him when they secretly won't because they're racist. I think it's likely that there are more people who will say they're voting for him when they're not, simply because they fear that they'll be labeled as racist if they say they're supporting McCain.

Monday, July 14, 2008

On the shoulders of giants

I assume this is a reference to the Isaac Newton quote "If I have seen farther than others, it is because I have stood on the shoulders of giants.". But my friend Megan passed this along to me, which is essentially a call to post about a classic paper in your field and the contributions it's made.

The papers which have had the most direct effect on my science have been relatively more recent, but thankfully, I do know some useful older ones as well. If I were feeling more ambitious, I'd tackle Sewall Wright's 1932 paper which laid out shifting balance theory, but that's not going to fit into my current time scheme. So I'll instead go with Lederberg and Lederberg's March 1952 classic Replica Plating and Indirect Selection of Bacterial Mutants in the Journal of Bacteriology

Though it's hard to think of it at the moment, at the time this paper was written there was controversy over the origin of mutations. Some people felt that mutations were always arising spontaneously. Others felt that mutations which conferred adaptation to a specific condition would be brought about by introduction of that condition. For example, if a cell were subjected to an increased salt concentration, mutations which enabled it to deal with a high salt concentration (maybe changes in ionic transporters, changes in the internal salt concentration, changes in detoxification machinery, etc) would be induced, and thus occur more frequently than they would in a cell not subjected to salt stress. Thought this may seem strikingly teleological, I feel it's important to remember that this was before the double helix nature of DNA had been demonstrated, so it was a time in which biology was even more of a black box than it is currently.

The Lederbergs devised a simple experiment to test this idea. They grew bacteria on agar plates without the presence of an antibiotic that the strain was sensitive to. They then stamped this master plate onto a sterile piece of velveteen, so some of the cells adhered to the pile. This velveteen was then stamped onto a number of fresh plates containing the antibiotic the cells were known to be sensitive to. If the mutations conferring resistance happened before exposure to the antibiotic, resistant colonies would form in the same location on the fresh plates, because they would have been derived from a resistant ancestor on the master plate. Conversely, if the mutations were induced by the presence of the antibiotic, there would be no correlation in location of the resistant colonies from one plate to another. The results clearly showed that the locations where resistant colonies grew were consistent across the replica plates made from a given master plate, showing that the mutations responsible for the adaptation arose in an environment in which they would not have been expected to be advantageous. This paper also details the equivalent experiment involving bacterial resistance to a virus which infects the wild type--again, resistance crops up in the same locations repeatedly, indicating that it is derived from changes which occur before exposure to the virus.

This paper also outlines the use of sterile velvet for replica plating--a technique I myself have used repeatedly in the lab to screen for certain types of mutations and/or genetic engineering. In general, it's fairly easy to screen most traits in one direction--if you want to find which bacteria are resistant to a given antibiotic, you put the antibiotic in their growth medium, and anything that grows will resist it. Sometimes, though, you want to select for the cells which are sensitive to the antibiotic, or which require the addition of a certain chemical in order to grow, or the like. Replica plating provides an efficient way to screen hundreds of colonies for these types of changes--make a master plates in the permissive environment (without the antibiotic, with any possible required nutrient, etc), and make replica plates on both the permissive and the strict environment (when the antibiotic is present, when a given compound is missing, etc.). Look for colonies which grow in the permissive environment but which don't in the sensitive one. There you go. To be more sure of yourself, you'll generally repeatedly test that it has the property you're looking for, but the odds are pretty good that it does, and it's a lot faster than other means of finding such negative properties.

So, thank you, Drs. Lederberg. this paper of yours not only established the importance of mutation prior to exposure to an environmental challenge, but also outlined a handy lab technique I've made repeated and systematic use of in my own experiments.

Thursday, June 5, 2008

An interesting concept, somewhat marred by an essential flaw

Recent list work: #5 (done), #9 (done), #32, #42 (done), #44 (done), #69, #70, #83, #85 (done).

Slate has an interesting article about color/racial bias potentials in professional athletics. It discusses some cases of white athletes getting higher pay than black athletes with comparable stats, whether that's economically justified based on the effects racial makeup of the team has on ticket sales, whether baseball umpires alter their calls on ball v strike based on the race of the batter/pitcher (and how omitting an important variable such as time of day can lead noise to be mistaken for signal), etc.

But there's a big flaw in the article.

The hook of the article is that the Celtics are going to be playing the Lakers in the 2008 NBA finals. On paper, the Celtics are a better team--better win/loss record, better point differential, long winning streaks against teams the Lakers themselves were playing. The Vegas oddsmakers have, on the other hand, favored the Lakers on the point spread. The article attempts to discuss whether Vegas has caught on to referee racial bias which tends to operate on the whole in favor of white players. Most likely no, but not for any reason discussed in the article. Fundamentally, oddsmakers are not really concerned with whether team A will beat team B by 5 points. They are concerned with whether 50% of the betting dollars will be on team A if you give team B an artificial boost of 5 points. Gambling establishments essentially want an equal amount of money on each possible outcome, so they can minimize their risks and make their profit from the house taking whatever cut it takes. It frequently amazes me how many people don't recognize this distinction.

Thursday, May 15, 2008

The culture wars continue

Today the CA Supreme Court is expected to hand down a decision on gay marriage. Proposition 22, aka the Knight Initiative, was passed back in 1999 defining marriage in California as being between one man and one woman. This ballot proposition almost caused me to switch my voter registration to CA from my native NY in order to vote against it, but I reasoned that the school budget vote in May would be more likely to be affected by my vote than this initiative, so I stayed registered in NY at the time. Gay couples have sued, oral arguments were yesterday, and a ruling is expected today.

This site has a decent synopsis of the expectations.

For the record, I support reasonable marriage equality. By that, I mean that marriages between any two consenting adults who aren't married to other people, and let's leave the sophomoric statements about "Everyone already has the equal right to marriage someone of the opposite sex, so you're not advocating equality but special treatment" out in the dust where they belong. I also respect that the proponents of this (to me) odious initiative at least went about it legally; I'm not happy with their result, but process matters to me, and so I'm far more fond of this statute than something like the Defense of Marriage Act which strikes me as so blatantly unconstitutional.

One of the things, though, that bothers me in the coverage of these matters is the repetition of things which are simply not true. "Unlike many other states, California also has a robust domestic partnership law, passed in 1999, which gives gay couples almost all of the legal rights and benefits afforded to married couples." This is a common perception--that if you create civil unions, you're creating something legally equal to a marriage, but merely calling it something different, so what's the big deal?

The big deal is that there are a number of ways that no domestic partnership law nor civil union is legally equal to marriage. None of them touch upon the federal marriage benefits--joint filing of federal taxes, lower inheritance taxes, the ability to use marriage to sponsor citizenship, family-related Social Security benefits, inheritance of a pension, etc. Even in CA, domestic partners may not file joint state tax returns. Spouses have legal privilege in court testimony; domestic partners nearly universally do not. Civil unions and domestic partnerships do not cross state lines, which is of far more concern today than the similarly awful anti-miscegenation laws from the 1930s--our economy is far more mobile now, and it's much more likely that any young couple will end up moving to a new state for their education or employment. There are hundreds of legal differences between marriages and either civil unions or domestic partnership agreements. This is a fact that is very rarely acknowledged in popular discussions of the issue. And, I feel, something that is to the tremendous disadvantage of those of us arguing for equality.

When you're arguing for the need to treat people equally, one of your best allies is the outrage some people will feel at the lack of equality. That outrage is going to be blunted when people feel the only difference is what something is called, rather than the pragmatic legal realities that are the bigger problem. Until the general public is made aware of host of legal differences between civil unions/domestic partnerships (or even the gay marriages in MA) and a federally-recognized marriage, I think it's unlikely that they will care enough to make a change.

Tuesday, April 22, 2008

An annoying lack of fear

Tomorrow I have my oral qualifiers. I turned in my written one -- a thesis proposal -- two weeks ago, and tomorrow will present about the work and answer whatever questions my committee decides to ask. I don't feel like I've done much of anything on this in the past week, and the reason is...I'm just not scared enough. I've been through quals before. I've been working on or thinking about this project for 4 years now, though for substantial portions of that time I was physically working on other projects. I've never feared public speaking, and I gave a version of this talk last week. After I did so, I asked the one biologist I know who heard the practice for feedback, and he told me I know too much about this subject, probably because I was able to give a reasoned answer to a question which was almost certainly asked as a joke.

So tonight I looked over my powerpoint to remind myself of the order of things, and I did another bit of analysis of some of the preliminary data and tossed it in there. I've bought food for the meeting (cheese, bread, pepperoni, fruit, and juice). And I've read much of a novel that I've read before and which has absolutely nothing to do with my work. I couldn't even get into the mood to bake cookies like I normally do for all committee meetings.

Here's hoping my lack of fear doesn't come back to bite me in the morning. Though I think it's unlikely, I recognize it's theoretically possible for my committee to fail me and tell me I need to leave the program. And yet, even writing that out doesn't send me into the panic I feel it should, with me reviewing the papers I've cited to be sure which author argued which point in which specific paper.

I suppose in the morning I'll find out whether this is the calm of reasonable confidence, or the calm of denial.

Update: I passed. The exam was a lot longer than I expected it to be (roughly 3 hours of me talking and being asked questions, nearly 3:30 hours by the time they'd decided I'd passed, brought me back in the room, and we finished discussing some strategies for the next steps and how to alter things for the grant I'll use this project to apply for in the fall. I felt like quite the idiot at a few points, in which I couldn't remember things which I know that I knew at points in the past, but it's done with. I now most likely don't have another stretch of time as scary as that waiting in the hall until I do the same thing at my actual dissertation defense.

Sunday, April 13, 2008

I'm not dead yet...

...just not been blogging lately.

I turned in my written qualifier exam last week, which was what was taking up the majority of my life until that point. I also got back page proofs for the encyclopedia article I wrote with my advisor; those are due back next week. I've filled out my taxes, and gotten a good portion of the way through preparing my oral presentation on my thesis project, so I've got a bit of a breather.

Today I found myself dealing with way too much information on a different front. I went grocery shopping, which I'm beginning to understand is a dangerous thing to do if you're well read in terms of ecology, health, and international relations.

For instance, let's look at the produce I bought.

I eat a lot of fruit, and for reasons I don't feel like going into at the moment I was limiting myself on fruit for the past couple of weeks, so I really wanted to buy some today. Because I'm the sort to overanalyze things, I ended up considering:

Is it better to buy fruit crops from Latin America or from greenhouses in the US? It's April in MI, and thus most fruit is not yet in season--our big local fruit harvests are mid summer (cherries) and fall (apples and pears), with some berries throughout the summer. When contemplating the blackberries on sale this week, I noted that they're from Ecuador, which presumably means that they've been transported a longer distance (higher CO2 emissions) and were grown under higher pesticide concentrations, which may remain stable in the water supply. Conversely, they were also grown in a climate more amenable to berry production in the first place, and probably required much less in the way of added fertilizers, and if they were farmed in large scale projects their harvesting efficiency is probably much better than in the small scale operations typical of most seemingly progressive farming. Then there's the consideration of whether this provides an economic incentive for licit agriculture in a region where workers will clearly switch to coca production if nothing else is economically viable, whether my purchase of a foreign farm product is lowering the long term economic viability of domestic farm production, whether or not that effect on domestic farm production is inherently a net bonus or a net negative, and whether I'm influencing the demand for migrant farm labor that is increasingly comprised of illegal immigrants. And then there's the consideration of whether since immigrants are, in general, harder working than people who stay in their native country (because they're willing to sacrifice so much for the perceived benefit for their children) which group it's better to reward.

And all of that is without even addressing the question of whether it would be better ecologically to buy fresh versus frozen berries, given the energy cost in the freezing process and transport in refrigerated conveyance.

Lest someone be tempted to tell me to go to a farmer's market--well, the local ones aren't open yet, and even if they were, the impact of the gas needed to get to the farmer's market might overpower any ecological benefit going could reap. Perhaps going would be able to reap other economic benefits, and the social benefits that changing economics of supply and demand would entail, but that's not terribly clear either.

Similarly, it took about 10 minutes to find a loaf of bread which wasn't horrendously expensive, was made of whole grains, and didn't contain high fructose corn syrup. That's less for health reasons (my metabolism is just fine with a large component of high fructose corn syrup in my diet) than it is my relatively insignificant economic protest against a farm bill which makes high fructose corn syrup more profitable for agribusiness than crops designed to be eaten as whole crops.

Then I got into considerations about recycling when it came time to buy something to drink. I recycle both plastic and aluminum, and in some ways I very much support deposits on cans and bottles to encourage their recycling. But given that I've got a recycling truck coming by my house once a week anyway, it seems a bit silly to care about getting things that I need to take back to the store. Also, while aluminum cans end with more packaging than do plastic bottles, aluminum recycling is less energy intensive and recovers a higher yield of the aluminum in the first place. Then again, the cardboard that the aluminum comes in is something the city only sometimes picks up--otherwise I need to drive it to the drop off center for cardboard recycling, which I admit I do rarely more because it's something of a pain than because it's better to wait until I've got a full load, as it's not on my way to anything.

Then there was the issue of bagging. I've got a set of canvas bags which I take shopping with me, so I don't have to rely on paper or plastic bags--it's one of those rare times when the responsible decision actually is clear. However, with the way self checkout tends to work, it's much more of a pain to use my own bags than the store bags, as the weight sensors will think I'm trying to steal something if I just put the empty canvas bag on the pad before I start scanning things. I usually end up having to stack the food on the sensors, pay, and then put it all in my bags, which makes me take more time than the average customer and slow down everyone else. Today, though, I bagged in paper (which is actually worse in terms of CO2 than plastic--the higher transport costs overmatch the sustainability arguments) inside my canvas ones. I've got some yard waste to get rid of, and the city will only take it if I put it in paper bags. I ended up getting dirty looks from a couple of customers, perhaps because they thought I was just posing at being responsible.

If this is what trying to be an informed, conscious shopper entails, I can see why most people aren't. It's a lot more work and a lot more time than simply grabbing what's on sale. I have a hard time imagining that I'd be willing to put this much time and thought into my grocery shopping if I had children, or was worried that my company might have another round of layoffs at any time, or any of the many other reasons most consumers aren't going to care where their fruit came from.