09 February 2006

A reality-impaired perspective on current events

As I mentioned a couple of days ago, NASA finally got around to firing the two-bit political hack that had been trying to make sure that their scientists published only those results that fit his restricted worldview. Today, the New York Times has his side of the story.

It's an interesting read. Apparently, he left because he was tired of being smeared by the media. The whole didn't actually graduate thing had nothing to do with it. Really. Trust him.

08 February 2006

Going Different Directions in the Same Space

As many of you know, I'm a graduate student in a zoology department. When I tell kids that, most of them think I'm studying to become a zookeeper. They also usually think that's something pretty cool. When I explain that I'm really studying to be a scientist who studies how animals change, it usually turns out to be a letdown. For some reason, kids are usually happier thinking that I might get eaten by the lion or stepped on by an elephant.

Anyway, what I actually study is speciation mechanisms. What that means is that I'm trying to look at the DNA of closely related species in order to figure out why they wound up as different species. There are a lot of questions left to answer, and lots of scientists are working in this area.

I'm guessing that right about now at least some of you are thinking something along the lines of, "Hey, wait a minute! Haven't you guys been telling us that Darwin figured that out way back when?"

What Darwin and that Wallace fellow that keeps getting left out of the story both managed to figure out is that new species are made by changing old species. They also figured out that natural selection was one way to make this happen - if some organisms are different from most of the rest of their species in a way that makes them more likely to survive and reproduce, and if the differences get passed to their offspring, then in time the bulk of the population will wind up with that trait. If this happens to only one population of a species, the changes can make that population so different that they won't be able to mate with the other populations. When that happens, you have two species where you used to have one.

That view is a little simplified, and we don't think that it is the only process that leads to the formation of new species, but it's more or less accurate. The reason that scientists are still gainfully employed working on the question of how you get new species is that the view is also a little bit corse-grained. It's like looking at a picture on a really old, low-resolution monitor. You can see things well enough to see what it is a picture of, but you don't see a lot of the details - and details can be very important.

Another way to look at this might be to use the way we grow up as an example. We know that there are children, we know that there are adults, and we know that adults happen when children grow up. You can look at a ten year old and a forty year old and know that one is a kid and one is an adult. Figuring out exactly when the change from child to adult took place is a lot harder, and so is figuring out what "growing up" actually means.

Those of us who study speciation spend a lot of time looking at geography. In part, we do this because looking at the geography can mean that you get to go lots of cool places to do your research. Mostly, though, we look at the geography because figuring out where the two populations were living in relation to each other when they split into different species can give us some good clues about how it might have happened.

There are basically three ways that you can arrange two populations in space relative to each other. Both populations can be living in the same place (we call this "sympatric"), the two populations can be living in different places ("allopatric"), or the two populations could be arranged so that they are mostly living in different places, but with an area of overlap between them ("parapatric"). That's a bit of a simplification, and there are some fairly obscure variations that can turn out to be important when you actually start to study things, but it's good enough for our purposes.

In theory, populations can split into different species in any of those three categories. There are some scientists who have developed mathematical models of the process of speciation, and those models all seem to indicate that it doesn't matter if the populations are allopatric, parapatric, or sympatric - given the right set of circumstances they can wind up as two different species.

That's the theory. When we take the theory to the field, what we find is that it's pretty easy to find examples of allopatric and parapatric speciation, but it's really hard to find clear cut cases where two populations living in the same place have split into different species. There are two resons for this. One is that it is a little easier for populations to split when they don't live in the same place. The other is that the way these things are defined makes it very hard to prove that the species were living in the same place when they split.

The exact definition of "sympatric" has actually been a little hard to pin down. For a long time, it basically meant that the populations weren't living in different places. For a long time this was good enough, but when people actually started to look at what happens to the individuals involved, it got a bit harder to pin down. For example, if one population of insects lives in the branches of the trees on a small island, while another population lives in the low bushes, are they really living in the same place? That might sound like it's just nit-picking, but when you go to look at the population genetics you find that seemingly trivial distinctions like that can make a really big difference in how likely it is that the populations will completely separate.

One of the researchers who models speciation recently came up with a more precise definition. He said that two populations can be considered to be truly sympatric when mating is random with respect to birthplace. Now that's pretty obviously an ideal that isn't often going to be achieved, but there can be situations that at least come close. You'd think that solved the problem, right? Unfortunately, you'd be wrong.

There are a fair number of scientists who really don't like the idea of sympatric speciation. For a long time, Ernst Mayr, who was an extremely influential evolutionary biologist, argued that populations could only separate into two species if they were separated from each other by some sort of barrier. He made a relatively persuasive case for that positio and argued his case with passion for decades, so it's no surprise that there are some scientists who are skeptical of the possibility of sympatric speciation. In the past, when scientists have presented cases where it looks like two species split while living in the same place, the skeptics have demanded proof that the species were never geographically isolated from each other during their divergence. Proving a negative like that is kind of tough, so the controversy over whether or not two species can actually split while living in the same place has continued.

In this week's issue of the journal Nature, two different papers are presented that offer pretty convincing proof that species have diverged in sympatry. In both cases, two species that are clearly more closely related to each other than to any other species are found living in places that make it extrordinarily unlikely that the populations were ever geographically isolated from one another.

In one case, two species of cichlid fish are found living in a small, isolated lake in Nicaragua. The habitat within the lake is relatively uniform, and the authors demonstrated that the two species are not reproducing with each other and are physically, ecologically, and genetically different. In technical terms, that's called a "grand slam." For this to be anything other than sympatric speciation, a founding population of fish would have had to arrived not once but twice. That's unlikely enough to begin with, before you start to take into account the similarities that these two species share with each other but not with any of their relatives in other nearby lakes. When you take that into account, it becomes extrordinarily improbable that they didn't split in that lake.

The second case involves two species of palm on Lord Howe Island off Australia. Here, again, the species seem to be reproductively, physically, and genetically distinct. They also flower at different times, and the genetic work showed evidence that selection was operating to increase the divergence between these species. This is another really solid case for sympatric speciation.

These discoveries should convince all but the most unreasonably skeptical that sympatric speciation almost certainly has happened. That means that we know that species can diverge in all three of the different geographic relationships, and that they probably have done so. That, in turn, tells us that speciation almost certainly doesn't always happen through the same mechanisms.

By this point, I've probably lost half the people who started to read this, and most of the rest of you are probably wondering why I thought something this confusing and boring is actually exciting enough to be worth blogging. In part, of course, it's because I am, as my brothers will cheerfully confirm, a hopeless science geek. But if you've read this far you're probably one too (or you're my mother), so that can't be all of it. Part of it is because this is hot research in my own field, but that's not all of it either - I don't write about every cool article I read.

The reason I thought this was worth writing about - the take-home message of this post - is actually pretty simple. Evolutionary biology is a very active field, and we continue to learn new and exciting things almost every day. It is a field populated by people who are eager and driven to learn new things about the way evolution works. It is not a cult of personality centered around one man who wrote one book almost 150 years ago, as some would have you believe.

07 February 2006

Nasa PR

A large number of bloggers this week have been all over the situation at NASA public affairs, where at least one presidential appointee has been attempting to silence any scientist that wants to report on things - like global warming - that don't fit well with the president's unreality-based worldview. (See my post earlier this week for links to some of the commentary.)

Blogger Nick Anthis reported yesterday that 24-year old Bush appointee and would-be scientific censor George Deutsch, who has been at the center of the scandal, did not actually graduate from college as his resume claimed. Today, the New York Times confirmed Mr. Deutsch's lack of degree. The Times also reports that Deutsch responded to this revelation by falling on his sword and resigning. One down, and an unknown number of unqualified political hacks to go.

Of course, this whole thing with Deutsch is just an amusing sideshow when viewed in light of the overall pattern of distorting science. It does, however, raise an important question: how did he get hired in the first place? Aside from his White House connections, Deutsch's only remotely relevant qualification was his alledged journalism degree. He has no background in science. His non-college experience is working on the Bush re-election campaign. The journalism degree seems to be it. Apparently, being an administration bootlicker is such a great qualification that nobody bothered to verify anything else.

Patronage - Gotta love it.

Educational Disparities

I had more fun than usual today - instead of doing labwork and going to class, I cut school and volunteered as a judge for the Hawaii Association of Independent Schools annual science fair. For those of you not familiar with our school system out here, HAIS covers the private schools on the island. Most are religious, but there are also a couple of private schools that don't seem to be religiously affiliated.

It was interesting, and it definitely wasn't what I was expecting. There were something like 45 entries in the category that I was judging (grade 9-12 research), and I got to talk to about 24 of the entrants. Along the way, I saw a couple of the worst research projects I'd ever seen, but I also saw some that totally blew me out of the water. There were several entries that could just as easily have been up at a scientific conference.

In some cases, the difference in quality was clearly related to the motivation and aptitude of the student. There were a couple of projects that were pure pseudoscience, and a few more that lacked any understanding of scientific method. There were also a couple of students who pretty obviously didn't know anything about what they were talking about. Other students knew more about their particular area of interest within their field than I did, and I wound up learning from them.

Unfortunately, a great deal of the disparity was also related to where the students went to school. This is great for the students that go to the schools that have extrordinary facilities. It's not so good for some of the others.

Some of the schools have science facilities available to their students that are better equipped than the lab I work in. One student, from Kamehameha Schools, did a project attempting to look at the structure of a particular enzyme across a range of taxa. Some of the work presented involved taking RNA, using an enzyme to convert it back to DNA, making a large number of copies of the DNA, and then sequencing the DNA. I asked the student where the work was done, thinking that it was a project done with a University of Hawaii researcher. The answer: "I did it at school." I said, "No, I meant where did you have the sequencing done." The answer: "Yeah, uh, we have our own sequencer." Their high school has a DNA sequencer. My lab doesn't have a sequencer.

Other students did not have access to anywhere near the same level of facilities. Where some students were doing their lab work in state of the art labs, and growing bacteria in temperature controlled incubators, others were doing their lab work on the kitchen counter and putting their bacteria out in the sun to incubate. Students at some schools had access to university researchers. Others did not. Some students participated in an intensive summer program that taught research methods. Others were being taught from the textbook, with the goal of being able to pass standardized tests.

Talking to the students was great. Some were clearly there because they had to be, and didn't really care about what they were doing. Others were highly motivated and extrordinarily enthusiastic - the type of student that you hope like hell goes on to a career in science.

Ranking their projects wasn't so great. I started from the bottom, and had no problems until I got up to the top half. That was when things started to suck. There were a few students there who were clearly motivated, intelligent, and creative, but who hadn't had access to anything near the level of resources that others did. Their projects, unsurprisingly, simply weren't as good as those with access to more people and equipment. Unfortunately, the student's potential isn't really something that I could give them a lot of points for - it was a science fair, it was about doing and presenting research, and the research just wasn't as good. And, if I did give them points for working with fewer resources, I'd be punishing others for having access to good resources. I just love problems that have no fair solutions, don't you?

I don't resent schools, like Kamehameha, that have lots of really, really good equipment, superb faculty, and special intensive science courses for interested students. I just wish everyone had access to that caliber of education. It would be expensive as hell, but we could do it. We could make teaching a high-paid, prestigious career. We could build the best education program in the world. It would even be the American thing to do, since it would give everyone a more level playing field for their career.

We won't, of course, because people don't like paying taxes, and the idiot with the Pennsylvania Avenue address isn't about to make the actual commitment to education that it would require.

But we should, damn it. We should.

06 February 2006

Support, my ass.

The White House has released the President's 2007 budget request, and there's not a lot of surprises there. Lots of projects are on the chopping block, defense and homeland security spending are up, the deficit is huge, the moron still wants to make his tax cuts permanent, and he wants the bill for that to mostly come out of programs that benefit the poor. Shocker, huh.

I'll probably blog some more on some of the science-related areas of the budget later on. Right now, there's one area that I want to look at first: the military pay raise. I know, it's not the most obvious place to start off, but that's where the vast bulk of our family income comes from these days, and it's always nice to see how the next year is looking. I also like to take a look and see if Bush is putting the government's wallet where his "support the troops" rhetoric comes from.

It will probably come as a shock to most of you (yes, that is sarcasm) to find that Bush talks a real good game, but when it comes time to go and actually do something, he's nowhere to be found. The proposed annual pay raise for the military next year is 2.2 percent. The economic assumptions that the budget is based on predict an inflation rate of 2.4 percent.

That's right. The same White House that tries to brand anyone who disagrees with their war as "unsupportive" of the troops has decided to show their support by suggesting a military pay raise that doesn't even match their own inflation prediction.

For some reason, that's not a level of support that impresses me.

05 February 2006

Clash of Values

I've read a few posts over the last few days, written by bloggers I usually enjoy reading, on the cartoons of the Prophet Mohammad issue. Wilkins comes closest to my own views, but none of the posts really manages to capture what I think is the essence of the issue.

This is both a simple issue and a complex one, all at the same time.

PZ is right about some of the complexities involved. There are some parallels between this situation and various ugly forms of discrimination and prejudice. There are also issues of perception and of national and ethnic identity. It is entirely possible, if not likely, that some of the anger these cartoons have inspired stems from the glaring economic disparity between the parts of the world doing the mocking and the parts being mocked. I think that those are real problems, but I think that the simpler issue is also the more important - at least at the moment.

That issue is freedom, and whether cultures based on the freedoms that provide the stable core for liberal democracies can coexist peacefully in the same world with cultures that demand that their values be given special treatment.

This case may have been started by a low-circulation Danish newspaper trying to piss off a religious group that is a distinct minority in their country, but it has rapidly turned into an international dispute involving the whole world. It has also brought to light an extremely alarming school of thought on freedom of expression.

The armed takeover or burning of embassies is bad, as are death threats. They're also nothing new in the stormy world of modern politics, particularly when we're talking about the Mideast. To put it another way, the violence is appalling but hardly surprising.

What's more alarming, at least in my opinion, are some of the views that various nations have expressed about what freedom of expression should mean. Newspaper editorials from Nepal and Bangadesh, demand that the freedom of expression be limited to exclude criticism of religion. Pakistan issued a statement declaring that freedom of expression does not extend to the freedom to insult someones religion, and the president of Afghanistan said that the publication of those comics was an act that, "must never be allowed to be repeated." Other Islamic nations have made similar statements.

The Muslim world wasn't the only place where governments have objected to the publication of the cartoons. A South African court has issued a ruling barring the publication of those images there. Our own State Department has been at best lukewarm in their support for press freedom in this case. And the Vatican informs us that, "the right to freedom of thought and expression...cannot imply the right to offend the religious sentiment of believers."

Of course, it should not come as a surprise that the Vatican is not in favor of the right to blaspheme. However, the right to blaspheme is absolutely critical in a secular society - and while people may bash secularism, the secular society has proven to be the single best way of creating an environment where everyone is free to worship (or not) as they see fit.

Without the freedom to blaspheme, there can be no true freedom of speech and there can be no true freedom of religion. These civil liberties are at the core of western democracy, and cannot be set aside just because religious people have had their feelings hurt.

The Commissar suggests that a good way to show support for the freedom of expression in this case is to reprint the cartoons in question. I am not going to do that. I fully support his right, and the rights of others, to piss off whoever they want. Personally, I think that the cartoons represent a gratuitous insult to Muslims, and I decline to personally participate in spreading them. Similarly, I fully support the right of the KKK to peacefully march through a community, but I refuse to put on a sheet and march with them.

The situation with these cartoons looks more and more like a clash of values with every day. I, for one, am not willing to have my freedom of religion and expression restricted to satisfy anyone's sensibilities. Many Muslims, on the other hand, appear unwilling to tolerate a society that allows people to insult Mohammad. I am optimistic enough to hope that we will be able to find a way to resolve this cultural divide to everyone's satisfaction, but I am realistic enough to realize that the hope appears faint.