17 September 2005

Wildlife pictures - Drosophila

There are very, very few organisms with scientific names familiar to the general public. So I was actually pretty psyched to find that Drosophila is familiar enough that it's in the spell checker dictionary. There's a reason for that, of course, and it doesn't have anything to do with wildlife. Drosophila melanogaster is the "fruit fly" that's been used in thousands of laboratory experiments over the years. Lots of people have gotten to see them in high school or college labs, crawling around in little tubes with food in the bottom.

D. melanogaster may be the popular member of the genus, but it's got a lot of company. This single genus contains an enormous number of species - well over 1000 have been described to date, and there are hundreds of species that have been collected but not yet described. There are species of Drosophila known from all over the world.

Many of them are native to Hawaii. Millions of years ago, a single species of Drosophila arrived in the Hawaiian Islands. The population that arrived was very small, perhaps as small as a single fertilized female. From that small start, an amazingly diverse fauna has evolved. Hundreds of species have been described to date, hundreds more have been collected but not yet formally described, and there is now way to know if we have discovered all of them yet.

The pictures show two of the species from one of the better-known groups of native Hawaiian Drosophila - the "picture-winged" group. These flies are giants among Drosophila - almost as large as house flies. The two flies pictured here are both about the same size, and the picture on the bottom has the edge of a quarter for scale.

The top picture is Drosophila silvestris, and the photo on the bottom is Drosophila heteroneura. Both are endemic to the island of Hawai'i (the Big Island), and both are usually found living in the same locations. They are closely related species, and can hybridize in the lab, where they yield fertile and vigorous offspring. In nature, however, they do not appear to interbreed.

Both pictures were taken with a 4MP Cannon digital camera, shooting through a binocular microscope at 6.3x.

16 September 2005

Let's get back into the reality-based community.

The president gave me a nice surprise earlier in the week when he expressed a willingness to take responsibility for the federal government's failings after Katrina. A very faint hope began to stir within me when I heard Bush accept responsibility - was it possible that the administration was starting to move back toward the reality-based community? Today, the president brutally dashed that hope. Despite a federal deficit that is already at monumental levels, the president has ruled out raising taxes to pay for the post-Katrina recovery. Instead, he wants to offset these new expenses with budget cuts in other programs.

Some realism would be nice. There are definitely a few places where there is fat left in the federal budget. One notorious example is the $250 million bridge to the Alaskan island with the population of 50. That's $5 million per resident, which does strike me as just slightly excessive. But lets put things into perspective, shall we? The total cost of that bridge works out to be approximately the same as the cost required to keep the war in Iraq running for six hours. If Bush somehow managed to go back and get rid of all of the pet projects Congress earmarked mony for in the transportation bill, he'd still only have recovered slightly more than 10% of the estimated cost of the hurricane cleanup.

We need to get back into the real world. We are running a war, and we have a massive domestic disaster on our hands. Those are things that the nation is going to have to pay for, one way or another. We can pay sticker price now, or we can put off paying for a while, and force our children to pay way, way more than the original costs. Let's be adult about things, for a flipping change. We need - all of us - to make a few sacrifices, for the sake of the future.

15 September 2005

Children and animals

I've been able to resist, for the most part, blogging about the cute things that my kids do, but there was an episode night before last that was just too good to keep to myself.

My dog, Ross, has been porking up a bit lately, and I'd been having a difficult time figuring out why. I hadn't been feeding him more, he hadn't been getting too many snacks, he hadn't been getting into the trash, so I just wasn't sure what was going on. Then, last night, I got a hint of one of the possible causes.

I woke up around 2, and went downstairs to get something to drink. When I did, I found that the lights were on, and my son (who is 6) was down there with the dog. They were both sitting on the kitchen floor, they were both eating Pop-Tarts, and they both looked up at me with exactly the same guilty expressions on their faces.

From what I was able to piece together, my son started this tradition a couple of weeks ago when he was sick and not sleeping well. The dog, who is a fast learner, decided that the tradition should continue, and has been waking him up for the midnight snacks. That was, at least, what the boy claimed was happening. I was a bit skeptical, but an empirical investigation conducted last night seems to have confirmed this scenerio. Dog and boy are now being kept isolated from each other at night.

14 September 2005

The Pledge of Allegiance case

I see that a California judge has once again ruled that the "under God" phrase in the pledge is unconstitutional. This ruling, particularly since it comes at a time when the Supreme Court is being reshaped by two vacancies, is going to stir up a great deal of interest in the legal process, in the actions of judges, and in many other aspects of our legal system.

Actually, it's already stirring people up. It only took me a few minutes to find a few interesting posts about this isssue on different blogs. A group called Project 21 issued a press release that attacked the ruling as an example of "judicial activism":
"This is yet another in a series of attacks on the religious traditions on which our nation was founded," said Project 21 member Kevin Martin. "For far too long, the liberals have used our courts as a way to create rules they cannot achieve popularly through an elected, representative legislature. If anything is unconstitutional, it is this vicious display of judicial activism."

After that almost obligatory display of contentless sound and light, the Project 21 press release went on to argue that the reference to God in the Pledge is simply a form of "ceremonial deism", and it is therefore not an unconstitutional establishment of religion. (I personally find it amusing that they argue, in the same press release, that the Pledge of Allegiance represents the "religious traditions on which our nation was founded" and that the pledge is "ceremonial deism" devoid of any real religious implications.)

I really don't have much of a problem with "ceremonial deism". If the Supreme Court wants to open their proceedings with the invocation, "God save the United States of America and this honorable Court," that isn't a big deal for me. As I understand it, they've always done things that way. If so, then I'd have to agree that the tradition is mostly just that - a tradition - and that the religous content is really pretty much secondary. I personally think that putting "In God We Trust" on currency is a bit pointless, but it doesn't reduce the value of the currency in the hands of an atheist, and I don't really think it would be worth the trouble to remove it.

I don't have much of a problem with references to God in historical documents, in old traditions, or in patriotic songs. If Newdow ever sues to keep a school from forcing students to sing the "Battle Hymn of the Republic", I would hope he gets his ass laughed out of court. Despite the theistic references in that song, it is an important part of our history, and there are good reasons to expose students to it. The fact of the matter is that even if religion has not officially been important to our nation, it has been very important to many of the people who have shaped our nation, and it is a part of many American traditions. Take, for example, Thanksgiving. The first Thanksgiving was very much the theistic event. Any explanation of the holiday should mention that. To do anything else would really corrupt the meaning of the event.

This particular case, however, is different. When the Pledge of Allegiance was written in 1892, and when it was adopted in 1942, it did not contain the words "under God". The pledge simply stated, "One nation, indivisable". (They obviously didn't write that part yesterday.) The words "Under God" were added to the pledge in the 1950s, by act of Congress. They were added for a specific purpose: to distinguish the United States and its form of government from the "Godless Communists".

That's not "ceremonial deism". That's not something that is just a historical part of the Pledge. That's not just doing things the way they were always done. That is the United States Congress writing a law that pretty much says that atheists are not as "American" as theists. That is an establishment of religion, pure and simple.

I just hope that more people on the courts have the courage to stand up and say that, no matter how unpopular that may be.

Everything that's wrong with FEMA in a nutshell...

There was an absolutely unreal story on NPR today about the disaster medical center that operated out of Louis Armstrong International Airport during the evacuation stage following Katrina. A number of physicians complained about difficulties in obtaining needed supplies. Apparently, FEMA officials were not sending in supplies unless the requisition forms were properly filled out and sent to the Baton Rouge headquarters. The lack of a working fax at the airport did not, apparently, enter into the equation.

NPR had part of an interview with Col. H. James Young, the FEMA official in charge of the airport, on Morning Edition today. What he had to say indicates some major problems in that organization (not that this is news at this point, of course). The audio from that segment is available online. The transcription below is my own.
Supplies showed up. We had what we needed to do what we needed to do... These doctors, they work in these ERs, in these big hospitals or wherever it might be, and they may not have certain procedures they need to go through. They can say, "I want this right now," and they have it. Well, this is the federal government, and it has procedures that we go through."

It really needs to be heard to be believed. This man - this very model of the modern inept bureaucrat - really sounds like he thinks that the problem is the expectations that the doctors have, not anything wrong with the system. Heaven forbid that the federal government give doctors, during an emergency, what they want in the shortest amount of time possible.

I'd like to suggest something a bit radical here. Maybe, just maybe, we should make sure that the people running things at FEMA understand that there's a time and a place for paperwork. In the middle of a massive medical crisis isn't it. That's when you put people who are not merely intelligent and qualified, but also creative and flexible thinkers in charge. That's when you let them improvise, to do what they need to do to get the job done now. Write down the expenses. Keep track of what is going where, as much as you can. But get the stuff there now, and do the triplicate BS later.

Fieldwork in strange and exotic localities.

There are lots of scientists, particularly in fields like geology and zoology, who choose their fields because of the opportunities for fieldwork. There is a romance to the idea of the rugged scientist wandering out in the deserted field looking for the evidence that will lead to the next big discovery. There is the lure of strange places, and untamed wilderness. There is a fascination with the wild. In the summer, the mind of the young scientist turns to the field. And then you learn about the need for funding, and hopes and dreams come to a crashing halt.

A very interesting article in today's New York Times reminds us that nature doesn't actually end where human occupation begins, or even in places where human occupation is at its most dense. There are geologists doing fieldwork deep in the wilds of New York City, where the glacial terrain of Central Park continues to yield new lines of evidence that may help us learn about some of the climate changes that marked the end of the last major glaciation.

12 September 2005

Sharing responsibility and accountability.

An editorial in today's Washington Post examines yet another group whose role in the Katrina fiasco needs to be examined: the United States Congress. So far, their actions have received relatively little scrutiny, but some of their actions (and inactions) seem to have played a part in setting the stage for the disaster.

With so many failures at so many levels of government, I'm starting to think that any investigation should be done by a bipartisan, independent commission. The 9/11 commission could serve as a model, as could the Warren investigation of the Kennedy assassination. Such a bipartisan, independent body would have the best chance of reaching findings that people can trust.

Drawing careful conclusions

Well, when I said that the last post would stir up some controversy, I wasn't wrong. In the comments section, someone has already accused me of "political correctness" for refusing to draw the conclusion that the two alleles reported in the study are being selected due to their effects on brain size. This accusation was predictable, and it is wrong.

Political correctness has absolutely nothing to do with the proper interpretation of this study. If I thought that the only explanation for the positive selection was the effect of the mutation on brain size, I would have no problem whatsoever in saying that. At present, however, we simply don't know what the exact effect of the mutation is.

We know that the gene is involved in brain size determination, but that does not mean that the mutation in question has anything at all to do with increasing or decreasing brain size. It doesn't mean that the allele results in better brain function. It doesn't mean that people with this allele are smarter than those without it. When the researchers report that an allele of this gene has been subjected to positive selection, and that the gene therefore continues to evolve adaptively, it means just that and nothing more. Determining why the allele is positively selected requires that we study the effects of the allele.

Here's an example that might help illustrate things: the sickle cell trait. I have not run the statistics, but I'm reasonably confident that the allele for this trait shows the effects of positive selection in some populations. Yet the allele does not have a postive effect on the normal functioning of the gene. In fact, the effect of this allele is extremely negative in homozygotes. The positive selection stems from the effect that this trait has in increasing resistance to a disease, not in its effects on the oxygen-carrying functions of hemoglobin.

For all we know, the situation with either or both of the alleles discussed in these two studies is exactly the same - they might actually have a negative impact on brain size, but be positively selected for other reasons. It is also possible that the reason that these alleles have been positively selected is because they result in an enormous increase in intelligence. But we don't know that, either.

Restricting the conclusions that you draw from a study to those supported by what the study actually demonstrates is not political correctness. It's just responsible science.

11 September 2005

Wake up, and smell the controversy

There are a pair of articles in this week's edition of the journal Science that are almost certainly going to cause some excitement and controversy in the field of human evolution. Controversies in this area are nothing new, of course, but these articles seem to have all of the necessary ingredients for a spirited debate. They also seem to be almost certainly destined to be miscited by any number of unsavory individuals.

Although the two articles have slightly different sets of authors, both come from the same laboratory, and both focus on the same topic: natural selection acting on genes involved in the development of the human brain. Two different genes were examined, and in both cases specific versions of the genes - alleles - were found to be present in frequencies that indicate that they have recently been (or still are) the subject of strong selective pressure. In both cases, the alleles appear to be very new - younger than the appearance in modern humans. Finally, and here is the bit that's going be the most controversial part of this, the selectively favored alleles are less likely to be present in people from certain geographic locales.

The first paper discusses the evolution of a the gene known as Microcephalin. This gene got its name because a lack of function in both copies of this gene causes a genetic disorder called microcephaly. Individuals suffering from microcephaly have brains that are extremely small, but which have normal structure.

The team of researchers had previously investigated the evolution of this gene within primates, and had noted that this gene appeared to have been the subject of strong positive selection in the lineage leading up to apes and humans. They report, in the Science article, that during the course of this study they noticed that one version (or allele) of this gene appeared to be very common in the humans that they had looked at. They also found that this version of the gene caused an amino acid change in the protein that it produces, due to a single mutation changing amino acid 314 from aspartate to histidine. This kind of thing is very exciting to people who do evolutionary genetics, so they decided to investigate further.

They looked at sequences for this gene from 89 different humans, with a wide range of geographic origins. They found that the region of the gene that they were looking at contained 220 different places where there were variations in the specific nucleotide ("DNA letter") at that position. They also found that there were 86 different alleles present in the population that they had examined. One of these alleles was extremely common compared to all the others. Out of the 178 copies of the gene (each person has 2 copies) that they looked at, 59 of them - 33% - were that one allele. 18 individuals were homozygous for that allele (meaning that both of their copies were that allele). The next most common allele was present in 11% of the copies.

That's the type of data that screams "selective pressure" the second you look at it. But it is possible to be more scientific about investigating it. One of the things that you can do is to use computer simulation to figure out what the probability is that you would see the same results if the allele frequency was the result of chance. The investigators used a set of very conservative estimates about human population dynamics, and ran the simulation 5,000,000 times. None of the simulations yielded the observed results. This is a very strong indication that the common copy of the allele is selectively favored.

The investigators also looked at the age of the allele and the geographic distribution. They found that the allele appears to be quite young (~37,000 years). They also found, and this is the part that is likely to stir up controversy, that the allele is much less common in sub-Saharan Africa than in the rest of the world. (It seems to be most common in populations from the Americas.)

The second article looks at the evolution of ASPM, which, like Microcephalin, is involved in the development of brain size. As in the first study, an allele was found to be present with a frequency far greater than one would expect if the allele was neutral. This allele turns out to be even younger than the Microcephalin allele reported earlier, with an estimated age of only about 5,000 years. It also shows an uneven geographic distribution. As you might expect, the younger allele is less widespread than the Microcephalin allele. It is most common in Eurasian and North African populations, and it is quite uncommon in Native American, sub-Saharan African, and some East Asian populations.

Two studies, both of genes involved in brain development, both demonstrating extremely strong indications that one allele has experienced very strong positive selection, and both indicating that the positively selected alleles are more common in Europeans than in most Africans. I suspect that these results are going to bring joy to what passes for the hearts of a number of slimebags. They shouldn't, but they will. They will because the pussbuckets in question are always willing to grab onto anything they think supports their narrow-minded beliefs with both hands. They shouldn't get excited because these results actually don't say anything about intelligence.

We don't actually know why those alleles have been selected. The genes are involved in the development of the brain, and in brain size, but the alleles could be favored for entirely unrelated reasons. It's possible, for example, that people with that version of the gene are less likely to suffer from some illness or another. Even if the alleles in question have been positively selected due to their effect on brain size, these are only two of a large number of genes that are involved in the development of intelligence. These two genes have favored alleles that are present in certain populations. Other genes may have favored alleles that are present in other populations.

These two studies should serve as an excellent reminder that evolution, even in humans, is a continuous and complex process. They should not serve as fodder for various fools and assorted idiots.

Follow up: In response to accusations from one of the people commenting on this post, I have put up, in a new post, a slightly more detailed explanation of why we need to be careful drawing conclusions from these studies.

Evans, Patrick D et al. 2005. Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans. Science. Vol 309, Issue 5741, 1717-1720.

Mekel-Bobrov, Nitzan et al. 2005. Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens. Science. Vol 309, Issue 5741, 1720-1722.

There is absolutely nothing...

...like having to write a proposal when it comes to sucking away every ounce of the interest and enthusiasm you once had for your project.

And I've got to do four by 15 October. I wonder if enthusiasm can be measured as a negative quantity.