02 June 2006

Read This

Go read this article. And remember it in November.

Friday Random Ten: The Conservative Edition

With the recent online publication of National Review's list of the top 50 Conservative Rock Songs, I decided to see if I could force a conservative worldview onto this weeks list of the ten songs randomly selected by my iPod.

1: Pave Paradise
Lilith Fair Live Version
This song has compelling lyrics ("Took all the trees, put 'em in a tree museum/charged the people a dollar and a half just to see 'em") that demonstrate the basic compatability between environmental conservation and an unregulated free market syste.

2: Life's Been Good to Me So Far
Joe Walsh
While some might see this as a being all about Hollywood values, it's really about that great American dream - wild success.

3: Cats in the Cradle
Harry Chapin
A sweet and loving tribute to the special relationship that fathers can have with their sons in modern suburban America

4: Radio Free Europe
Becaues Europe wouldn't have any freedoms without us, so they damn well better remember to agree with everything that we say and do.

5: Taxman
The Beatles
OK, this one's really on their list. Hell, it's probably Grover Norquist's ring tone.

6: Born in the USA
Bruce Springsteen
Conservative to the core, this song trumpets American Pride at full volume. Just remember to ignore the lyrics.

7: The Imperial March
John Williams
I can't do it. There's clearly no way I could possibly draw any kind of connection between this one and modern conservativism, no matter how hard I try.

8: Lola
The Kinks
A nice, traditional values account of boy meets girl, girl takes boy home, girl turns out...

9: The Times, They Are A Changing
Bob Dylan
That's right, you liberals have had it all your way for way too long now. We conservatives are gaining ground, and we'll start to govern any day now.

10: The Proclaimers
King of the Road
This remake of the depression-era hobo classic should make us downright nostalgic for the days before those communistic, New-Deal, so-called safty net programs.

01 June 2006

Me and the ESA

I've had a day or so to recover from yesterday's revelation that I have to get Endangered Species Research Permits to cover the possibility that I might take some of the newly-listed endangered Hawaiian Drosophila along with the ones that I'm after. The paperwork is definitely going to be a royal pain in the ass. That's absolutely certain. Because I am conducting scientific research, I need a scientific research permit; in order to get a scientific research permit, my research must have a conservation benefit for the involved species. This, in turn, means that I am actually going to have to pay more attention to the endangered species than I had initially intended.

As annoying as all of this is, it's a good thing.

The reason that we have the Endangered Species Act (if only for the moment) is not to penalize business and cripple America's ability to compete globally. The purpose of the ESA(wingnut objections notwithstanding) to permit the federal government to take private land without compensation. The purpose of the ESA is not to make it easier for us touchy-feely liberal types to get in touch with nature. The purpose of the Endangered Species Act is to try and make sure that our grandchildren and great-grandchildren live in a country as rich in biodiversity as the one we have now. It's not perfect - we are still losing species. In fact, the ESA's more or less just a finger in the dike. But it's all the protection that many of these species have.

One of the botanists at UH told me that there was, about 100 years ago, a researcher there who liked to make "century collections" - collecting and preserving 100 samples of a plant, and sending the samples off to herbariums around the world. Apparently, there were a couple of cases where he only got up to about 80 or so, and nobody's ever been able to find the plant since. I don't know whether this is true or not, but either way it's a pretty damn good cautionary tale. As much as I'd like to follow the example Bill Murray set in Ghostbusters, things really shouldn't work that way. Scientists are perfectly capable of harming the environment if they are not careful. The ESA paperwork and oversight makes sure that our research will not just increase knowledge, but will also aid in the recovery of the endangered species, and this benefit far outweighs the inconvenience that results.

But the paperwork's still gonna suck.

31 May 2006

What are these people smoking?

New York City just lost a big chunk of federal homeland security money. According to the New York Times, this was at least in part because the federal government didn't like the way that the money was being spent, but an assessment of risk was also part of the equation. I'm not in a position right now to assess how the money was spent, but as a former New Yorker I was somewhat shocked by part of the risk assessment:
New York officials were given a one-page tally that explained, in part, how the region's risk-based standing was calculated. The document said the region had no "national monuments or icons," four banking or financial firms with assets of over $8 billion, 28 chemical or hazardous material sites, as well as nearly 7,000 other possible important, high-risk targets, like hospitals or major office buildings, a tally that some city officials said had major omissions or errors.

"It's outrageous that these bean counters don't think the Statue of Liberty, Empire State Building and Brooklyn Bridge are national monuments or icons," said Jordon Barowitz, a spokesman for Mayor Bloomberg.
Not to mention Times Square, the Broadway theaters (or, for that matter, Radio City Music Hall), the New York Stock Exchange, Yankee Stadium, Central Park, a couple of dozen world-famous museums, etc, etc, etc. I swear, this has to be a "small government" strategy - they're trying to make the federal government as incompetent as possible, in the hope that we give up on it instead of trying to fix the problems.

We interrupt this broadcast...

...for the following sounds:

*thud* *thud* *thud* *thud*

Thank you.

The preceeding sounds have been brought to you courtesy of a graduate student who has just discovered that the possibility that his study might result in the capture of insects newly-listed as endangered species almost certainly means that federal scientific permits will be required before fieldwork can begin.

We now return you to your regular blog, already in progress.

30 May 2006

For Congress, Wherever You Are:

First, they came for your library and bookstore records.
And Congress said, "Damn Straight. Anyone reading both the Koran and The Anarchists' Cookbook is clearly a terrorist, and needs to be shipped off to Gitmo."

Then they came to listen in on your overseas phone calls.
And Congress said, "Great idea. We need to know if that cab driver in New York is badmouthing the president to his parents back home."

Then they came to get your domestic phone records.
And Congress said, "That's right. We need to check on anyone placing frequent calls to the falafel joint down the street."

Then they came for some files in the office of a congressman who had just been caught on tape accepting a $100,000 bribe, $90,000 of which was found in his freezer.
And Congress said, "Hey, wait! You can't do that to us! We've got ill-defined and poorly spelled out Constitutional rights! We're going to hold hearings on this right away!"

29 May 2006

How many species 3: an answer, and some more questions.

In a previous post, I presented an example of one of the questions that evolutionary biologists face. In this example, I described three populations of closely related insects, presented a few details about their distribution, and gave the results for some laboratory-based breeding studies that were conducted with these populations some years back. I then asked people to guess how many species the three populations were divided into by scientists. Their answers, and some questions, can be found in comment threads both at The Panda's Thumb and at The Questionable Authority.

If you look at the answers that people have given, you will see that all three possible choices (1 species, 2 species, and 3 species) have received some votes. The most popular answer is that there are 2 species, with populations A and B being put together as a single species, and population C being given status as a separate species. The people who have chosen this option focused on the obvious differences in fertility for the crosses involving population C. The person who voted for three species did so based on the high likelihood that all three populations are on separate evolutionary tracks. The people who voted for a single species did so based on the fact that, despite the male sterility, population C is still interfertile with populations A and B. Several people also asked for more information. I'll try to satisfy some of those requests in this post.

All three arguments are good ones, and I can't say that any of them is flat out wrong. I can, and will, tell you which of those positions matches the current scientific classification for the group, but that does not mean that the other two are necessarily wrong. This group definitely falls into a grey area. The three populations are somewhere in the process of differentiating from each other, and drawing the line becomes a bit tricky in these cases.

Populations A and B are currently considered to be in the same species - Drosophila grimshawi. Population A is the Molokai population; population B is found on Maui. There is also a population of these flies on Lanai. Population C is considered to be a separate species, D. pullipes, and is endemic to the Big Island.

The data that I presented on the fertility of male hybrid offspring was taken from Alan Ohta's 1977 Dissertation. A published version of the material can be found in:
Ohta, Alan T. 1980. Coadaptive Gene Complexes in Incipient Species of Hawaiian Drosophila. The American Naturalist. v. 115(1), pp.121-131.
Here's where it gets fun, though: I only gave you part of the situation with this group in the example, and the part that I did talk about is actually the more clear-cut part.

In addition to the populations that I talked about in the earlier post, there are also populations on Lanai, Oahu, and Kauai. The Lanai population acts much like the Molokai and Kauai populations. This isn't surprising, since the channels connecting Maui, Molokai, and Lanai are narrow and shallow - so shallow, in fact, that the three islands were connected several times during the ice age. As a result, it is common for evolutionary biologists to treat those islands as a single entity, often referred to as either the Maui Complex of islands, or "Maui Nui" ("Big Maui"). The Oahu and Kauai populations do not fit in quite as well with either the Maui Nui populations or with the Big Island population.

I'm not going to present numbers this time the way I did last time (see the reference cited above if you're interested), but I am going to try to provide more of a broad overview. Some of this was already covered in the earlier post, of course, but I'm going to include it to try to keep everything in context.

General characteristics:
Pretty much all of the extant Hawaiian Drosophila are restricted to the native forests above 1000'. This is probably related in part to human-caused habitat changes, but in the case of the picture-wings (including the species discussed here) the restriction is more climate-related. These species prefer cooler temperatures than other Drosophila species, and tend to do poorly at temperatures over about 68 F (20 C).

Physical Appearance:
The Big Island flies (D. pullipes) can be distinguished from the others only on the basis of some minor color changes in the legs and sides of the thorax. All of the other populations are physically indistinguishable from each other.

Ovipositional Behavior:
This is the most obvious phenotypic difference separating populations. The Oahu and Kauai populations and D. pullipes will only deposit eggs in the presence of rotting bark from plants of the genus Wickstroemia. The Maui Nui populations will ovideposit virtually anywhere. Larvae have been reared from 12 plant families, including 2 that are entirely invasive to the islands (the figure of 14 that I gave in the comments was incorrect). To answer a question asked earlier, the Maui Nui populations have been known to use Wickstroemia, but I think it's unclear whether that is a retained trait or whether they're simply indiscriminate. Looking at the study (Montgomery, 1975) that determined this, it appears that their larvae has been reared out of pretty much any plant found in the same climate/vegetation zone as the flies. It should also be noted that specialized ovipositional behavior is the norm in the picture-wings. Only four other species are known to use more than three families, and only one is known to use more than grimshawi.

All of the populations can be crossed successfully in the lab. As I previously reported, the Maui Nui populations are fully interfertile with each other, but most of the crosses involving D. pullipes produce sterile male hybrids and decreased numbers of fertile female hybrids. (For the exact numbers, see Ohta, 1980). The Kauai and Oahu populations are interfertile with each other, and produce infertile males when crossed with D. pullipes.

Here's where it really starts to get interesting, though: when crossed with the Maui Nui populations, the Oahu and Kauai populations produce fertile hybrids, but the fertility of the F2s (the offspring of hybrid x hybrid matings) is decreased, as are most of the backcrosses (hybrid x parental species). This is particularly true for crosses involving a hybrid and the popuation used for the male parent of the hybrid, but much less so when the backcross is with the female parental population. Again, the numbers can be found in Ohta, 1980, but here are the high points: the smallest drop in the F2 fertility was from 90% to 50%. The smallest drop for backcrosses into the male parental population was from 93% to 63%. This indicates that while the differentiation between these populations isn't as great as that involving D. pullipes, it's still substantial.

Genetic Distances:
In his dissertation, Ohta examined about a dozen allozyme loci (those are enzymes where more than one version [allele] of the enzyme is present in the group you are looking at). He computed Nei's genetic distances for the different populations.
Here's a quick summary:
Within the Maui Nui populations, the largest distance separates the Lanai and Molokai populations (0.246), and the smallest separates Molokai and Maui (0.05).
The Hawaii population (D. pullipes) is most similar to the Molokai population (D=0.245) and most distant from the Kauai population (D=0.419).
The genetic distance between Kauai and Oahu, despite their behavioral and morphological similarity, is larger than any of the distances involving D. pullipes (0.375).
The greatest genetic distances are those separating the Oahu/Kauai populations from the Maui Nui populations - the range is from 0.576 (Kauai x Lanai) to 0.760 (Kauai x Maui).

The new questions:
So, now that we've got a bigger view of the picture, how should the group as a whole be handled? In particular, what should (or, for that matter, can) we say about evolution in this group, and how should we classify the relationship between the Oahu, Kauai, and Maui Nui populations? I'll post on this again in another couple of days - let's see what the comments bring this time.

Montgomery, Steven L. 1975. Comparative Breeding Site Ecology and the Adaptive Radiation of Picture-Winged Drosophila (Diptera:Drosophilidae) in Hawaii. Proceedings of the Hawaiian Entomological Society. V. 22(1), pp.65-103

Ohta, Alan T. 1980. Coadaptive Gene Complexes in Incipient Species of Hawaiian Drosophila. The American Naturalist. v. 115(1), pp.121-131.

28 May 2006

How many species 2: What is a species, and Why does it matter?

One of the questions asked in the comments of the previous post in this series is quite pointed, and very much on topic for this discussion, so I'm going to take a minute or two to answer it. I'll give the answer to the example in another post, that will shortly follow this one. Karl asked:
So why are you asking that question? How is "species" defined. Does it really have a definition? Does it matter? Isn't "species" just a modern reaction to the biblical term "kinds"
Now that I've taken a few minutes to think about it, I'm starting to remember why I was dodging that question. I could write a long, rambling discourse on the topic, but in all honesty the best I can do for a definition of "species" is to paraphrase Justice Stewart's concurring opinion in Jacobellis v. Ohio: I might not ever be able to intelligently define the term, but I know it when I see it.

If you ask working biologists to give you a definition for "species," most will provide you with some version or another of Ernst Mayr's Biological Species Concept:
"species are groups of interbreeding natural populations that are reproductively isolated from other such groups."
In practice, however, most working biologists tend toward the "Justice Stewart" species concept, especially when their own preferred organisms are involved. It's a simple (and common) problem, really. Mayr's definition looks absolutely fantastic on paper, but it has this nasty habit of falling all to pieces when confronted by reality. We keep using Mayr's definition when asked to give one because (to paraphrase another famous guy) it is the worst possible definition for "species" - except for all the other ones that people have tried.

The next question, of course, is why we keep trying - why we think that it is important to try - if "species" is such a hard concept to define. Opinions differ on this, and I can only give you my own. It matters because we are trying to describe something that really exists. Some people do disagree, and believe that what we call "species" are simply human groupings, but I think they're wrong. I think that species really do have a biological existance, independent of our own intellectual activities.

The reason that we have a hard time coming up with a definition of species that works for everything is that there isn't one. Different types of organism keep themselves sorted out in groups in different ways. Mayr's definition works (at least in theory) for organims that are sexually reproducing. It goes all to hell when confronted with asexual organisms, and it gets worse when you toss plants into the mix - they do the wierdist damn things as they evolve.(Go read John Wilkins' paper on the topic, since he does a much better job explaining this.) Because evolution is an active, ongoing process, you will also find - no matter what definition works best for your organisms - some groups that are pushing the boundaries between species. Mayr's definition explicitly lumps together anything that can successfully interbreed, but what do you do when two populations successfully interbreed only 0.001% of the time in the lab, and never in nature? What do you do when they can be hybridized in the lab 100% of the time, but when they consistently refuse to interbreed with each other in the wild? What do you do when two populations will only produce sterile males when crossed, but always produce fertile females?

One of the best examples of this problem involves Lions and Tigers. Female Tigons (the hybrid offspring of a male tiger and a female lion) are fertile, and potentially could serve as a means of moving genes from tiger populations into lion populations or vice versa. This means that tigers and lions are potentially interfertile, and under a strict application of the biological species concept would be considered to be a single species. Of course, we "know" that they are not. Tigers and lions do not interbreed in the wild, are very different in appearance, and have very different behaviors. If they are not different species, the term becomes essentially meaningless.

So, to sum it up, species are real, and there are definitions for "species." The best definition will depend on the group of organisms that you are looking at, and no matter how you define "species," you will probably still find some group or another that is at a point in evolution where it doesn't quite fit the definition you're using. To sum up the summary, life is pretty damn messy.

But it does matter. When we look at living things (as our most distant human ancestors did) we see species. We can tell that living things are divided into groups, and that each individual is more similar to the other members of the group than it is to any other group. (Usually, anyway.) It matters because it is the way nature behaves, and because that is what we are trying to describe and explain.

It's a tired analogy, I know, but dealing with "species" really is a lot like dealing with the concepts of "child" and "adult." We know that there are differences between children and adults. It takes no real insight to look at the two and identify significant distinctions between the groups. The problem comes when you try to come up with definitions of "child" and "adult" that are capable of unequivocally distinguishing the two. It can't be done - there is no sharp distinction between the two there to identify. The same could be said for other age-based distinctions, like "adolescent" and "senior citizen." We recognize those as "real" groups, sharing numerous common features, even though we can only come up with arbitrary methods for distinguishing them from the neighboring class. The same is true for "species." We can see that they are real in nature, and that organisms really do form distinct groups. We just can't come up with a definition that will always allow us to distinguish a single species with very distinct populations from two species that sometimes interbreed.

Religious Discrimination and National Cemeteries

It seems that the National Cemetery Administration (part of the VA) is having some difficulties comprehending both the spirit and letter of the Constitution. The widow of an Afghanistan casualty wants to have an emblem representing his religion placed on his government-provided memorial. The VA is currently refusing. The problem is simple - they will only place approved religious emblems on the markers, and the marker that she wants isn't one of the following approved symbols:
Christian Cross
Buddhist Wheel of Righteousness
Hebrew Star of David
Presbyterian Cross
Russian Orthodox Cross
Lutheran Cross
Episcopal Cross
Unitarian Church Flaming Chalice
United Methodist Church (Cross)
Aaronic Order (Cross)
Mormon (Angel Moroni)
Native American Church of North America (teepee)
Serbian Orthodox Cross
Greek Cross
Bahai Nine-Pointed Star
Atheist (Atomic-symbol with "A" in center)
Muslim (Crescent and Star)
Konko-Kyo Faith
Community of Christ
Sufism Reoriented
Tenriko Church
Church of World Messianity (Izunome)
United Church of Religious Science
Christian Reformed Church
United Moravian Church
Christian Church
Christian and Missionary Alliance
United Church of Christ
Humanist Emblem of Spirit
Presbyterian Church (USA)
Izumo Taishakyo Mission of Hawaii
Soka Gakkai International (USA)
Sikh (Khanda)
Christian Science (Cross and Crown)
Muslim (Islamic Five-Pointed Star)
Raise your hand if you know about all of those groups. Anyone? As hard as this might be to believe, there is actually a religion practiced by people in the American military that does not appear on that list: Wicca.

That's right, Sgt. Stewart was a Wiccan, his wife and daughter are Wiccans, and they would like the government to treat his faith with the same respect that they offer the members of Izumo Taishakyo Mission of Hawaii. Approving a religious emblem for the Wiccans should be a no-brainer for the VA. The Army, after all, has recognized Wicca as a faith since the late 1990s. In fact, my wife tells me that Wiccan services were held by one of the units when she was at the National Training Center at Ft. Irwin. So far, however, the VA has not seen fit to act - despite requests for approval of a Wiccan emblem dating back to 1997, and despite their approval of several other emblems since then. In fairness, I should note that the VA has said that a decision would be coming "soon." Two months ago.

I would call this an outrage, but that would be a gross understatemnt. I would say that I am surprised, but given that Bush spoke out against Wiccans in the military while mismanaging Texas, and given his propensity for pandering to Christian extremists at every opportunity, I am not.

I do think, however, that something should be done.

The VA Undersecretary for Memorial Affairs is William F. Tuerk.
The snail-mail address is:
U.S. Department of Veterans Affairs
National Cemetery Administration
810 Vermont Avenue, N.W.
Washington, D.C. 20420

I was only able to locate general hotline phone and email information:

Go ahead and contact those numbers anyway - I used to work on a constituent hotline, and I can tell you that if nothing else, there will be a report generated on the number of calls an issue is getting.

You should also contact your Congresscritters. Let them know that you vote, and (if appropriate), remind them that this is an election year.

(via Dispatches from the Culture Wars)