09 June 2006

Moving day

Well, it's moving day here at The Questionable Authority. I've been picked up as part of the newest group of bloggers to move over to scienceblogs.com. I've been working on the new site for a few days now, and I've actually got several posts up over there.

You can find the new blog at: http://scienceblogs.com/authority/

The posts that are already here will stay here, but I probably won't be updating much anymore. Hope to see you all at the new place!

07 June 2006

The hydra

It's just been reported that the leader of al-Qaeda in Iraq has been killed by an American air strike. I hope it's true, but even if it is I don't know how much good it will do. We've lopped another head off the beast, but there are plenty more where that one came from.

05 June 2006

Elections, RFK, Rolling Stone, and Salon.com

A couple of days ago, I posted a link to a Rolling Stone article written by Robert F. Kennedy, Jr. In that article, RFK Jr presented what he considered to be evidence that the Ohio presidential vote suffered from widespread fraud, and that Kerry was robbed of the presidency as a direct result. In the comments for that thread, Jason presented a link to an article at salon.com that rebutted the RFK piece. I had some time this weekend to read the salon article and to go back and re-read the Kennedy piece. Some thoughts:

There seems to be little doubt that RFK Jr. at best misinterpreted and at worst played fast and loose with his statistics. Many, if not most, of his most sweeping allegations seem to be much, much less well supported than he made them appear. Kennedy's conclusions - particularly the conclusion that the election was stolen - should be taken with a grain of salt.

At the same time, there also does seem to be more to some of the allegations than Manjoo's Salon article indicates. One example of this can be found in the county-by-county vote totals. Manjoo rightly points out that Kennedy's focus on how Kerry did compared to "down-ticket" candidates is not supported by past history. At the same time, there do seem to be some slightly strange numbers out there. In Agulaize County, for example, 3,142 more votes were cast in 2004 than in 2000. Bush received 3,246 more votes in 2004 than in 2000. Kerry received more votes than Gore did, but fewer than the total received by Gore and Nader in 2000 (Nader was not on the ballot in 2004 in Ohio. There were more registered voters in 2004, so the percentage turnout between the elections wasn't huge - it was 69.3% in 2000, and 70.4 in 2004. For the vote count in that county to be legitimate, the Democrats would have had to have had an enormous drop in turnout while the Republicans received a massive gain, or every single new voter would have had to vote for Bush, and 104 votes would have had to flip to Bush from the 3rd party candidates in 2000. Neither scenario is impossible, and the numbers are not a smoking gun. But they strike me as highly improbable.

Do I think that Bush stole the election in Ohio? I don't think that there's enough evidence to say that for certain. I do think that there is more than enough evidence of misconduct there to make watching them closely this year a very, very good idea.

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)

26 May 2006

How many species?

I've got a little question to keep people busy over the long weekend.

There are three populations of an organism. The populations are physically separated from each other as a result of geographical factors. Geographically, they are arranged in a more or less linear fashion. The geographic details are as follows:

Population A is the northwestern population. Population B lies to the southeast, and is eparated from population A by a minimum of ~14km. Population C is southeast of population B, and separated by about 50km.

Populations A & B are identical to each other in appearance and in a key reproductive characteristic. Population C differs very slightly in appearance, but is substantially different in the reproductive characteristic.

The organisms (flying insects) were captured and bred in the laboratory. Experimental crosses were made for the different combinations of these three populations, with the following results:

Male from A x Female from A:
91% of male progeny fertile

Male from B x Female from B:
99% of male progeny fertile

Male from C x Female from C:
92% of male progeny fertile

Male from A x Female from B:
98% of male progeny fertile

Male from B x Female from A:
93% of male progeny fertile

Male from B x Female from C:
0% of male progeny fertile

Male from C x Female from B:
0% of male progeny fertile

Male from A x Female from C:
0% of male progeny fertile

Male from C x Female from A:
69% of male progeny fertile

Female offspring had somewhat better fertility than the males, which is not unexpected in this group, for reasons I'll discuss in another post. Female offspring were fertile in the cases where the males were sterile, but the number of offspring surviving to maturity was greatly reduced in those crosses overall (around 10% of what was seen in the control crosses) and the fertility of the female hybrids was reduced compared to the control crosses.

My question for you is this: How many different species should these three populations be grouped in? Provide an explanation for your answer. Oh, and if you hadn't guessed, this isn't a hypothetical case. I've removed the names so that you can't see what the "right" answer is.

I'll talk about the currently accepted scientific grouping sometime on Tuesday.

25 May 2006

Uncommon Dissonance

Over at Uncommon Descent, DaveScot seems to have forgotten that the theme of the blog is Intelligent Design, and gone off on an anti-ACLU rampage. So far today, he's managed to post three items assaulting ACLU positions.

One isn't really worth mentioning - it's just a link to "stoptheaclu.com." That site is mostly focused, at least right now, on promoting efforts that are currently underway in the House of Representatives to prohibit courts from awarding legal fees in Establishment Clause cases. This is intended, apparently, to make it possible for local communities to violate the first ammendment without running the risk of having to pay as much if they are sued and lose.

The second is a copy of a First Ammendment Center press release about the ACLU recently forcing some high schools to exclude prayers from their graduation proceedings. (Appearently, the students at one of the schools decided that their classmates' rights weren't worth respecting no matter what the courts said.) For an interesting perspecive on the problems with prayer at major public events, I'd encourage people to take a look at this article at WorldNetDaily - a site that I usually don't endorse.

The third is an article about a lawsuit that the ACLU just filed in Kentucky on behalf of a supporter of Westboro Baptist Church. For those of you not familiar with that wonderful religious institution, those are the "God Hates Fags" folks. Recently, they've taken to protesting at the funerals of troops killed in Iraq, carying signs that say things like, "Thank God for IEDs," to promote their claims that the deaths of the troops are god's punishment because the US tolerates homosexuality. Kentucky recently passed a law intended to stop the Westboro assholes from protesting at the funerals. The law bans any protest activity of any kind, whether disruptive or not, whether spoken or written, that takes place within eye or earshot of the funeral, or within 100 yards of the funeral, unless they have the family's consent. (See here for the ACLU's complaint.) The ACLU's argument in this case, and as much as I despise Westboro and everything they stand for I think the ACLU is right, is that the law is extrordinarily overbroad and an unconstitutional restriction on free speech and expression. As an aside, I have to wonder if DaveScot and the rest of the wingnut community would have been so pissed at the ACLU if this had happened as the result of the protests Westboro Baptist used to run at funerals for AIDS victims.

What I really love about DaveScot's complaints, though, is this: when he was running around trying to defend his idiocy in falling for a well-known anti-ACLU scam, he said:
The ACLU has certainly stood against prayer in public school even if led by students in extra-curricular settings like graduation ceremonies and football games. There is not one iota of doubt in my mind that the ACLU would love to do the same thing to prayer in the military. Prayers led by commissioned and non-commissioned officers in the Corps are common. The military builds and maintains chapels on military bases. They employ religious clerics whose job is spiritual counseling and leading worship services. Anyone that thinks the ACLU wouldn’t stand against that if they could get away with it needs their head examined. They simply know the American public wouldn’t tolerate it and the ACLU would be so harmed they might never recover as an organization. So they bite their anti-religious tongues in the interest of self-preservation.
Gotta love it.
The ACLU is defending Westboro Baptist, which DaveScot refers to as "vile" (proving, I suppose, that the old adage about a stopped clock might just be right). The ACLU has defended in the past the free expression rights of Nazis and the KKK. But they won't take on military chaplains, he says, becuase it would be too unpopular.

Somebody needs to buy DaveScot a clue, because he's in desparate need of one and obviously can't afford it himself. If there is one thing that the ACLU has proven, time and time again, it is that they do not care how unpopular the cause. If they think that someone's rights are being violated, they'll take on the cause no matter how scummy, sleazy, dishonest, repulsive, or reviled the plaintiff might be. Hell, they've even come to the aid of Rush Limbaugh. If that doesn't prove it, I don't know what will.

23 May 2006

Isn't that like...

Over at Uncommon Descent, Bill Dembski says that he has purchased the domain name "pro-science.com"

Is it just me, or is that just a little bit like Henry VIII buying pro-marriage.com? OJ Simpson buying WhoKilledNicole.com? King Herod buying BethlehemDayCare.com...

22 May 2006

DaveScott and new depths of slime

Over at Uncommon Descent, Dembski lackey DaveScot is plumbing new depths of dishonest, slimy behavior. The attempt is nothing new for him, of course, but this time he may actually have managed to tap previously unreachable depths.

Here's what happened:
A friend of DaveScot's sent him an email claiming that the ACLU is about to go after the government because they don't like to see soldiers or marines praying while in uniform. DaveScot posted this email on Uncommon Descent, along with a request to pass it along to everyone you know. A number of people who read Uncommon Descent immediately informed him in the comments that the letter is, in fact, a several-year-old scam that has been thoroughly discredited by pretty much everyone who has bothered to check the facts. DaveScot responded to this by slightly altering the message, deleting the comments that pointed out the scam, and posting a brief comment responding.

The original message read:
If you look closely at the picture above, you will note that all the Marines pictured are bowing their heads. That's because they're praying.

This incident took place at a recent ceremony honoring the birthday of the corps, and it has the ACLU up in arms. "These are federal employees," says Lucius Traveler, a spokesman for the ACLU, "on federal property and on federal time. For them to pray is clearly an establishment of religion, and we must nip this in the bud immediately."

When asked about the ACLU's charges, Colonel Jack Fessender, speaking for the Commandant of the Corps said (cleaned up a bit), "Screw the ACLU. GOD Bless Our Warriors, Send the ACLU to France."

Please send this to people you know so everyone will know how stupid the ACLU is Getting in trying ! to remove GOD from everything and every place in America. May God Bless America, One Nation Under GOD!
Here's how it appears after DaveScot's editing. The changes are so minor that I'll highlight them in bold to make them easier to spot:
If you look closely at the picture above, you will note that all the Marines pictured are bowing their heads. That’s because they’re praying.

This incident took place at a recent ceremony honoring the Birthday of the Corps, and it has the ACLU up in arms. “These are federal employees,” says a rumored spokesman for the ACLU, “on federal property and on federal time. For them to pray is clearly an establishment of religion, and we must nip this in the bud immediately.”

When asked about the ACLU’s charges, former Marine Sergeant David Springer, speaking for all his brothers in uniform said (cleaned up a bit), “Screw the ACLU. GOD Bless Our Warriors, Send the ACLU to France.”

Please send this to people you know so everyone will know how stupid the ACLU is Getting in trying to remove GOD from everything and every place in America. May God Bless America, One Nation Under GOD!

What’s wrong with the picture? ABSOLUTELY NOTHING
Let's look at those changes. We'll set aside, for the moment, idiot boy's amazing arrogance in claiming to speak for everyone in uniform. (I know for a fact that he does not.) That aside, he removed the name of the ACLU spokesman, instead calling him "rumored," and substituted his own name for the name of the Marine spokesman. That's it. The attack against the ACLU is left fully intact.

DaveScot made those changes after being told that the letter is a hoax, and that THE ACLU HAS DENIED THE ALLEGATIONS. DaveScot provides his justification for this in the comments to the post:
To everyone who’s pointed out that the ACLU story is a fabrication according to snopes.com - that’s hardly the point. The pictures of Marines praying are real. The fighting and dying to protect the interests of the United States is real. The request to pray for them is real. So I removed the fake names, noted the ACLU statement is rumor, and quoted a very real former Marine Sergeant’s sentiments instead. If anyone has a problem with that they can KMA. Google that.

HOO RAH! Semper Fi!
You gotta love it.

Never mind that there's a difference betweeen the ACLU's statement being "a rumor" and being a well-documented fabrication. Never mind that he doesn't just quote his own sentiments, but also claims that his sentiments are those of everyone in uniform. Never mind that he actually labeled the ACLU spokesman and not the entire incident as a "rumor." Just look at the logic. It's a real picture of marines praying, so that means that it's OK to bash the ACLU. What a scumbag.

Still, the incident is worth noting for reasons beyond just the personal failings of DaveScot. It illustrates those quite well, while simultaneously illustrating a common creationist trait - being too much of a skeptic to accept any evidence for evolution, while simultaneously being credulous enough to accept anything, no matter how clearly false, that supports your own preconceptions.

15 May 2006

Tonight's Presidential Address

In a little less than four hours, the president is scheduled to address the nation. The subject of the address is immigration, and it has been widely reported that Mr. Bush will announce that he is sending the National Guard to help secure the border with Mexico. The president will undoubtedly give a number of reasons for this in the address (I predict that we will hear about 9-11 once or twice tonight) but the real reasons are purely political.

Bush is in desparate need of some sort of "win" right now. His poll numbers are heading toward Nixon-land. He's under 70% support from Republicans, and under 60 with Conservatives right now. His popularity with Democrats, Liberals, and Independents is getting so low that it risks becoming statistically indistinguishable from zero. He really doesn't care too much about the people who are against him, but the drop with the base is starting to really concern the administration.

They need a win. They need to show that they can get together with congress and solve a problem, and the solution needs to be bipartisan - involving both moderate and conservative Republicans. Right now, immigration is probably their only hope - social security, taxes, and health care definitely won't work anymore, and the war is off limits.

Unfortunately, immigration isn't working out too well. The House of Representatives wants to round up and bring to justice all of the illegals, and ship home all 12 million of them. The president and the senate want an immigration bill that is at least slightly responsive to reality, and recognizes that we might not actually be able to afford 12 million one-way airfares just now. Instead, they want to allow illegal aliens who have been here for long periods of time without getting into trouble to move into a legal status.

Right now, neither group is willing to budge, so the president is stepping up. In a bold move, he's sending thousands of National Guard troops (who, we all know, have nothing better to do with their time) down to the border. He's hoping that this will show the House Republicans that he's serious about enforcement, so that they'll back down enough to let some sort of guest worker program pass.

To put it another way, our troops are being entrusted with a mission of critical importance. They are being sent to guard our border from the tired, the poor, the huddled masses yearning to breathe free. Their mission there is to allow the Republicans to make a deal with the Republicans, saving the President from political disaster.

13 May 2006

A killer is a killer is a killer

Over at Uncommon Descent, DaveScot is once again angry with Kevin Padian. This time, it is because Padian dared to suggest that the only thing separating suicide bombers from the murders of abortion doctors is that one commits suicide and the other doesn't. DaveScot apparently thinks that murdering someone because of your religious views is somehow more acceptable, or at least less heinous, if you have a specific target in mind than it is if you are indiscriminate in your attack:
Suicide bombers kill/wound as many as possible, they don’t know who the victims are, they don’t care whether the victims have done anything wrong (perceived or real), and in their indiscrete targeting even kill people of their own creed.

Conversely, in the United States there have been only two abortion doctors murdered (AFAIK) and in both cases the murderer knew exactly who he was killing, perceived the target as a serial murderer of innocent children, and didn’t kill anyone else.
I could point out that DaveScot neglects some facts while attempting to excuse homicidal lunatics. He fails to mention that several other doctors were saved only by poor aim. He also conveniently forgets the whole Eric Rudolph episode - Rudolph, you will recall, killed an off-duty cop and severely wounded a nurse in a clinic bombing in Alabama. DaveScot is so eager to distinguish between the homicidal fanatics who share his faith and those that do not that he failed to mention any of that.

Ultimately, though, those points are really not all that relevant to the basic point that Padian was making (and that DaveScot was objecting to. His point was simply that suicide bombers are motivated by something different than the depression that is more typically implicated in suicide. Rather than being victims of an illness, the bombers are motivated, as are the murders of abortion providers by a belief that their action is righteous, and will be seen by God as such. In that, the suicide bombers are equivalent to homicidal anti-abortionists. (Please note that I am not describing all opponents of abortion as homicidal. Most are not.)

If DaveScot wishes to draw some type of distinction between homicidal Christian abortion opponents and homicidal Islamic suicide bombers, I suppose that he can. It is certainly true that there have been fewer killers of abortion providers than there are suicide bombers, and that the suicide bombers kill more people per incident. In my mind, though, those are distinctions that lack any substantive difference - Dante's Hell might have had many levels, but nobody consigned to hell was suffering anything less than eternal torment. Similarly, it might be possible to fit the different killers with different descriptions, but ultimately a killer is a killer.

12 May 2006

Googling terms.

Via Stochastic (Seed Magazine's in-house blog), we find that those dedicated purveyors of all things Intelligent Design over at Telic Thoughts have decided to compare the volume for the Google searches of "Intelligent Design" and "Darwinism". They're all happy about the results and the trend, but they forgot one thing: most (sane) people don't usually refer to evolution as "Darwinism." For a more reality-based view of the trends, take a look at this one. And by all means, look at the regional popularity of the terms.

11 May 2006

Wiretaps, investigations, and Yiddish

Back when I was in high school, I was an intern in the branch of the New York City Mayor's Office that handles telephone complaints. It was an interesting job, and I learned a lot. A great deal of this education was provided by a Hasidic Jew named Isaac, who worked at the desk right in front of me. He was a master at the fine art of subtly penetrating the obtuse workings of the city bureaucracy. He didn't use those skills too much - he found the frontal assault to be much more fun - but he knew them and taught them well. Besides the practical politics, he also taught me a little Yiddish - just enough to let me swear proficiently.

One of the very first words that I picked up from him was 'chutzpah.' He used the word to describe the qualities that I would need to exhibit if I was to have any hope of accomplishing anything in New York City Government. When I asked him what the word meant, he had to stop and think for a minute or two. Chutzpah, he said, is a one-word description of a fairly complex personality trait, and that there was no word in English that adequately captured the concept. I asked him if he could describe the trait, and he paused again for a second or two of thought. "OK, I tell you what chutzpah is. Chutzpah... you take a dump on your neighbor's doorstep, then ask to borrow his toilet paper, you got chutzpah."

That was a while ago - back during the Dinkins administration. If I asked him the same question today, he'd have a much easier time describing the concept. All he'd have to do is show me this Washington Post Article.

It seems that, in what has to be the most absolutely amazing exhibition of pure brazenness ever demonstrated, the "Justice" Department has managed to shut down an internal investigation into whether or not some of their lawyers might have committed ethical violations while involved in the President's Warrentless Wiretapping program. The reason that the investigation ground to a halt? The investigators were refused the security clearances that they needed to look into the matter because the actual details of the program are extremely sensitive national security information, and restricted to the smallest possible group, so the investigators didn't have - wait for it - "need to know." Without the details of the program, they were unable to determine if their lawyers committed any ethics violations, and the investigation has now been closed.

Gotta love it.

If the Democrats were smart - meaning that the rest of this post is a wishful fantasy - they'd make oversight an issue in this year's elections. This congress has been completely derelict in their responsibility to watch the actions of the executive branch, so the president has been allowed to do pretty much whatever he damn well pleases. That should end. Congress doesn't just have the right to do oversight, they've got a responsibility to do it, and they've been absolutely remiss when it comes to meeting that responsibility. Democrats should be campaigning on that issue, and they should be doing it heavily. It might be a national issue, not a local one, but Congresscritters have obligations to more than just their district. They also have responsibilities to the nation. If they don't want to carry them out, they should be encouraged by their employers to find other work.

10 May 2006

The Land of the Endangered.

The State of Hawaii is one of the smaller states in the Union. According to Wikipedia, we're 43rd out of 50 in size, 42nd in population, and, at 3000km from the nearest continent, we're as isloated as you can get. We may be small and out of the way, but there's a lot that we have. We've got a great climate - we're the only state that's entirely in the tropics. Being in the middle of the ocean helps there, too, since all that water helps to moderate the climate even more. It also gives us some really great beaches, world-class surf spots, and truly excellent snorkling and diving.

There's something else that being isolated does for us. It's the reason that we're the endangered species capital of the United States. We're so far out in the middle of the ocean that it is very difficult for new species to get here. The few that have made it have become the founders for evolutionary radiations, resulting in the origin of thousands of species unique to Hawaii. These species have been hit hard as a result of human actions. One in four species (329/1312) on the United States endangered species list is endemic to the Hawaiian Islands.

Yesterday, the list of endangered species in Hawaii got longer. The United States Fish and Wildlife Service added eleven species of Drosphila to the endangered species list, with one more species being listed as threatened. Each of the twelve species is found on only on a single island.

For those of you not familiar with the Hawaiian Drosophila, let me provide a quick intro. The genus Drosophila is best known because of Drosophila melanogaster, the legendary "fruit fly" that geneticists and students of biology have worked with for decades. ("Fruit fly" is in quotes because Drosophila are not actually fruit flies, but I'll refrain [for now] from descending to the depths of dorkdom necessary to go into detail on the difference. For now, suffice it to say that the distinction is at least semi-important to people who work with the group in the field.)

As I was saying, D. melanogaster is the best known member of the group, but it is far from the only one. There are literally thousands of species in the genus. Almost a quarter of them are found only in the Hawaiian Islands. The twelve flies being listed are members of a group of the Hawaiian Drosophila known as the picture-wings. (Pictures of two picture wings, one of which [D. heteroneura] is one of the newly-listed species, can be found in an earlier post here.) Each of the listed species has a range restricted to a single island. Most of them will only breed on a small number of plant species (1-3). They are extremely rare - surveys in their habitat areas don't turn up more than a couple of flies. Listing these species as endangered, under the circumstances, is such a complete no brainer that it's a wonder that it only took five years of work and a lawsuit to get it done.

But here's the kicker - the only thing that really distinguishes these twelve picture wings from the other hundred or so in the group is that they are a bit more rare. The vast majority of the group are limited to one island, and the vast majority are limited to a small number of plants. It's possible to catch a few more during surveys, but the difference isn't really all that much - none of these insects are what anyone would consider to be common.

It gets even better. The picture wings, ironically enough, haven't been the focus of this attention because they are the rarest of the Hawaiian Drosophilids. They've gotten the attention because they're the best studied group. The truth is, we don't actually even know how many species there are for sure. Entirely new species have been described within the last few years, and it is quite probable that there are more to be found.

Described species or not, formally listed or not, there are a lot of species in Hawaii that are very rare and at risk of extinction. Listing these twelve species is good, especially since the lawsuit settlement also mandates that critical habitat be designated for these species. It's good, but it's hardly enough. Unless we want to lose biodiversity faster than we can discover and describe it, we need to do far more to protect the native Hawaiian species. And, of course, we need to put more time, effort, and money into studying our ecosystems while we still have them.

09 May 2006

Lack of updates apology

Sorry for the recent lack of updates here. I was sick as a dog for a good chunk of last week, and have family in town. It's also the end of the semester, so grades are coming due and I still have a load of grading to do. Updates will probably remain a bit sporadic for the next day or two, but should get back to normal after that.

Oh, and there may be some changes to the blog in the next week or two.

02 May 2006

Surprise, surprise, surprise.

There's an interesting letter in this week's Nature (subscription required). The author of the letter, Michal Jasienski, compared the frequency of use for the words "surprising" and "unexpected" in the scientific literature to their use in other academic literature and in standard English. He found that the two words both appear in scientific writing much, much more commonly than they do elsewhere:
The word 'surprising' appears 12 times more frequently in the natural sciences than in standard English and 1.3 times more frequently than in social sciences, arts and humanities. The word 'unexpected' appears 39 times and 2.2 times more frequently in the natural sciences than, respectively, in standard English and in non-science academic
He attributes this phenomenon to a desire for publicity:
Although natural phenomena can indeed sometimes be surprising if they are against our expectations, being 'surprising' is not an inherent quality of nature. Does scientists' use of this term in their publications truly represent genuine surprise at their results? One might think that academic machismo or realism would cause scientists to downplay their surprise, but, on the other hand, overstating the level of astonishment may occur when striving for media attention.
Ewan, over at Complex Medium, agrees that publicity is probably the reason for the frequent use of "surprising" and "unexpected." Tara, at Aetiology, does not - although she does wonder if the words in question might be overused.

Personally, I think that being surprising is pretty much an inevitable consequence of our current level of understanding of nature. We've learned enough to know that there is a hell of a lot that we don't know, and we're continuing to develop tools that let us poke a little farther into our ignorance. If we weren't being surprised on a regular basis, it would imply that we actually have a pretty good handle on the nature of nature - and that really would surprise me. That's one of the reasons for the frequent use of the term.

Another reason that we scientists use those words so often is that "surprising" and "unexpected" is where we live. It's where we do business. It's what we are looking for. We are trying to answer questions that we don't already know the answers to. If you're not being surprised on a regular basis, you're probably not doing real science.

28 April 2006

Friday Random Ten: The "Who the Hell am I" version

I was seriously considering writing a serious post today. Howard Kurtz has an interesting post about blogs over at the WaPo site, which fed into some thinking I've been doing about the subject. That's going to have to wait a day or two, though.

My fellow graduate students have honored me by making me one of the four department grad representatives for the next year (put another way, there was a popularity contest and I lost), so I now have to suffer through the same meetings that the faculty go to. After 2 hours working on the question sets for the diagnostic exams that are given to entering graduate students, I am totally unable to put together much in the way of coherent thought.

So, instead of an incisive and insightful post on the broader implications of blogging, here's a Friday Random Ten. (Which you'll probably enjoy more anyway, so this is kind of a win-win thing.)

1: Silver Spring
Fleetwood Mac

2: Me and Bobby McGee
Arlo Guthrie (Live in Sydney)

3: Livin' in America
Black 47

4: Turn the World Around
Harry Belafonte

5: Appalachian Spring - "The gift to be simple"
Leonard Bernstein/New York Philharmonic

6: Snoopy and the Red Baron
The Royal Guardsmen

7: A Little Respect

8: Hawaii 78
Israel Kamakawiwo'ole

9: Downtown Baghdad Blues
Black 47

10: Jack and Diane
John Mellencamp

Yesterday's song lyrics, and today's problems

Waist Deep in The Big Muddy
Pete Seeger, 1967

It was back in nineteen forty-two,
I was a member of a good platoon.
We were on maneuvers in-a Loozianna,
One night by the light of the moon.
The captain told us to ford a river,
That's how it all begun.
We were -- knee deep in the Big Muddy,
But the big fool said to push on.

The Sergeant said, "Sir, are you sure,
This is the best way back to the base?"
"Sergeant, go on! I forded this river
'Bout a mile above this place.
It'll be a little soggy but just keep slogging.
We'll soon be on dry ground."
We were -- waist deep in the Big Muddy
And the big fool said to push on.

The Sergeant said, "Sir, with all this equipment
No man will be able to swim."
"Sergeant, don't be a Nervous Nellie,"
The Captain said to him.
"All we need is a little determination;
Men, follow me, I'll lead on."
We were -- neck deep in the Big Muddy
And the big fool said to push on.

All at once, the moon clouded over,
We heard a gurgling cry.
A few seconds later, the captain's helmet
Was all that floated by.
The Sergeant said, "Turn around men!
I'm in charge from now on."
And we just made it out of the Big Muddy
With the captain dead and gone.

We stripped and dived and found his body
Stuck in the old quicksand.
I guess he didn't know that the water was deeper
Than the place he'd once before been.
Another stream had joined the Big Muddy
'Bout a half mile from where we'd gone.
We were lucky to escape from the Big Muddy
When the big fool said to push on.

Well, I'm not going to point any moral;
I'll leave that for yourself
Maybe you're still walking, you're still talking
You'd like to keep your health.
But every time I read the papers
That old feeling comes on;
We're -- waist deep in the Big Muddy
And the big fool says to push on.

Waist deep in the Big Muddy
And the big fool says to push on.
Waist deep in the Big Muddy
And the big fool says to push on.
Waist deep! Neck deep! Soon even a
Tall man'll be over his head, we're
Waist deep in the Big Muddy!
And the big fool says to push on!

27 April 2006

Some slightly belated carnie barking

The latest editions of my three favorite blog carnivals are now available. If you've got the time, take a look at them (and if you don't, what are you doing reading this, anyway).

The 11th Edition of the Carnival of the Liberals is now available at And Doctor Biobrain's Response Is... While you're there, be sure to take a look at today's post.

The 64th Carnival of Education is available over at The Education Works. If you're interested in learning more about education, that's the place to go.

Finally, the 52nd issue of Tangled Bank is now available over at The Inoculated Mind. Give that a look if you want to see some of the best science posts from the last couple of weeks.

My daughter's revenge

My daughter has been having some homework and study habit issues lately that have lead to some stress for her. She hasn't been doing her spelling homework, and she has been doing poorly on spelling tests. This issue came to a head a couple of days ago, when I received a note from her teacher alerting me to the problem.

The daughter and I had a bit of a long talk about this yesterday (punishment in and of itself), and she's been handed a substantial "no computer, no TV, no nothing" sentence as a result. She thinks that this is massively unfair, because it's not like spelling is really important, and said so. I told her she was wrong, and the conversation ended there.

Today, I did a talk to her class for career week. Instead of just doing a talk, I decided it would be fun to spend most of the time answering questions. In retrospect, that might have been a bit of a mistake.

The Daughter (hand in the air): "What does DNA stand for?"

Me: "Deoxyribonucleic acid."

The Daughter (attempting to radiate wide-eyed innocence): "How do you spell that?"

26 April 2006

Somewhere, John Henry is smiling.

I've got to admit it - when someone told me that Bruce Springsteen was going to be releasing a whole album of Pete Seeger covers, my first response was to yawn. I like the stuff he's done with the East Street Band, but I've never been much of a fan of his solo efforts. I really didn't know what to expect from this one, but it definitely wasn't much. I suppose I figured it would probably be another Bruce + guitar album - probably quiet, almost certainly acoustic.

When the album popped up in my Tuesday morning email from iTunes, I decided to take a couple of minutes to sample a track or two. I did that. Then I sampled a couple of more. Then one or two more. Then I bought the album.

I don't exactly know how to describe it, except to say that it's good. It's Shakespeare, the way it's meant to be done. Springsteen got together with a large group of musicians - fiddles, horns, drums, banjo, washboard, jug (I think), and recorded something that sounds like a really good jam session. It's not a choreographed studio album. It's a bunch of people making music and enjoying themselves along the way.

The song choices are pretty damn good, too. The title track (We Shall Overcome) was a little weak (it sounds like Bruce is trying to channel early Dylan), the rest of the tracks are a well-chosen mixture of civil rights related pieces (Jacob's Ladder, Eyes on the Prize), working man's songs (John Henry), and just plain fun music (Ol' Dan Tucker, Froggie Went A Courtin'). I really can't remember the last time I've found an album that I've enjoyed so much.

25 April 2006

But does Barbara still like him?

President Bush's has been having problems in the polls for a while now, and his numbers just keep dropping. A CNN/USA Today/Gallup poll just released puts his approval numbers at under a third (32% +/-3). That's probably not the number that has him feeling the most pain right now, though. That honor most likely goes to the pitiful 33% approval number from last week's FOX News poll. If things get much worse, he's only going to have his immediate family left on the plus side of the equation.

21 April 2006

Earth Day Concerns

Today, there was an Earth Day fair on campus. I had a little time during lunch, and wandered on through. Strangely, I found myself becoming more and more annoyed as I moved through the displays. It took me a while to figure out exactly why. It was the lack of topicality of some of the displays.

Before I go on, I want to make it clear that most of the displays were both relevant and interesting. A couple looked at things like sustainable agriculture and aquaculture. There was a display, including a portable processing unit, from the local biodiesel group. Another highlighted low cost and relatively high efficiency solar cells, suitable and affordable for home use. For me, those are exactly the kinds of display that are exactly what Earth Day should be used to highlight.

But then there were the other displays. There were a couple wandering around in what I thought was a display of a sadomasochistic relationship, before I figured out that it was just a recreation of Abu Ghraib. He was wearing the black suit and hood, and she was passing out fliers demanding the trial of Bush et al for crimes against humanity. Our local communist was there, with lots of copies of Revolutionary Worker. Another few people, somewhat more moderate than the first pair, were circulating with a petition demanding Rumsfeld's resignation. Another group was working the immigration issue. Those were the types of display that annoyed me.

It's not that I don't think that those are views that are entitled to be displayed. Hell, I agree with some of them. It's just that they aren't Earth Day issues.

The planet is too important to politicize in any way, and it is certainly too important to make it a partisan issue. Addressing the problems that are facing the planet is going to need to involve everyone. We need to involve more people, with a wider range of views, in the solution to the problem. Linking Earth Day, the environment, and environmental issues to a wide array of unrelated (not to mention controversial) positions is not going to accomplish it. Instead, it risks painting the environment as another purely liberal issue, alienating those we most desperately need to convince.

Friday Random Ten, the Pau Hana edition

My own department here at the University of Hawaii might not make the top ten graduate school lists, but there are still plenty of good reasons to go here. One of them is our Friday afternoon Pau Hana. Getting together out on our building's lanai for beers, pupus, and conversation gives us something to look forward to at the end of the week.

This week, my iPod seems to be looking forward to Beers as much as I am.

1: On A White Sandy Beach Of Hawai'i
Israel Kamakawiwo'ole

2: Sitting On the Dock of the Bay
Otis Reading

3: Real Good Looking Boy
The Who

4: Can You Picture That?
Dr. Teeth And The Electric Mayhem Band

5: Bubble Toes
Jack Johnson

6: Blues Traveler
The Hook

7: Man On The Moon

8: It's 5 O'Clock Somewhere
Jimmy Buffett

9: I Can See Clearly Now
Jimmy Cliff

10: Ob-La-Di, Ob-La-Da

20 April 2006

National Priorities

It's that time of the year again - the military needs more money if they are going to keep fighting in Iraq and Afghanistan. This time, the pricetag is in the vicinity of 100 billion dollars.

$100,000,000,000 is a lot higher than any of the previous emergency bills, in large part because the administration had been doing its best to hide the true costs of the war by putting off equipment repairs. The war has gone on for long enough now that further delay has become impossible, according to the Washington Post article linked above:
[Army Chief of Staff GEN] Schoomaker said as much at a Senate Armed Services Committee hearing in February, when he remarked that a "bow wave" of costs "pushed forward from previous years" is now cresting.

Pushing back the costs was dishonest, but that's nothing we haven't come to expect from this administration, and that's not actually my biggest complaint about the size of my bill. What pisses me off is the pork.

That's right, the congress has decided to use the military emergency spending bill to fund projects in their district that are completely unrelated to the war. In what is probably the most glaring example, Mississippi's two Republican senators added a $700 million earmark to the bill. The earmark will fund relocating a rail line that was just rebuilt after Katrina (for $250 million) away from the coast, making the casino developers happy:
The real impetus appears to be economic. For more than half a dozen years, Mississippi officials, development planners and tourism authorities have dreamed of the complex restructuring of Mississippi's coastal transportation system that Lott and Cochran now want to set in motion. Under the plan, the CSX line -- which runs a few blocks off the coast line -- would be scrapped. CSX would move its freight traffic to existing tracks to the north owned by rival Norfolk Southern.

Then U.S. 90, a wide federal highway that hugs Mississippi's beaches, would be rebuilt along the CSX rail bed. The route of the federal thoroughfare would be turned into a smaller, manicured "beach boulevard" through cities such as Biloxi, where visitors could "spend more time strolling among the casinos and taking in the views," as the Governor's Commission on Recovery, Rebuilding and Renewal put it.
What a sense of priority. Getting an unsightly rail line away from the tourists is very important. Actually giving the people in the military enough of a pay raise to match the inflation rate this year: not so important.

19 April 2006

Full Sleeze Ahead!

According to the Washington Post, a very interesting television add is being run in the Ohio 6th. The commercial is an attack add, calling candidate Bob Carr, "too far left to work with Republicans in Washington," and characterizing him as a, "liberal Democrat." The add is paid for by the National Republican Congressional Committee.

OK, so far there's nothing surprising about this, right? After all, you'd hardly expect the Republicans to run an add supporting a Democrat in a congressional election. That's true enough, but here's the kicker: Carr isn't the Democratic candidate for the district. At least not yet. He has to win the primary first.

A Republican attack add against the Democratic candidate in the general election is an attempt to hurt that candidate. A Republican attack add against a Democrat running in a primary is an endorsement. (Unless, of course, you think that Democratic voters are looking for a candidate who isn't a liberal, and who wants to work with Republicans.)

The NRCC is running the attack adds in an attempt to get themselves a nice, weak candidate to run against in the fall:
If Carr wins, there is no reason to suppose that he will be a formidable candidate in this open district, being vacated as incumbent Democrat Ted Strickland runs for governor. Carr once ran a hapless campaign, as a Republican, in Michigan. He lost that race in 1996 to Rep. Bart Stupak (D) by 71 percent to 27 percent.
Gotta love it. It's not even may yet, and the Republicans are already doing their best to run a nice, dirty, dishonest campaign.

18 April 2006

Show Up.

How involved in politics should scientists be? What factors are important when it comes to making that decision?

For some of us, the answer to that comes fairly easily. One or two of us managed to evade the stereotype of the scientist-of-the-future, and caught the involvement bug because we were popular enough to win a role in student government early in our lives. A few of us were caught in a different stereotype - the children of the flower children - and have never known what it is like to not be involved in political causes. A bunch of scientists are just plain incapable of keeping their noses out of anything they bump into, whether it directly involves science or not.

The decision is harder for others. There are a few scientists who really do have an ivory tower mindset, and actively try to avoid anything that smacks of politics. Many put so many hours into their science that they don't have any to spare for politics. More are apathetic to politics, or disillusioned, or simply unaware of the issues.

Both the involved and uninvolved should read a new article in PLoS Biology. The article, "Scientific Illiteracy and the Partisan Takeover of Biology," provides both reasons to get more involved in the political process and some hints as to where the efforts of scientists might most effectively be focused.

The article, written by Liza Gross, focuses on the work of Dr. Jon Miller, who has spent decades studying the public perception of science. Some of what he has to say is depressing (if not terrifying). Some of his message raises the possibility that there is still hope. All of it is worth reading.

The key point made in the article is this:
"The era of nonpartisan science is gone."

That's a fairly bold statement, but it is true.

As the article points out:
It's not that Americans are rejecting science per se, Miller maintains, but longstanding conflicts between personal religious beliefs and selected life-science issues has been exploited to an unprecedented degree by the right-wing fundamentalist faction of the Republican Party. In the 1990s, the state Republican platforms in Alaska, Iowa, Kansas, Oklahoma, Oregon, Missouri, and Texas all included demands for teaching creation science. Such platforms wouldn't pass muster in the election, Miller says, but in the activist-dominated primaries, they drive out moderate Republicans, making evolution a political litmus test. Come November, the Republican candidate represents a fundamentalist agenda without making it an explicit part of the campaign. Last year, Miller points out, former Senator John Danforth, a moderate Missouri Republican, wrote in a New York Times opinion piece that for the first time in American history a political party has become an arm of a religious organization. The United States is the only country in the world where a political party has taken a position on evolution.
So what is a scientist do do? Miller has a suggestion that might come as a shock to some. If you don't like the way that the fundamentalists treat science, then get involved:
The era of nonpartisan science is gone, says Miller, who urges scientists and science educators to learn the rules of this new game and get behind moderate Republicans as well as Democrats to protect the practice and teaching of sound science. Given the partisan attack on evolution and stem-cell research, he thinks scientists need to learn more about how the political process works. They need to be willing to run for the school board, write $500 or even $5,000 checks to support moderate candidates, and defeat Christian right-wing candidates. “Scientists need to become involved in partisan politics and to oppose candidates who reject evolution or attack scientific research,” he says. “It takes time, money, and paying attention to the issues.”
For most scientists, both time and money are limiting resources, but that is a hurdle that must be overcome. In politics, the decisions are made by those who show up. If we want things to change, we need to get involved.

Not everyone has money to donate to a political campaign. Time, on the other hand, is something else. We might not have as much of it as we want (or need), but we always have some. Running for the school board takes a lot of time. Speaking during the public comment period of a school board meeting takes a lot less. Writing your congresscritter takes even less - in fact, you could have written one in less than the time it's taken you to read this. You might not be able to do much, but there's no excuse for doing nothing. It's time to show up.

A Brief Pop Gen Primal Scream

Right about now, at the tail end of a long and painful homework assignment, I have a strong urge to take my population genetics textbook and give the next person who tries to tell me that there's no math in evolution a good whack upside the head.

And any time that a single individual represents more than half of an organism's great-great-grandmothers, you should be allowed to just list "too high" as the inbreeding coefficient, and to hell with figuring all the possible routes through the pedigree.

17 April 2006

Sally Jacobsen, the Northern Kentucky University professor who decided that her emotions should dictate what speech is allowable on campus, has been removed from her teaching duties and will retire at the end of the semester.

Interestingly, however, she is apparently still refusing to confirm or deny whether or not she was personally involved in destroying the display. The entire incident was an absolute disgrace, but that's the part that pisses me off the most. This self-righteous fool has the strength of her convictions right up to the point when it looks like serious consequences are pending - and not an inch further.

16 April 2006

The Real Enemy in the War on Christian Holidays

It occurs to me that Bill O'Reilly and other members of the paranoid right have managed to totally miss the boat when it comes to figuring out who is responsible for the whole overblown "War on Christian Holidays" thing. They've focused their venom against the ACLU and anyone else who wants the religious message kept out of any governmental acknowledgment of the holiday. The people who just want to be able to celebrate Christmas and Easter as secular holidays aren't the ones that they should blame. They should, if they are going to be angry at anyone, focus their wrath against those who actually made it possible to celebrate Christmas and Easter as something other than a religious event.

Look, I've read the Bible, and there's nothing in there about a really, really fat guy trying to squeeze down a skinny little chimney with a massive sack of cheap, plastic toys. The only mention of rabbits that I can think of isn't in the New Testament - it's way back in the food laws section of Leviticus. In that passage, the rabbit is not identified as a distributor of painted eggs; it's misidentified as an animal that "chews the cud" (it's chewing something, folks, but it ain't cud).

If the Christian Right wants to get angry at anyone about the secularization of Christian holidays, it should be the people who secularized them in the first place. Those fine folks who make the cards at Hallmark come to mind. Mattel Toys probably bears some of the blame for the whole secular Christmas thing, along with Toys'R'Us. If you're looking for a specific target for Easter blame, maybe you should complain about the folks who make the Cadbury Cream Eggs, or those disgusting little Peeps.

15 April 2006


The current Chairman of the Joint Chiefs, Gen. Peter Pace, had some interesting things to say in defense of Rumsfeld recently:
"As far as Pete Pace is concerned, this country is exceptionally well-served by the man standing on my left," General Pace, chairman of the Joint Chiefs of Staff, told reporters at the Pentagon. "Nobody, nobody works harder than he does to take care of the P.F.C.'s and lance corporals and lieutenants and the captains. He does his homework. He works weekends, he works nights.

"People can question my judgment or his judgment," he continued, "but they should never question the dedication, the patriotism and the work ethic of Secretary Rumsfeld."
That's almost a non-denial denial. To the best of my knowledge, none of the recent criticisms of Rumsfeld have involved his dedication, patriotism, or work ethic. In fact, I have little doubt that he is dedicated to something, works very hard, and considers himself to be a patriot. I think he's unbelievably stubborn, irresponsibly unwilling to face the possibility that he might be wrong, and mindnumbingly incompetent. Oh, and I definitely question his judgment, too.

14 April 2006

Free Speech 101

Here's a quick lesson in how freedom of expression works:

Everyone get's to make their opinions known. That means everyone. Including people who have views that you don't like. Your right to freedom of speech does not include the right to keep other people from expressing their opinions.

A professor of Literature and Language has demonstrated a criminal lack of understanding in this regard - and I do mean criminal. According to several sources, including the Cincinnati Enquirer, Prof. Sally Jacobsen led a group of students from one of her graduate-level classes in destroying a display of 400 crosses that had been set up on the school grounds by an anti-abortion group:
"I did, outside of class during the break, invite students to express their freedom-of-speech rights to destroy the display if they wished to," Jacobsen said.

Asked whether she participated in pulling up the crosses, the professor said, "I have no comment."
The professor may not have wanted to comment on whether or not she participated, but there is a picture of her participating available on the campus paper's website. Apparently, she encouraged and participated in this act of censorship and vandalism because she didn't like the way the display made her feel:
She said she was infuriated by the display, which she saw as intimidating and a "slap in the face" to women who might be making "the agonizing and very private decision to have an abortion.

Jacobsen said it originally wasn't clear who had placed the crosses on campus.

She said that could make it appear that NKU endorsed the message.

Pulling up the crosses was similar to citizens taking down Nazi displays on Fountain Square, she said.

"Any violence perpetrated against that silly display was minor compared to how I felt when I saw it. Some of my students felt the same way, just outraged," Jacobsen said.
Wow. What an amazingly arrogant, obnoxious, and self-righteous piece of work she is.

For the record, the student group that erected the display had, as Jacobsen could easily have discovered had she bothered to ask, obtained the school's permission. And I strongly suspect that she's nowhere near as concerned about the appearance of NKU endorsing the message when it's one she approves of.

Personally, I think that the anti-abortion group's position on abortion is wrong. I've seen plenty of anti-abortion displays, including graveyard-type displays like the ones in question, and I really dislike them. If I had the power to pick and choose what opinions are allowed to be expressed, I definitely wouldn't allow those. And that's exactly why I shouldn't be given that power - and why nobody should have it.

Fortunately for Northern Kentucky University, their president has a much better grasp on what freedom of speech means than that idiot that they are, at least for the moment, employing:
"I am very disappointed that this happened," Votruba said. "At a university, the opposing views should be able to bump up against each other. Responding with pamphlets or speeches would have allowed the power of ideas to compete."
I'm an extrordinarily big fan of the tenure system, and a huge fan of academic freedom. In this case, however, neither should provide enough of a shield to protect that clueless idiot's job. Actually, neither should provide any shield at all. Like freedom of speech, academic freedom only works when it protects all parties. It certainly does not extend to including the right to suppress any offensive view anywhere on campus. Professor Jacobsen at the very least inspired, and almost certainly participated in, an action that violated the free speech rights of the anti-abortion group, was antithetical to the basic principles of academic freedom. Along the way, she appears to have committed at least criminal destruction of private property, and possibly theft.

The university has promised to take action against anyone involved in the incident, and I hope they stand by their word on that. In addition, the anti-abortion group has decided to press criminal charges against those involved. Good for them. This professor needs to learn that others have the right to their own opinions, even when they differ from her own. She also seems to need a refresher course in actions and their consequences.

(Via Dispatches from the Culture Wars)

Aplications of Evolution 4 - Migration and Sex

In recent years, the costs associated with genetic studies have dropped dramatically. That isn't much of a surprise. When the two main tools used in modern genetic studies, the polymerase chain reaction (PCR) and DNA sequencing, were first developed, they were extrordinarily labor intensive. Initially, PCR required the scientist to spend hours and hours moving the samples from one water bath to another. DNA sequencing required the researcher to determine the order of bands on a gel by eye - determining a single sequence could easily take a whole day. Later, methods were developed to automate these processes, and they became much less labor intensive. Instead, they were simply very, very expensive.

Fortunately, technology tends to become cheaper over time, and this has proven to be as true for molecular genetics as it was for CDs and DVDs. In recent years, the costs have dropped dramatically. This means that using genetic techniques has now become feasible for many more researchers, and that they are being used to address many more questions. In many cases, the addition of genetic tools to a study has led to some amazing and sometimes unexpected results.

One interesting example just appeared in the "online early" section of papers for Molecular Ecology. (This means that the paper has been reviewed and accepted by the journal, and will appear in print in a future issue.) In this paper, a group of wildlife biologists used both radio-tracking and genetic techniques to look the effect of the Ventura Freeway on the Los Angeles area populations of bobcats and coyotes. The authors examined two types of data: they looked at the movement of individual animals that had been captured and radio collared, and they looked at the genetic structure of the populations. What they found is that many animals migrate from one side of the freeway to the other, but that few of the migrants are reproductively successful.

The authors used three study locations. Two were on the north side of the freeway, but separated from each other by a major secondary road. The second was south of the freeway, across from the northeastern site. This experimental setup let the authors compare the effect of the freeway to the effect of the secondary road. Over the seven years of the study, they radio collared and tracked 110 coyotes and 87 bobcats. Genetic samples were collected from all of the animals they captured.

The radio collar data allowed the researchers to see where the animals were moving. This technique has been around for a while, and is still used today. They found that only a small percentage (4.5% of coyotes; 11.5% of bobcats) of the animals they studied were observed to cross the freeway. A much larger percentage (~50%) of the animals crossed major secondary roads.

OK, there's nothing surprising about that. Anyone whose ever watched Wile E Coyote and the Roadrunner square off can tell you that coyotes and highways aren't a real good mix. The bigger the road, the bigger the problem for the animal. That makes sense. However, the road is not an absolute barrier to the migration, and it only takes about one migrant per generation to keep populations from drifting apart, so it looks like the highway won't significantly fragment the bobcat and coyote populations. That's good news, because a fragmented population is usually at a greater risk of extinction than an intact one.

If the radio collar data does a good job at predicting the migration rate, the genetic data should show that there aren't big differences between the animals at the three study sites. To examine this, the authors used a series of statistical tests to determine whether the individuals sampled should best be considered to be a single population, or separate populations. They found that the coyotes grouped into two distinct subpopulations, and that the bobcats grouped into three. A second series of tests was used to determine how distinct the populations were from each other. This demonstrated that there were statistically significant differences between the populations. These results indicate that there is a very low level of migration between the populations.

So what's going on here? The radio collar data seems to point to a much higher migration rate than the genetic data demonstrates. What could cause such a difference?

It all comes down to that perennially popular topic - sex. It looks like physical migration across the freeway is relatively common. The genetic data actually supported this, too. Some individuals with the genetic signature of the south of the freeway populations were found north of the freeway, and vice versa, indicating that there are migrants. The reason that the populations show so much genetic divergence in the face of all that migration is simple: the migrants aren't reproductively successful. Their genes aren't winding up in the gene pool, and from a genetic perspective any migrant that doesn't reproduce doesn't count.

This is one of those experiments that screams to be repeated. If the pattern is real and holds true for a wide range of taxa, it implies that populations might be more easily separated than suspected, which might, in turn, imply that evolutionary divergence is also even easier than suspected. Even if the findings only apply for territorial animals such as bobcats and coyotes, they might require substantial changes in how those species are managed.