Science Blogging in London

Next week I’ll be in London for Nature Network’s Science Blogging Conference. It’s entirely possible that I’m looking forward to the trip as much as GrrlScientist is, and not just because I’ll be hanging out in the UK for a week afterward. Both ScienceBlogs and the Nature Network host groups of bloggers who are interested in and write about science, but there are also quite a few differences between the two groups. It’ll be interesting to sit down with folks there and look at our different perspectives. Hopefully, everyone will be able to take away something new from the discussions.

After the conference, I’m planning on doing some scientific sightseeing. I’ve been to London before, but that was a family trip, and there were some constraints on what I could do and where we could go. (To put it another way, I could only get away with boring everyone else so much without facing a revolt.) This time, I’m going to try and get to a few more places that have strong history of science ties. Down house is definitely on the agenda, as are trips to Oxford and Cambridge. Aside from that, I’m leaving things up in the air a bit. Suggestions are, of course, welcome.

For-Profit Scientific Publishers and the Culture of Entitlement

I used to have a hard time explaining the anger, resentment, and hostility that many scientists feel toward the big academic publishing houses. It’s been getting easier, though. Recent events have, unfortunately, provided people with an experience that makes it easier to relate to what the academic community has been going through.

Gas prices are going up. You’ve been combining trips, cutting your milage as much as you can, driving a more efficient vehicle, and your fuel costs are still going up. You drive home from work, stopping along the way to put $30+ dollars worth of gas into the 10 gallon tank in your Prius. You sit on the sofa, turn on the news, and hear that Exxon-Mobil just reported quarterly profits of about $1,500 per second. The price of something that you need to buy is going through the roof, it’s making things inconvenient for you, and the people who sell it are making money faster than the mint can print it. How happy are you?

If you want to understand the anger that the major publishing houses are generating, that’s a good place to start.

Publishers don’t make money at anything close to the clip that Big Oil does, but they’re not doing badly. Elsevier is probably the biggest fish, and they come in at a respectable $1,700 per minute. That’s 60 times less than Exxon-Mobil, but it’s still a nice chunk of change.

The university libraries that make up a large proportion of their customers have been feeling the pinch more and more. The cost of the journals has been rising at a much higher rate than inflation. This means that either the library need to receive a significant budget increase every year (and if you’ve ever worked at a university you know exactly how easy that is to do) or they need to cut spending somewhere else to make up the difference.

It’s important to remember that access to journals is, for scientists, as much of a necessity as gasoline. In fact, it can be easier to cut utility usage than it is to cut journal use. If it’s a sunny day, I can turn the lights off in the lab. But if I can’t get access to the most recent developments in my field, I’m not going to be able to work effectively.

So far, the situation that I’ve described with journal prices is similar to the gasoline analogy I presented. Both are necessities (at least under certain circumstances). Both have been increasing in price. And the providers of both are making large profits, while their customers suffer.

That’s where the analogy ends, though, because scientists are not only the end customers for journals, they’re also the people who provide the content. For free. If you want to continue the analogy, you’d have to pretend that during the whole time that gas prices and profits have been rising you were spending five or ten hours a week working on an oil rig, and that you’re doing it without pay.

The Academic Senate at UC Santa Cruz summed this up well in a 2003 resolution:

Online journal charges have, however, been rising much faster than comparable prices, and Elsevier prices have been in the lead. Library acquisition budgets are increasingly being driven by unsustainable increases in journal prices. Elsevier’s revenues and profits have been rising fast in recent years. Their profits were up 26% in the last year. Elsevier’s prices are not proportional to the use of these journals made by UC faculty. Access to Elsevier journals costs the UC system 50% of its online budget, and use of these journals is only 25% of total online journal use.

UC Faculty members are important players in Elsevier’s journals. 10-15% of the content is written by UC faculty, 1000 faculty are on the boards of Elsevier journals, and about 150 faculty are senior editors for those journals.

The University of California started negotiation with Elsevier seven months ago, seeking to establish a sustainable relationship with Elsevier. Those negotiations have not yet concluded but there is a chance they will break down if Elsevier is unwilling to price its product in an affordable way that avoids punishing annual price increases that are 2 or 3 times the Consumer Price Index rate of inflation.

The relationship between publishers and the scientific community is not a partnership. It’s parasitic.

And it gets worse, because the parasite doesn’t even have the decency to try and hide what it’s doing. Instead, the major academic publishers seem to feel that they are entitled to continue to make enormous profits selling scientific research to scientists at outrageously inflated prices.

This sense of entitlement has been at its most obvious where the open access movement is involved. Publishers like Reed Elsevier fought tooth and nail against legislation that would require researchers to make a copy of their work freely available within a year of publication. Along the way, they claimed credit for the entire peer review process, slighting the editors and reviewers who actually do the work – for free – for them. Then, when they finally give in after fighting tooth an nail against open access requirements for years, they brag about their “leadership” when it comes to making their products more accessible.

Were it not for their track history, I suspect that neither the Mad Biologist or I would have been quite as irritated when they “borrowed” some of our work for internal use. With the track history, though, seeing our words sitting, without proper credit, permission, or attribution, on a page that bears a prominent notice protecting their copyright becomes something more. It goes from being a minor discourtesy to being another symptom of the company’s lack of respect for the people who do the bulk of the work to produce their profits, and provide the bulk of their customer base.

Reed Elsevier caught copying my content without my permission

Update: 13 Aug. I’ve added a new post that I think provides a clearer explanation for the reason that this sort of behavior is such an irritant when it comes from a company like Elsevier.

Like most bloggers, I have an ego. I’m not mentioning that by way of apology, but as an explanation for why I was browsing through my sitemeter statistics last Friday. Every now and then, I head over to sitemeter, call up the view that lets me see what websites referred people to my page. If I see a link that’s coming from a source I don’t recognize, I browse over and look to see what people are saying about me. Yeah, it’s sad. Yeah, it’s shallow and self-centered. And, yeah, I know a bunch of you have your own blogs and do it too.

Anyway, I’m almost at the end of the list from the last 100 hits when I come across this link. I don’t recognize it, so I click on it and I’m taken to this page. (I saved it as a pdf because I’ve got a feeling that it won’t be accessible at the link for much longer.) That page contains the majority of a post about open access that I wrote a few weeks ago.

The vast majority of the content on that page was written by me. All but the first 13 words in the “comment” at the top of the page were taken from my article. The remainder of the page contains the first 60% of my post. The links I included in the original have been omitted, but the text itself is unaltered. The source that is given for the material is simply “ScienceBlogs.com”. My name is not given, and the only link to the original article is in the section of the page marked “related links.” The copying that took place in the “comment” section is entirely unacknowledged. The only mention of copyright occurs at the bottom of the page, and reads, “Copyright © 2008 LexisNexis, a division of Reed Elsevier Inc. All rights reserved. ”

I was not asked for, and did not give, permission for my work to appear on that page, much less in that format. Needless to say, I felt a little slighted.

The website in question appears to be a custom version of the LexisNexis search engine. This particular version appears to be Elsevier’s own custom version, intended for internal use. I don’t have conclusive proof of that, but the title bar at the top of the page reads, “Elsevier Corporate”, and the person who accessed my blog from that page had an IP address that’s registered to MD Consult, which is an Elsevier subsidiary. My guess is that Elsevier’s keeping track of news articles and blog posts that mention them, along with the context in which they’re mentioned.

So, someone at Elsevier apparently made a copy of something I wrote criticizing Elsevier, and made that copy available to whoever has access to their (apparently not well-secured) house version of LexisNexis. This might technically be a copyright violation, but if it is it’s basically just the electronic equivalent of clipping a news article, photocopying it, and sticking the copies in co-workers’ mailboxes. Is this really something that I should care about?

Clearly, I think it is, or I wouldn’t be writing this post.

This blog, like almost all blogs, is an open-access publication. There’s no charge to read this blog. If you’ve got an internet connection and time to waste, you can scroll through the things I’ve written to your heart’s content. The thing is, open access doesn’t mean that nobody gets paid.

If you’re reading this material on my blog, you’re going to see some ads. The ads bring in income for the Seed Overlords. They use that income to cover the not-insignificant costs of running this online Zoo. They also pay me (and the rest of the bloggers). The more people read my posts, the more opportunities there are for someone to actually look at one of the ads, and the more I get paid. I don’t get paid when people read this on someone else’s website.

Advertising-supported web publishing is a business model that Elsevier understands quite well. In fact, it’s a business model that they use. They run a cancer information site that’s open accessand supported by advertising. And because they get paid only for the ads that appear on their site, they have a copyright policy that prohibits reposting their material on other sites without their consent.

That’s not the only time that Elsevier has shown a very acute awareness of where their money comes from. They’ve consistently opposed open access initiatives around the world, because open access requirements would have a very large impact on their bottom line. In fact, they’ve gone to great lengths to try to protect their income stream. As you may remember, they were one of the publishers involved in the astroturf group “PRISM” that their attack dog PR expert put together to lobby Congress in opposition to an open access initiative.

Elsevier has spent a great deal of time, energy, and money in an effort to get people to respect their income flow. They apparently didn’t bother to think about mine.

I’m not upset about this because of the money, though. (It’s not like I get paid all that much anyway.) I went into the financial aspect partly because it’s a clear illustration of Elsevier’s thoughtlessness, and partly because I’m not entirely certain that they will understand any other basis for objecting to their actions. The money isn’t the real issue. The real issue is respect.

Scientists provide the content for Elsevier’s journals. They donate their time to review, and often edit, the articles that appear in the journals. They make up the bulk of the audience for the journals. Yet Elsevier has, time after time, demonstrated a complete lack of respect for scientists and the scientific community. It’s not a surprise that they would decide to grab my post, while ignoring my rights to my own material. It’s simply another example of where their focus is: intellectual property matters if and only if it’s theirs.

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!

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.

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.

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
REM
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.

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.

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:

ARRRRRRRGGGGGGGHHHHHH! F---! F---! F---! No!
*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.

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!"

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.

Hybrids:
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.

References:
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.

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)
Hindu
Konko-Kyo Faith
Community of Christ
Sufism Reoriented
Tenriko Church
Seicho-No-Ie
Church of World Messianity (Izunome)
United Church of Religious Science
Christian Reformed Church
United Moravian Church
Eckankar
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:
public.inquiry@va.gov
1-800-827-1000

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)

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.

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.

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...

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.

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.