The Seguin Gazette-Enterprise and Misrepresentation of Pianka.

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**Update- 7 April 06, 18:00 HST -**
All of the Sequin Gazette-Enterprise articles linked to in this article are no longer available through those links, and I am currently unable to find them as live links elsewhere on their site. I will be emailing the paper for comment shortly, and will attempt to contact them by phone for an explanation if that does not work.
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It's been several days since the attacks on University of Texas ecologist Eric Pianka first began, and there's no end in sight. Yesterday, Texas governor Rick Perry's office compared Pianka to the Nazis, and today he is being required to talk to the FBI so that they can make sure that he's not a terrorist. Meanwhile, various portions of the right-wing community are continuing to rave against Pianka - the Uncommon Descent folks alone have no less than four posts up on the topic today.

Also today, the Seguin Gazette-Enterprise (the local paper that got the ball rolling on this whole affair) posted the transcript of another, more recent, speech by Pianka. This is interesting because the transcript is for the same speech discussed in the April 2nd Gazette-Enterprise article that was picked up by the Drudge report, sparking the national outcry. Having the transcript available makes it much easier to critically examine the news article about the speech, and to see how well the material in the article reflects what was actually said.

The easiest way to do this, I think, is to look at the way direct quotes are used in the article, and then at the same quote within the context of the speech. It's as close to objective as I'm going to be able to get. The direct quotes will be placed in a bold font to make them easier to find.

From the article:

A University of Texas professor says the Earth would be better off with 90 percent of the human population dead.

"Every one of you who gets to survive has to bury nine," Eric Pianka cautioned students and guests at St. Edward's University on Friday. Pianka's words are part of what he calls his "doomsday talk" - a 45-minute presentation outlining humanity's ecological misdeeds and Pianka's predictions about how nature, or perhaps humans themselves, will exterminate all but a fraction of civilization.

From the transcript:

Now it is only a matter of time until Ebola got here evolves and mutates a little and it will be airborne, and then I think we might finally get a take. And when it sweeps across the world — we're gonna have a lot of dead people. Every one of you that is lucky enough to survive gets to bury nine. Think about that. I doubt Ebola is gonna be the one that gets us. I think it will be, uh, something else.

But did you ever wonder why things like SARS and now what the Avian Flu are continually cropping up? They're cropping up because we were dumb enough to make a perfect epidemiological substrate for an epidemic. We bred our brains out, and now we're being pegged. The microbes are gonna take over. They're gonna control us as they have in the past. Think about that.

If you look closely, you will see that the two sentences in bold do not entirely match. The newspaper quoted Pianka as saying "every one of you who gets to survive." The transcript has him saying "every one of you that is lucky enough to survive." It's a small difference, I know, but I think it is significant - especially since it seems to be part of a trend.

A little later in the article, we read:

So what's at the heart of Pianka's claim?

6.5 billion humans is too many.

In his estimation, "We've grown fat, apathetic and miserable," all the while leaving the planet parched.

The solution?

A 90 percent reduction.

Looking at the transcript, here's what we see in context:

The great North American saltgrass prairie and we just took it and turned it all into agricultural lands. We exterminated the bison, wiped out the Indians, totaled the prairie dogs and those black-faced ferrets. We just erased an eco-system. Now this is very nice for Americans because that rich topsoil has allowed us to grow food and we can feed ourselves and the rest of the world and we've grown fat and apathetic and miserable as a result of it. We've lost the bison — we've lost an awful lot and we'll never be able to recover.

I do need to give the author some credit here - Pianka did use the quoted words. He did not do use them to refer to humanity as a whole, as the Gazette-Enterprise implied, and he didn't use them in reference to population growth per se. But he did use those words in pretty much that order.

I'm not sure that the same thing can be said about the next quote I'm going to look at:

"[Disease] will control the scourge of humanity," Pianka said. "We're looking forward to a huge collapse."

I realize that I didn't provide much context for that, but I didn't really think that it was necessary. I've got nothing to compare it to. Neither "scourge of humanity" nor "looking forward" appear anywhere in the text of that speech. Those phrases are also absent from the incomplete transcript of the Texas Academy of Sciences speech posted at the Pearcey Report earlier today. It is entirely possible that Pianka said those things at some point in time, but it does not appear that they were included in the 31 March speech. The page with the transcript does note that there are some missing portions, so I'll give the paper the benefit of the doubt for the moment, but the omission is troubling.

Here's another chunk from the newspaper article:

As of press time, Pitts - who sent his appeal via email Saturday - had received no response from the university, but he says, "It's too early for any responses to have been made." Meanwhile, Pianka urges humanity to heed his call to be prepared, saying "we're going to be hunters and gatherers again real soon."

"This is gonna happen in your lifetime," he told his St. Edward's audience. "Do you wanna go there? We've already gone there. We waited too long."

I apologize, but I won't be able to provide a single quote that contains both phrases. It would be far too long - over 1100 words separate "hunters and gatherers again real soon" from "This is gonna happen."

Here's the context for the first part:

It's just a matter of time until the planet changes really bad. Some meteorological people have models that show thresholds where it shifts just instantly overnight. What I'm waiting for is when you go to the supermarket and there are no more Triscuits on the shelves and you say to yourself, "Hey, where did Triscuit come from, anyway."

We've lost touch with the reality of where food comes from. We're completely mislead. It's just a commodity that's bought and sold and people make money on it. You've got to think, you've got to think — and remember, humans were hunter/gatherers not that long ago and I think we're gonna to be again very soon.

And the second:

The U.S. Fish and Wildlife recently released caribou off the islands off of Alaska to help the Eskimos, the Aleuts, get protein. And the herds from these islands — there were several islands — all grew exponentially just like the human population's been growing for quite a few years and then they ate everything they could eat and the populations crashed.

This is what's going to happen to us. This is gonna happen in your lifetime. Does that look like fun? Do you want to go there? You've gone there. We waited too long.

Both of those quotes, read in context, are alarmist. But they are talking about completely different threats. Coupled together, they say do make a nice quote, but it's not what Pianka actually said. As was the case with the other quotes, it's a fairly small difference, but the cumulative effect is to cast Pianka in the worst possible light.

I'd almost be willing to write off the misquotes to poor memory and notetaking by the reporter, but the same trend shows up in a quote taken from written material:

The professor's not the only one who can articulate this concept. Because Pianka includes his doomsday material in his coursework, Ebola and its potential play a notable role in some students' studies. A syllabus for one course reads:

"Although [Ebola Zaire] Kills 9 out of 10 people, outbreaks have so far been unable to become epidemics because they are currently spread only by direct physical contact with infected blood. However, a closely-related virus that kills monkeys, Ebola Reston, is airborne, and it is only a matter of time until Ebola Zaire evolves the capacity to be airborne."

It is here that some say Pianka ventures from provocative food for thought to, as Wilkins said, "very extreme material" that violate many people's views - including his own - about the treatment of human life. While many praise Pianka's boldness and scientific know-how, others say he crosses an ethical line in his treatment of Ebola's viability as a killer.

The quote does not actually appear in Pianka's course syllabus. Instead, it appears on a website that lists reasons to take the class. Here it is in full context:

During the past quarter of a century, world population has increased from about 3.4 billion people to over 6.4 billion, an increase of over 85%. In some parts of the world, human populations are growing even faster.

If humans do not control their own population (and we seem unwilling and unable to do so), then other forces will certainly act to control our population. The four horseman of the apocalypse (conquest, war, famine, and death) are all candidates. Most likely, lethal virulent microbes like HIV and Ebola zaire will set limits on the growth of human populations. HIV, by allowing infected hosts to survive years while they spread the virus and infect new hosts, has already become a pandemic, but it will be years before it decimates the human population. Although Ebola kills 9 out of 10 people, outbreaks have so far been unable to become epidemics because they are currently spread only by direct physical contact with infected blood. However, a closely related virus that kills monkeys, Ebola reston, is airborne, and it is only a matter of time until Ebola zaire evolves the capacity to be airborne.

It's clear that Pianka is not advocating the use of Ebola as a weapon in this passage. Instead, he is warning that a devistating epidemic is a likely outcome of continued population expansion. Interestingly, the reporter doesn't bring that up later on, when speculating on Pianka's motives for discussing ebola:

Though Pianka turned down requests for a sit-down interview, he maintains he is not advocating human death.

Does he believe nature will bring about this promised devastation? Or is humanity's own dissemination of a deadly virus the only answer? And more importantly, is this the motive behind his talks?

Responding to these very questions, Pianka said, "Good terrorists would be taking [Ebola Roaston and Ebola Zaire] so that they had microbes they could let loose on the Earth that would kill 90 percent of people."

This quote appears to come from an exchange captured in an audio recording posted on the paper's website.

Here's my attempt at a transcript:

Reporter: "My question is, do you believe that this is something that's going to come about naturally? Do you believe that this is something that humanity needs to take a step to cause? Because that's what's being said..."

Pianka: "Oh..."

Reporter: "...and there's a big difference in that."

Pianka: "Oh.. I think that umm [incomprehensible- I honestly can't tell for sure whether or not he used the word "good" there, but I don't think he did.] er... terrorists would be taking one of these and one of those other ones and trying to combine them so that they had a microbe that they could [let/set?] loose on the earth that would kill 90% of the people. I don't think they are that sophisticated...

Reporter: "...OK, but yes or no question, do you advocate that?"

Pianka: "I don't advocate killing people."

Reporter: "OK."

I have a hard time looking at the quote from the article, listening to the audio of the actual exchange with the reporter, and viewing what was written as anything other than a deliberate attempt to make Pianka look bad. It seems clear to me that the first part of Pianka's answer was the result of him mishearing or misinterpreting the reporter. I think that was clear to the reporter, too. She cut his answer off to ask him point blank whether he was advocating terrorism.

The article in the Seguin Gazette-Enterprise contains numerous misquotes and out of context quotes. All of them err in the same direction - making Pianka look bad. It is almost impossible to believe that this is the result of anything other than deliberate effort on the part of the paper.

On Science Education (or: I Want To Be PZ Myers)

I have a confession to make. (Yes, another one.) I want to be PZ Myers when I grow up and finish my PhD. Well, a sort of watered down version of him anyway. I'm not so sure about the whole agressively godless thing. And I can almost certainly do without the cephalopod fetish.

Ok. So I don't really want to be PZ. I just want his job. Or one a lot like it. I like doing research. I enjoy new problems, and I love finding solutions. But I also like to teach - I really enjoy it - and professors at research universities just don't do enough of it for me. Most of the professors in my department spend a quarter or less of their time in the classroom. I want more time working with undergraduates than that.

That's the big advantage that I see in teaching at a liberal arts college instead of a research university. The smaller schools exist to teach. In the research universities I've seen, the undergraduates may be the excuse for having a department, but the departments exist to do original research. Teaching seems to come in second as often as not.

Here's the thing, though. To get to the point where I'm reasonably qualified for a position teaching in the science department at a liberal arts college, I need to complete a PhD in the sciences. The PhD program I'm in is, like most others, entirely research focused. This means that the expectation is that the grad students will put most of their time into their research, take only classes related to their research, and do as little teaching as possible. We're required, at least in theory, to have one year of teaching experience before graduation. It is uncommon for students to TA for more than a year unless they can't find any other source of funding. Many advisors actively discourage their students from taking classes that are interesting but unrelated to that student's specific research area.

My department is not atypical in this regard. In fact, the majority of the faculty have been very supportive of my desire to get more teaching experience. Several of them have helped me with questions I've had about teaching, and in improving my skills. Ultimately, however, I am a student in a program that's designed to produce researchers. It is definitely not designed to produce educators.

So how does this tie in with science education?

As Janet pointed out in a post on her blog earlier today, the folks who teach science at the K-12 grade levels are not usually people who majored in science. They are people who took some science classes in college, but most majored in education. Of the fraction that completed an undergraduate science major, few have done any graduate-level work in science - which means that few have had substantial exposure to the practice of science.

Once a student reaches college, they get to take science classes taught by a real, live scientist. That's someone who has finished a PhD in their field, conducted original research, and knows how the scientific community functions. Their graduate program was almost certainly like the one that I'm in - focused on producing the next generation of researcher.

To put it another way, the people who teach students science before college have lots of training in education and little in science, while those who teach student science in college have lots and lots of training in science, but little to no formal training in education.

I'd like to go out on a limb here, and suggest that this situation is absolutely insane. It's bloody stupid. Look, and education degree is fantastic. If I've learned one thing from TAing the last two semesters, it's that teaching is a hell of a lot more difficult than it looks. Being able to effectively teach a subject requires much more than knowledge of the subject. To teach well, you have to be able to structure the course appropriately, present the material at a reasonable rate, present the material in a way that can engage at least a few of the students, write exams that actually test what you teach, explain why an answer is wrong instead of just saying that it is - and that's just a partial list. But you do need to understand the material.

The current system is set up to produce people who are skilled in either teaching or science. It isn't set up to produce people who are trained in and good at both. That needs to change. If we are going to have any hope in fixing science education in this country, we will need lots of people who can do both.

Guilty Pleasures

I have a confession to make.

From time to time, in my own home and out of view of my children, I yield to temptation and read something written by Tom Clancy. It's wrong, I know, but it's hard to resist. The man's politics might have started to the right of John Birch Society (and drifted rightward over time), and his the mindset of his characters is overly righteous and simplistic, but his stories are decent escapist novels. If I need to turn off my brain for a while, Clancy isn't the world's worst way to do it. The thing is, though, unlike a large number of wingnuts, I know that it's just a story.

Fieldwork 2: Minor Difficulties

This is a plant that is known locally as "Spanish Bayonet."


These are your pants after you fall into some.


Any questions?

Prayer and the Military

Some of our more self-righteous congresscritters have been making to have the president sign an executive order guaranteeing evangelical Christian military chaplains the right to pray in Jesus' name. To their credit, the organization that represents the majority of military chaplains has come out against this move.

Here's the bottom line:
Military chaplains pray in two different types of circumstance. They pray when they are conducting religious services for people who share their beliefs, and they pray in circumstances when people who do not share their beliefs are required to be present. Nobody is questioning the right of chaplains to pray as they wish when they are conducting the services appropriate to their own denomination. However, when praying in a situation when people from other religious traditions are present, it is entirely inappropriate for a chaplain to deliver anything but a non-denominational prayer.

The executive director of an organization that represents some evangelical chaplains and is pushing for the executive order is quoted in the Washington Post article linked above:

But Baugham said evangelical chaplains must represent the church that endorses them for military duty, and "they are not authorized to give nonsectarian prayers."

That position is extrordinarily odd, particularly coming from a group that endorses chaplains for military duty. According to this army website, a chaplain's endorsement from their faith group should certify that the candidate is, among other things, "Sensitive to religious pluralism and able to provide for the free exercise of religion by all military personnel, their family members and civilians who work for the Army."

Any chaplain that cannot be sensitive to the differing beliefs of others in their unit is simply unfit for the needs of the military, and should be discharged.

Fieldwork 1: Packing

Preparation is absolutely essential to doing good fieldwork. Some of the preparation includes obvious tasks like figuring out where you are going to go, why you are going there, and how you are going to spend your time when you get there. Figuring out how you are getting there is usually a good idea, too, as is making sure that you have any and all paperwork that you will need. That's often a bit harder for scientists, becuase there are frequently extra permits and permissions to be obtained. There's also the matter of setting up your schedule once you get on site. Time is precious, and it's common to have to budget time tightly to make sure everything gets done.

Let's put it this way: fieldwork doesn't often happen on a moment's notice. When it does, it's usually because something extrordinary has happened somewhere in the world, creating a research opportunity that might not be available for long. (Most people refer to these as 'natural disasters'.)

It's also important to make sure that the logistics for the trip are lined up ahead of time. Food and shelter come under this category, of course, but I'm mostly talking about gear. You need stuff to do science, and there's nothing worse than finding out that you aren't going to be able to get all the data you need because you forgot to bring something important. That's why you'll find scientists (like me) who would ordinarily pack for a two-week vacation without using a list putting together detailed packing checklists for fieldwork. Putting together the checklist is usually followed by staring at it for a while to make sure you haven't forgotten anything, packing it all, unpacking it to make sure you haven't forgotten something, re-packing it, and wondering what you've forgotten.

Anyone want to take bets on what I'll forget?

Into the field

I've been trapped in the lab for the last few months, but that's about to change. I'm heading out into the field tomorrow morning, on a short trip to the Death Valley, California area.

The fieldwork I'm going to be doing isn't really related to my own research, but I'll take what I can get. Actually, it will be nice, because I'm going to be getting back to my roots. Back when I was first getting into science, I started out intending to be a paleontologist. Evolution interested me, and I was very interested in broad-scale, macroevolutionary events. But somewhere along the way I was seduced by the Dark Side, and was overcome by the lure of molecular techniques.

This week, I get to be a paleontologist again. A group of six grad students and two professors at UH, including myself, are working on a review paper. The topic of the review is the origins of animal life, and we thought it would be a good idea to get to get more familiar with the field. We're heading to Death Valley because it's a site that has some nice places to see the evidence for Precambrian animal life.

We'll be staying just south of the National Park, in a little town with a population of about 80. I've got a hunch that internet access will be a little hard to come by, so I probably won't be able to post too much before I get back on Thursday.

Friday Random Ten

The Friday Random Ten is a blog meme of uncertain origins that's been around for years. I keep meaning to do one, and every week (until now) I forget.

Directions: Fire up the iPod, set to shuffle songs, hit play. List the first ten songs that come up. Don't cheat.

This week, my iPod seems to be a bit more random than usual.

1: Louis Armstrong and Duke Ellington
It Don't Mean A Thing if it Ain't Got that Swing
2: The Clash
Should I Stay or Should I Go Now
3: Pearl Jam and Neil Young
Rockin' In the Free World
4: Pete Seeger
The Erie Canal
5: Sean Na'auao
Fish and Poi
6: U2
Pride (In the Name of Love)
7: The Who
Baba O'Riley
8: Black 47
Living in America
9: Buffalo Springfield
For What It's Worth
10: The Muppets
The Muppet Show Theme

Last Night

Somewhere around two this morning, I had to get up to take care of one of a father's most important duties: monster patrol.

I've done it before, but this time was different. For starters, it was both kids who woke me up. Usually it's just one. Second, the monster was hiding somewhere different. Usually, it's under the bed or in one of the bedroom closets. This time, for some strange reason, it seemed to be in the bathroom. That's what I could gather from the kids, anyway. When they're under the blankets, it can be hard to understand everything.

I wasn't really that surprised. We were having a hell of a thunderstorm last night, and I figured that was probably the cause. In the probably futile hope of reclaiming my bed from the kids, I dragged myself out of bed and staggered out to take a look at the bathroom.

Damn near pissed myself when I got there. There was this really freaky sound coming out of the bedroom. It's almost impossible to describe - it was sort of like a whimper, but with this strange echo effect, and something that sounded sort of like heavy breathing going on, too. I wasn't sure what it was, but it probably wasn't the pipes.

After taking a minute to recover, I mustered up my courage, turned on the lights, and lunged into the bathroom. And found the dog.

It turns out that the thunderphobic canine, banished from the master bedroom, had taken refuge, whimpering and panting, in the bathtub.

If we can keep it.

As Ben Franklin left Independence Hall during the final day of deliberations during the Constitutional Convention, a woman is reported to have stopped him and asked:

“Well, Doctor, what have we got—a Republic or a Monarchy?”

Franklin responded:

"A Republic, if you can keep it."

If we can keep it. There's the rub. Somehow, it seems like that just keeps getting harder to do.

The problem here, as in way too many other areas of American life, probably rests with the godawful state of our educational system. Far too many Americans seem to hold the mistaken view that we live in a democracy, and that the majority should be able to impose its will on the minority.

For example:

Who cares if there’s a “sizeable Mormon community”. They don’t have to sing Christmas songs if they don’t want to or they can ask that traditional Mormon pieces be added. This is America and Christmas along with Christmas carols are a longstanding tradition of a vast majority. Christmas is a national holiday and tragic as it is for the loony left it hasn’t been renamed Winter Solstice Celebration yet. Anyone that doesn’t like that is welcome to move to a country where they don’t celebrate Christmas. I’ll help them pack and pay for a one-way ticket on a banana boat out of here.

Here's another example, from a resolution currently on the floor in the Missouri State Legislature:

Now, therefore, be it resolved by the members of the House of Representatives of the Ninety-third General Assembly, Second Regular Session, the Senate concurring therein, that we stand with the majority of our constituents and exercise the common sense that voluntary prayer in public schools and religious displays on public property are not a coalition of church and state, but rather the justified recognition of the positive role that Christianity has played in this great nation of ours, the United States of America.

Way, way too many people, apparently including some legislators, just don't seem to understand why we have the system of government that we do.

We don't live in a democracy. We live in a republic. We live in a republic because many of the drafters of the Constitution were at least as afraid of democracy as they were of monarchy:

From this view of the subject it may be concluded that a pure democracy, by which I mean a society consisting of a small number of citizens, who assemble and administer the government in person, can admit of no cure for the mischiefs of faction. A common passion or interest will, in almost every case, be felt by a majority of the whole; a communication and concert result from the form of government itself; and there is nothing to check the inducements to sacrifice the weaker party or an obnoxious individual. Hence it is that such democracies have ever been spectacles of turbulence and contention; have ever been found incompatible with personal security or the rights of property; and have in general been as short in their lives as they have been violent in their deaths.
James Madison, Federalist #10.

The Constitution was very intelligently designed to set up a system of government that protects the rights of the minority from the tyrany of the majority. That's why changing the Constitution is such a difficult process. It's not supposed to be something that the majority can do anytime they want. If it was otherwise, we would live in a very, very scary place - a place where the rights of the minority could be revoked by the majority at any time, for any reason.

I'm sorry to rant for so long on this, but it's important. The narrow-minded bigots who advocate for those kinds of "Christian Nation" and "if you don't like it, move" positions are attacking our fundamental values. They are trying to remake the country in their own twisted image, and they are trying to remake it as something far different from the Republic that the signers of the Constitution worked so hard and risked so much to establish.

Unfortunately, it really seems like those ignorant, jingoistic fools are becoming more common. At a minimum, they're becoming more vocal, and in our modern media world that can sometimes amount to the same thing. Franklin was right - we have a republic only as long as we can keep it.

We're going to need to work at that, I'm afraid. That's why groups, like the ACLU, that are willing to stand up for the rights of the minority are so critical right now. They provide a voice to people who are willing to fight the majority to protect their rights. Without them, it would be much, much easier for the majority to act like a tyrant.

Last Throws

It would seem that our vice-president's grasp on reality is about as good as his marksmanship. On Sunday, he did Face the Nation. During the interview, the following exchange took place:

SCHIEFFER: Mr. Vice President, all along the government has been very optimistic. You remain optimistic. But I remember when you were saying we'd be greeted as liberators, you played down the insurgency 10 months ago. You said it was in its last throes. Do you believe that these optimistic statements may be one of the reasons that people seem to be more skeptical in this country about whether we ought to be in Iraq?

CHENEY: No. I think it has less to do with the statements we've made, which I think were basically accurate and reflect reality, than it does with the fact that there's a constant sort of perception, if you will, that's created because what's newsworthy is the car bomb in Baghdad. It's not all the work that went on that day in 15 other provinces in terms of making progress towards rebuilding Iraq

That's right, he really said that his ten-month old claim that the insurgency is in its "last throes", and other similar claims, were "basically accurate and reflect reality".

I caught that on the air when it happened. One of my neighbors was there, too. I think he probably put it best when he said, "if you believe everything they say in Washington, the insurgents have had more last throes than a nymphomaniac in a frat house."

Plantinga, Intelligent Design, and Uninformed Opinions

One of the better posts mentioned in yesterday's Tangled Bank can be found over at Adventures in Science and Ethics. In that article, Janet provides a clear and detailed explanation of the limits of scientific expertise. As she reminds us, scientists are not near-omniscient beings, endowed with some sort of infailable ability to assess ideas across all the fields of scientific research. Scientists are primarily qualified to comment on matters within their own field. If a scientist is not an expert in an area of science, he or she should give the scientists within the other field the benefit of the doubt, and assume that they have a better understanding of their own area. As Janet points out, scientists (and other adademics) should be responsible enough to know their own limitations.

This sense of responsibility seems to be somewhat lacking among some of the more prominant proponents of Intelligent Design. It's shown up in any number of places, including a recent article by well-known philosopher Alvin Plantinga.

Plantinga pontificates at length on Judge Jones' ruling in the recent Kitzmiller v. Dover Intelligent Design lawsuit, but his rant seems to be entirely disconnected from the actual facts of the case - or, for that matter, any real understanding of what the ID proponents actually advocate.

The monumental depth of Plantinga's ignorance becomes clear fairly early on in the paper, when he discusses the Intelligent Design view of evolution:

Consider, for example, the claim that ID is just creation science in drag, as it were. That ruling is relevant in that previous court decisions have gone against creation science. But the kind of creation science those decisions had gone against is characterized by the claim that the world is a mere 6,000 to 100,000 years old, rather than the currently favored age of 4 billion or so years old.

Second, those creationists reject evolution in favor of the idea that the major kinds of plants and animals were created in pretty much their present form. ID, as such, doesn’t involve either of these two things

It is possible that Plantinga is correct here, since it is notoriously difficult to determine what ID, "as such," actually involves for any particular aspect of science. (That's the inevitable side effect of having a "theory" that entails no positively testable hypotheses.)

The problem for Plantinga's argument comes when one moves from the undefined principles of an idealized "Intelligent Design as such" to those of Intelligent Design, as outlined in the various "resources" provided to the Dover High School students. A quick look at the "textbook" at the center of the case is all it takes to see that Plantinga's position does not hold up well when evaluated using reality-based criteria:

"Intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks, and wings..."
(Of Pandas and People, quoted in Forrest trial testimony)

That may not reflect Plantinga's view of Intelligent Design, but it clearly involves the idea that the major kinds of animal were created in more or less their current forms, and it clearly links that concept with the definition of Intelligent Design. It's also a view that the Discovery Institute doesn't seem to have too much of a problem with - they've called the book that it appears in "an excellent educational resource."

It seems clear to me that Plantinga is talking about some form of Intelligent Design that exists only in the realm of the ideal. Here, on Earth, we are dealing with a different form of Intelligent Design. The form of Intelligent Design that we are coping with doesn't have much to do with working on developing new scientific knowledge in the future. Instead, it is about what some people want to teach in the secondary school classroom right now.

Plantinga might have been able to see this if he had taken the time to look at what ID proponents do, rather than just what they say.

Tangled Bank #49

Tangled Bank #49 is now available over at Living the Scientific Life. Tangled Bank is almost always very good, and this one is better than most. It's laid out better than most, and there are a number of extrordinarily good submissions.

For the love of God, stand up for something

Yet again, the Democrats in congress are doing their best to dodge an issue. What a bloody shock. This time, the issue is Senator Russell Feingold's recent motion to censure the president for operating an illegal wiretapping program.

The Republicans, secure in their knowledge that their majority is sufficient (at the moment) to defeat any such motion, called for an immediate vote on the motion. The Democratic Leadership, proving yet again that they are incapable of demonstrating the leadership or moral courage needed to do light a match in a dark cave without first conducting extensive polling on the issue, are acting to postpone any vote for the moment. Essentially, they're filabustering Feingold's motion. The excuse for this inaction, as provided by Harry Reid, is that the motion deserves more thought and consideration.

Yeah, right. There are lots of things out there that deserve more thought and consideration. This really isn't one of them. What the president did is somewhat, but not entirely, known. Congress has attempted, somewhat pathetically, to extract more information. The administration semi-politely told them where they could stick their request. No further action has been taken, and no further action appears to be forthcoming.

Legal scholars have weighed in all over the place on the president's justification ("I'm a wartime leader.") for the program. Either you buy his argument or you don't. If you do, you don't think he did anything illegal. If you don't, you think he did soemthing illegal. If he did something illegal, he should be censured. If he didn't, he shouldn't. If you haven't figured out where you stand on this one by now, you haven't been paying attention.

What the Democratic delay tactics are all about is not taking a stand. They don't want to risk pissing off their base by going on record against censure, and they don't want to risk pissing anyone else off by (heaven forbid) going on record for censure. So, yet again, we find the Democratic leadership standing around trying to figure out which way the train's going - presumably so that they can jump in front and get run over again.

For crying out loud, why can't they take a stand. At this point, I'd settle for almost any kind of stand. OK, it's nice that they aren't the Republicans, but it would be even nicer if they were something more than the "not-Republican Party". The country is in deaparate need for leadership, and right now it doesn't look like anyone's willing to step up.

Yes, I'm slacking off on blogging again.

There's nothing like two or three nights of checking the base calls from the sequencer by eye for sucking the will to live (and all other motivation) clean out of your system. I'll be done in another day or two - for these two loci.

In the mean time, I'd like to wish a belated happy birthday to PZ. (Your dried squid is in the mail.)

If you're looking for something else to read right now, go take a look at a nice rant over on Evil Monkey's blog - it does a fantastic job at capturing modern science.

Applications of Evolution - More on the gall wasp

A while back I put up a couple of posts about an invasive gall wasp that's threatening a species of tree unique to Hawaii.

In the first of those posts, I made a few predictions, based on my understanding of ecology and evolution, on how researchers might be able to control the gall wasp infestation:

Ultimately, however, it may be impossible to save the Wiliwili without some sort of biological control. So let's assume that a decision is made to look for one. Normally, we would look to the species' native habitat to find a parasite or predator. Unfortunately, we don't actually know what the native range of this species actually is. It was only described for the first time last year, and it seems to be an invasive in all of the places that it has been found. The world is a really big place, and we have a limited amount of time until the Wiliwili follows countless other Hawaiian species into extinction. So where do we start to look?

Africa. Since this species hasn't been described from there at all yet, what makes us think that we should look there?

Evolution.

There are a number of related species of gall wasp in South Africa, including some that utilize Erythrina trees. There are also Erythrina trees that are native to this area. As I understand it from conversations with other grad students here, these trees do not appear to be experiencing the same sort of massive infestation that is being seen here in Hawaii. This indicates that one of two things is happening there. Either the South African Erythrina have an innate defence mechanism protecting them from the gall wasps (this is unlikely, as the gall wasps can and do breed using these trees) or there is something else, most likely a predator or parasite, keeping their population in check. This is the type of more stable ecological relationship that we expect to see in areas where the species evolved.

I don't know whether or not sufficient funding will be found to do this, but I predict that a thorough study of the gall wasps in South Africa will turn up a predator and/or parasite capable of controlling the gall wasp population. (Or that the Erythrina trees have a defence mechanism protecting them from gall wasps.) I also predict that, again pending sufficient funding, that molecular studies will show that the wasps invading Hawaii are relatively closely related to species from South Africa.

I'm a big believer in scientific integrity, and I believe that scientific integrity includes reporting negative results and incorrect or falsified hypotheses. With that in mind, I find that I must take this opportunity to admit that part of my hypothesis was not, in fact, entirely accurate. Researchers have not found a parisite or predator that targets these wasps in South Africa.

They found it in Tanzania.

An update in today's Honolulu Advertiser reports that a state entomologist spent two months in Tanzania earlier this year, and discovered a species of wasp that feeds on the larvae of the species of wasp that's killing the trees. He went to Tanzania, it appears, because he was a good bit more careful with his preliminary research than I was when I wrote the initial article:

Ramadan, a 54-year-old native of Egypt who has been working for the state agriculture department since 1997, studied the situation and recommended searching for a natural enemy in Tanzania because the country, which borders the Indian Ocean, has more than 15 Erythrina species.

Aside from that, the reasoning behind the approach was essentially what I outlined above. He went to look for wasps in an area where the wasps and trees were believed to co-exist. What he found was encouraging. He brought back a species of wasp that seems to successfully eliminate about 95% of the larvae of the tree-killing wasps.

The wasp has been tested against the invasive, and appears to be effective. They are now testing it for side effects (they want to make sure it won't kill things that it shouldn't). Those tests will probably take at least a year, but it looks like there may still be some hope for the Wiliwili.

Blonde Equilibrium

I was originally planning to hold off on starting a series of posts on the genetics of evolution until next week, but John Wilkins recently found a myth that's just too good to ignore.

According to this legend, a World Health Organization study conducted a few years ago revealed that the natural blonde is scheduled to become extinct by the year 2202. The reason given for the imminent demise of the unperoxided flaxen haired is that blonde hair is caused by a recessive gene, and too few people now carry that gene. Since two people who carry the gene must meet (and do certain other things) in order to produce a blonde, the number of blondes is decreasing.

The myth is in fact just that - a myth. It was a wildly successful hoax carried out by someone pretending to be on the WHO staff. They were able to get a large number of media outlets to bite, and the story received international attention when it was first released. Despite a World Health Organization 'clarification', it would appear that some media outlets still haven't quite figured out what's going on.

Still...

The looming extinction of the natural blonde is a legend that's probably going to stick around for a while, for a couple of reasons. For starters, there's a certain ironic appeal to having the blonde meet the fate of the dodo. More importantly, though, the scenario sounds plausible enough. There do seem to be more dark haired people around than there used to, and if natural blonde's aren't meeting and mating as much as they used to, then why shouldn't we expect the blonde to go extinct?

That's a classic population genetics question if there ever was one, and it's one that I'll be looking at in this post (and, hopefully, in a few follow-ups). There are a few different ways to look at the question. We'll start with the easiest, but there is a little bit of vocabulary to get out of the way first.

It's just two terms, but they are important words in genetics. The first is "locus" (plural: "loci"). You can think of a locus as a single gene. (To be a little more specific, a locus is a specific location at a chromosome.) The second is "allele". An allele is one possible version of a gene. Since humans have two copies of each chromosome (one from each parent), we can have either two identical alleles or two different alleles at any locus.

Now back to the blondes.

The question of whether or not the blonde hair allele will disappear from the human species can actually be treated as the simplest situation in all of genetics: it's called a one-locus, two-allele model. This means that the trait (in this case, hair color) is controlled by a single gene, and there are only two variations of the gene in the population. In the case of human hair color, it's not really that simple, but because blonde hair is a recessive trait, we can get away with pretending that it is. We'll just call the dominant allele "not blonde" (and we'll represent it with 'B') and the recessive allele "blonde" ('b'). It's simpler to do it that way, and the math comes out the same.

Let's assume that 1% of humans are natural blondes. That means that they carry two copies of the 'b' allele. If we assume that people don't choose who they marry based on natural hair color, we can use this to figure out how common the 'b' allele is in the population. The equation for that is easy. If 'b' is the probability of picking a random allele from the populaiton and finding that it is a 'b', then the percentage of people with two 'b' alleles will equal b*b. We know that b*b = .01 (or 1%), so b must equal 0.1.

To put it another way, if one percent of the people are blonde, then ten percent of the alleles are the blonde allele. (Which means that 90%, or 0.9) of the alleles are the 'B' allele.

That's the case in the first generation, but what happens in the next one? That's the key question. If the next generation has a smaller percentage of blonde alleles, then blondes may be on the way out. So how do we find out what's going to happen next?

It turns out that there is a famous genetic principle that provides the answer to that pressing question. It's called Hardy-Weinberg equilibrium, and it says that, given certain assumptions (which we will discuss later), then the allele frequencies won't change. 10% of the alleles in the next generation will still be 'b' alleles. There's a famous equation that goes with that, but it's got exponents and other annoying mathy things, so I'll skip it for now. If you don't want to trust me, you can always google it.

The assumptions are where things get a little tricky. For Hardy-Weinberg to work, a number of conditions must be met. The population must be very large, there can't be migration into or out of the population, there can't be mutation, and there can't be any form of selection going on. It's clear that there will be few cases where this is true, but there are lots of cases where it comes close.

The blonde gene, if we consider the entire human race, is one of them. The mutation rate for the gene is going to be so low we can ignore it, the population is very large, and if we are talking about the whole planet, there's not a lot of migration to worry about. Selection is a possibility, of course, but peroxide's taken that one out of the equation.

Since the Hardy-Weinberg conditions are met on a global level, we can safely say that the frequency of the "blonde allele" isn't going to change in the species as a whole. That means that blondes won't ever go entirely extinct.

That takes care of the gene that causes blondeness. But what about the number of blondes? Will that change? Actually, it might - in fact, it's likely to drop. That's becuase of ethnic differences and our increasingly international society, and it's what I'll talk about when I write the next post in the series.

Grading papers

"Don't worry, they're going into medicine."
-Grad student in my lab, looking at the lab reports I was grading.

I just finished grading this week's batch of lab reports for the 400-level animal physiology class I'm TAing. I'd like to share a few of the better little oopsies committed by the students this time:

"the heart recovery rat"
"has been use din the past"
"as needed overtime"
"The student with the least amount of excercise a week was tide with"

"two data were collected during this experiment"
"fitness is an important indicator of mortality"
"Fourteen individuals (six males, nine females)"

Evolutionary Genetics - Introduction

[A] curious aspect of the theory of evolution is that everybody thinks he understands it.
-Jacques Monod

I enjoy my job. I love getting out into the field to do research. I love studying populations of organisms. I think that the questions that I look at are interesting, and that a lot of the answers are pretty cool.

The problem is that it's hard to explain to people exactly what it is that I do. In part, that's because evolution is really a lot more complicated a field than most people realize. The popular view of evolution is more or less that Darwin figured out that species evolve through natural selection, and that's that. People with more background than average in evolution understand that there are other things that come into play, too, like genetic drift.

It is accurate to say that evolution and drift cause species to diverge. In the same sense, it's accurate to say that World War I started because some lunatic Serb blew an Archduke away. In both cases, the explanation only just begins to touch on what is really going on.

I'm still just getting started as far as blogging is concerned, and I'm just getting started in my career as a scientist. I'm probably going to want to talk about my work a lot over the coming years. To make things easier to follow, I'm going to start a series of posts that will outline in as simple terms as I can manage the basics of evolutionary genetics. I'm hoping to make those posts a weekly feature on this blog. The first real post in the series will appear next Monday.

I've got some ideas for topics, but I'm also willing to take suggestions. Feel free to add them to the comments of this post.

Not a lot this weekend

I've been handed a heavy schedule of spring cleaning for this weekend, so I probably won't have a lot of time available to update this between now and Monday. On Monday, I'll be kicking off a new series of posts on how scientists study evolution.

Informed Dissent

As many of you have already heard, the Discovery Institute has released its list of scientists who "Dissent from Darwinism." The New York Times decided to look a bit beyond the DI press release, and actually took a look at some of the signers and their motives. Other bloggers, including PZ Myers and Josh Rosenau, have already looked at the NYT article and the list itself. I'm not going to attempt to redo their work. Instead, I'm going to take a look at the DI's response to the New York Times piece.

Predictably, the Discovery Institute's Media Complaints Division is a bit upset about the tone of the article. They tried to make sure that the author of the Times piece received the proper spin before the article came out, but despite their best efforts the article still took a fair look at their list.

One of the things that upset the DI was the article's focus on the signers' disciplines. The Times article pointed out that biologists and biochemists make up a minority of the names on the list (30%, according to the Discovery Institute). The Discovery Institute doesn't think that this is worth considering. From the preemptive strike:

Of course, the list also includes many scientists specializing in chemistry, physics, engineering, mathematics/statistics, and related disciplines. But since Darwinists continually assert that their theory has implications for many other scientific fields, why shouldn't scientists from these other fields have the right to speak out? Moreover, it's remarkably cheeky for Darwinists to claim that only biologists have the right to express views about evolution when many of Darwinism's leading public defenders in America aren't biologists. For example, Lawrence Krauss of Ohio (who the New York Times deems qualified to defend evolution on its op-ed page) is a physicist, not a biologist. And Eugenie Scott, the director of the National Center for Science Education, has a degree in anthropology, not biology. If Chang raises this bogus argument in his article, I hope he also quotes my response.

At first glance, that seems to be a reasonable point. Why should it matter if scientists who "dissent" have experience in a relevant field, especially if the discipline of a scientist supporting evolution is irrelevant?

In this case, it comes down to the basis for the opinion. A scientist who is relatively unfamiliar with evolution but who supports it anyway is basically expressing his or her confidence in the scientific process and the scientific community. In the same way, I know little about relativity, but I recognize that the theory of relativity is considered by physicists to be well-supported. I understand the scientific process, and I trust physicists to do their jobs correctly. I do not presume to understand physics better than they do. In cases such as this, the background of the scientists is not all that relevant. What matters is the scientist's understanding of the nature of science and the role of the scientific community, because that is the foundation for the opinion.

A scientists who is dissenting from something in another field is making an entirely different - and much more radical - statement. What that scientist is saying is that he or she does not trust the scientists in the other discipline. Instead, that scientist is directly judging the work done in another field, based on some factor other than trust in the scientific process.

In those cases, the background of the "dissenting scientist" becomes much, much more relevant. We need to know something about the scientist's background in order to figure out how seriously to take that dissent. In particular, we need to know if their position is an informed dissent. We need to know if that scientist has the background needed to be able to independently, fairly, and above all competently assess the science involved.

Long time again

It's been a long weekend for me, and I haven't had much of a chance to blog - as both the people who look at this regularly know. Things have calmed down a bit now, so I should be getting back into the swing of things real soon now.

Rejoicing in Ignorance

PZ Myers already trashed this incredibly, painfully, dangerously, arrogantly stupid op-ed that appeared in the usually intelligent WaPo. PZ, as always, does a good job of informing this idiot that he is a stinky brown object floating around in the gene pool. Ordinarily, I wouldn't waste much time trying to add to what Myers wrote, but in this case I think there's something that he missed - and Cohen is just too damn stupid for me to resist commenting.

Richard Cohen wrote his article in response to an LA Times report about children dropping out of high school after repeatedly failing algebra. That is a legitimate problem, and it is one that we desparately, desparately need to address as a nation. We need to educate our children. All of them. Not just the ones who can afford to go to a private school, or the ones who are lucky enough to live in a good school district. Schools may be a local responsibility, but this has become a national problem, a national crisis, and it really is in need of a national solution.

Cohen, in his article, proposes a solution that is the intellectual equivalent of fixing an ingrown toenail by amputating the foot. His idea: if people can't pass algebra, don't make them take it.

Arithmatic - the part of math that Cohen claims to be competant at - teaches you how to answer a problem. Algebra teaches you how to set the problem up. It does, Cohen's pathetic assertions notwithstanding, teach you how to reason. In fact, it teaches you how to reason in ways that you really do use in everyday life.

Here's the thing, Gabriela: You will never need to know algebra. I have never once used it and never once even rued that I could not use it. You will never need to know -- never mind want to know -- how many boys it will take to mow a lawn if one of them quits halfway and two more show up later -- or something like that.

That's a word problem, and it is the kind of thing that algebra teaches you to solve. Here's another example: You're at the gas station on your way home from work. You don't have a credit card, it's three days until payday, and you know that you are going to need to put five gallons into the tank to keep the car running until then. Gas is at 2.50, and you have 15 dollars left. You also need milk. If you buy a gallon of milk, will you have enough money left for the gas you need?

Word problems suck, but you rarely run into anything else in the real world. Some people may be lucky enough that it doesn't matter too much if they miss the answer by a little bit. Cohen may have enough money to pay the landscapers no matter how many are working. Others aren't so lucky. Gabriella may need to figure out how far she can stretch that last 15 bucks.

In fact, the educational disparities in this country make it much more likely that Gabriella will find herself in just that situation. I grew up in the Bronx. We weren't as poor as others in the neighborhood, but we weren't exactly rich - we sat right on that border between working-class and middle-class. When you are coming from that kind of inner-city background, there aren't a lot of ways to do better. A fortunate few might have the athletic or musical skills that can lead to fame and fortune. The military is an option for some, but you need to get through high school before they'll take you - especially if you want training in something high-tech. You might win a lottery jackpot. Or you can get educated.

For most people, education is the only way out of poverty. Education is the only way to get a job that will pay something more than minimum wages. Education is the only viable path to a better life.

That's simple reasoning, but it apparently escapes Cohen. Of course, that's not much of a surprise. After all, he has this to say about reasoning:

Gabriela, sooner or later someone's going to tell you that algebra teaches reasoning. This is a lie propagated by, among others, algebra teachers. Writing is the highest form of reasoning. This is a fact. Algebra is not. The proof of this, Gabriela, is all the people in my high school who were whizzes at math but did not know a thing about history and could not write a readable English sentence. I can cite Shelly, whose last name will not be mentioned, who aced algebra but when called to the board in geography class, located the Sahara Desert right where the Gobi usually is. She was off by a whole continent.

Let me see if I've got that right: Writing teaches reasoning better than math. We know this because people who are good at math are bad at writing. An example of this is someone who is good at math, but doesn't know where the Sahara is. Yeah, writing has definitely taught this guy how to reason.

I'm not trying to argue that the humanities and social sciences are unimportant, or even that they are less important than math and science. They're all important. They're all part of a good education. They're all things that you need to know if you are going to succeed in our modern society.

Especially if you're not lucky enough to start out ahead.

Molecules and Evolution.

I spend a lot of time on this blog writing about evolution, and about Intelligent Design, and about why one is bad and the other good. This time, I'm going to try to do something a little different, and discuss one of the many lines of evidence for evolution: the similarities that we see when we compare DNA sequences from different animals.

The example that I'm going to use is hemoglobin from humans and chimps. Hemoglobin is a protein that is found in red blood cells. The hemoglobin picks up oxygen in the lungs and carries it to the different tissues. Hemoglobin is not a single molecule. It is a complex protein that is made of several smaller proteins. Each of those proteins is produced by a gene. We're going to look at one of those genes: alpha-globin.

The National Institutes of Health maintains a database known as GenBank. GenBank's basically Google for hard-core biology geeks. It's an international database where scientists store DNA and protein sequences. I rummaged around there, and came up with a alpha-globin DNA sequences from a human and a chimp. I'll put these sequences in pairs of lines, with the human sequence on top and the chimp sequence on the bottom.

Human: ACT CTT CTG GTC CCC ACA GAC TCA GAg AGA
Chimp: ACT CTT CTG GTC CCC ACA GAC TCA GAa AGA

Human: ACC CAC CAT GGT GCT GTC TCC TGC CGA CAA
Chimp: ACC CAC CAT GGT GCT GTC TCC TGC CGA CAA

Human: GAC CAA CGT AAG GCC GCC TGG GGT AAG GTC
Chimp: GAC CAA CGT AAG GCC GCC TGG GGT AAG GTC

Human: GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG
Chimp: GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG

Human: GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC
Chimp: GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC

That's only part of the sequence, but it's pretty representative. I showed the first 150 "letters" of the DNA sequence. There's one difference in these 150 bases, and the full sequence shows 99% similarity.

I've shown you that humans and chimps have very similar alpha-globin gene sequences, but so far that's all I've shown you. I haven't explained why I think that this similarity indicates evolution instead of something else. After all, it might just be that the gene does the same things, and that explains the similarity.

The gene does, in fact, do exactly the same thing in chimps that it does in humans. The gene makes a protein that is part of hemoglobin in both species. In fact, even though the genes are slightly different, the portion of the gene that I showed the sequence for makes exactly the same protein in both species. There is a difference in the DNA sequence, but not in the protein sequence.

Our proteins are strings of amino acids joined together in a line. There are twenty amino acids that we use in our proteins. The "genetic code" that tells our body the order that the amino acids should go in uses three letter DNA "words" to indicate each amino acid. There are four DNA letters, so there are 64 possible words. That's a lot more words than we need, so most of the amino acids have more than one "word" assigned in the code.

This means that there are literally hundreds of possible DNA sequences that could make exactly the same protein sequence that we see in human and chimp alpha-globin. The sequences that humans and chimps use are almost identical. They aren't exactly the same, but they are really close. The sequence for an orang-utan is a bit more different.

These slight differences, more than the similarities, are what makes us view this as evidence for evolution.

Bloody stupid media

It looks like the media got a bit pissed at Scott McClellan during the press briefing today. Why? Because they weren't promptly informed that the Vice President accidentally shot his hunting partner.

Useless whining schmucks.

They have been routinely mushroomed by this administration over the past five years on a virtually limitless range of subjects. They have very rarely demonstrated anger about any of this. (Of course, it's possible that they still haven't noticed.) They could have gotten angry about being lied to on a policy story - it's not like that hasn't happened - but, no. Instead, they pitch a fit because they weren't told about a story that looks to be more fodder for the Daily Show than serious news.

Dude, my bad.

oops.

Darwin Day

Today is the 197th anniversary of the birth of Charles Darwin. In honor of this, I've tried to pull together a mini-blog carnival of posts related to Darwin and evolution.

The Darwin Day website has a list of events from around the world that were (or are being) held today in celebration of Darwin's birthday. Scanning the list, it looks like most of these are scientific lectures about evolution and evolutionary biology.

Scientists aren't the only ones who are giving talks and making presentations today. Today is being marked as Evolution Sunday in hundreds of churches across the United States. This event was put together by a the same person who started the Clergy Letter Project, which has collected over 10,000 signatures of clergy who support teaching real science in the science classroom. For those interested, their website has a list of links to some of the sermons.

Darwin's birthday and evolution have gotten some attention from bloggers recently, too. PZ has a picture and an excerpt from a biography of Darwin. Actually, pictures seem to be a real theme for today. There are a couple of other photographs on blogs, Olduvai George has a nice portrait of a young Darwin, and Jennifer Forman Orth gives us an iconic image of Darwin in an unlikely place.

There are also several blog posts that have gone up in recent days that fit this occasion well. Tara Smith, over at Aetiology, was kind enough to write a post about how evolution relates to her own research. 10,000 Birds wrote a post earlier this week that presents a nice discussion of evolution and birds. Over at Daily Kos, there's a brief history of the evolution of humans since the big bang. Alun touches on the evolution of religion in a post, and there's an article on evolution written by Niles Eldredge over at The Virginia Quarterly Review. Finally, I wrote a small piece about how we get new species the other day that seems to fit the occasion.

Happy Birthday, Charles.

A reality-impaired perspective on current events

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

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

Going Different Directions in the Same Space

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Nasa PR

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

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

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

Patronage - Gotta love it.

Educational Disparities

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

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

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

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

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

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

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

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

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

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

But we should, damn it. We should.

Support, my ass.

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

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

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

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

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

Clash of Values

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

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

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

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

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

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

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

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

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

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

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

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

Politicizing Science

Work and a Blogger issue have kept me offline for the last day or two, and lots of other people have weighed in on the latest Bush administration attack on science, but I still wanted to throw in my .02.

The Bush administration apparently gave some political idiot with no experience or background in science a job as a public affairs hack at NASA headquarters. From this position, idiot-boy has seen fit to try (with a notable lack of success) to muzzle a well-known climate scientist, and to make sure that the NASA website doesn't do anything to piss off creationists.

The irony of all this going on at the same time that Bush is wandering around talking about the need to improve our standing in science is impressive, but that's really all that's remarkable about this event.

I'm pissed off about it, but entirely unsurprised. This is just the Imperial Presidency in action again. The sole mission of this administration right now is to make the president look good. Everything else comes later. We've seen it with regard to the warrentless wiretaps (sorry, I forgot, that's been rebranded as "terrorist surveilance"), we've seen it with Iraq, and we're seeing it now with science.

It's bad. It's fundamentally wrong. It's scary. It's threatening our democracy. But it's not a surprise.

Tangled Bank #46

Tangled Bank 46 is now available at the new Adventures in Science and Ethics digs. Enjoy.

reflexes

Wesley Elsberry, over at The Austringer, posted a link to a cool little test of reflexes. I blew about ten minutes on it, and found that it was difficult to make it past five seconds. Interestingly, though, I also found that if I could make it past the first five seconds, I would almost always survive for longer than 15 seconds. (Best time: a little over 22 sec).

One Nation, Divided.

There's an invitation, over at Radio Open Source, for bloggers to write their own version (BOTU) of the State of the Union address. It's a last minute kind of thing, so we get a few minutes or a couple of hours to pound out our attempts at something that the White House spends months at.

With that in mind, here's my take:
==

Today, more than at any other time since the Civil War, America stands divided. Half of all Americans, it seems, can almost always be counted on to have an opinion strongly opposed to the other half. The divide seems to stretch across almost every aspect of our culture.

We did not seek to become a nation divided, but that is what we are. The divisions have deepened in recent years, and at times it seems that the gap is unbridgable. But bridge it we must, for, as Lincoln said, "A house divided against itself cannot stand."

We cannot fail to close this gap, for if we do we will be faced with a crisis worse than what Lincoln was faced with. At that time, the divisions in the nation cut cleanly across geographical divides. Now they do not - colors on the map may paint a picture that looks clean, but these divisions run deeper, and they run through the middle of areas that are painted a single color on televised political maps.

How we choose to deal with this the divide will define our nation for years to come.

We have, at this moment, a choice between two paths. We can continue down the path that we have been - a path of ten-word policy soundbites, a path where distorting the arguments of your opponents is the norm, a path where every policy decision is treated as a win or lose contest by the two main parties.

That is the path to national destruction, but we can continue along it until it reaches its end. We can choose to fail.

We can also choose to succeed. That is the harder path, because it will require a massive shift in our political culture. It will require us to stop looking at our political opponents as the enemy, and it will require us to stop acting that way.

It will require us, most of all, to truly recognize that a diversity of ideas and ideals is a strength.

It may require us to compromise with each other, but it need not. Bipartisanship can be good, but sometimes a partisan position is the right choice, and sometimes it is better to pick one position than to try to blend two radically different approaches. The right choice will be different at different times, and on different issues.

We do not need to embrace the milquetoast middle. What we need is honest and open debate on the issues. We need to work with each other sometimes, and to not hold a grudge when we need to work against each other. We need to argue the issues fairly, and to conduct open debates.

We need, in short, to do nothing more than to recommit ourselves to a system of government that recognizes the value of opposition, and the strength of diversity.

The Spineless

PZ Myers has posted two different installments of Circus of the Spineless over at Pharyngula. The first features some of our favorite invertebrate animals. The second features some of our least favorite invertebrate humans. Enjoy.

All in a day's work...

There's nothing in the world like being a biologist on a beautiful Sunday in Hawaii.

One of the other grad students in the lab, Lindsay, is doing her dissertation work on the Laysan Albatross, and offered to show the rest of us her field site at Kaena Point. For those of you who aren't familiar with it, Kaena Point is the northwestern tip of Oahu. A fair amount of the tip of the island is a nature preserve, with good reason. A number of seabirds have breeding colonies there, Hawaiian monk seals are frequently seen on the beaches in the area, and there is a great deal of native vegetation. Oahu's environment has been massively disturbed by humans, and Kaena Point is one of the few natural areas left that hasn't been entirely ruined by human contact.

Lindsay is keeping tabs on this particular colony, checking on the progress of nests and eggs, figuring out which birds are mates, and who is responsible for which nest, and other such things. The rest of us were there partly to assist her and partly to sightsee.

This group of birds are the unmated crowd. They haven't yet been able to successfully mate, and are just hanging around the edges on the colony. Most of these had run across Lindsey before, and had the leg bands to show for it. Another couple did not, but took off before we got close to them. One wasn't so lucky, and got grabbed.

Kim's holding the bird for Lindsay, who is taking a blood sample. Nori is all set to apply pressure to stop the bleeding. The blood sample will be used for genetic work later on. (It's so much more fun doing the population genetics for a real population than it is working on things that only live in the lab.)

Lindsay and Kim take a second to pose for a picture with the bird. The bird is now wearing a pair of leg bands, and has donated a small amount of blood to further scientific advancement. Everyone looks so nice and calm. Even the bird almost looks content in this picture. It looked so nice and easy I figured I could give it a shot the next time. As it turns out, I was mistaken.



Yes, that is birdshit on my pants. A couple of minutes after that shot was taken, the bird managed to wiggle its beak free and take a couple of nips out of me. Lindsay got her blood sample, but I think the bird got more of mine.

By the time we got back to the parking lot, I was hot, tired, and sweaty. I had mud and birdcrap all over my clothes. I had a bit of sunburn on my face, except for a couple of little patches where the band-aids covered up some bird bites. I had scratches on my arms from albatross claws and from thorns. And I was totally and completely happy.

It wasn't just because we had seen monk seals and humpback whales, either. The charismatic megafauna are fun to look at, and it's nice to get some pictures of them, but the real joy comes from something else.

I'm not sure how to describe it, either. I think the closest I can come is that it's the joy of the active persuit of knowledge. It's what Feynman called the "kick in the discovery" and "the pleasure in finding the thing out." It's knowing that even if this isn't your project, your research, you are still part of something more than just a walk on the beach. It's wondering what makes things tick, and how this little piece fits into the puzzle of reality. It's the knowledge that no matter how much gets figured out this time, there will always be something else to learn later on. It's the childlike delight in poking at something just to find out what happens if you do. Being a part of the neverending story of science is just plain fun, and words alone simply can't do it justice.