A slow awakening.

Scientists, as a whole, are massively, epicly conservative.

That statement is not, of course, meant to describe the political leanings of most scientists - that's a whole different story. When I say that scientists tend to be conservative, I mean that in the sense of being cautious and slow to change. If you don't believe me, just ask any grad student who has the misfortune of presenting a new idea to their advisor.

It's not a surprise, really. Caution is a major part of scientific training. We are trained, trained again, and trained some more in the art of caution. We are warned about taking risks. We are warned not to try to squeeze interpretations out of the data that are not supported by the data. We are really pushed to note when others fail to be cautious. A healthy skepticism is the hallmark of a good scientist. Couple a tendency to be cautious with the "ivory tower" mentality that is still all too common in the academic world, and you have the makings of a population of individuals who will normally steer well clear of anything that has the stench of politics about it.

But a change, long overdue, is in the air. Slow and reluctant to anger and slower still to take action, like Tolkien's Ents, scientists are starting to wake up and get involved. Scientists are starting to find their voice, and an anger that has been kept submerged beneath the dignified facade of the academic community is starting to boil to the surface. It's been a long time coming.

There are any number of reasons for this anger, particularly in recent years. As Chris Mooney has documented in a recent book, the current administration has distorted scientific research on issue after issue. They have twisted, distorted, and outright lied about scientific research. The president has publicly belittled government scientists. In the view of the Bush White House, any time that some paid industry shill says something that contradicts the concensus of the vast majority of the scientific community, it means that "the jury is still out" on the issue.

Yesterday, Mooney summed up both the situation and the reason that we should care about it quite nicely in an OpEd piece:

Today we are facing a full-fledged national crisis over the role of scientific information in public policy-making. It's a subtle crisis in some ways, often obscured by the complexities of scientific disputation. But it is a crisis nonetheless, one that threatens every one of us because it affects not only public health and the environment, but the way we treat knowledge itself in American society.

That may sound alarmist to some. Personally, I think it might be an understatement.

We live in a world where science plays a huge part in all of our daily lives. It has become so important, so ubiquitous, that we no longer even notice it. It is, for most Americans, part of the natural background, no more noticable than the air. It is also, for most Americans, no less critical. Modern medicine and pharmacology, electronics and computers, the way we produce food, even things as mundane as the way we make sure that food gets distributed properly - all of these things are driven by recent advances in the sciences. If everything that is the product of a scientific advance made in the last fifty years were to vanish tomorrow, millions would be dead within a week. It's bad enough that so few people in the US understand science. Taking advantage of this, and trying to get people to misunderstand science, is utterly immoral.

Tangled Bank #38

The latest edition of Tangled Bank is available at Living The Scientific Life. There are lots of links to explore in this one, and lots of good writing.

The next edition of Tangled Bank will appear here on 19 October. Submissions can be sent to host@tangledbank.net.

Some musings on science and intelligent design

I wasn't really planning to be blogging right now. In fact, I was planning on being asleep right now. I put in a nice, relaxing, 13-hour day in the lab today, so I was feeling a bit tired by the time I was ready to go home. Unfortunately, the caffine is still with me, and I was too wired (and too tired) to get to sleep right away, so I decided to take a few minutes to catch up on some of the things that I'd missed during the last couple of days of the Dover trial. Boy, was that a stupid idea. Now, I'm too wired to get to sleep, too tired to get to sleep, and way, way too pissed off to get to sleep.

Strangely, though, it took me a while to figure out exactly why. The quotes from creationists that popped up in the articles weren't really anything that I hadn't seen hundreds of times before. Some complete schmuck of a lawyer asserts that evolution requires atheism:

Creationism requires a student to first affirm the creed that God created the heavens and the earth, and the theory of evolution requires that a student affirm the creed that there is no God. Both are exclusive claims, neither is scientific, neither can be empirically verified.

An utter jackass of a columnist tries to simultaneously argue that Intelligent Design isn't a scientific theory, and that it is science:

In truth, intelligent design isn't a scientific theory but a restatement of a timeless argument: that the regularity and laws of the natural world imply a higher intelligence -- God, most people would say -- responsible for its design. Intelligent design doesn't argue that evidence of design ends all questions or disproves Darwin. It doesn't make a religious claim. It does say that when such evidence appears, researchers should take it into account, and that the weaknesses in Darwinian theory should be acknowledged as forthrightly as the strengths. That isn't primitivism or Bible-thumping or flying spaghetti. It's science.

A second idiot with a law degree tries to paint the ID proponents as being on the side of America, mom, and apple pie:

As the courtroom drama unfolds in Harrisburg, consider the words of one parent — a mother of five — who lives in the school district.

Sheree Hied told a reporter: “I think we as Americans, regardless of our beliefs, should be able to freely access information — because people fought and died for our freedoms.” That’s what America represents — the freedom to explore all sides of an issue.

For some reason, I don't even find it as funny as usual that, despite all the assertions that Intelligent Design isn't religion, pretty much everyone pushing it is a proud member of the Christian right.

None of this is news to me. I'm used to seeing people who call themselves Christians pissing in the well of truth in a frantic effort to discredit evolution. I'm used to seeing assertions that evolution is a weak theory, packed with gaps. I'm used to reading the argument that when it comes to learning about evolution, students shouldn't be taught what the right answer is, they should get to pick whatever answer they believe is best.

So why, tonight, am I so totally pissed off?

It's probably got something to do with reading that bullshit after putting in a very long day, on a weekend, doing original research in evolutionary biology. It might have something to do with seeing a pair of lawyers and a columnist confidently, despite their own lack of scientific credentials, expressing the opinion that the work I do is nonsense. It might just be that I've finally reached the end of my patience. Or all of the above. Or all of the above, coupled with the revelation that a Dover High School janitor was apparently allowed to get away with burning a mural depicting human evolution.

Actually, after reading that last article again, I'm starting to feel my anger fade away a bit. More than anything else, it clarifies the issues for me, and reminds me that this really isn't about science. This is a conflict between worldviews, pure and simple. On one side, we have empirical fact. On the other, we have a group of people who find themselves, sadly, feeling threatened by what they believe empirical fact is telling them. I could almost feel sorry for them, if it wasn't for the way that they keep demanding that my children be exposed to the version of "reality" that they've cooked up to save their own religious perspective.

I see the future...

...and it's going to be light on updates for the next couple of days.

I've got my first real grant proposal due on 15 October, and my advisor wants to see a full draft by Tuesday. That's a bit painful, since I've barely started. But this is an in-house grant, and if he doesn't sign off as recommending funding, I don't get funded. So I'll be finishing a draft by Tuesday. There's even a chance that I can finish this without having my brain liquify and dribble out my ears. But I'm not optimistic.

Circus of the Spineless

The first edition of Circus of the Spineless is now available at Milkriverblog. Take a look. There's an enormous about of diversity within the inverts, and you'll find posts discussing strange worms, giant squid, flies, bugs, and a host of other invertebrates.

Some more on relevant expertise

It really never ceases to amaze me. Perfectly rational people, most of whom would never consider having their barber do their heart surgery (or their surgeon do their hair, for that matter), have no problem rendering judgement on the validity of complex scientific theories. In an earlier post, I mentioned an example of this happeining with evolution. At the moment, another example of this sort of thing can be found in the comments section of a recent post that mentioned Einstein.

Personally, I'd be the first to say that there are things in relativity that sound silly to me. They sounded silly to a lot of physicists when the theory was first published, too. Yet relativity was accepted fairly quickly by most physicists. It might be that relativity is wrong, and if so, I expect that we'll find that out someday. At the moment, however, a hell of a lot of physicists who understand the math and the experiments that have gone into establishing relativity think that it's a pretty good explanation of the way things work. That's good enough for me.

I still don't understand why this doesn't work for everyone.

Ahhh. A nice way to start the day.

I turned on the TV this morning, to some nice news. Tom DeLay, who has come to symbolize nasty politics at its worst, has just been indicted.

I'd love to blog more on this now, but it's time to run to school.

A few anniversary musings.

On 27 September 1905, a paper was published in the journal "Annalen der Physik". The paper, titled, "Ist die Trägheit eines Körpers von seinem Energieinhalt abhängig?" ("Does the Inertia of a Body Depend Upon Its Energy Content?"), was only three pages long. It was the fourth published by the same author that year. None of the four papers was immediately embraced by the scientific community. In fact, most were initially considered to be fairly controversial. At the time, the author of the papers had neither a doctoral degree nor an academic position. He had a few prior papers to his credit, but was essentially an unknown in the field of physics.

Within a relatively short period of time, those four papers would be recognized as having revolutionized the field of physics. The author, who was a relatively obscure Swiss patent clerk in 1905, would become one of the icons of our time.

One of the interesting things about these papers is that all of them were theoretical. Not one presented experimental data. What they did do, however, was make predictions that could be experimentally tested. As the various hypotheses proposed in those papers past test after test, they became more and more accepted within the scientific community. One of the equations - the one published in the 27 September 1905 paper - is probably the best known equation in physics: E=mc².

It is one hundred years to the day from the publication of that paper. At this time, science is faced with a group of people who claim that they have a brand new theory that explains how life started on the planet, and how individual species may have originated. Their theory has, thus far, not had much of an impact on the way that scientists actually conduct science. The proponents claim that their new hypothesis has sparked a controversy within science. The vast majority of the scientific community, including every major scientific organization in the United States, disagrees, saying that the "hypothesis" in question is too atrocious to make it even that far.

What separates them from Einstein? The proponents of the atrocious hypothesis would probably say that there isn't much that separates them from Einstein. More rational people disagree. Einstein worked within the established proceedures of the scientific community. They do not. Einstein's work made testable conditions. Theirs does not. Einstein's hypotheses were tested a number of times before becoming accepted. Theirs cannot be tested.

The biggest difference is this: Einstein did not appeal to the public and to school boards to have his work taught to public schoolchildren. Some of his work is taught to schoolchildren, but that came naturally, as his work gained respect and acceptance within the scientific community and made its way into textbooks.

Our modern Intelligent Design proponents have no hope of their work taking that course, and they know it. Their hypotheses make no testable positive predictions. This does not bother them much, however, because they do not appear to be investing much in the way of resources toward doing actual scientific research.

As a result, 100 years after Einstein's paper on mass-energy equivalence was published, there is a trial in Pennsylvania. The ID folks bypassed the normal scientific process, and forced their religiously-motivated fake science into a school, in flagrant disregard of the rights of those who do not want their children to be exposed to religious lies disguised as science.

Happy anniversary, Albert.

More amusement, courtesy of the Discovery Institute.

From an article in the York Daily Record:

Luskin said Miller inaccurately characterized intelligent design as a concept that focuses on what evolution doesn'’t explain. Luskin said intelligent design stands on its own as an explanation of life and the origins of species.

It is untrue that intelligent design requires a supernatural being. Intelligent design doesnÂ’t suggest who a designer is, Luskin said.

Contrary to Miller'’s comments, Luskin said, intelligent design is a testable theory.

Michael Behe, a professor of biological sciences at Lehigh University, has written about how protein and protein interactions could not evolve. His article was printed in 2004 in Protein Science, a publication of the Protein Society, Luskin said.

So let's see if I've got this right:
It is wrong to suggest that Intelligent design merely focuses on what evolution doesn't explain. ID stands on it's own, and makes testable predictions. This can be clearly seen if you look at Behe's paper, which argued that evolution can't explain the evolution of protein interactions.

Wow. I guess even a hint of anything that remotely begins to faintly resemble something that might once have been briefly exposed to intellectual honesty is just too much to ask from these guys.

More on Dover

I don't have as much time to blog tonight as I'd like. Instead, I'm working on a couple of things that aren't on my top ten favorite things list - designing PCR primers and grading lab papers. I did steal a few minutes here and there to look at some of the news stories relating to the Dover lawsuit, which opened today.

Some good articles:
There are three articles that are especially worth a look:
There's a truly outstanding article in the Washington Post, that provides a nice, simple explanation of evolution. There's a couple of places where I think that they might have simplified a bit too much, but as a whole this article is the best treatment of the issue that I have seen in the media in years. (hat tip: Pharyngula)
The New York Times also has some decent coverage, http://www.guardian.co.uk/religion/Story/0,2763,1579199,00.html.

The WaPo piece, in addition to the good coverage on evolution, has an amusing little quote from the Discovery Institute's John West:

Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.

(In fact, some "junk" DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.) In any case, West said, it is up to Darwinists to prove ID wrong.

A few things worth noting here:

The Intelligent Design "prediction" is interesting for a couple of reasons. To begin with, one must wonder as to exactly how they develop their expectations for this designer. They expect the designer to be intelligent enough not to leave lots of junk in the genome. Yet they are entirely unconcerned by any number of features in humans alone that smack of incompetent engineering. Why, for example, do our eyes have blind spots? Who put together the specs for my lower back? Flatfeet don't seem too intelligent to me, either. Of course, all of that pales next to the decision that was made to, as the old engineering joke puts it, run the sewer piping right through the middle of a recreational area. It's funny. Anything intelligent about the way that organisms are put together is, they feel, good evidence for an Intelligent Designer. Anything unintelligent about the way that organisms are put together, on the other hand, is just proof that we can't know the Ineffable Plan of the Designer. Who isn't necessarily God. Really.

Another interesting thing that I noted is that, somehow or another, the Discovery Institute doesn't seem to have focused anything in the way of research funding or energy into trying to find the purpose for the junk DNA. One really must wonder why. They are the main source of ID funding, and they think that they have a testable hypothesis out there. So why were they lobbying school boards instead of testing that hypothesis?

Finally, it is not up to us to prove them wrong. That's not how it works. If you think that you have come up with a good hypothesis, you need to go out and test it. You don't get to say, "This is how things are, and I'm right about that unless you prove me wrong." That sort of thing might work on a kindergarten playground. It doesn't work in science.

Dover News carnival.

This morning, I took a few minutes to look at a number of the various news articles about the upcoming Dover Intelligent Design lawsuit. The articles that I looked at seem to present a wide range of views, and a few of them were actually quite good. Initially, I was just planning on commenting on one or two. After reading a few, I thought it might be a little more fun to present a bunch of them blog-carnival style.

So, without further ado, here they are: the good, the bad, and the ugly.

The good:

One of the best things about Google's News Search is that it allows you to read articles that you would not ordinarily have access to. In particular, it gives you access to local columnists at small newspapers. The quality of these columnists varies widely - almost as widely as the quality of blogs. However, there is at least one thing that can be said for the local columns: they give you a chance to see a take on a story that isn't the same as that in the endlessly duplicated wire-service stories.

The Dover coverage in the Sunday papers included a couple of pretty good articles from local guest columnists. In the South Carolina newspaper The State, there is an article by Furman University professor Wade Worthen. Worthen tackles, head on, the major reason that the debate over Intelligent Design has taken place in the public arena: "There is no debate within the scientific community; that's why intelligent design proponents seek to legislate their truth in the political arena."

A former high school science teacher wrote a good op-ed piece for the Springfield News-Leader. Mr. Cunningham, pulling no punches, begins his article by presenting his opinion of how Intelligent Design should be taught: "Since intelligent design has no scientific substance, there is no controversy with evolution to teach to a science student. What should be taught about intelligent design, if anything, is that it is a hoax." The wording may not be the most diplomatic I've seen, but I really can't argue with that assessment. He also makes a good point about the scientific status of Intelligent Design: "If intelligent design had any substance, young biologists worldwide would be straining to win laurels by disproving current evolutionary theory in favor of intelligent design." Truer words haven't been spoken. There's nothing like being right at the center of a big, massive, ugly, blood-on-the-floors scientific debate when it comes to making a name for your self.

Brad Kurtzburg, writing for Elites TV, put together a nice little piece that tells the story as-is, without searching for "balance". I particularly liked the way he juxtaposed two short paragraphs:

The Dover school board claims it just wants students to be aware of the existence of intelligent design as an 'alternative to evolution.' It also denies that intelligent design in 'religion in disguise.'

The school board is being supported by The Thomas More Law Center which uses litigation to promote what it calls 'the religious freedom of Christians and time-honored family values.'

Bill Toland of the Pittsburg Post-Dispatch has two articles, both good, on the upcoming trial. The first article starts out on a light note:

If "intelligent design" supporters weren't so quick to rebuke those who connect their mission to the Bible, it would be tempting to borrow from the Old Testament and describe the upcoming federal trial over the issue as a legal version of David vs. Goliath.

Instead, we'll let the defendants in this case, which pits Dover Area School District against parent plaintiffs, to describe the trial in their own words.

"It's almost David vs. Goliath," says Richard Thompson, of Michigan's Thomas More Law Center, which is defending the York County, Pa., district.

The rest of the article is a touch more serious, and raises some excellent points that have been overlooked in too much of the press coverage:

"It's an attempt by the ACLU and Americans United for the Separation of Church and State to intimidate this tiny school district in Pennsylvania," he said. "They want to make an example of this small school district."

The parents, their attorneys and most scientists and educators see it the other way around.

Intelligent design is pseudo-science, they say, but a well-orchestrated one, funded by Christian literalists who oppose the theory of evolution and promoted slickly during the past 10 years by religious groups. They say intelligent design supporters are disingenuous when they claim their argument has no religious implications, because intelligent design's top advocates have already let the cat out of the bag. Intelligent design opponents point to the words of Phillip Johnson, devout Presbyterian and father of the theory:

"Our strategy has been to change the subject a bit so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools."

Toland's second article is largely based on an interview with Ken Miller, and discusses the scientific failings of Intelligent Design in some depth.Perspectivess from other scientists are featured in a couple of more articles - one good example is from a North Carolina TV station.

Mary Warner, writing for the Newhouse News Service, has an a excellent article in the Cleveland Plain-Dealer. She gives a nice description of the scientific standing of evolution:

Evolution - the theory that all life descended from common ancestors over eons through natural selection - is a mainstay of modern science.

"There are probably more scientists who believe Elvis is alive" than scientists who reject evolution, says Ed Larson, a Pulitzer Prize-winning author on America's battles over evolution.

She then goes on, later in the article, to give a slightly different perspective on the matter, from one of the lawyers for the defense:

Attorney Richard Thompson, arguing now for the board, says its purpose was "valid and clearly secular" - to inform students of "the existing scientific controversy" about evolution.

That's a vitally important point that all too frequently is missed when reporters try to be balanced: this is not a controversy of two evenly matched sides, or even one where a significant minority is struggling against the majority. This is a "controversy" where an extremely tiny minority (the Discovery Institute claims 400; there are hundreds of thousands of scientists in the US alone) is waging a political battle against the vast majority of scientists. This point is also made in a column available on the News 24 website.

The York Daily Record continues it's extraordinarily good coverage of the Dover Biology policy with a few more noteworthy articles. One of these examines what is at stake in this trial. The other http://ydr.com/story/doverbiology/86717/ discuss the issues surrounding the testimony being demanded from reporters for two local papers.

Last in this category, but by far not least, there is an interesting column written by a Presbyterian pastor from Virginia. I'm not sure that I agree with everything that he's written in the article, but the overall perspective is definitely thought-provoking.

The Bad: (or at least not too good)

Two of the major wire services, AP and Reuters, have written articles that are, for the most part, factually accurate, but which make far too much of an effort to "balance" their coverage by presenting statements from both sides. As a result, both articles let some real whoppers from ID proponents slip by unchallenged.

The AP article has this doozy, from the head of the law firm representing the defense:

"All the Dover school board did was allow students to get a glimpse of a controversy that is really boiling over in the scientific community," Thompson said.

It might have been reasonable to note at this point that virtually every major scientific organization in the country has issued some sort of statement saying that Intelligent Design is unscientific, or that the body of peer-reviewed Intelligent Design research is small enough that even an incompetent carpenter could count it with ease.

In the Reuters article, the Discovery Institute's Director is given a pass on this bit of hyperbole:

"It's a disturbing prospect that the outcome of this lawsuit could be that the court will try to tell scientists what is legitimate scientific inquiry and what is not," West said. "That is a flagrant assault on free speech."

It really would have been reasonable for the reporter to note that the lawsuit does not seek to limit scientific research in any way. It simply wishes to limit material taught in public school science classrooms to actual scientific material, rather than badly-disguised religion.

A community columnist for the La Crosse Tribune seeks balance, as well:

There is one more rule to this debate. Students must listen to each other and be respectful of other ways of looking at the issue. Evolutionists need to give up their attitude of intellectual superiority. Intelligent design or creation advocates need to give up their attitude of moral superiority.

Debating evolution and exposing its flaws might inspire some young student to find the answers for those flaws. Then again, maybe some other theory is correct. Maybe this kind of critical discussion will show us that alternative answer.

Would that it were that simple. I'd personally love to see students taught about the controversies within evolutionary biology. Unfortunately, there are two problems with this approach. The first is that doing so would require students to learn far more biology than they have been. This isn't necessarily a bad thing, but it may not be realistic given time and resource constraints. The second problem is even simpler: none of the things that the Discovery Institute people claim are "flaws" in evolutionary theory actually are. Adding them to the curriculum would reduce the quality of scientific education, not improve it.

The Christian Post doesn't seem to be any more of a fan of balanced coverage than I am. Unfortunately, their lack of balance leans far to the other side - they include a lengthy section on Behe, but don't mention any of the scientific opposition to his claims.

The Ugly:
In addition to letting you see columns from places you never would have otherwise looked, Google News also lets you see letters to the editor that you never would have seen. I'm convinced that seeing the columns is a good thing. I wonder a bit about the letters.

A letter to the Danville Advocate-Messenger raises a number of old creationist talking points, then concludes with this gem:

Yet it [evolution] continues to be promoted as fact. Why? Because evolution is nothing more than the denial of the existence of a Creator.

The greatest asset evolutionists have is the reluctance of ordinary people to explore and learn the true scientific evidence - and therefore the deception continues to be perpetrated. You don't have to be a scientist or engineer to understand the facts. Many competent scientists have written a great deal about these truths in plain, everyday English.

My study of scientific research proves that "we are fearfully and wonderfully made," or in other words, we have been awesomely, intelligently designed by an infinite, benevolent God. The question is: Are we really looking?

His study of scientific research.... It's funny. I didn't find this sort of thing to be quite so irritating a couple of years ago. Of course, I've invested at least a couple of thousand hours in studying evolutionary biology over the past couple of years.
OK. It is true that you don't need to be a scientist or an engineer to understand the facts. But it helps. (Actually, I'm not sure why someone would expect an engineer to understand evolutionary biology. I don't necessarily expect them to not understand it, but it's not exactly something that they are trained in.)
The problem here is that the creationists are good at putting their message into simple and easily understood prose. Scientists are not as good at this. The fact that the entire message of creationism is simplistic plays a large part in this, as does the fact that science is vastly complex.

The final letter to the editor, and final entry in this post, comes from someone who has a very valuable message to share. Youwon'tt find it in the text of the message - it's just in the subtext. The message is this: there really are places for kooks outside of the internet.

That wraps it up for this brief and biased digest of the Sunday paper coverage of the Dover Battle. I hope you've enjoyed it.

Responsibility

There were anti-war rallies today in several different cities. Watching the news reports from the rallies, I am left with painfully ambivalent feelings. As I've written before, I very strongly feel that we have an absolute responsibility to do everything in our power to make sure that we don't leave the Iraqis worse off now than they were when we invaded.

I don't think that anyone can argue if I say that the Iraqis are worse off now than they were when we invaded. Being freed from the yoke of a dictator is a fantastic thing, of course, but it's probably not quite as wonderful as being able to walk down the street without wondering if you are about to become another innocent bystander.

Some argue that we are the cause of the violence, and that things will get better if we leave. We are the cause of a lot of the violence, but I don't know that it will get better if we leave. Al Qaeda didn't have any significant connection to Iraq before we invaded, but they are sure as hell there now, and they really are opposed to democracy. I see absolutely no reason to believe that they will simply leave Iraq alone if we pull out. I think it's more likely that they will continue to fight against whatever government is in place when we leave.

Let me be clear. I do not like this war. I do not think it was a good idea. I do not think that the administration took any of their prewar responsibilities - making sure that they were using all the best intelligence available to make their decisions, listening to the army chief of staff, planning what to do if we weren't greeted with candy and flowers, postwar planning in general - seriously. At best, the administration was incompetent, at worst they were downright dishonest.

Mistakes were made.

Scratch that. The passive voice doesn't do that justice. People in the administration, starting with the president and the cabinet, made lots of mistakes. Some of them were minor, but a tragically large number have been major. They have gotten us into a war, their pitiful excuse of an exit strategy didn't work out, and now we're in a bad place. Those things have happened, and they are responsible for them, although it is extraordinarily unlikely that they will ever be held accountable in any real sense of the word.

Unfortunately, they made those mistakes while leading the United States. That means that we are responsible for them, too. It doesn't matter what you think of Bush. It doesn't matter whether or not you think that his victories have been "legitimate". He is the president. That is reality. How he became president does not change that fact. Whether or not he should have the power to drop the entire country into a quagmire that makes quicksand look like rock is irrelevant. He has that power, and he has used it. And there we are.

Right now, one of the many forces holding us in that muck is responsibility. We have a responsibility to do our best - our full, complete best - to fix the things that we have messed up. We may not be able to do so ourselves, but we still have a responsibility to make sure that things do get fixed. Maybe we can find someone else who would be willing to help, but unless or until that is firmly in place, we are stuck.

The thing about this particular force, though, is that it is largely self-imposed. Nobody is standing there with a stick forcing us to do our duty. Responsibility can only hold us there as long as we decide to let it. Ignoring, escaping, or denying our responsibility has a seductive allure. We can pull our forces out of Iraq in a very short period of time, if we so choose. We don't have to let any more of our men and women come home maimed or in body bags. We don't have to stay in a situation which has made IED an acronym almost as familiar and unpleasant as IRS. We can just walk away any time we want.

It gets better - if we pull out and walk away, we won't have to sacrifice anything tangible. It won't cost us a single dollar - in fact, we'll save about a billion dollars a day. That's enough money to fund an enormous number of schools. In less than a year, the savings will cover the clean-up costs from Katrina. The deficit will be reduced, and we won't be putting such a huge burden on our children and grandchildren.

So what the hell, why not. After all, what's responsibility. It's just a word, right? It's not even like it describes something concrete - it's nothing but an abstract concept. It's not even one of the sexy abstract concepts, like freedom, or liberty, or mom's apple pie.

In my eyes, however, responsibility is a noble cause. Responsibility means doing what is hard, for no other reason than that it has to be done. What frustrates me almost to the point of rage is that I seem to be almost the only one who feels this way. To my right, the world seems to be filled with people who don't think that things have really gone all that wrong. To my left, people seem to be focusing on bringing everyone back from Iraq now, regardless of our duty. Why is it so hard to admit what the rest of the world knows - we've really screwed up this time. Why is it so hard to admit that making mistakes also makes us responsible for making sure that they are fixed?

The tools of the trade

I have finally reached the point where I have assembled enough information to begin working on my PhD project - or at least the preliminary experiments. I don't know how well this will work, but I'm going to try to put together a series of posts as I go along that explain, as simply and clearly as I can, the kinds of things that I am doing, and the reasons that I am doing them.

One of the things that I'm going to be trying to do with this series is to learn how to talk about science at a level that can be understood by people who don't have much of a background in science. Because of that, I would greatly appreciate critical feedback and suggestions. The first real post in the series will go up tomorrow, and I'll try to get something in the series up at least every couple of days.

Chutzpah, pure chutzpah

There's an article in today's York Dispatch about the upcoming Intelligent Design lawsuit. This particular article discusses the rats leaving the sin Discovery Institute's principled decision not to support the Dover school district in this case. Most of the quotes from the various DI talking heads is the usual stuff, but there was one statement attributed to Casey Luskin that displays a disregard for reality that is below and beneath even the rather loose standards of the Discovery Institute:

He [Luskin] said the Discovery Institute is "not trying to hinder their case in court," but the organization wants intelligent design to be debated by the scientific community, not school boards

"Debated by the scientific community, not the school board."

I was honestly shocked to read that. After almost a decade of following the various creationist strategies, I thought I'd seen every type of dishonesty possible, but this really takes things to an all time low.

"Debated by the scientific community, not the school board."

That's just about as far as you can get from everything that the Discovery Institute has actually done. Their fellows spend inordinate amounts of time pushing their philosophy in political forums, particularly educational ones. The scientific output of the Discovery Institute, measured in terms of material published in peer-reviewed scientific journals, is absolutely pitiful. The output of the Discovery Institute, measured in terms of press releases, op eds, letters to the editor, and other attempts to push their message in the public arena, is impressive.

But don't just take my word for it. The Discovery Institute has a list of "Peer-Reviewed and Peer-Edited Publications Supporting the Theory of Intelligent Design" up on their website. Scanning down the list, one can quickly count 34 separate items. Looking a bit more closely, one finds that three items are listed twice - once in the "featured articles" section at the top, then again in the appropriate section further down. Looking closer still, one finds that they listed a book which was edited by two of their fellows as one item, and then listed five chapters from that same book as separate items.

The following items are listed as "Articles Supportive of Intelligent Design Published in Peer-Reviewed Scientific Journals":

• S.C. Meyer, “The Origin of Biological Information and the Higher Taxonomic Categories,” Proceedings of the Biological Society of Washington, 117(2) (2004): 213-239.
• M.J. Behe and D.W. Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, 13 (2004): 2651-2664.
• W.-E. Lönnig & H. Saedler, “Chromosome Rearrangements and Transposable Elements,” Annual Review of Genetics, 36 (2002): 389-410.
• D.K.Y. Chiu & T.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4(3) (September 2002): 766-775.
• M.J. Denton & J.C. Marshall, “The Laws of Form Revisited,” Nature, 410 (22 March 2001): 417.I.
• M.J. Denton, J.C. Marshall & M. Legge, (2002) “The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology 219 (2002): 325-342.

That's a grand total of six articles that have been published within the last five years, for an average of 1.2 articles per year. That publication rate wouldn't be considered to be overly impressive coming from a single scientist, let alone from ten. It's even less impressive when you consider the fact that the DI's center for The Renewal of Science and Culture has about 40 fellows.

Over the same period, the Discovery Institute and its fellows have released dozens, if not hundreds, of press releases and op-eds advocating that their views be taught in public school classes in various parts of the country. Its fellows have testified before school boards and textbook adoption committees. They have waged, in short, a very agressive public relations campaign (even going so far as to hire a well-known public relations firm) trying to build popular support for their views.

Those are not the actions of a group of people who want to debate their views within the scientific community. Those are the actions of a group of people who are hoping that they can use a miniscule number of peer-reviewed articles as a scientific fig leaf to cover a religious agenda. If they really wanted to debate their views within the scientific community, they would be doing just that. They would be formulating and testing hypotheses, doing experiments, writing papers, and focusing their efforts at convincing scientists. They would certainly not be putting the vast bulk of their efforts into public relations.

They also wouldn't have been saying things like this:

[from a DI press release] The Discovery Institute today faulted defenders of Darwin's theory for refusing to defend their views before the Kansas State Board of Education and for being afraid to answer tough questions about the scientific problems of modern evolutionary theory.

“Darwinian scientists showed contempt for science and the citizens of Kansas by refusing to appear before the State School Board,” said Dr. Jonathan Wells, a biologist at the Discovery Institute’s Center for Science and Culture.

"Debated by the scientific community, not the school board." What utter, unmitigated hypocrisy.

Tangled Bank 37

The latest edition of Tangled Bank is available at Milkriverblog. Tony's clearly put a lot of work into this, and it's paid off. Enjoy.

Toxic Soup

Over the past couple of days, several articles have appeared in various places about the dangers from toxic materials in areas devastated by Katrina. All have discussed the environmental risks, health risks, and other dangers. The picture that these articles paint is grim. Even some of the more upbeat articles, contain phrases that are a bit alarming ("a toxic gumbo like we've never seen,"). The optimistic end of the timeframe for the entire city being safe to resettle is expressed in months. The pessimistic end... let's just say that it's pretty pessimistic.

The contamination comes from many sources. In fact, it is not at all an exaggeration to say that the contamination is coming from virtually everywhere. Many of the articles have listed household items as a source of contamination, and a few have even mentioned some of the more common household hazards. I'm going to do something that is (I think/hope) a little bit different. I'm going to take a look, in detail, at the household hazardous materials that are in my carport, and at the dangers of each.

It's actually pretty easy to find out what hazards, if any, are associated with items in your house. One of the various federal requirements (I believe it's OSHA's, but I'm not positive) is that Material Safety Data Sheets (MSDS) be available for pretty much any kind of chemical product that's sold in the US. They aren't very hard to find, usually. It's usually just a matter of going to the manufacturer's website and hunting around until you find them. If they're not available there, you can usually find them through google if you're persistent enough. I did that for the stuff that's out in the storage cabinet in my carport.

I went out, took a quick inventory, went on line, and started hunting. Listed below is what I found. I've grouped things into categories based on a rough assessment of how bad they are. The links on the item names should bring up MSDS sheets.

• Mostly Harmless:




• Fertilizer, 16-16-16, ~5kg. The ecological effects are listed as unknown, and there might be some. Large increases in the nutrient content of a body of water can lead to algal blooms and other unpleasantness. Right now, there's no way to know if the household fertilizer releases will have any impact.
  
• RoundUp weed killer, ~1L. I really wasn't expecting the weed killer to wind up in this category, but it is minimally toxic and readily biodegrades.




• Not Too Bad




• Raid roach spray, 3 cans, don't know how full. The MSDS isn't all that helpful. All the ecological and long-term toxicological sections are listed as "unknown".


• Bleach, ~6L. Poisonous and a short-term health risk. Long term/environmental also unknown.


• Windex. ~2L. Not too bad healthwise, but there's a "keep out of watersheds" warning in the MSDS.




• Not Good




• Prestone Anti-Freeze (about 1L or so). Ethylene Glycol is not good for you. It's a poison and it can cause mutations. In addition to birth defect concerns, this also raises cancer concerns. According to the MSDS, no conclusive link has been found between antifreeze and cancer, but the short-term toxic effects alone are enough to put it into this category.


• 10W40 Motor Oil, 3 quarts. The toxicological and ecological sections are listed as "unknown", but I don't think it takes an Einstein to figure out that motor oil is bad for stuff.


• Acetone, ~500mL. Not good to breathe, not good to drink.


• lacquer Thinner, ~5L. A tasty mix of methanol, xylene, toluene, ethyl benzene, and acetone. Yummy.




• No Clue




• Paint. Don't know what kind - the label is covered with paint. 2 or three partially congealed cans of this stuff. It's blue, but that's about all I know.


• One unlabeled jar of something that I'm almost sure is more fertilizer. I seem to remember borrowing something from one of the neighbors to use on an orchid. (This kind of thing is worth a hefty OSHA fine when it happens in a lab.)

That's just from one small carport locker. Inside the house, there's a whole cabinet of assorted cleaning supplies. Ammonia, oven cleaner, scrubbing bubbles, more bug spray, more windex, and who knows what evil is lurking under the sink.

If half that stuff spilled in the lab at one time, I'd have to call the environmental safety folks to come over, clean it up, and drop 50 pounds of paperwork on my head. If it spills in my house during a flood, and is still there when I get home, someone (probably me) is going to have to clean it up. Probably nothing bad will happen right then, and probably the exposure won't cause long-term problems, but it might. The risk is definitely there. But that's only a very small, very localized part of the problem.

Take the list from my house, and assume that it is excessive. Assume that I've got more hazardous gunk in my house than 75% of the general public (actually, it's probably no worse than average). If so, and assuming that only 10,000 homes were badly flooded in the New Orleans area, that's still a total spill 2,500 times greater than the quantities I listed above. Let's put that into perspective: 1250 L of acetone, 12,500 L of thinner, 1875 gallons of motor oil, and that's just the start.

That's also just the household chemicals. There's still gas stations, dry-cleaners, carpet-cleaners, and a whole mass of other small businesses that deal with lots of chemicals. Then there are the landfills, and the superfund sites, and the petrochemical industries, and everything else. "Toxic gumbo" is probably an understatement. This situation is simply a nightmare. So far, the major oil spills alone total millions of gallons. There have been several news reports indicating that there is so much oil in some of the flood-deposited gunk that the testing labs are having problems detecting anything else.

And it gets worse.

Some of the stuff is going to wash away fairly quickly, but some of it is going to settle out into the sediment. The sediment is the mud that people are going to have to clean out of everything. That's not going to be easy. Some of that sediment is going to linger - maybe not in houses, but in yards, and parks, and other places.

A lot of the stuff that washed away quickly, and a whole lot of the stuff that settles out, is going to wind up in nearby bodies of water, like Lake Pontchartrain. Besides the short-term ecological effects, which are simply impossible to predict, there are also long-term effects that are impossible to predict. One question is going to be how much of the toxic material is going to accumulate in tissues. Will fish from that lake be edible any time soon? What about shellfish in the Gulf near New Orleans?

The sad and simple truth is that we just don't have any basis for predicting any of the effects of the toxic disaster. Nothing like it has ever happened in the United States before. It will, quite literally, be decades before we know what the long-term effects are. There are probably going to be some, and they are probably going to be bad, but that's about all we can say right now.

Cleaning this up is going to be difficult, but it is not going to directly involve most of us. Preventing a repeat of this, on the other hand, is something that should involve all of us. Do yourself, and the rest of us, a favor. Go out to your garage, or carport, or shed, or whatever. Look at the hazardous materials that are there, figure out what you really need to keep, and properly dispose of the rest. The regulations for this will vary from place to place, and it may be inconvenient. Do it anyway. After all, next time the toxic sludge might be in your livingroom.

DNA and RNA (and Birdnow).

PZ Myers has, over at Pharyngula, taken issue with a remarkably ignorant essay written by Timothy Birdnow. Birdnow has responded with a new blog, PZ has responded to part of the response, and so the fun begins. At the risk of being seen as just piling on to an easy target, there are a couple of important points that I don't think have been raised yet. The first has to do with exactly what constitutes the "building blocks of life"; the second has to do with basic competence.

Below is a quote from the exchange between Birdnow and Myers where the question of the "building blocks of life" is raised:

Birdnow:
What, you may ask, is the connection between Einstein`s proof of atoms [his explanation of Brownian motion] and Darwinism? Darwinism argues that all life evolved from a less complex state. Following the chain of life backwards, one eventually comes to the most basic unit of life-deoxyribonucleic Acid (the DNA molecule). The DNA molecule is composed of the even simpler RNA molecule, and is the fundamental building block of life. It is the largest, most complex molecule in nature. According to Einstein`s theory, the original DNA (and RNA) Molecules should not have formed and survived since there are being constantly buffetted by energized atoms. The establishment of life required energy, and that energy meant that the nascent DNA was exposed to more energetic particles which should, logically, have prevented the formation of such a large and complex molecule. That this molecule not only formed but spread suggests different mechanism at work then those proposed by the Darwinists.

Myers
DNA is not made of RNA. They are two molecules with similar structures, but different sugar backbones and a small difference in the bases.

Birdnow:
Oh, so now we have two completely different molecules as the building blocks of life! Life did not begin once, but twice from seperate building blocks! You know, Doctor, that DNA is fundamentally an advance on RNA. You are playing games here, and it does not disprove a thing I have said.

Both DNA and RNA are very important to life, and they are currently important for different reasons. They are also both representatives of only one of the types of molecule that are of fundamental importance to life. Both DNA and RNA are macromolecules (big molecules) made by stringing together (polymerizing) a large number of smaller molecules. DNA and RNA are both members of the class of macromolecules known as nucleic acids. Nucleic acids have three main parts: A sugar molecule, a base, and a phosphate group. DNA and RNA differ in the sugar that they use (RNA uses ribose; DNA uses a ribose that is missing an oxygen). Both use four different bases, and share three of them (adenine, guanine, and cytosine). The fourth base in RNA molecules is uracil, while the fourth base in DNA is thymine.

In addition to nucleic acids, there are also proteins, sugars, and lipids (fats). All of those are also critical to life as it now exists. Proteins are important in allowing cells to carry out chemical reactions, sugars are important for energy storage and transfer, and lipids are important in creating the barriers that separate the inside of the cell from the outside. All of these are fundamental building blocks of life as we know it.

I've stressed that these are important to current life for a reason. Just because something is critically important now does not mean that it has always been critically important. For example, the keystone at the center of an arch is totally critical to the structural stability of the arch. Remove the keystone, and the whole thing collapses. The keystone, however, is the last structural component added to an arch. Prior to the placement of the keystone, the structural stability is provided by scaffolding. After the placement of the keystone, the scaffolding is redundant, ugly, and unnecessary, and it is quickly removed.

I'm not trying to suggest that there used to be some sort of "scaffolding" that took the place of one or more of these types of macromolecule - we don't know that. I'm simply trying to point out that the current importance of nucleic acids does not necessarily imply that nucleic acids were always as important as they are now. That is one of the things that origin of life research is currently examining.

It is possible that neither DNA nor RNA was critically important to the development of life. It is possible that both were. It is possible that either (or both) were very important, but not in the same way that they are today. Right now, those aren't questions that we can answer.

What I can say, however, is that Birdnow is entirely wrong when he claims that "DNA is fundamentally an advance on RNA." DNA is better than RNA when it comes to the long-term storage of genetic information. RNA tends to degrade relatively quickly, and stability is important if genetic information is going to be reliably stored and transmitted to the next generation. RNA, however, is better than DNA at a number of other tasks. In addition to being used to take the information from DNA to the ribosomes for use in constructing proteins (messenger RNA), RNA strands also make up part of the ribosomes (ribosomal RNA). RNA is also used to collect the amino acids that are added to the protein (transfer RNA). For these tasks, a single-stranded RNA molecule works much better than double-stranded DNA.

DNA is no more of an advance over RNA than humans are an advance over the cockroach. DNA is different from RNA and does different things than RNA. Similarly, if you want a poem written or a city built, you want a human. If you want something that is likely to live through a nuclear holocaust, the cockroach is a better choice. Along the same lines, the hammer is not an advance over the wrench. Different tasks simply call for different tools - and this happens to be as true within the cell as it is at a construction site.

In addition to the misconceptions over DNA and RNA, Birdnow's uninformed diatribe also provides an illustration of a very interesting phenomenon: the tendency of people who have a minimal understanding of science to believe that they are as qualified, if not more qualified, to comment on scientific issues as professional scientists are. Let's take another look at part of Birdnow's statement:

You know, Doctor, that DNA is fundamentally an advance on RNA.

Later on in the post, he goes on to complain of part of Myers response:

This is the old ``I know more than you and I say so`` canard.

When Myers complains - entirely correctly - that Birdnow displays a massive knowledge deficit in the field of biology, Birdnow is apparently highly offended:

Boy, if that isn`t the pot calling the kettle black! The main reason I wrote this was because I became increasingly irritated with the monstrous arrogance and utter closed mindedness of Darwinists such as Dr. Myers. Perhaps, Dr., if you found this essay hard to understand you should find yourself a fifth grader to explain it to you. You don`t seem to have a command of logic.

Birdnow, who is a property manager, apparently feels that his understanding of biology is secure enough that he can tell a professional biologist what is what. Similar beliefs about the nature of science seem to be very common, as was pointed out over at Photon in the Darkness a while back. The people over at American Thinker, who posted the original Birdnow piece, seem to find this completely normal. Yet, in virtually any other area of American society, such beliefs would be considered completely ridiculous.

In fact, scientists who dare to suggest that they might be more qualified to comment on scientific matters than non-scientists run the risk of being branded as "elitists". It's not elitism, folks, it's specialization. Modern society is far, far too complex for everyone to be good at everything. Most people select career paths that are specialized fields, and they are (normally) better at their own field than they are in other fields. This means that they are (normally) better able to develop informed opinions about matters within their fields than are people who lack the strong background in that area.

I suspect that Tim Birdnow knows a hell of a lot more about property management than I do. I also suspect that when the roof is leaking at a property that he is responsible for, he calls a roofer to fix the problem, not a plumber. Yet, despite this, he thinks that he has a sufficient knowledge of biology to publicly claim that, "Any way you look at the issue, Darwinism is on the ropes."

Mr. Birdnow, if I tried to tell a plumber how to fix a sewer problem, I'd look like a fool. And rightly so. If I tried to tell you how to manage property, I'd look like a fool. And rightly so. When you try to tell me that you know more about biology than I do, you look like a fool. The truth is that, as far as anyone can tell from reading your post and response, you don't know diddly squat about biology, geology, or paleontology. Your writing is, in fact, jam packed with misconceptions, misunderstandings, and outright errors.

When I tell you that, I am not being arrogant any more than a teacher is when they point out errors in a student's test. I am presenting an evaluation of your work that I am actually qualified to make. PZ Myers is even more qualified (much more qualified) to make that evaluation. Both of us have taken numerous classes in biology, both of us have undertaken research, both of us know the field. We understand biology, and we can tell when other people don't. You don't.

Suggesting that I may be more qualified than you are to determine how well you understand biology is also not "elitism". It is specialization. The fact that I am a biologist does not make me any better or worse, in a general sense, than a butcher, a baker, a property manager, a janitor, or any other trade. It just means that I know more about biology than people who aren't biologists, and that I am, for that reason, more qualified to make statements about biology than people who aren't biologists. I don't know why so many people have a problem with that.

Another interesting human evolution-related paper

An interesting paper by a group of researchers from the Max Planck Institute for Evolutionary Anthropology has appeared in the latest edition of the journal Science. The researchers have taken an interesting approach to investigating the differences between humans and chimps - they have used a relatively new genetic tool known as microarray analysis to examine the differences in gene expression between the chimps and humans. Their results are interesting for two different reasons. First, it is always interesting to learn more about the differences that separate us from our nearest relatives. Second, this paper has actually used the human-chimp relationship as a model system to investigate some basic evolutionary questions.

Before we get into the meat of the paper, a bit of an introduction is called for. The single, most basic lesson that is taught about the way that genes work in the cell is known as the Central Dogma: DNA is transcribed to produce RNA, and RNA is translated to produce protein. It's a nice, clearly stated concept, and it has the added virtue of often being true. DNA is transcribed into RNA, and the RNA is "read" in the cell's ribosomes to produce the various proteins that carry out most of the cell's functions. The Central Dogma is simple and relatively easy to understand.

Like most statements that are simple and easy to understand, the Central Dogma is not entirely true. There are some cases where the RNA is the final product, and does something else besides code for a protein. The RNA sometimes gets edited before it is used to make a protein. Some of the DNA has functions other than directly making protein. Genes work in more complex ways than those specified in the Dogma, and the Dogma doesn't cover all of the important parts of what goes on in the cell.

One of the things not covered by the Central Dogma is the matter of gene regulation. This is an important process in all living things, and is particularly important in complex multicellular organisms. Every cell has all of the DNA needed to do everything that the organism does, but not every cell actually does everything. In fact, after the early stages of development, no cell does everything. Different types of cells develop in different tissues and organs, and need different amounts of different proteins at different times.

I'm not going to get into the fine details of gene regulation here. For the purposes of understanding this one paper, it is enough to know that different cell types are going to need to make different amounts of various proteins at various times. Since these proteins are made from RNA, we can find out active a given gene is in a cell by looking to see how many copies of the RNA transcript for that gene are floating around in the cell.

Microarray analysis provides us with a method for comparing the amount of DNA expression for various genes in the same types of cell in two different species. The details are fairly complex, and you don't really need to understand them to get the basic gist of what was done in this paper, but if you want to know more, you can look here.

In the experiment reported in the Science article, the researchers used microarrays to examine the relative expression of different genes in humans and chimps in a number of different tissues - heart, kidney, liver, testis, and brain.



On the left, I have reproduced figure 1 from the Science article. This figure shows the differences in gene expression observed in the various individuals sampled. The samples that begin with "C" are chimps, and those that begin with "H" are human. The lines indicate the size of the difference, with short lines indicating little difference, and long lines indicating a great deal of difference. These results are quite interesting.

One of the things that they show is that in the sampled tissues, the greatest similarity in gene expression levels between humans and chimps is actually in the brain, while the greatest differences are in the liver. This probably isn't what you might have expected to see. After all, the differences in thought and behavior are generally considered to be enormous between humans and chimps. So what do these results actually indicate.

In the opinion of the paper's authors, these results demonstrate the importance of neutral changes in evolution. In such a model, most genetic change accumulates in places where it does not positively or negatively affect survival. The heart, the kidneys, and the liver function more or less the same in humans and chimps, and the figure shows that the differences in gene expression within humans and within chimps are similar to the difference between the two groups. Such a result indicates that selection has not been a large factor driving the divergence in expression in those tissues. Selection does appear to have been a factor in the differences in the testis, and it may have been in the brain.

So what might all this mean? The authors of the paper sum it up well:

we find that the patterns of evolutionary change in gene expression are largely compatible with a neutral model, in which different levels of constraints acting in different tissues add up for single genes. These evolutionary constraints act in a similar manner on the coding regions of DNA sequences and thus lead to parallel patterns in expression and sequence evolution. In contrast to the overall picture of selective neutrality, two examples of putative positive selection stand out. First, testis shows an excess of expression differences between species and an enrichment of both expression and amino acid sequence differences on the X chromosome. Second, the brain, although under more constraints than the other tissues, has an excess of gene expression and amino acid changes on the human lineage compared to other tissues. This suggests that evolutionary changes at both the level of gene regulation and the level of protein sequence have played crucial roles in the evolution of certain organ systems, such as those involved in cognition or male reproduction. Consequently, the modest number of sequence differences in genes between humans and chimpanzees cannot be taken as evidence that regulatory changes would necessarily be more important than structural protein changes during human evolution. Rather, both types of changes are likely to have acted in concert.

It's going to be interesting to see what the response to this paper is. In some ways, the findings back up some of the things that we've long suspected about the divergence of chimps and humans - in particular, that the differences might be mainly due to selection acting on a fairly small number of traits. In other ways, such as the suggestion that changes in proteins might be as important as changes in gene regulation, this paper may challenge the traditional model of human/chimp divergence. This kind of mixed result is kind of nice to see. It hints that we haven't been entirely wrong in the past, but that there is still plenty more to learn about what drove the speciation process that split us from the chimps.

Reference:
Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees
Philipp Khaitovich, Ines Hellmann, Wolfgang Enard, Katja Nowick, Marcus Leinweber, Henriette Franz, Gunter Weiss, Michael Lachmann, and Svante Pääbo
Science 16 September 2005: 1850-1854.

Wildlife pictures - Drosophila

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



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

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


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

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

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

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

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

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

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

Children and animals

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

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

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

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

The Pledge of Allegiance case

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

Actually, it's already stirring people up. It only took me a few minutes to find a few interesting posts about this isssue on different blogs. A group called Project 21 issued a press release that attacked the ruling as an example of "judicial activism":

"This is yet another in a series of attacks on the religious traditions on which our nation was founded," said Project 21 member Kevin Martin. "For far too long, the liberals have used our courts as a way to create rules they cannot achieve popularly through an elected, representative legislature. If anything is unconstitutional, it is this vicious display of judicial activism."

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

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

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

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

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

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

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

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

NPR had part of an interview with Col. H. James Young, the FEMA official in charge of the airport, on Morning Edition today. What he had to say indicates some major problems in that organization (not that this is news at this point, of course). The audio from that segment is available online. The transcription below is my own.

Supplies showed up. We had what we needed to do what we needed to do... These doctors, they work in these ERs, in these big hospitals or wherever it might be, and they may not have certain procedures they need to go through. They can say, "I want this right now," and they have it. Well, this is the federal government, and it has procedures that we go through."

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

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

Fieldwork in strange and exotic localities.

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

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

Sharing responsibility and accountability.

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

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

Drawing careful conclusions

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

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

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

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

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

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

Wake up, and smell the controversy

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

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

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

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

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

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

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

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

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

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

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

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


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

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

There is absolutely nothing...

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

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