A clean sweep in Dover

The York Dispatch is reporting that eight out of the eight incumbent school board members in Dover have lost their bids for re-election to pro-evolution candidates. Wes already gave the preliminary results in an earlier Panda's Thumb post. What I'd like to do is talk about the implications a bit.

First, it's worth noting that voter turnout was higher in Dover than in other school districts, and that the school board was the reason. If you look at the official election results page for the county, you will see that voter turnout for the county was about 20%. (This speaks rather poorly for us as a country, even if it is an off-year election, but that's another issue.) The turnout in two of the four Dover districts hit the 40% mark, a third district was at 35%, and the last 23%. People care about this issue.

It is also worth noting that this was a hotly contested election. If I've done the relatively simple math correctly (not necessarily a safe assumption at this time of night), it looks to me like the Dover CARES candidates won 52:48. That's actually a lot more significant than it looks at first glance. Dover is heavily Republican, as the rest of the results indicate, and the Dover CARES candidates were running as Democrats. They may have only gotten 52% of the vote, but the Democrats running for County Commissioner and Inspector of Elections each only managed to get 35% of the vote.

People do care about this issue, and it appears that they care about good education for their children. The candidates from Dover CARES have managed to demonstrate, once again, that getting up off of your ass and doing something can really make a difference. Don't ever underestimate that.

If you are reading this, and you are not already doing something offline, start. Talk about the issues with your friends and neighbors even - especially - if they are on the other side. If you can, host something like Cafe Scientifique. Get involved with the local school board or PTA, particularly if you have children in the district. Sure, it requires time, and who has time. Sure, it is inconvenient. But it is the right thing to do.

Now comes the hard part: once you get involved, stay involved. The fight over whether science education in America should be governed by science or religion is one that is not going away any time soon.

Let's take the news from Dover not just as a sign that it is possible for people who get involved to make a difference. Let's take it as a sign that we can make a difference - if and only if we get up, get involved, and stay involved.

Wells, and the future of ID

Jonathan Wells just reposted an article over at ID: The Future that he wrote about a year ago. The article is a fictional account looking at the history of the ID movement from now until 2025. Here's what Wells thinks will lead (or will have lead - I never can keep track of the right tense in these future history pieces) to the downfall of Darwinism:

Surprising though it may seem, Darwinism did not collapse because it was disproved by new evidence. (As we shall see, the evidence never really fit it anyway.) Instead, evolutionary theory was knocked off its pedestal by three developments in the first decade of this century-developments centered in the United States, but worldwide in scope. Those developments were: (1) the widespread adoption of a "teach the controversy" approach in education, (2) a growing public awareness of the scientific weaknesses of evolutionary theory, and (3) the rise of the more fruitful "theory of intelligent design."

For the moment, I will ignore the first two points. The entire "Teach the Controversy" approach at the moment is built around Well's book Icons of Evolution, which is about as misleading and incorrect a book as I've ever read. If you want more information on that, there is a nice collection of material available at the TalkOrigins Archive.

Instead, I am going to look at his predictions regarding the rise of Intelligent Design. After all, teaching that evolution is wrong might make legions of religiously motivated anti-evolutionists happy, but it does nothing on its own to advance Intelligent Design. A negative argument against evolution might show that evolution is wrong, but it does nothing to show that any alternative is right. At the moment, the ID movement only has a negative argument. They have not defined the "theory of Intelligent Design," and they have not tested it. In fact, one of the witnesses for the pro-ID school board in the recently concluded Dover Trial testified that he thought ID was "too young" to have developed testable hypotheses yet.

Since this is the case, I think it might be interesting to see what Wells thinks ID will be able to do (someday in the unspecified future):

The third and perhaps most decisive development was a series of breakthroughs in biology and medicine inspired by the new theory of intelligent design... For years the controversy remained largely philosophical; then, in the first decade of this century, a few researchers began applying intelligent-design theory to solving specific biological problems.

I'm not sure exactly what "intelligent-design theory" is just yet, and I doubt that anybody else is either. There definitely didn't seem to be much of a concensus about it during the defense's case in Dover. That makes it a bit more difficult for me to figure out how this "theory" is going to lead to advances. Let's see what Wells thinks:

Darwinists immediately declared the other 95 percent "junk"-molecular accidents that had accumulated in the course of evolution. Since few researchers were motivated (or funded) to investigate garbage, most human DNA was neglected for decades. Although biologists occasionally stumbled on functions for isolated pieces of "junk," they began to make real progress only after realizing that the DNA in an intelligently designed organism is unlikely to be 95 percent useless. The intensive research on non-coding regions of human DNA that followed soon led to several medically important discoveries.

We will ignore the fact, for the moment, that Wells is misrepresenting the current state of scientific research in this area. There is actually plenty of work being done on "junk" DNA, and that there are actually some evidence-based reasons to think that at least some of the junk DNA is junk. We also know that some of the non-coding regions do have functions. In many cases, for example, the regions of DNA that code for proteins are separated by a certain distance from regions of DNA that regulate the gene. The length of the separation is important, but the sequence is not.

Scientists do not believe that some of the DNA is junk because we are "committed Darwinists". We believe that some of the DNA is junk because there is evidence that indicates that some of the DNA is junk. The accumulation of non-functional DNA in the genome can readily be explained as the byproduct of common descent, but that is not the reason that we think it's junk.

But let's set that aside for the moment. Where's the "intelligent design guided" research? Where are the preliminary results? What is the methodology? Where's the Beef?

If you think that there will be massive benefits to study in this area, why aren't you out doing it?

Wells goes on to talk about another area of study:

Another insight from intelligent-design theory advanced our understanding of embryo development. From a Darwinian perspective, all the information needed for new features acquired in the course of evolution came from genetic mutations. This implied that all essential biological information was encoded in DNA. In contrast, intelligent-design theory implied that organisms are irreducibly complex systems in which DNA contains only part of the essential information. Although a few biologists had been arguing against DNA reductionism for decades, biologists guided by intelligent-design theory in 2010 discovered the true nature of the information that guides embryo development.

This is another misrepresentation of the state of science. The role of environmental factors in development has been under investigation for quite some time, and I doubt that there are very many scientists around right now who think that DNA determines everything. In fact, I was at a seminar on Friday that discussed experiments conducted on the development of some fish in an environment designed to simulate microgravity. The effects were quite noticable. Of course, it sounds like Wells is suggesting something more than genotype-environment interactions here, so it will be interesting to see what his scientific research demonstrates.

You are doing scientific research, aren't you, Jonathan?

You do have experiments running, don't you? You have projects ongoing in your lab righ now, right? You do have a lab, don't you? So where are the preliminary results? What is the experimental design that you are using? What methods of data collection are you using? Where is that beef?

All three of these developments-teaching the controversy, educating people about the lack of evidence for evolutionary theory, and using intelligent-design theory to make progress in biomedical research-were bitterly resisted by Darwinists in the first decade of this century. Defenders of the Darwinian faith engaged in a vicious campaign of character assassination against their critics in the scientific community. Meanwhile, their allies in the news media conducted a massive disinformation campaign, aimed primarily at convincing the public that all critics of Darwinism were religious zealots.

For crying out loud, Jonathan, WHERE'S THE DAMN BEEF? What you've just put up there sure isn't beef - it's a low quality, vinegary wine.

Let's be clear. We are not opposing you because of our ideology. We are opposing you because we think that you are wrong. In fact, you are wrong on several different levels. Your positive evidence for Intelligent Design is absent. Your negative arguments against evolution are incorrect and misleading. If you want us to stop opposing you, show us the beef.

And don't even try whining about evil Darwinists refusing to fund or publish your stuff. All new hypotheses face uphill battles for funding, but you folks have it easy. All you've got to do is divert some of that money the Discovery uses to push it's message into the schools into bench research. The annual budget there could fund a couple of reasonably good labs.

So why isn't this being done? What's the excuse this time? When are you going to stop talking about your vision of the future of ID research and start doing ID research?

No bucks, no Buck Rogers

Money makes science go. Without money, we cannot conduct experiements, and without experiments, you have no science. On a more personal note, without money, I can conduct no experiments, and without experiments, I can get no degree. This is why I was so stressed out a couple of weeks back when I was hammering out my proposal, and that was why I was so happy today to find out that I've been granted some funding from the agency I submitted the proposal to. It's only about 2/3 of what I asked for, but every dollar helps.

Some (beter late than never) Carnival Barking

New editions of both Circus of the Spineless and Tangled Bank were published this week. Enjoy.

The Dover Case - Closing Arguments

The closing argument delivered on behalf of the plaintiffs in the Dover, PA Panda lawsuit by Eric Rothschild is available via the ACLU of Pennsylvania's website. It is a powerful argument, and it is well worth reading in full.

Maui Pictures 1: Haleakala Silverswords

Now that I've had a few days to get caught up on work, I've finally got a little time to sit down and go through some of the pictures from my Maui trip. I'm going to post some of the more interesting ones here from time to time.

The first picture, below, was taken on 30 October 2005, on the Sliding Sands Trail inside Haleakala Caldera. Haleakala Caldera really cannot be adequately described. It is an almost completely alien place, a landscape that looks more appropriate to a Sci Fi movie than to anything on Earth.



The plants in this picture are Haleakala Silverswords (Argyroxiphium sandwicense ssp macroencephalum). This subspecies is only found high on the slopes of Haleakala, and within Haleakala Caldera. It is federally listed as an endangered species.

The plants in the lower left of the photo show the normal form of the plant. The silvery appearance of the leaves is due to fine, reflective hair-like projections that cover the leaves. These reflect light, protecting the plants from the high intensity solar radiation that they receive, growing as they do at high altitudes and tropical latitudes. The individual leaves are small and narrow, minimizing water loss in this dry, windy environment.

The Haleakala Silversword has what is known as a monocarpic life history. This means that the plants grow for several years (up to 20 in the case of the silversword) before producing a single flowering head. After flowering once, the plant dies. Several of the plants in this picture have recently flowered, and are dead or dying.

A. sandwicense is part of a group of endemic Hawaiian plants known as the Silversword Alliance. This group consists of the genera Argyroxiphium, Wilkesia, and Dubautia, all of which are the descendents of a single species that arrived in the Hawaiian Islands, probably from North America, millions of years ago.

More information on this species can be found at Wikipedia.

Losing what little respect I had left for Kerry.

For the record, I voted for Kerry. I wasn't thrilled with the man, but I thought he was a far better choice for president than Bush. I really, really, really wish he had won the election, and the fact that I have lost a great deal of respect for Kerry since then should not be taken in any way, shape, or form as implying that I am supporting Bush in any way, shape, or form.

Since the election, I have been steadily losing respect for Kerry. I donated a small amount of money to his campaign, and as a result, I am on an email list for direct email from him. The fact that he lost has not discouraged him from sending repeated emails out to this list in recent months. For some reason, the emails since the election seem to be pushing views that are a bit to the left of where he was when he was running. More and more, he strikes me as a politician in the mold of the legendary French radical who saw the crowd go by and said, "There go my people. I must find out where they are going so that I can lead them."

Of course, that description fits damn near every politician in the country right now.

Today, I got an email from Kerry that put out a proposal that really made me wonder what the man is smoking. He is proposing, and asking people to sign a petition supporting, a "plan" in which 20,000 US troops are withdrawn from Iraq following the December elections there. I don't care what side of the debate you are on when it comes to troops in Iraq. That plan is not only stupid, it is downright dangerous, and the man should know better.

The "premise" of the plan appears to be that elections in Iraq make things better when it comes to dealing with the insurgency. Personally, I think that the insurgents have done a reasonably good job of disproving that. They are more active some months than others, but there doesn't seem to have been any long-term trend toward a drop in their activity since the last elections there. Elections per se do very little to help the immediate security situation (the long term effects may be different, but that is yet to be seen). Using the election as a reason to pull out a limited number of troops makes no sense at all.

That's why the idea is stupid. It's also dangerous. In fact, it's even more dangerous than pulling out all of our troops. If we do that, I personally feel that we will be immorally reneging on the responsibility that we have to leave Iraq no worse off than when we started. However, American troops will no longer be at risk under that plan. Under the Kerry proposal, we will be left with a security situation that is probably no better than it was when we pulled out the 20,000 troops, but there will be fewer Americans on the ground. This, in turn, will place the troops that remain at an even more elevated level of risk than they are now.

Kerry, being both a veteran and a man who aspired to be Commander-in-Chief, should know better.

The Air Force Academy and Religion

A first ammendment lawsuit has been filed against the Air Force, over the issue of proselytizing. The plaintiffs in this case, including four active-duty officers who are recent graduates of the Air Force Academy, feel that they have the right to not be exposed to proselytization while on duty. The same set of guidelines that lead to the lawsuit have also come under fire from Christian Evangelicals, who feel that the guidelines go too far in restricting their rights to spread their religious message.

The relevant portion of the first amendment states, "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;". The problem in this case is that it isn't possible to satisfy both clauses at the same time.

On one side, there is the issue of establishment, and the issue of coercion. Senior officers in the military have extrordinary power, particularly over those who want to be career military. A single bad performance review from a superior can totally kill any chances for future advancement. Not pissing off the boss is hugely important. Under those circumstances, it is difficult to see how an "invitation" by a commanding officer to pray at the start of a staff meeting could be seen as something akin to an order, or why subordinates would be very reluctant to say anything if the religious statements of a superior were making them feel uncomfortable. The commanding officer is the representative of the government, and given the nature of the military it is difficult to see how the governmental function could be overlooked, particularly during duty hours. That is a de-facto establishment of religion. On the other side, there is the issue of free excercise. Evangelical Christians believe that it is their religious duty to evangelize. If you tell a commanding officer that he cannot tell his subordinates about his religious beliefs, you are restricting his right to freely excercise his religion.

This is going to be an interesting case to follow.

I'm back.

The trip to Maui was very interesting. I didn't actually get to collect anything, but I now have a much, much better idea of what not to do next time. In science, that can sometimes be almost half the battle right there. I'm wading through hundreds of inbox messages, but might have something worthwhile to post later today.

Missing the Point

I was just looking at an interesting article in the Brunswick (Maine) Times-Record. It seems that the president of the Bowdoin College Democrats, Alex Cornell du Houx, is off to Iraq. He is a member of the Marine Reserves, and his unit has been activated in preparation for a December deployment to Iraq. Despite his vocal opposition to the war, Cornell du Hoax is putting his uniform on, putting his political aspirations on hold, and doing his duty. (Something similar happened out here in Hawaii last year with one of the members of the State Legislature.)

The president of the Bowdoin College Republicans (who is also the secretary for their national organization) made some amazingly petty and small-minded comments about Cornell du Houx's pending deployment:

Daniel Schuberth, a leader of the Bowdoin College Republicans and College Republican national secretary, said, "I applaud Mr. Houx for his service, just as I applaud any other soldier who is brave enough to take up arms in defense of his country. I find it troubling, however, that one of the most vocal opponents of our president, our country and our mission in Iraq has chosen to fight for a cause he claims is wrong. Mr. Houx's rhetoric against the war on terror places him in agreement with the most radical fringes of the Democratic Party, and I am left to question his logic and motivation."

Although I've already seen some progressive blogs beating up on Schuberth, I've actually heard similar sentiments from people who are far to his left when talking about my own family situation. A couple of people have actually said things to me along the lines of, "but if you are opposed to the war, how can you let your wife go off and fight there? if she is opposed to the war, why is she going?"

Anyone who raises such questions demonstrates a lack of understanding of the proper relationship between the military and the civil power in a democracy. In order to for a nation to remain a democracy, the military must be subordinate to the civil power. To put it bluntly, the military does not get to decide if they want to fight somewhere. They are told to, by the politicians. If it works the other way around, it isn't a democracy. It's a military dictatorship.

People who have a committment to the military, and who fulfill their committment despite their opposition to the war, are acting in the finest traditions of the United States. By acting in this allegedly illogical manner, they are doing their part to protect our country. In fact, they are doing so twice - from enemies foreign, and from enemies domestic.

Another dry spell coming up.

I'm going to be off-island for the next few days, cut off from the internet. I'll be living in a tent, out in the wilds and the weather, isolated from the civilized world, doing fieldwork - generously giving of myself to advance science. Unfortunately, I don't get much sympathy for the sacrifice, since I'll be doing all of this on Maui.

I get back to Oahu on Tuesday evening. Updates will resume shortly thereafter.

Lying under oath

Scooter Libby really should have taken lessons from former Dover School Board Member Bill Buckingham. You really can tell obvious, outrageous lies under oath. Just make sure that you have a well-documented OxyContin addition to fall back on to protect you from the perjury charges later.

And there I thought I was at least a little bit scientific.

You fit in with: Humanism Your ideals mostly resemble that of a Humanist. Although you do not have a lot of faith, you are devoted to making this world better, in the short time that you have to live. Humanists do not generally believe in an afterlife, and therefore, are committed to making the world a better place for themselves and future generations. 0% scientific. 80% reason-oriented.

Take this quiz at QuizGalaxy.com

Of course, after all the fun we had putting together my first research proposal a couple of weeks back, my advisor might agree with that 0% thing.

Shamelessly mooching my first meme-like project.

I just finished setting up an online map of Questionable Authority readers over at Flappr. If you click on the link, you can add yourself to the map.

I've mooched this from Pharyngula, who mooched it from Crooked Timber.

Evolutionary Trees

David, over at Science and Sensibility, has used the blog family tree that The Commissar to form the basis for a phylogenetic tree. Phylogenies are tree-like diagrams of evolutionary relationships. They are a very common tool in science, and David does a really fantastic job at explaining them. It's definitely worth a look.

Hat Tip: Pharyngula

(Postscript:) In the unlikely event that anyone is interested in knowing, I group with the Pharyngulids.

Absolutely unforgiveable

The New York Times reports that the White House is threatening to veto any anti-torture legislation that reaches the president's desk without an exemption for the CIA. Such a bill, sponsored by Republican senator John McCain, was recently attached as an ammendment to a military spending bill. The ammendment passed the senate with a 90-9 vote.

The White House is reportedly opposed to the ammendment because, "the president needed maximum flexibility in dealing with the global war on terrorism." Personally, I vote with the 90 senators who feel that presidential flexibility to deal with terrorists should stop short of the kind of things normally seen in bad S&M spam.

The courage to do the right thing...

...does not come easily, and it does not come without a price. We should always remember that, and we should always remember with the greatest respect those true heroes who have the courage needed to stand up for what they know to be right, even in the face of their own government.

Rosa Parks, who passed away last night, had the courage to face the consequences for doing the right thing. In the process, she proved that a single person, doing the right thing, can change the world for the better. I can think of no higher praise, and no better legacy, than that.

Behe, positive arguments, and negative arguments

If you've been following the posts at Panda's Thumb and other pro-science web establishments lately, you've seen a lot of criticism of Behe's testimony at the Dover trial. You will probably see more, as more of the transcripts become available. It's not so much a matter of piling on as it is a matter of the transcripts having so many different bad points to comment on. It's like a really bad blog article, but one that took place over three solid days of testimony.

This installment in the increasing body of work addressing Behe's substandard arguments will examine some of the things that he said on the stand about there being positive arguments for intelligent design. The material that I will be commenting on can be found during his direct testimony. The transcript is available in pdf format here.

There are two separate, relevant quotes. I'll provide them first, then comment on them. The first brief exchange is found on page 86. The questioner is Mr. Muise of the Thomas Moore Law Center. The answer is from Behe:

Q. Do you have an opinion as to whether intelligent design posits a positive argument for design?

A. Yes, I do.

Q. What is that opinion?

A. Yes, it does.

The second quote is a bit longer. It begins on page 90, and continues on 91:

Q. Now I want to review with you the intelligent design argument. Have you prepared a slide for this?

A. Yes, I have. On the next slide is a short summary of the intelligent design argument. The first point is that, we infer design when we see that parts appear to be arranged for a purpose. The second point is that the strength of the inference, how confident we are in it, is quantitative. The more parts that are arranged, and the more intricately they interact, the stronger is our confidence in design. The third point is that the appearance of design in aspects of biology is overwhelming.

The fourth point then is that, since nothing other than an intelligent cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that the design seen in life is real design is rationally justified.

Although Behe claimed that ID makes a positive argument, his summary of "the intelligent design argument" is fundamentally a negative argument. That is, inferring design is justified due to a lack of evidence for natural causes rather than as a necessary inferrence from the evidence. This becomes obvious here:

...since nothing other than an intelligent cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that the design seen in life is real design is rationally justified. [emphasis added]

That's not only a negative argument, it's two separate negative arguments. Concluding design is justified, according to Behe, because (a) no natural cause has (in Behe's unhumble opinion) been shown to be capable of creating the appearance of design; and because (b) the explanations offered by modern evolutionary theory are not sufficient (again in his unhumble opinion) to qualify as a natural cause capable of explaining the appearance of design.

Perhaps someday someone will make a positive argument for design. The argument made by Behe, however, was not (his testimony of a few minutes earlier notwithstanding).

This morning's dose of hypocrisy

It would appear that Senator Kay Bailey Hutchinson, Republican of Texas, thinks that perjury is a crime when a Democrat does it, but a "technicality" when committed by a Republican. Isn't it nice that our country is being lead right now by people with such firm moral standards?

A couple of thoughts on Intelligent Design and Blame

The current success of the Intelligent Design movement in the United States is not entirely the fault of scientists and science educators. But, sadly, we really haven't done all that much to hinder their social, political, and cultural progress. A heroic few - Genie Scott, Wes Elsberry, Nick Matzke, and the rest of the full time staff at NCSE - have worked full-time at opposing anti-evolutionists. A number of other scientists and academics have invested a large amount of time into fighting anti-evolutionism. Their work has been fantastic, but the focus of the work has been a bit narrow.

I don't mean that as a criticism of NCSE and the others who have been working to fight the anti-evolutionists. There are a lot of anti-evolutionists out there, they spew forth massive volumes of misleading garbage, they are threatening the education of children all over the United States, and they desparately need to be opposed.
With the number of people working at opposing them so small and their resources so limited, there is no way that NCSE could have any other focus than on responding to the anti-evolutionists.

Unfortunately, reacting to the anti-evolutionists is not going to be enough to win the day. Anti-evolutionism is a popular position these days, and it is being promoted heavily on many religious fronts. Tactical victories in courtrooms will not change this, and such victories might not even be enough to shift the initiative away from the anti-evolutionists.

If we continue as we have been, we will lose this fight. It does not matter if we have the weight of all of scientific evidence on our side. It does not matter that we are right. It does not matter that their position is anti-scientific. It does not matter that their outlook on reason is pre-rationalist. It does not even matter that their efforts to integrate their own religious perspective into all aspects of American culture is entirely counter to the vision that the founding fathers had for a republic without a state religion. Those things should matter, of course, but sometimes the popularity of a movement matters more than whether or not the views that it advances are intelligent, healthy, or correct.

Although the enemies of science claim that this is a scientific debate, we know that this is not the case. We understand that their opposition is primarily based in religious beliefs, and in a deep philosophical distaste for the concept of having a cousin swinging from a frame in a zoo while eating bananas. What we don't seem to grasp, however, is that treating this as simply a matter of science versus nonsense is not going to work in the long term. We must begin to treat this as what it is: a battle for the hearts and minds of the next generation.

At the moment, we are losing this battle. Mostly, this is because we haven't been showing up. The Christian right has youth ministers. They have services targeted entirely for young adults. They have tried, and largely succeeded, in creating an environment where it is cool to be a young, conservative Christian. For the most part, our outreach has been absent. We recruit scientists as we always have, and we do very little to make sure that we are exposing everyone to the joys of science from a young age.

This is where we need to do more. We need to get scientists into all classrooms at all levels. We particularly need to get scientists into classrooms in areas that are distant from the academic habitats that we are usually restricted to. We need a real grassroots effort at selling science to the public. I have never met a scientist that was not addicted to science. I have never met a scientist who did not have a true love for the process of discovery. Unfortunately, we are very good at hiding our love of nature behind the clinical language of science. That's the one thing that we need to get worse at.

Accidentally committing an act of honesty?

A quote from John Calvert in a recent article caught my eye:

“it’s just another example of science interfering with education,” Calvert said.

I've got to give Calvert credit here. It's not often that you see someone sum up the entire intelligent design movement in just nine words.

European Relations

It would seem that our relations with Europe have taken yet another turn for the worse, with the inane decision by a Spanish judge to issue international arrest orders for three American soldiers (see WaPo story for more details).

The arrest orders result from a tragic incident that occurred in 2003, during the invasion of Baghdad. An American armored unit was holding territory in Baghdad, and was being attacked both by small arms fire and by indirect fire (artillery and mortars). The troops knew that the Iraqis had been using spotters to direct artillery, and were trying to find the spotters, in part using information intercepted from captured radios. From the intercepts, they became aware that a spotter was in the process of trying to call in fire from a high-rise building in the area.

At the Palestine hotel, near the site of the battle, several reporters were observing the battle from balconies. Some of the reporters had cameras set up on tripods, and at least one was observing the action using binoculars. When the soldiers saw a reporter on a balcony using binoculars, with some sort device on a tripod next to them, they believed that they had found the artillery spotter, and fired a tank round into the building, killing two journalists. One of the journalists was a Spanish citizen. This incident is reported in detail in the book Thunder Run.

The incident was tragic, and an international media group, after an investigation, believed that the incident could have been prevented had the soldiers received better information about the hotel, which was well known to be occupied by journalists. An army investigation also concluded that the incident was an accident, and that the troops had acted within the rules of engagement.

This incident falls into the "bad things happen in wars" category. Reporters try to see what's going on. They use things like binoculars to do this. Artillery spotters try to see what's going on, in order to better direct high explosives toward their enemies. They use things like binoculars to do this. Soldiers who are on the receiving end of artillery fire have an understandable dislike of artillery spotters, and will do whatever they can to make them stop. Under the circumstances, it can be understandable for them to mistake a reporter on a distant balcony with binoculars for an artillery spotter on a distant balcony with binoculars.

The Spanish government doesn't see things that way. They have demanded that the US government either permit them to take statements from the soldiers involved, or to allow a Spanish delegation to quiz them. The US government has refused, so a Spanish judge issued the detention orders.

It is possible, I suppose, that the Spanish government is acting in good faith here. Stranger things have happened, or so people say. I'm not so sure. I've got to wonder exactly how likely it would be that this whole thing would be happening were the curent Spanish government not so opposed to the Bush administrations and its policies.

Be afraid. Be very afraid. And pissed off, too.

Well, it seems that it has been more possible for Big Brother to watch us than we thought. So much so, in fact, that had this information come from a less reputable source, and without confirmation from manufacturers and government sources, I would have written it off as a psychotic conspiracy theory.

It appears that the government can look at documents produced by many color printers, and determine the time and date that the document was produced, as well as the serial number of the printer that the document was printed on. Doesn't that make you happy you sent in the product registration card? By the way, there are no laws that would prevent the printer manufacturer from handing over the registration information to the government upon request. "Request" here, by the way, means just that. Request. Not subpoena, not court order. Just "request".

The research that has lead to this discovery was conducted by the cyber-rights group Electronic Frontier Foundation, and their report can be found here. They are continuing to collect information from various printers, but have already succeeded in cracking one of the codes used - it was so tough to crack, so secure, it took their intern a whole week to figure it out. If you think this is crazy, join the crowd. If you think this couldn't possibly be the case, and that the folks at EFF have suffered mass paranoia, read the Washington Post story on this, which includes confirmations from both IBM and the Secret Service.

Here's the quote from the Secret Service:

"It's strictly a countermeasure to prevent illegal activity specific to counterfeiting," agency spokesman Eric Zahren said. "It's to protect our currency and to protect people's hard-earned money."

Here are the excuses given by some of the involved companies:

Xerox spokesman Bill McKee confirmed the existence of the hidden codes, but he said the company was simply assisting an agency that asked for help. McKee said the program was part of a cooperation with government agencies, competing manufacturers and a "consortium of banks," but would not provide further details. HP said in a statement that it is involved in anti-counterfeiting measures and supports the cooperation between the printer industry and those who are working to reduce counterfeiting.

What pisses me off about the situation - and it should piss you off, too - is this: this was done, and has apparently been done for a long time now, without the knowledge of the vast majority of people using the printers. The government, banks, and big business went and put together a set of measures to protect their own interests. These measures involve a technology with chilling implications both here and in other countries - especially those with repressive governments and no civil rights protections. The measures were put in place to make life easier for the banks, businesses, and law enforcement, and they were put in place without the knowledge of the public.

If the printers that we buy stamp identifying information on every page that they spit out, this is something that we sure as hell had the right to know. We also sure as hell had the right to participate in an open discussion of this policy, its implications, and the possible costs and benefits associated with it. We definitely should have been able to take part in the discussions in order to ensure that our own interests were being looked after here, not just the interests of the goverment and corporations.

Of course, had we been informed about this from the start, that might not have worked so well for the government and corporations. We might have rebelled at the concept. We might have demanded that some sort of unreasonable privacy protections - like legal due process - be put into place to protect our right to privacy. We might not have purchased printers with that "feature". Doing an end run around the public was definitely the convenient thing for the feds, the banks, and the printer manufacturers to do.

It just wasn't the right thing.

This situation screams for an investigation. Who made these decisions? What the f--k do they think gave them the right to make those decisions without informing the public? Who in the government was involved in setting this up? What people at what levels of the government knew about this, and what gave them the delusion that they had the right to leave the public in the dark?

Most importantly, are there any other little surprises out there that we haven't been deemed worthy of knowing?

Tangled Bank #39

The Tangled Bank

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us.
-Charles Darwin

The Tangled Bank is many things. It is a famous metaphor used by Charles Darwin in the passage quoted above. It is the blog carnival that you are reading right now. And it is a very good description of modern science.

Once upon a time, science was considered to be a largely academic endeavor. Academic scientists, like academic historians, English professors, and other such university types, were largely secure in their ivory tower. Commercial, political, and other "applied" aspects of science were frowned upon. This is still sometimes the case, of course, but the distinctions have become more and more blurred. Science, now more than ever, is part of modern life, and life is more connected to science. The difference is no longer clear. As in the picture of the tangled bank above, it's not really possible to pick a point where pure science ends and applied begins.

Now that my little introductory sermon is done, on to the links:

Before we get to the posts discussing scientific discoveries, we have a some reminders that science is a field that is, above all else, a human occupation. And we humans are, of course, what we are.

Ms. PhD of YoungFemaleScientist shows us that the practice of science is sometimes different from the ideals, and that people don't always live up to their responsibilities. GrrlScientist has a post that compliments this one rather nicely, discussing some of the university politics that interfere with some of those minor things that the schools do - the little things, like educating students.

From Dr. Mom, we have a nice article about the giant squid, and how it relates to the loss of prestige that scientists have experienced in American culture. (This blog was new to me, and may be new to you as well. If it is, take some time to look through some of the other posts, too. There's a series in progress on how to write a scientific paper that's shaping up to be particularly good.)

On a more somber note, Orac provides us with a needed reminder that the history of the euthanasia and eugenics movements include far more than just the history of Nazi Germany. Sometimes crimes against humanity start at home.

This week, we also have a pair of posts on the love-hate relationship between economics and the environment. The perspectives the two take are somewhat different from each other, and I'm not sure whether or not I agree with either of them, but it is definitely worth remembering that the relationship between humans and our environment is complex, and that when we look at the effects that we have on the environment we cannot ignore the effects that the environment has on the way we live.

Shifting from the practice of science to actual scientific news, we'll start with the realm of the very large, out at galactic scales. In one of the very few "pure" science posts for this edition, The Bad Astronomy Blog, gives us a nice look at the Andromeda galaxy using two different types of imaging: visible light and infrared.

At the moment, a hurricane with a name that starts with "W" is roaming the Atlantic. This storm is getting some attention, since the list of storm names ends with "W". The next tropical storm in the Atlantic (if there is one) will receive the highly original name of "Alpha". The sheer number of storms this year, coupled with the strength of Katrina and Rita, has lead to a great deal of discussion about the relationship between hurricanes and global warming. If this type of thing interests you, you might want to take a look at the Oxford University Press Blog, which gives us a short interview with author Kerry Emanuel on Hurricanes and Global Warming.

Moving on, Dr. Freeride reminds us that this is National Chemistry Week. On the lines of chemistry, the applications of chemistry, and the increasingly blurry distinction between pure and applied sciences, we get a reminder from In the Pipeline that Big Pharma does Real Science, too. (Even if the criteria for success are slightly different than they are for academics.) There's also an interesting article on biochemistry and trust at Twochemists.

I don't know exactly how to classify the next entry. It might be physics, it might be chemistry, it might be an environmental post - it's a mini-tangled bank all by itself in some ways. Sometimes the simple solutions are the best solutions, and sometimes you get really lucky and the simple solution to one problem turns out to solve a whole bunch of other things, too. Political Calculations blogs about some of the unexpected benefits that may come from a rubberized pavement designed to reduce noise.

In the field of the cognitive sciences, Dave Munger has an article over at Cognitive Daily about how humans learn the deceptively simple process of pattern recognition.

We've got a few field-biology submissions this week.
10000 Birds reports on a recently published article on Barn Swallow mating. The report demonstrates something that many of us already suspected - the odds of successful monogamy increase if you put effort into continuing to look good even after the honeymoon.

One of the nicer things about fieldwork is that you can often see more interesting (or at least photogenic) things in the field than you do in the lab. Over at Henry's Webiocosm Blog, there's a picture that reminds us that life has a way of turning up and hanging on even in the most unexpected places. On a more seasonal note, there's a nice picture of variability in leaf colors over at the Botany Picture of the Day website. The post that it's attached to is worth reading, too.

Jennifer Forman Orth, of The Invasive Species Weblog, comments on a recent case that appears to demonstrate that the financial penalties that may occur if you get caught after causing problems by introducing a pest to an area probably don't outweigh the benefits to doing it in the first place. The issue of invasive species is one that I've been thinking about a lot lately, since the effects of a new invasive out here in paradise are becoming more noticeable as time goes on. The post of my own that I link to is an old one, but if you check back in a day or so there will be a large, but not happy, update to the story.

We also have a number of posts about genetics this week. Some of them are more reality-based than others, but all are interesting. EvolGen decided to address a cartoon character's question about whether or not a somewhat atypical set of relationships constitutes incest. The scenario might seem a bit silly, but it takes a nice look at the mechanics involved in figuring out genetic risks.

Keats' Telescope brings us an article on the amount of "free" DNA that can be found in ocean sediments. This research has some interesting implications, particularly when it comes to the utility and validity of genomics work with "environmental" samples.

Aetiology discusses the vast diversity that seems to exist within each species of bacteria. It's interesting stuff. We tend to forget that something in excess of 99.99% of all life that has ever lived on this planet, by any measure you choose to use, is some sort of bacteria. Their genetics are very different from the life we usually look at, and we are only just beginning to fully grasp the depth of the evolutionary and medical implications that this raises.

PZ Myers reminds us that there can be more to the way that DNA works than just the order of As, Ts, Cs, and Gs with an article on Tourette's Syndrome.

There's also a few posts worth looking at (here and here) that discuss an article in Science about intellectual property rights and the human genome. Apparently, lots of genes have been patented so far, some of them more than once. Allowing people ot patent chunks of human DNA sequence has its good and bad points, I guess, but it does feel a bit creepy sometimes. As long as they don't start requiring us to get tattooed with the patent numbers, I guess I can live with it.

That pretty much concludes the posts that were submitted to me for this edition of Tangled Bank. There do, however, seem to be a couple of big things missing. I received only one submission that was directly related to creationism this time. That's particularly strange, since there is currently a major lawsuit underway in federal court related to a Dover, Pennsylvania school board policy. Anyone interested in the trial can find pretty much all the information that they want over at The Panda's Thumb. There's also a good series of posts available there on bird flu, which is the other big gap in this week's posts.

That wraps it up for this one, folks. It's been a pleasure hosting this, and I hope to do it again someday.

The next edition will be posted on November 2, at The Examining Room of Dr. Charles. Submissions can be sent to Dr. Charles, to PZ Myers, or to host@tangledbank.net.

Tangled Bank

The next Tangled Bank will be posted here on Wednesday morning, so if you haven't yet done so, please send your links to host@tangledbank.net

Hope and Fear, from just one paper.

As much as I like to think of myself as being a middle-of-the-road kind of guy, politically speaking, I tend to lean far more to the left than to the right. Typically, I am not someone who normally manages to agree with Charles Krauthammer on very much, if anything. But his Friday article on the genome sequencing and reconstruction of the 1918 Spanish Flu virus provides a solid summary of both the desparate need that scientists have for that information, and the all-too-real reasons to be very afraid of the consequences of having that material available in the public domain.

Famous last thoughts

Advisor: "You just need to remember, Mike, when you start working on your proposal, that the expectations are going to be a bit higher than you've been used to."
Me (thinking): "Yeah, right. No sweat. No way is this going to be any harder than the last few things I've written."

Dog Bites Man

I was going to title this post something like, "Casey Luskin totally misunderstands and misrepresents something related to biology," but the title I settled on seems to sum up the news level involved much more concisely. In this instance, Casey attempts to explain away some of the evidence for human-chimp common descent that was presented by Ken Miller during his testimony last week in the Dover case.

I'd like to be able to quote the entire relevant portion of Dr. Miller's testimony here, both because it establishes the context for Luskin's ill-founded critique, and because it is a beautifully elegant and simple explanation of a powerful piece of evidence that supports the common ancestry of apes and humans. However, it is too long for that to be convenient. If you want to read the whole thing for yourself - and I encourage you to - you will find it starting on page 22 of the pdf file linked above.

Luskin starts off by taking some gratituitous digs at the status of evolution, deliberately misunderstanding the reasons for Miller's testimony, and with some other inanities. He then moves on to his main complaints with Miller's testimony:

Miller made his prediction that there was a fusion event simply by counting chromosomes in apes and humans—not by analyzing the chromosomes themselves.

Miller started off his "prediction" by simply observing that humans have 23 pairs of chromosomes and apes have 24 pairs; therefore two ape chromosomes were fused into one human chromosome. Miller claims that this simple chromosome-counting requires a fusion event if common ancestry is true.

Actually, Dr. Miller did more than "chromosome counting". This is fairly obvious after just a cursory reading of the testimony.
Miller:

Now, what that means, Mr. Walczak, is that you and I, in a sense, are missing a chromosome, we're missing a pair of chromosomes. And the question is, if evolution is right about this common ancestry idea, where did the chromosome go?

Now, there's no possibility that that common ancestry which would have had 48 chromosomes because the other three species have 48, there's no possibility the chromosome could have just got lost or thrown away. Chromosome has so much genetic information on it that the loss of a whole chromosome would probably be fatal. So that's not a hypothesis.

Therefore, evolution makes a testable prediction, and that is, somewhere in the human genome we've got to be able to find a human chromosome that actually shows the point at which two of these common ancestors were pasted together.

As you can see, the reason for Miller's prediction goes a bit beyond the, "apes have 48, we have 46, so we must have had 48 once, too" line that Luskin presents. The prediction is trivially obvious - if you understand the slightest thing about common descent. If humans and apes are closely related, then their genomes will, we expect, be very similar. This means that if we are short a chromosome pair in comparison to apes, then that genetic material needs to be somewhere.

Mr. Luskin, however, has some ideas about other things that could be responsible for the chromosomal patterns that we see:

Why couldn't it be the case that the common ancestor had 23 distinct chromosomes, and one chromosome underwent duplication in the line that led to apes? Or maybe the common ancestor had 20 distinct chromosomes and there have been 4 duplications events in the ape line, and 3 in the human line?

The short answer to Luskin's question is that the different chromosomes are, well, different. We have looked at them. We have sequenced them. They are not obvious duplicates. They have different genes. That would, to me, seem to argue strongly against the pattern that we see being the result of a series of recent duplication events. Of course, I'm kind of strange when it comes to formulating opinions about stuff like that. I think that evidence actually means something.

Casey continues:

or maybe the ancestor had 30 distinct chromosomes and there have been 6 fusion events for ape-line but 7 fusion events for the human-line.

Do you see my point? Simple chromosome-counting or comparisons of numbers of chromosomes does not lead common ancestry to make any hard predictions about how many chromosomes our alleged ape-human common ancestor had. So, under Miller's logic, there is no reason why a chromosomal fusion event is a necessary prediction of common ancestry for all upper primates.

Casey might actually have a point here, if his representation of Miller's argument had even the faintest resemblance to reality. However, the argument is nowhere near as simplistic as Luskin makes out. (Shocking, that.)

Not content with mere error, however, Luskin descends into sheer inanity:

In fact, if we find evidence that humans have two distinct chromosomes that have evidence of fusion (i.e., let's say human chromosome #2 has fusion evidence, and then, hypothetically, we also find evidence for fusion on human chromosome #9), then under Miller's logic, if apes lack any evidence for a fused chromosome, then this should count against common ancestry. Thus, at the present time, absent a full analysis of fusion evidence in our chromosomes, we cannot necessarily say that the presence of one fused chromosome in humans is a prediction of common ancestry. Much more research still needs to be done.

Wow. Now there is an argument that lacks honesty, integrity, reason, intelligence, and logic. And all at once, too. Where to start...
First, Casey's so-called argument is based on the assumption that unless we know everything, we know nothing. That's a rather pitiful attempt to dodge actually looking at any evidence ever. Second, Casey somehow or another manages to assume that we actually don't know about the other chromosomes. The fact is, we have a pretty good idea about human and chimp chromosomes. It's one of the things that you pick up after years of study - particularly when you do little things like sequence the entire genomes of humans and chimps.

Luskin decides not to quit while he's behind:

So I am more than willing to acknowledge and affirm that Miller did provide some very good direct empirical evidence for a chromosomal fusion event which created human chromosome #2. But I'm more interested in two other questions: if we accept Miller's chromosomal fusion evidence as accurate, then (1) is his chromosome fusion story good evidence for Neo-Darwinian common ancestry between humans and apes? Or (2) does it perhaps pose great problems for a Neo-Darwinian account?

The answer to question (1) is "NO" and the answer to question (2) is "YES!"

This should be good.

The fusion-evidence implies that some of our ancestors likely had 48 chromosomes. But Miller has not provided any evidence that the individual with 48 chromosomes was historically related to modern apes. (I grant that our chromosome #2 has banding patterns similar to two ape chromosomes, but given that our chromosome structure is generally similar to that of apes anyways, it is not a stretch to assume that any 48 chromosome ancestor of you and me had a chromosome structure similar to apes, regardless of whether or not that individual was related to apes. Claiming that banding pattern similarities is evidence of common ancestry with apes simply invokes the “similarity = ancestry” argument, and thus begs the question.) It is entirely possible that our genus Homo underwent a chromosomal fusion event within its own separate history.

OK. First, we expect, based on common ancestry, to find that our chromosome structure is similar to that of apes. The Intelligent Design folks, on the other hand, expect that... well, actually, this is another case where ID predicts absolutely nothing.

Second, we do not claim that the chromosome banding patterns are evidence for common ancestry because they "look similar". Chromosome banding patterns are yet another area that we have been researching for decades. We know that they are heritable characters. In fact, they are heritable characters that are shared between humans and apes. That is evidence for common descent.

As far as the third point is concerned, the chromosome fusion certainly could have taken place any time after the human-ape split. Nobody I know of is claiming that the chromosome fusion is the reason that we are different from apes. It is evidence that we share a common ancestor with them, and it may have played a role in the divergence, but it may also have played no role whatsoever.

Luskin, however, fails to grasp this:

All that evolutionists have claimed is that this fusion event occurred after the split that led to humans, so it occurs only in the human lineage. Evidence of a chromosomal fusion event is not evidence that our line leads all the way back to apes.

Given that we had a 48-chromosome ancestor, we don't know if our 48-chromosome ancestor was an ape or not. For all we know, our 48-chromosome ancestor was a part of a separately designed species, as fully human as anyone you meet on the street today. There is no good reason to think that going from a 46-chromosome individual to a 48-chromosome individual would make our species more ape-like.

Common descent could not have been falsified if there was no evidence for a fusion event, but common descent certainly is not refuted by the presence of a fusion event. The question now stands, does this fusion event provide any evidence for common ancestry between humans and apes? The answer to that question is no.

That last paragraph is a bit confusing, and I'm not entirely sure what he's trying to get at. Let me try to make the reality-based view a bit more clear. Based on everything that we know about our relationship with apes, we could quite firmly predict that there would be a chromosome fusion, and we could predict which chromosomes would be involved. The prediction turned out to be correct. Had it not turned out to be correct, that would have been a very, very large problem. It would, in fact, have refuted our common descent-based expectations. Personally, I think that the fact that the predictions of common descent were so clearly met is powerful evidence in favor of common descent. But again, that's just my own reality-based view.

Luskin, after presenting a fancy (but meaningless and misleading) animated gif, moves on to his next line of misunderstanding:

Under Neo-Darwinism, genetic mutation events (including chromosomal aberrations) are generally assumed to be random and unguided. Miller's Cold-Fusion tale becomes more suspicious when one starts to ask harder questions like "how could a natural, unguided chromosomal fusion event get fixed into a population, much less how could it result in viable offspring?"

That is actually a relatively reasonable question, and the concepts involved can be confusing. I'll try to explain them as clearly as possible, as I respond to each of Casey's points.
Casey:

(1) In most of our experience, individuals with the randomly-fused chromosome can be normal, but it is very likely that their offspring will ultimately have a genetic disease. A classic example of such is a cause of Down syndrome.

This is actually not quite true. Down syndrome is caused by duplication of chromosome 21, resulting in the victim having not the normal two, but rather three copies of the chromosome. A chromosome fusion is not a duplication. A chromosomal fusion occurs when two different chromosomes get stuck together, forming one larger chromosome. Someone with a chromosome fusion has no more, and no fewer, copies of any particular gene than someone without that fusion. They are likely to be genetically normal.
Casey:

(2) One way around the problem in (1) is to find a mate that also had an identical chromosomal fusion event.

Actually, all that is necessary for successful reproduction is for the chromosomes in one individual be able to line up with the other individual's chromosomes. This is entirely possible in the case of a recent fusion, particularly since the same chromosome sequences are present in both individuals.

In some cases, differences in chromosome number can result in the offspring being sterile. This is, in fact, what happens in mules. However, that type of thing doesn't happen right after a fusion. It happens once enough changes have occurred in the fused chromosomes that they can no longer line up with their unfused counterparts.

There are actually some populations of Drosophila species that are polymorphic in their number of chromosomes. That means that, within the species, some individuals will have the chromosome fusion, and others will not. The two types interbreed freely.

Luskin concludes:

Miller may have found good empirical evidence for a chromosomal fusion event. But all of our experience with mammalian genetics tells us that such a chromosomal aberration should have resulted in a non-viable mutant, or non-viable offspring. Thus, Neo-Darwinism has a hard time explaining why such a random fusion event was somehow advantageous.

If it were to turn out that the fusion of two chromosomes can only result in a viable individual if the fusion event takes place in a highly unlikely and highly specified manner, then we may actually be looking at a case for a non-Darwinian intelligent design event in the history of the human genus.

Actually, none of our experience with mammalian genetics tells us that a chromosome fusion should have resulted in either a non-viable or a non-fertile offspring. In fact, our knowledge of Drosophila genetics - coupled with our evolutionarily-informed understanding that fly genetics are not all that different from mammalian genetics - tells us that these sort of fusions don't usually have any impact on the viability or fertility of the offspring.

Mr. Luskin's criticisms are, as always, poorly informed. Dr. Miller, unlike Casey, understands biology and evolution. His choice of the chromosome differences between humans and apes was a very good example of evidence for common descent.

It really does matter if it's right.

I just read, for the second time, an article by Doug Kern that's available at Tech Central Station. After my blood pressure came back down a bit, the article got me to thinking. The tone of the piece is annoying and condescending, and there is far more in it that is wrong than is right, but it illustrates a number of the political problems that we face all too well.

The title of the article is, "Why Intelligent Design is Going to Win." The thesis statement is short and simple: "Intelligent Design theory is destined to supplant Darwinism as the primary scientific explanation for the origin of human life. ID will be taught in public schools as a matter of course."

The first flaw, of many, in the article is in this thesis statement. One thing which, I think people frequently fail to fully understand is that the current battle over Intelligent Design has absolutely nothing to do with anything other than getting ID taught in public schools. It certainly has nothing to do with the actual validity of the "theory". It has still less to do with what the primary scientific explanation for the origin of human life will be. Intelligent Design could be force fed down the throat of every American schoolchild for the next century, but that will not make it the primary scientific explanation for the origin of human life. Scientists will continue to study evolution, until such time as evolutionary theory is supplanted by another scientific theory. That will happen only if empirical, scientifically testable hypotheses are presented, tested, and if they pass repeated tests.

Allow me to be clear on one point here: I am not arguing that teaching Intelligent Design to every child in every school in America would accomplish nothing. If I believed that, I'd be pretty damn silly to be arguing about it. Actually, I think that teaching Intelligent Design in the public schools would accomplish a large number of things. It would, for starters, prove that if you try hard enough, you really can obfuscate your way around the constitution. It will also serve to put a set of religious beliefs into the public school classroom - beliefs that run counter to my own - and force me to pay to have those beliefs taught to my children. It will further reduce the already pitiful level of scientific literacy in our country. It will accelerate a brain drain that is already taking place, and it will serve to hasten the country's slide from first-world status. That's just some of what teaching Intelligent Design will accomplish.

Kern goes on to present the reasons that he believes that Intelligent Design will one day rule the country:

ID will win because it's a religion-friendly, conservative-friendly, red-state kind of theory

Please note that this may be true, but it says absolutely nothing about the scientific merits of Intelligent Design. I hope it isn't true, but I am afraid that it is.

Kern gives some reasons to justify this statement:

The most vocal non-scientist proponents of ID are those delightfully fertile Catholics, Evangelicals, and similarly right-leaning middle-class college-educated folk -- the kind whose children will inherit the country. Eventually, the social right will have the sheer manpower to teach ID wherever they please.

That was one of the statements that had me almost literally seeing red. The founders of our nation shed blood to establish a society founded, in part, on the principle that the government should not be used as a tool to advance religion. Kern apparently believes that once they have enough people, the religious right can ignore that, and push religious beliefs on the remaining minority - despite the fact that we have a constitution specifically to protect the minority from the tyranny of the majority. What's worse is that this jackass doesn't seem to find anything wrong with that position.

Kern goes on:

Belief in ID does nothing to make believers less capable in science or engineering. No geek in the world will find his computer mojo diminished because of his opinions on irreducible complexity. To the contrary: ID might make biology and the natural sciences more appealing to believers who might otherwise find science to be too far removed from God's presence.

Actually, belief in ID does make you less capable in biology. That's the result of the whole "evolution is the core concept that unites biology" thing. Another article, this one on Jeb Bush and ID, makes the point quite nicely:

University science professors and a national group that had concerns about how science curriculum was rewritten in Minnesota say it's ironic that Florida would spend hundreds of millions of dollars to woo The Scripps Research Institute to the state, yet hire a top educator who does not accept Darwinian evolution — something Scripps scientists say they prove every day in their experiments.

Not satisfied with the hole he's dug for himself, Kern goes on to provide more of the reasons that he thinks ID will win: "2) ID will win because the pro-Darwin crowd is acting like a bunch of losers." Well, I guess that's as good as any to throw out the cornerstone of biology - the people who support it act like losers. Kerns continues:

Vitriol, condescension, and endless accusations of bad faith all characterize far too much of the standard pro-Darwinian response to criticism.

Vitriol is common, and it is becomming more common. It would be nice if we could all maintain our composure as nicely as Douggie "they're acting like losers" Kerns does, but it can be hard sometimes. This is especially true for scientists in the face of the continuing creationist assault. We spend hours working in the field and lab for every minute that they spend spewing out their nonsense to non-scientific audiences. Keeping cool becomes increasingly difficult under the circumstances. There are also frequent accusations of bad faith. That's because the creationists frequently display bad faith. Don't just take my word for that. Go look at the trial transcripts from this week, where numerous witnesses document the efforts that the Dover school board made to add creationism to the curriculum, before settling on the current ID maneuver. Then look at the way that they keep claiming that their motives were entirely secular. Look at the Meyer affair. Or the Leonard affair. Or at any number of other incidents through the years.

Here, though, we again find one of the more frustrating realities that we are faced with. We are dealing with opponents who will make inaccurate, misleading, and dishonest claims, and then claim that we are whiners when we point that out. It must be nice to argue without having to worry about your scruples acting up. I really should try it someday.

Kerns continues:

A reasonable observer might note that many ID advocates appear exceptionally well-educated, reasonable, and articulate; they might also note that ID advocates have pointed out many problems with the Darwinist catechism that even pro-Darwin scientists have been known to concede, when they think the Jesus-kissing crowd isn't listening.

Back in the good old days of usenet, this sort of thing used to be called the "lurkers support me in email" argument. Making a blanket statement about things that go on behind the scenes, without providing evidence to support any of it, is a common strategy. It's not a particularly honest strategy, but it is common. To the best of my own knowledge, as someone who has put a hell of a lot of time into both dealing with creationist lunacy and into studying evolution, the Intelligent Design folks have not made a single contribution to the field in any way - and that includes pointing out substantive problems with evolution.

The next reason that he gives is my favorite: "ID will win because it can be reconciled with any advance that takes place in biology, whereas Darwinism cannot yield even an inch of ground to ID."

Isn't it a wonderful argument? What he's saying boils down to this: ID will win because it can't possibly be refuted. To a lawyer like Kerns, that's a fantastic strength in an argument. To a scientist, that's proof that an argument is completely non-scientific in nature. Lest you think that I am somehow misrepresenting Kerns, here's the rest of this argument:

So you've discovered the missing link? Proven that viruses distribute super-complex DNA proteins? Shown that fractals can produce evolution-friendly three-dimensional shapes? It doesn't matter. To the ID mind, you're just pushing the question further down the road. How was the missing link designed? What is the origin of the viruses? Who designed the fractals? ID has already made its peace with natural selection and the irrefutable aspects of Darwinism. By contrast, Darwinism cannot accept even the slightest possibility that it has failed to explain any significant dimension of evolution. It must dogmatically insist that it will resolve all of its ambiguities and shortcomings -- even the ones that have lingered since the beginning of Darwinism. The entire edifice of Darwinian theory comes crashing down with even a single credible demonstration of design in any living thing. Can science really plug a finger into every hole in the Darwinian dyke for the next fifty years?

I really wish I could give this to the judge in the Dover case. This sums up, better than anything else that I have seen, the scientific principles involved. Evolution is a scientific theory. It has been subjected to tests, it is being subjected to tests, and it will continue to be subjected to tests. It stands a very real chance of failing some of these. It might, conceivably, be shown to be wrong. If it is, we will have to replace it with a better explanation, and that new explanation will have to be tested, retested, and tested again. If it fails, it will have to be replaced with a better explanation, and the process will continue. That is how knowledge advances. Intelligent Design, on the other hand, cannot be subjected to tests. It cannot be proven wrong ever, under any circumstances. It will be an explanation that cannot be replaced. That is how knowledge stands still.

Kerns has a couple of more reasons for his belief, relating to a perceived need to change the way science works in order to accommodate information theory (he seems to be blissfully unaware that information theory is doing just fine as things are) and the ability of humans to perceive design. (He argues that just because we are hardwired to detect design doesn't mean that design isn't there.) In the interests of getting a decent night's sleep, I'm going to slide past those and move on to his conclusion:

The only remaining question is whether Darwinism will exit gracefully, or whether it will go down biting, screaming, censoring, and denouncing to the bitter end.

It's tempting to let the nation go to hell in its own, uniquely American way, but I can't. For some strange reason, I think that it is important for us to give our children the best education that we can. In my mind, a twisted, unrecognizably distorted view of science doesn't begin to enter that picture. Mr. Kern might hope that we will go gently, but that will not happen. Intelligent Design is bad science, it is worse theology, and it is built on a foundation of dishonesty. The entire world could embrace it, but that wouldn't change those basic facts.

Not one of the reasons that Kerns gave to support his belief in the inevitable success of Intelligent Design has anything to do with the question of whether or not Intelligent Design is correct, or even whether it is scientific. To a certain degree, this makes sense. The battle over ID is not a scientific one, but a political struggle. Sadly, whether or not a position is right or wrong has become totally irrelevant to modern politics. Perception, spin, and how to manipulate popular opinion matter. Truth is meaningless.

I am not a politician. I am a scientist. Like most scientists, I believe that reality matters. Truth matters. Science matters. This may place me at odds with politicians. It may not endear me to Kerns and his ilk. It may not make me popular. None of that matters. I will not "go gracefully." I will stand up for what I know is right. To teach Intelligent Design is to lie to our children. That is wrong, and it does matter.

Another Dover news carnival

After spending most of the week stranded deep in the mire of proposal writing, I've rewarded myself with a day off. Actually, it's not so much a matter of rewarding myself as it is a matter of attempting to resusitate the last remaining shreds of my sanity. So instead of continuing to pickle my brains in the volumnous literature surrounding the history of genetic divergence in various species of Drosophila, I decided to take some time to skim through a number of the news articles that the Dover trial has spawned in the last week. (Why I thought this would help maintain my sanity should serve to indicate just how brain-corroding the scientific proposal process actually is.)

Rather than taking as inclusive a look as I did last time, I think I'm mostly going to focus on the more annoying articles this time. It might just have been my mood this week, but it certainly felt like there was a heck of a lot more stupidity being aired this time.

To lead things off, we have an editorial in the York Daily Record. This was somewhat disappointing, since their coverage of the whole Dover affair has been, overall, outstanding. (I should probably note that the author is a copy editor, and that this may constitute "community opinion" rather than that of the editorial board. In his piece, titled: "Don't settle for separate but equal", Dave Dentel writes:

The truth is that anyone who’s being intellectually honest will admit that science can never be divorced from religion, that a person’s philosophical outlook will always affect how he or she interprets nature’s phenomena. Honest people will also admit that Darwinism supports a definite philosophy about nature, one that is hostile to theistic faith held by many Americans.

This is why I find the Dover plaintiffs’ arguments disingenuous. Their witnesses, like many adherents to Darwinism, insist modern science respects religion when in reality it marginalizes it and usurps its authority.

Mr. Dentel needs to learn that "his religion" is not necessarily equal to "all religion", and that there is a big difference between "hostile to theistic faith" and "hostile to a theistic faith". There are plenty of people out there who really do believe that science provides the best explanation for the way that the physical world works, but that science also only explans how the world works. The why questions are not addressable by science, but that does not make them any less real. Dentel goes on to conclude with this set of concerns:

What does this means for students? It means that explicitly and implicitly they’re taught that science trumps faith.

It means they learn that men in white lab coats — the ones who offer medicines, iPods and weapons of mass destruction — speak with greater authority than pastors, rabbis and priests. It means they’ll be told the reason they exist is no reason at all, just chance, mutation and blind law.

And chances are they’ll believe it, because after all, it’s based on science.

Mr. Dentel, scientists do speak with more authority than pastors, rabbis, and priests - when it comes to the nature of the physical world. That does not mean that scientists should be accepted as speaking with authority when they talk about things, like meaning, that are beyond the nature of science. If students believe that science trumps faith, it is because fools like you - or, for that matter, like Richard Dawkins - continue to insist that there is an absolute, either/or choice between science and religion.

Moving along, the Kingsport (Tennessee) Times-News ran an article on "local debate". I honestly can't tell why they used the word "debate" in the headline, since there really wasn't much of one there. They presented the malformed opinions of some twit of a "biology" teacher at a local "Christian" school, and then, presumably for balance, decided to close the article with the "contrasting" views of a lawyer/preacher who is a firm Intelligent Design proponent. The net effect of the article was to convince me that Kingsport is definitely not going to appear on the list of the ten places I want to move to. (This news will probably come as a relief to them, too.) The article quotes one Dora Phillips, who, it is alleged, is a "biology" teacher at a local "Christian School":

Phillips does not pretend to be unbiased about her approach.

"We have our own bias that are opposed to evolutionists' views. Evolutionists have biases too."

She's right. I freely admit it. I'm biased. I have a massive, bias that nobody will ever be able to shift me from. I firmly believe that it is an absolute moral wrong to teach children material that is nothing short of a flat-out lie. Phillips continues:

"Good science is based on three things: observations, the ability to measure those observations, and the repeatability of those measurements and observations. If those three things are not there, then it is a theory, not science," she said. "Creationists have not seen God design the universe, but evolutionists have not seen anything evolve from one species to another species, so we have a little more support than the evolutionists."

Wow. I realize that this is a private school, and that it doesn't receive government funding, but I still can't believe that anyone finds it acceptable to have someone who clearly lacks any comprehension of the way science really works teach the topic. The article then shifts the focus of the "debate" from this so-called "teacher" to Doug Tweed, who is a Methodist minister and a lawyer:

"This is not a case about defending religion. This is a case about defending truth as it is being discovered in the scientific community, and at the same time, trying to shed some light on the fact the position taken by the plaintiffs, even though they deny it, also has a religious motivation to deny the existence of God," Tweed said.

No, Doug. This isn't about anything that is being "discovered in the scientific community." Were it, there would actually be some discussion taking place in the scientific community. Not in courtrooms, not in schoolboard meetings, not in newspaper op-eds, but in scientific journals, at scientific conferences, and above all else, in laboratories.

Next on our list of unintelligent commentary on intelligent design, we have an opinion piece by Charlie Mitchell, editor of the Vicksburg (Mississippi) Post. Mitchell attempts to depict the current court case as a battle between the extremists on two sides of a religious battle:

Evolution has become the norm in science textbooks — underline science. In some jurisdictions, creationists have objected. Although they may want more, they insist that "intelligent design" must at least be mentioned.

This, in turn, spurred the ever-vigilant church-state separation crowd into fits of protest. They insist that for a teacher to mention the possibility of a guiding force in the universe is tantamount to trying to trick vulnerable little minds into becoming — oh no — Christians. Few will admit it, but from their narrow view, they believe Christians are the bane of human existence.

It's interesting, in a way. The more obvious it becomes in court that the Dover school board was motivated by religion, the more desparate people like Mitchell become to depict those opposed to the Dover school board as being motivated by religion, too.

That paragon of Moonie virtue, The Washington Times, has an OpEd on the topic by one Woody Zimmerman. Mr. Zimmerman, in a farily short article, manages to trot out just about every tired old creationist standard that the world has ever seen. I particularly enjoyed this one:

Darwinism's "holy grail" would be species-crossovers found in the fossil record to fill those pesky "gaps." But the grail remains elusive. Occasionally a jawbone or tooth, etc., has been proclaimed as evidence of a long-sought "missing link." These hopes have died when the artifact traced to one species or another, never to an intermediate.

As far as fighting creationists goes, I sometimes think that it would be better if we never found another intermediate - because, as far as jokers like this are concerned, every time we find an intermediate it just gives them two new gaps to complain about - one on each side of the new find.

There's more idiocy out there, but that just about does it for my tolerance this week. But don't worry. The trial's not over for a while yet, so we should see plenty more foolishness before it's all over.

Apologies for the lack of posts.

I've been spending the last few days deep in proposal hell. There is a fine line to walk, when you are putting together a proposal for your first independent research project, between outlining something that is too broad to be an answerable question, and too narrow to be anything interesting. Thus far, I have managed to fall off that line several times in each direction. But, the n-th time's the charm, and I think I've got it nailed this time. I'll find out for sure on Tuesday, when I (once again) meet with my advisor to discuss the proposal.

Hopefully, it won't go like the last time:
Me: So what do you think?
Advisor: Well... ... ... ... ... ... ... it's well written, but ... ...

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.