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.

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.