24 September 2005


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

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

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

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

Mistakes were made.

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

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

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

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

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

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

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

22 September 2005

The tools of the trade

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

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

21 September 2005

Chutzpah, pure chutzpah

There's an article in today's York Dispatch about the upcoming Intelligent Design lawsuit. This particular article discusses the rats leaving the sin Discovery Institute's principled decision not to support the Dover school district in this case. Most of the quotes from the various DI talking heads is the usual stuff, but there was one statement attributed to Casey Luskin that displays a disregard for reality that is below and beneath even the rather loose standards of the Discovery Institute:
He [Luskin] said the Discovery Institute is "not trying to hinder their case in court," but the organization wants intelligent design to be debated by the scientific community, not school boards

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

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

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

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

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

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

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

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

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

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

They also wouldn't have been saying things like this:
[from a DI press release] The Discovery Institute today faulted defenders of Darwin's theory for refusing to defend their views before the Kansas State Board of Education and for being afraid to answer tough questions about the scientific problems of modern evolutionary theory.

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

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

20 September 2005

Tangled Bank 37

The Tangled Bank

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

Toxic Soup

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

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

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

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

  • Mostly Harmless:

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

  • Not Too Bad

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

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

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

  • Not Good

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

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

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

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

  • No Clue

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

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

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

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

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

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

And it gets worse.

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

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

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

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

19 September 2005

DNA and RNA (and Birdnow).

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

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

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

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

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

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

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

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

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

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

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

In addition to the misconceptions over DNA and RNA, Birdnow's uninformed diatribe also provides an illustration of a very interesting phenomenon: the tendency of people who have a minimal understanding of science to believe that they are as qualified, if not more qualified, to comment on scientific issues as professional scientists are. Let's take another look at part of Birdnow's statement:
You know, Doctor, that DNA is fundamentally an advance on RNA.
Later on in the post, he goes on to complain of part of Myers response:
This is the old ``I know more than you and I say so`` canard.
When Myers complains - entirely correctly - that Birdnow displays a massive knowledge deficit in the field of biology, Birdnow is apparently highly offended:
Boy, if that isn`t the pot calling the kettle black! The main reason I wrote this was because I became increasingly irritated with the monstrous arrogance and utter closed mindedness of Darwinists such as Dr. Myers. Perhaps, Dr., if you found this essay hard to understand you should find yourself a fifth grader to explain it to you. You don`t seem to have a command of logic.

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

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

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

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

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

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

18 September 2005

Another interesting human evolution-related paper

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

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

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

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

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

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

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

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

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

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

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

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

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