Then a research team from Duke University came along and changed all that.
First they demonstrated that the appendix does have a function :
the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.
Proposed function of appendix as providing support for growth of bacteria essential to the function of the intestine.
Then they show  that
Although the appendix has apparently been lost by numerous species, it has also been maintained for more than 80 million years in at least one clade, supporting the idea that the structure has a vital biological function.
Part of the phylogenetic tree showing that the appendix most likely evolved more than once (red, appendix present; gray, appendix absent). Note that this part of the tree doesn't show that the monotremes (platypus, echidna) and some marsupials also have something that looks like an appendix.
Both of these papers separately point to evidence that the human vermiform appendix is not a useless structure. The interpretation is not in question - no biologist do (should) not have any problem understanding the implication of this, namely that the status of the appendix has changed to one of use, but that while Darwin was wrong about this particular point, this conclusion in no way takes anything away from evolutionary theory as a whole. Creationists are guaranteed to jump out and imply that this means there is a problem with evolution, but it cannot be said with enough emphasis that it in no way means that. Again, evolution can explain such organs of no use, but creationism can't. That one structure is no longer considered neutral with respect to fitness does not mean that such neutral organs don't exist. Examples:
- leg bones in whales
- eyes of blind cavefish
- pelvis remnants in snakes
- the human tailbone
- human goose bumps
- human muscles to move the ears (I'm very skilled at this myself)
A question of semantics
What do we call such organs/structures/behaviors that no longer serve any function? If we distinguish between those that used to have one function but now has another (penguin wings, for example) and those that used to have a function, but now doesn't at all (see list above), then I personally find it most useful to call only the latter vestigial. However, some people use the term in both cases (Jerry Coyne is said to do so in Why Evolution Is True, for example), but I find it more informative to call the former structure exapted, preadapted, or co-opted (I use co-opted, because the first to are usually used a nouns, exaptation and preadaptation - and that reminds me that Todd Oakley still owes me to explain what the difference between these three are).
So, I'll say that the human appendix is not a vestigial organ.
A question of politics
All of the above is really fairly straightforward (but exciting) science discourse. However, our own PZ Myers has reacted rather strongly in a post, Darwin and the vermiform appendix.
Before I go on, let me make a few things clear before anyone says otherwise: PZ is a great blogger, when blogging about science as well as about creationism and all things related to either one. I happen to be fairly aligned with him in terms of politics as well as on religion (we are both atheists), and I agree with him on most issues that he brings up on his blog. Notably, I side with him on the question of "Crackergate," "Expelled from Expelled," and share his disdain for the faitheists, just to name a few.
The post from today about the human appendix paper is the first example where I strongly disagree with PZ. He doesn't so much talk about the scientific paper itself, but instead about an article in ScienceDaily, Evolution Of The Human Appendix: A Biological 'Remnant' No More, in which we are introduced to the evolutionary significance of the study:
Now, some of those same researchers are back, reporting on the first-ever study of the appendix through the ages. Writing in the Journal of Evolutionary Biology, Duke scientists and collaborators from the University of Arizona and Arizona State University conclude that Charles Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant. Not only does it appear in nature much more frequently than previously acknowledged, but it has been around much longer than anyone had suspected.Parker then said
"Maybe it's time to correct the textbooks," says William Parker, Ph.D., assistant professor of surgical sciences at Duke and the senior author of the study. "Many biology texts today still refer to the appendix as a 'vestigial organ.'"
Darwin simply didn't have access to the information we have. If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution.Here is, then, the relevant passage from Darwin :
He also was not aware that appendicitis, or inflammation of the appendix, is not due to a faulty appendix, but rather due to cultural changes associated with industrialized society and improved sanitation. Those changes left our immune systems with too little work and too much time their hands – a recipe for trouble.
That notion wasn't proposed until the early 1900's, and we didn't really have a good understanding of that principle until the mid 1980's. Even more importantly, Darwin had no way of knowing that the function of the appendix could be rendered obsolete by cultural changes that included widespread use of sewer systems and clean drinking water.
Not only is [the vermiform appendage of the caecum] useless, but it is sometimes the cause of deathHe doesn't use the term vestigial, but instead is very careful (I gather) to say that it no longer has any use (in fact, it isn't even just neutral, per Darwin's observation, but detrimental).
Here are a few quotes from PZ's post about the ScienceDaily article, and my answers to each of them:
It's rather unseemly to collect a lot of data that Darwin did not have, run it through PAUP 4.0 on a fast computer, map the data onto a molecular consensus phylogeny, and cackle gleefully over discovering something Darwin did not know. Really, it doesn't make you a better scientist than Darwin."Cackle gleefully" ? Who, Parker? "Make you a better scientist" ? Where does this come from? Parker isn't implying any such thing.
To make it even worse, people who do this can't even make the corpse-fight a fair fight — they have to stuff the pathetic dead body with straw. In this case, they're padding Darwin's investment in the appendix a fair amount. They cite one work by Darwin, The Descent of Man, which mentions this issue. He wrote one whole paragraph on the topic, and here it is, in its entirety;Go to PZ's post to see the quote, which includes the sentence I quote from Darwin above, where he labels the appendix as 'useless.' People criticize the work of dead scientists on scientific grounds as a matter of routine. There is absolutely nothing wrong with it. Indeed, this is the way things must be, in order for science to progress. PZ would agree, I know, and I am puzzled why he would scold Parker in this manner.
Note why Darwin classed this appendage as vestigial: because it is greatly reduced compared to the homologous organs in non-human relatives, and because it currently exhibits a great range of variation, which is apparently non-functional. These are criteria which the paper in question does not refute at all. Darwin does say that the appendix is "useless", and the paper will show some evidence that that is wrong. It's also irrelevant.It is not relevant that the appendix is useless? The hell?! PZ harps about the semantics - vestigial vs. useless - but then ignores the meaning behind Parkers's words. Parker clearly means 'useless' when he says 'vestige'. Of that there can be no doubt. How can it be irrelevant whether the appendix has a use, when that is what both papers are all about? (It can't, and it isn't.)
The reason why it is irrelevant is that the presence of some function is not part of the definition of a vestigial or rudimentary organ
If a portion of the gut, a digestive organ, is diminished in size such that it no longer contributes to the primary function of the organ, but does retain a secondary function, such as assisting in immunity, or as the authors of the recent paper will argue, in acting as a reservoir of bacteria for recolonizing the gut, then it is still a vestigial organ. It has lost much of its ancestral function.PZ is using one definition of the word, and not the other (see semantics above).
I mentioned that I'd point out errors in Darwin's understanding. They're there, but note that seeing them now 150 years after he wrote his big book does not make me smarter than Darwin, nor does it invalidate the overall picture of his theory.And Parker neither said nor implied anything to that effect. In fact, he goes to great length to emphasize that "Darwin simply didn't have access to the information we have," and "If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution." That, and the rest of the Parker's words above from the ScienceDaily article.
Most of my complaints here are with the abysmal presentation of the ideas in it by the popular press, aided and abetted by the scientists themselves. Just keep in mind that whenever these press releases that declare "Darwin was wrong" appear, it's usually an example of grandstanding and the regrettable tendency of competitive scientists to think the way to impress people with the importance of their work is to get into a penis-measuring contest with poor dead Chuck.I was very careful to put "Darwin was wrong" in the title of this post. This is the "abysmal presentation" that PZ is referring to. PZ co-authored a letter to the New Scientist, when they printed those exact words in big letters on the cover of the January 2009 issue. (That cover story was about the uprooting the tree of life, and how parts of it isn't at all like a tree, but a network. I agree it was foolish to choose that headline for the cover, but, luckily, as things have turned out, it didn't really have much of an effect as far as I have seen.) I also think it is impressive when scientists can finally prove Darwin wrong on something. If no one else have been able to do it for almost 150 years, then let us indeed celebrate it with much fanfare whenever someone can. Darwin would have been proud.
I think PZ has got the heebie-jeebies. He is at the forefront of defending evolution against creationist imbeciles, so it is understandable that he dislikes it when scientists gives them ammo for their cannons (note to self: find a better idiom). However, when communicating science, we should not be hesitant to say things the way they are, and in this case "Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant." Trying to boost your scientific work in the popular media by such statements is fair game. It's very hard to get people interested, and I personally applaud Parker for the way he did it, and for standing up for "poor dead Chuck" at the same time. Yeah!
Lastly, let me briefly say how disagreeable I find the discourse in the comments to many of PZ's posts, this one in particular. People call each other names for voicing opinions not shared by the majority of the commenters. Accusing them of trolling is standard practice, akin to shouting 'witch' back in the middle ages, and one is a 'fucktard' when they don't like you. But worse than that, ScienceBlogs is a place for science bloggers, and the number one trait of a good scientist is skepticism. Pharyngulites as a group don't have too much of it; commenting how much they are in agreement with PZ on whatever he writes about, spiced with sublime derogatory terms, seems to be a hobby of hundreds of regular visitors. A few quotes from comments to the post in question:
"some idjits think that makes the whole work of the innovator wrong."
"As Prof. Myers points out, Darwin was wrong about a lot of things. So what?"
"Picking a fight with Darwin over it is just stupid."
"So, basically, they didn't understand what Darwin meant by "vestigial" because they didn't do all their homework."
It's not all bad, though. Here's one dissenting voice: "If we are to refer to all homologous structures with different functions as vestigial, it seems to have become a useless term."
Exactly my point.
 Darwin, C. 1871. The Descent of Man and Selection in Relation to Sex.
 Randal Bollinger, R., Barbas, A., Bush, E., Lin, S., & Parker, W. (2007). Biofilms in the large bowel suggest an apparent function of the human vermiform appendix Journal of Theoretical Biology, 249 (4), 826-831 DOI: 10.1016/j.jtbi.2007.08.032
 Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, & Parker W (2009). Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of evolutionary biology PMID:19678866
Bill Parker sent me an email in reply, and I have elected to make it a separate post: More on the appendix.