Last night, I [asked](http://scienceblogs.com/pharyngula/2009/08/looking_for_an_article.php) for a copy of an article (I have plenty now, thanks!) that was getting a lot of press. The reason I was looking for it is two-fold: the PR looked _awful_, expressing some annoying cliches about evolution, but the data looked _interesting_, good stuff that I was glad to see done. Awful and interesting — I'm a sucker for those jarring combinations. My favorite pizza is jalapeno and pineapple, too.
I'm going to split my discussion of this article in two, just to simplify dealing with it. This is the awful part. I'll do the interesting part a little later.
The paper is about the appendix, that tiny little organ in your gut that doesn't have a whole lot of obvious function. The point of the work is to try and show that yes, it does something — which is fine and interesting, although I will quibble a bit with their interpretation. Where they go awry, though, is in trying to pick a fight with a dead man, and making that the focus of their public relations.
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.
"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.'"
Charles Darwin is dead. Your research can't be very cogent if your approach to drum up interest is to dig up a 120-year-old corpse and kick it around; is there anyone _alive_ who disagrees with you who can put up a more informative and entertaining struggle? What this does is pick this one fellow as a symbol of the whole edifice of evolutionary theory, which has the advantage of making one's work seem very, very important (even if one is stacking the deck to do it), but has the disadvantage of giving every creationist on the planet something to masturbate over, and they're icky enough without your help.
It's also annoying. Charles Darwin was wrong about many things — I'll even give an example at the end of this article — and it's part of the nature of science that _everyone's_ work will be revised and refined over time, and some of us will even be shown to be completely wrong. 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.
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; it was presented briefly as part of a long list of human rudimentary structures, such as wisdom teeth, muscles of the ear, and the semilunar fold of the eye.
With respect to the alimentary canal, I have met with an account of only a single rudiment, namely the vermiform appendage of the caecum. The caecum is a branch or diverticulum of the intestine, ending in a cul-de-sac, and is extremely long in many of the lower vegetable-feeding mammals. In the marsupial koala it is actually more than thrice as long as the whole body. (46. Owen, 'Anatomy of Vertebrates,' vol. iii. pp. 416, 434, 441.) It is sometimes produced into a long gradually-tapering point, and is sometimes constricted in parts. It appears as if, in consequence of changed diet or habits, the caecum had become much shortened in various animals, the vermiform appendage being left as a rudiment of the shortened part. That this appendage is a rudiment, we may infer from its small size, and from the evidence which Prof. Canestrini (47. 'Annuario della Soc. d. Nat.' Modena, 1867, p. 94.) has collected of its variability in man. It is occasionally quite absent, or again is largely developed. The passage is sometimes completely closed for half or two-thirds of its length, with the terminal part consisting of a flattened solid expansion. In the orang this appendage is long and convoluted: in man it arises from the end of the short caecum, and is commonly from four to five inches in length, being only about the third of an inch in diameter. Not only is it useless, but it is sometimes the cause of death, of which fact I have lately heard two instances: this is due to small hard bodies, such as seeds, entering the passage, and causing inflammation. (48. M. C. Martins ("De l'Unite Organique," in 'Revue des Deux Mondes,' June 15, 1862, p. 16) and Haeckel ('Generelle Morphologie,' B. ii. s. 278), have both remarked on the singular fact of this rudiment sometimes causing death.)
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.
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 — Darwin obligingly concedes that evolution will salvage some utility out of organs with little retention of their original function, but which are present as a consequence of contingency. He discusses this at greater length in _On the Origin of Species_, and here is a significant chunk of the relevant writing.
Organs or parts in this strange condition, bearing the plain stamp of inutility, are extremely common, or even general, throughout nature. It would be impossible to name one of the higher animals in which some part or other is not in a rudimentary condition. In the mammalia, for instance, the males possess rudimentary mammae; in snakes one lobe of the lungs is rudimentary; in birds the "bastardwing" may safely be considered as a rudimentary digit, and in some species the whole wing is so far rudimentary that it cannot be used for flight. What can be more curious than the presence of teeth in foetal whales, which when grown up have not a tooth in their heads; or the teeth, which never cut through the gums, in the upper jaws of unborn calves?
Rudimentary organs plainly declare their origin and meaning in various ways. There are beetles belonging to closely allied species, or even to the same identical species, which have either full-sized and perfect wings, or mere rudiments of membrane, which not rarely lie under wing-covers firmly soldered together; and in these cases it is impossible to doubt, that the rudiments represent wings. Rudimentary organs sometimes retain their potentiality: this occasionally occurs with the mammae of male mammals, which have been known to become well developed and to secrete milk. So again in the udders in the genus Bos, there are normally four developed and two rudimentary teats; but the latter in our domestic cows sometimes become well developed and yield milk. In regard to plants the petals are sometimes rudimentary, and sometimes well-developed in the individuals of the same species. In certain plants having separated sexes Kolreuter found that by crossing a species, in which the male flowers included a rudiment of a pistil, with an hermaphrodite species, having of course a well-developed pistil, the rudiment in the hybrid offspring was much increased in size; and this clearly shows that the rudimentary and perfect pistils are essentially alike in nature. An animal may possess various parts in a perfect state, and yet they may in one sense be rudimentary, for they are useless: thus the tadpole of the common salamander or water-newt, as Mr. G. H. Lewes remarks, "has gills, and passes its existence in the water; but the Salamandra atra, which lives high up among the mountains, brings forth its young full-formed. This animal never lives in the water. Yet if we open a gravid female, we find tadpoles inside her with exquisitely feathered gills; and when placed in water they swim about like the tadpoles of the water-newt. Obviously this aquatic organisation has no reference to the future life of the animal, nor has it any adaptation to its embryonic condition; it has solely reference to ancestral adaptations, it repeats a phase in the development of its progenitors."
**An organ, serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other.** Thus in plants, the office of the pistil is to allow the pollen-tubes to reach the ovules within the ovarium. The pistil consists of a stigma supported on a style; but in some Compositae, the male florets, which of course cannot be fecundated, have a rudimentary pistil, for it is not crowned with a stigma; but the style remains well developed and is clothed in the usual manner with hairs, which serve to brush the pollen out of the surrounding and conjoined anthers. Again, an organ may become rudimentary for its proper purpose, and be used for a distinct one: in certain fishes the swimbladder seems to be rudimentary for its proper function of giving buoyancy, but has become converted into a nascent breathing organ or lung. Many similar instances could be given.
I've highlighted the part most important for this discussion. Darwin did not discuss the appendix or caecum at all in the _Origin_, but this description does apply. 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.
I do not understand why this is so hard for so many people to comprehend. Biology is plastic and opportunistic. Accidents of history will always still be incorporated into the whole of the organism; we make do, or we die. Just because something _is_ does not mean that the entirety of its nature is the product of selection.
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. You can see one 'error' in the quote above: we are now pretty certain that the original function of the swimbladder in fish was respiratory. It evolved first as a supplement to the gills, providing access to the rich oxygen content of the atmosphere, and was secondarily adapted to function for bouyancy. Hah, silly Darwin, that he did not know a detail of paleontology and phylogeny that would be worked out a century after his death!
He also made a more substantial error. He wondered how organs became smaller over time, and his answer was, unfortunately, a bit Lamarckian and also a bit muddled.
It appears probable that disuse has been the main agent in rendering organs rudimentary. It would at first lead by slow steps to the more and more complete reduction of a part, until at last it became rudimentary,- as in the case of the eyes of animals inhabiting dark caverns, and of the wings of birds inhabiting oceanic islands, which have seldom been forced by beasts of prey to take flight, and have ultimately lost the power of flying. Again, an organ, useful under certain conditions, might become injurious under others, as with the wings of beetles living on small and exposed islands; and in this case natural selection will have aided in reducing the organ, until it was rendered harmless and rudimentary.
"Disuse" is the magic word there: if a cavefish lived in the dark and never used its eyes, the idea was that its progeny would then have smaller eyes. This is not correct, but it was a central part of Darwin's invalid theory of heredity. This is a much more substantial failing of Darwin's work, but again, I can't claim credit for figuring this out; it took the work of Mendel to get the core of genetics puzzled out, and then it took a whole generation of scientists to work out how genetics and evolution fit together. We can say "DARWIN WAS WRONG!" about that, but we can't really say that about his treatment of vestigial organs in general, which seems to hold up fairly well…perhaps because Darwin himself was not so fervently committed to the absolute adaptedness of every single feature of every single organism as some of his later followers.
That said, I'll move along to the substance of the paper next, which really does have some good stuff in it. 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.
Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W (2009) [Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix](http://www3.interscience.wiley.com/journal/122544996/abstract). J Evol Biol. 2009 Aug 12. \[Epub ahead of print\]