Nicholas Wade has a very peculiar review of Richard Dawkins’ book, The Greatest Show on Earth, in the NY Times Review of Books. It’s strange because it is a positive review which strongly agrees with Dawkins’ position on the central importance of the theory of evolution in biology in the first half…but the second half is a jaw-droppingly stupid attack on a small point in the book. Wade has a very absolutist and wrong view of the definitions of some terms, and he goes on and on, whining about a topic that he doesn’t understand himself.

There is one point on which I believe Dawkins gets tripped up by his zeal. To refute the creationists, who like to dismiss evolution as “just a theory,” he keeps insisting that evolution is an undeniable fact. A moment’s reflection reveals the problem: we don’t speak of Darwin’s fact of evolution. So is evolution a fact or a theory? On this question, Dawkins, to use an English expression, gets his knickers in a twist.

Oh, man. Wade has really waded into it. This is a subject that has been amply discussed and explained and expounded upon, and I’m surprised that Wade is not only unfamiliar with it, but has thrown away half of his review in a misbegotten error of his own devising. Take it away, Stephen J. Gould:

In the American vernacular, “theory” often means “imperfect fact”—part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is “only” a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can’t even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): “Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science–that is, not believed in the scientific community to be as infallible as it once was.”

Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts don’t go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s in this century, but apples didn’t suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin’s proposed mechanism or by some other yet to be discovered.

Moreover, “fact” doesn’t mean “absolute certainty”; there ain’t no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science “fact” can only mean “confirmed to such a degree that it would be perverse to withhold provisional consent.” I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory–natural selection–to explain the mechanism of evolution.

If he’d just written that one little paragraph, it would have been mildly embarrassing for him…but he just keeps stuffing his foot down his throat. It’s a good thing he keeps his pants on to hide the spectacle of his shoe poking out of his butt.

He [Dawkins] seems to have little appreciation for the cognitive structure of science. Philosophers of science, who are the arbiters of such issues, say science consists largely of facts, laws and theories. The facts are the facts, the laws summarize the regularities in the facts, and the theories explain the laws. Evolution can fall into only of of these categories, and it’s a theory.

Whoa. Scientists everywhere are doing a spit-take at those words. Philosophers, sweet as they may be, are most definitely not the “arbiters” of the cognitive structure of science. They are more like interested spectators, running alongside the locomotive of science, playing catch-up in order to figure out what it is doing, and occasionally shouting words of advice to the engineer, who might sometimes nod in interested agreement but is more likely to shrug and ignore the wacky academics with all the longwinded discourses. Personally, I think the philosophy of science is interesting stuff, and can surprise me with insights, but science is a much more pragmatic operation that doesn’t do a lot of self-reflection.

As for his definitions…sorry, but these ideas simply do not fit into the tidy pigeonholes Mr Wade wants to make for them. Evolution is both a fact and a theory. Trying to cram it into one category does violence to both evolution and his cognitive roll-top desk.

And Wade goes on with more! Here’s where we really need philosophers; they could have much more fun shredding the blithe assumptions Wade flings about.

Other systems of thought, like religion, are founded on immutable dogma, whereas science changes to accommodate new knowledge. So what part of science is it that changes during intellectual revolutions? Not the facts, one hopes, or the laws. It’s the highest level elements in the cognitive structure—the theories—that are sacrificed when fundamental change is needed. Ptolemaic theory yielded when astronomers found that Copernicus’s better explained the observations; Newton’s theory of gravitation turned out to be a special case of Einstein’s.

If a theory by nature is liable to change, it cannot be considered absolutely true. A theory, however strongly you believe in it, inherently holds a small question mark. The minute you erase the question mark, you’ve got yourself a dogma.

I don’t even like his dig at religion. There’s a funny thing about religious dogma: it evolves. It changes slowly, usually, and it’s not on the basis of reason or evidence, but more often to bend to popular expediency — I’d agree that it isn’t knowledge that changes it, but the utility of accommodating a human institution to popular perception.

I kind of agree with the general statement that facts won’t change (but as I’ll say below, the facts do shift as they are argued over), but it is possible to change the conceptual framework, the theories, we use to integrate a collection of facts into a useful model in our brains. It is entirely possible for a new model to emerge that does a better job of explaining the history of life on earth someday. After all, it’s already happened, and look, Darwin’s theory still remained a fact!

Darwin’s theory was expanded and replace roughly 70-75 years ago, with the incorporation of the science of genetics into that framework. Darwin was working with a seriously flawed idea of heredity, and all his ideas about the transmission of traits were wrong. Pangenesis was completely scrapped and replaced with Mendelian and population genetics. I can’t imagine a more radical change than that happening any time in the future — we have a solid grip on the rules of heredity now, and what we expect is refinement and the addition of details.

But notice that what happened was a reversal of Wade’s claim. A massive bolus of ‘facts’ were inserted into the theory, but the core of the theory itself, the idea that species changed over time driven by forces of selection, remained. Why? BECAUSE THAT IS ALSO A FACT. We have piled evidence high that shows the earth is old, there have been a succession of forms, that the properties of populations change from generation to generation, that all the diverse forms of life on earth are linked by molecular relationships that fit nicely into a tree of descent. A subsidiary assumption that generations changed by the transmission of acquired characters was discarded, but the big picture was unchanged…and was actually made sharper and stronger.

Any future hypothetical theory that is a better model must incorporate these facts of evolution. It’s one of the reasons creationists aren’t doing science, because they are compelled by ideology to reject the evidence. There will be no theory that denies that human beings are apes and the children of apes, no matter how objectionable creationists find that, because that is a fact. We’ll argue over the mechanisms, whether it was selection-driven or mostly chance divergence, whether group selection played a role, over which fossil fits most closely to the main path of the population that led to us, etc., etc., etc., but the fact of our ape ancestry and nature is established.

One more quibble: Wade insists that every theory must retain that little question mark of doubt, and that is true. However, it also holds true for the facts of science; we can have a fair amount of confidence in the data, but no one considers a published result to be unquestionable. It happens all the time that different labs will wrestle over the data, and the interpretation of the data. It’s one of the factors that drives science, that we work hard to confirm and disconfirm everything. What you’ll actually find when you look at the daily routine of science is that the theories are generally stable and are not strongly questioned — it takes such a massive amount of contradicting data to overthrow a theory that it’s hardly likely that your average individual or research group can demolish a major theory like evolution, or cell theory — and most of the haggling and conflict is over the day-to-day details. You know, that stuff that Wade would try to stuff in his pigeon hole labeled “facts”.

Wade concludes his little diversion into fantasy philosophy with a strange dig at Dawkins that suggests he doesn’t like his book much after all.

He [Dawkins] has become the Savonarola of science, condemning the doubters of evolution as “history-deniers” who are “worse than ignorant” and “deluded to the point of perversity. This is not the language of science, or civility. Creationists insist evolution is only a theory, Dawkins that it is only a fact. Neither claim is correct.

True, neither is crorrect…but then, I guarantee you that Dawkins does not consider evolution to be “only a fact.” Only someone who had not read his books with comprehension could come away with this freakish idea that Dawkins is unaware of the “cognitive structure of science.”

I agree that Dawkins’ words are relatively uncivil, but I’d argue that they’re too civil, and that we need more incivility. Wade does not seem to agree that creationists deny the depth of human history (I don’t understand how he could find fault with the FACT that believing the world is 6000 years old requires blindness to 13 billion years worth of time), or that by promoting false beliefs about our origins they are not merely passively unaware, but are malevolently ignorant, or that using Gould’s definition of a fact, they are in denial “to such a degree that it would be perverse to withhold provisional consent.” Those are the facts that Mr Wade claims to be able to recognize, but ignores in this case.

I also will not accept sad tut-tutting over a lack of civility when Wade so obliviously compares Richard Dawkins to Savonarola. Savonarola? Really? You compare a gentlemanly scholar who writes books to oppose the rising tide of lunacy in the world to a book-burning puritanical fanatic who opposed the Renaissance and sought the death of homosexuals??

Hypocrite.

Since I just chastised the misleading presentation of this paper in the press (and I must emphasize that the odd focus on Darwin is not in the paper at all), we can now take a closer look at the paper itself. The data is actually cool to see, and represents a large amount of work; I still have some criticisms for the interpretation, though. The fundamental question is whether the structure of the appendix was specifically selected for, and the authors are on the side of ‘yes’. I’ll come down on the side of ‘maybe’.

But first, an important caveat. Creationists have long been yammering about the appendix: they are absolutely positive that it must have an important function, because God wouldn’t put it there unless it had a purpose. This paper will not help them. The heart of the work is a phylogenetic analysis of the distribution of the appendix in mammals which uses evolutionary theory: no evolution, this work vanishes in a puff of logic. If creationists try to claim this paper proves something they’ve been claiming all along, then they didn’t read it and didn’t understand it — it’ll be a clear case of circular illogic.

To follow along with the story, you have to be clear on the layout of a small piece of mammalian plumbing. The little cartoon below illustrates the juncture of the small intestine with the large intestine, a portion of your gut that you’ll find inside your abdomen on the lower right side.

When you eat something, it first goes into the stomach, where it’s treated to an acid bath, some enzymes, and a lot of muscular churning to break it up. Then it’s squirted into the small intestine (colored orange), where the acids are first neutralized and more enzymes are tossed onto the watery, mushy soup that the food has been rendered down into, called chyme. The primary job of the small intestine is to suck all the nutrients out of the chyme and pass them on to the circulatory system.

Once as much of the good stuff has been leeched out of the chyme as your system can do, the soup is passed on to the large intestine (salmon colored in my cartoon). This stuff is still very watery — if you’ve ever experienced diarrhea, that’s what it is at this point. The primary job of the large intestine is to resorb water from the waste, condensing it down into the thick, pasty glop we all know and love as excrement. The large intestine is basically the sewage treatment plant here.

The interesting thing about the transition is that it makes a couple of other odd dead-ends. The cecum (pink) is a small pouch that goes nowhere, while the appendix (red) is a slender projection from the cecum. These are variable in size both within a species and between them — some humans are born without an appendix, and within the majority that have them, there’s at least a two-fold variation in size. Between species, the variation is even greater: most mammals don’t have an appendix at all, and some have huge ceca and appendixes. The enlarged cecum in most of these species is used as a fermentation chamber, in which hard-to-digest food resides while resident bacteria help break it down.

The diagram below illustrates some of these forms — to confuse you slightly, they’re all upside down from my cartoon, with the appendix always drawn at the top.

The cecal appendix (a through l) or
appendix-like structures (m through o) in a
variety of mammals. The cecum ⁄ appendix
is oriented toward the top of each drawing,
the distal end of the small intestine toward
the left and the proximal end of the large
intestine toward the bottom. (a) human,
Homo sapiens; (b) Pongo pygmaeus, orangutan;
(c) Lepilemur leucopus, sportive lemur;
(d) Lasiorhinus latifrons, Southern hairy-nosed
wombat; (e) Oryctolagus cuniculus, rabbit;
(f) Phalanger gymnotis, ground cuscus; (g)
Anomalurus derbianus, scaly-tailed flying
squirrel; (h) Trichosurus vulpecula, common
brushtail possum; (i) Bathyergus suillus, Cape
dune mole-rat; (j) Atherurus africanus, brush-tailed porcupine; (k) Castor canadensis, beaver; (l) Microtus pennsylvanicus, meadow vole,
shown with a partially uncoiled large bowel;
(m) Phascolarctos cinereus, koala; (n) Ornithorhynchus anatinus, platypus; (o) Tachyglossus
aculeatus, echidna.

These images are taken from the Smith et al. paper, and illustrate its greatest strength — it consolidates a lot of scattered information about the distribution of appendixes in one place. They also discuss the variability of morphology; it seems there is some ambiguity in exactly what an appendix is. They used a strict definition of the appendix as “a relatively narrow and extended, close-ended structure at the apex of the cecum that is clearly distinguished from the cecum by a relatively abrupt change in the diameter of the bowel between the cecum and the appendix” and discovered that there were cases it did not cover. Some species had something that clearly looked like an appendix, but didn’t have a cecum. Others had a a cecum that gradually tapered into a slender tube, lacking that abrupt change in diameter. That complicates the analysis, so they actually did two: one that used the strict definition and excluded some cases, and one that used a broader definition that included every species that had something vaguely vermiform dangling off the appropriate region of the gut. They then mapped the distribution of appendixes onto a consensus phylogeny of the mammals, and produced the tree diagram below.

The tree on the left is using the strict definition of an appendix, and the one on the right uses the broader definition. Taxa that have an appendix are in red, taxa in which there is a mixture of species with and without an appendix are in blue, and those without any appendix at all are in gray.

(Click for larger image)
Phylogenetic tree of mammalian relationships with appendicular characters mapped onto it. A mammalian molecular consensus
phylogeny was taken, and appendicular and cecal characters were mapped onto the constraint tree as described in the Materials and
methods. Results from Analysis 1 are shown by solid lines, which indicate the presence of a true appendix. Results from Analysis 2 are shown
by the solid lines and by the checkered lines, the checkered lines indicating the presence of an appendix-like structure. On the left are
shown results from analyses considering all taxa with variable expression of the appendix the same as taxa with consistent expression of
the appendix. On the right are shown results considering all taxa with variable expression of the appendix as a separate state (indicated by
the blue colour). Colour and pattern codes are as follows: grey, appendix absent; red, appendix present; red checkered, appendix-like structure
present; blue, appendix variable; Blue checkered, appendix-like structure variable.

That’s interesting: the only groups that have an appendix are the Glires (rodents and rabbits), primates, monotremes, and some marsupials. There’s definitely a pattern to the distribution: it is not the case that the appendix is a random glitch in the organization of the gut, but is maintained consistently in some lineages for as long as 80 million years, and is consistently lost in others.

The data are useful to have and provide considerable food for thought; where I disagree with the authors is in the interpretation of that data. I don’t think purely morphological data give us enough information to resolve the issues they bring up.

Here’s what the authors conclude from that distribution. The most parsimonious explanation is that the ancestral state of mammals was to lack an appendix, so that the majority of extant mammals are exhibiting the primitive, appendix-less state. The appendix then independently evolved 2-4 times, with the lineages that acquired it also marked by frequent secondary loss of the structure. They argue that this necessarily implies an adaptive function for the appendix, otherwise it would not have been retained in so many of the primates and glires.

They also provide a possible function. In many cases where the cecum is very large, that function is digestive — this is an area of the gut that can be expanded into a fermentation chamber. In others, like us humans, it is too small to have that role, but what it may be is a small reservoir of bacterial biofilms that are resistant to loss during diarrheal episodes, and provide a source for rapid recolonization of the gut flora after disease strips them away. They have demonstrated the presence of biofilms in the appendix, and also in the proximal colon of outgroups that lack appendixes — so this property of supporting colonies of bacteria in this region of the gut is ancient.

I’m not entirely convinced. If the appendixes in marsupials and euarchontoglires are actually homologous, that should imply that their last common ancestor had a cecum/appendix…and the pattern is explained by widespread and frequent loss of the organ. The authors acknowledge this idea, but admit that there’s also a problem with analyzing it: it depends on loss being far more likely than gain, and there aren’t any probabilities that we can assign to such events. Fair enough. It does mean, though, that this analysis is insufficient to come up with an answer.

What I’d like to see is patterns of gene expression. That region in the plumbing where the small intestine becomes the large intestine is an interesting transitional zone which must be defined by some kind of patterning molecules; furthermore, I’d expect some kind of gene regulatory network has to be at work in that area to specify the different regions of small intestine, cecum, appendix, and large intestine. What are those genes? Which ones are expressed in the different regions? How do they interact and how are they regulated? You can see how my brain is turning over: I want to know about the developmental and molecular events going on here. That’s where we’ll be able to resolve the questions of appendix evolution.

I’m also unconvinced by the argument that retention of a feature for 80 million years is necessarily evidence of selection for a specific function. Another possibility is that it is entirely structural: there is a patterning pathway that sets up the transition from small to large intestine, and as a side effect it defines a few intermediate zones, the cecum and appendix. These are mostly harmless, and so are retained as entirely neutral characters that are not easily pared out without disrupting gut function. I say mostly harmless, because one lesson of the phylogeny is that a lot of lineages seem to have edited the structure out altogether. Again, it could just be loss of a neutral character, but it could also be an indication that usually, the appendix is a detriment.

A more solid answer would emerge if, for instance, the molecular networks behind the formation of the appendix in monotremes and humans were compared, and found to use the same toolkit of genes — then we’d have to regard it as highly probable that they are homologous, and the last common ancestor had an appendix. Or conversely, if the mechanisms used by the afrotheria, the xenarthra, and the other mammalian groups that lack an appendix to switch off appendix development were identical, that would suggest that the last common ancestor of the eutheria had that mechanism, lacked an appendix, and those euarchontoglires definitely did re-evolve the appendix.

Show me trees built from genes, then maybe I’ll accept the interpretation with more confidence! I just think that one thing these data do show us is that the appendix is a remarkably labile organ, making the appearance or absence suggestive but not conclusive.

As for the argument that one function of the appendix that is significant in modern human populations is as a bacterial reservoir for recovery of gut flora after losses due to disease, that seems entirely reasonable. However, the fact that the appendix has an incidental function that can be useful to individuals in specific circumstances does not mean that the appendix isn’t a vestigial organ, nor does it necessarily mean that its retention has been selected for. That some modern human populations have significant mortality from diarrheal symptoms (from cholera, for instance) seems to me to be a relatively trivial factor in a study that shows persistence of the appendix over many tens of millions of years, especially when no evidence of differential survival by individuals having or lacking an appendix is known.

I’m being a bit negative here, but it’s largely because that distribution is so interesting and suggestive, and points the way to where we should be looking to answer the question of why we have an appendix. I also have my biases — I incline more to believing the organ is mostly neutral in us, and favor explanations based on the architecture of the gene regulatory networks — and would really love to see some molecular data behind the pattern (I also think it might resolve some of the complications and ambiguities of the morphology).

It’s a good paper, but I get a rather different message from it. What it says to me is, “More genes! More development!” But then, I confess that that’s what most papers say to me, anyway.

Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W (2009) Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. J Evol Biol. 2009 Aug 12. [Epub ahead of print]