Oh, the martyrs of AiG!

I’ve really gotten under the skin of the frauds at Answers in Genesis — now Terry Mortenson is whining about my cruelty and lying frantically.

Last week I gave a lecture in the Creation Museum on “Millions of Years: Where Did the Idea Come From?” This is based on my PhD research. The next day the well-known (and self-proclaimed) atheist Dr. P.Z. Myers, a biology professor at the University of Minnesota-Morris, wrote a blog post about me with his usual caustic language. After labeling me a “crackpot,” he then proceeded to critique my lecture . . . without even hearing it (not very academic, is it?) . . . and to accuse me of being ignorant of historical truths that he explained to his readers. He also accused me and other creationists of believing things that neither I nor any other informed creationist believes.

No, I did not critique his lecture; I criticized his plainly stated premise, that our understanding of the age of the earth does not come from the evidence, but “comes from anti-Biblical worldviews (or philosophical assumptions) being imposed on the geological evidence”. Anyone could see that if they read the article, but once again AiG is afraid to link to me.

I’m not sure what specific things I’ve accused creationists of believing — most of my article was about the history of geology. However, he and his cronies at AiG do believe in something that is truly absurd: that the earth is only 6,000 years old. There’s not much I could add that is more damning than that.

Visiting North Dakota

It’s right next door, but I haven’t been to North Dakota that often. There are a couple of dates planned that will change that, though: on 24 September, I’ll be in Fargo for a free movie night with the Red River Freethinkers.They’ll be showing Julia Sweeney’s Letting Go of God at the Fargo Theater at 6pm, and then for an anti-climax, I’m giving a lecture.

If Fargo is just too darned congested for you, I’ll also be speaking at Minot State University in Minot, ND on 5 October — deep in the heart of the state. I’ll put up more details about that later.

Evolution of the appendix?


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]

Watch Maine

Maine recently legalized same-sex marriage —hooray and all that, but we don’t get to be complacent about it now. There is a proposition on the ballot for November, Proposition 1, that would revoke marriage equality, and as you might expect, conservative forces are gearing up to promote this bill. Greta Christina has some suggestions for how you can help defeat this hate bill…and explains why you should.

Cruel, cruel tease

If you’re like me, you are eagerly awaiting the release of Dawkins’ next book,
The Greatest Show on Earth: The Evidence for Evolution(amzn/b&n/abe/pwll), and you’ve probably already put in your preorder at Amazon. It’s kind of like the anticipatory excitement for the Harry Potter books, only for hardcore geeks.

To whet your appetite, there is a short extract from chapter one available online. And alas, you have to wait until 22 September for the whole thing. We’ll have it read by the 23rd, right?

Want more? Here’s an excerpt from chapter two.

The educated/ignorant divide

This is a very interesting analysis of Unscientific America: the authors weren’t only shallow in identifying solutions to the problems they identified, they completely missed the big one. This is an informative chart.

American variation in science literacy is enormous. Data from Salzmann & Lowell (2008)

We’ve got a large number of science-literate students in the top-performing category (which is good), but the average is relatively low (not good). I know this is really obvious, but I have to say it anyway, since I’m afraid many Americans will read this: the only way that can happen is if there is a huge number of students who are also really, really bad at science. Our country has an educated/ignorant divide to match our ugly rich/poor divide.

Here’s a personal story to make the abstract real. It’s back-to-school time in Florida, and the budget isn’t there.

Science teachers are feeling the pinch at Journeys Academy, Seminole’s new alternative school.

“My science teachers handed me three pages of things they’d like to have, but because of the hard budget times, we weren’t given an opening budget for science,” Principal Michael Icardi said.

That means a big need for “microscopes and balances and those types of things.” His team, Icardi said, will have to be “creative.”

If you don’t have the basics, if science teachers are told by their administrators that they have to replace essential tools with their imagination, it’s only going to get worse. If you want to fix science literacy in America, the answer isn’t going to come from the top with the training of a thousand Carl Sagans — we need to give a few tens of millions of students a decent lab experience, a little knowledge of critical thinking, and the intellectual tools to aspire to something better.

Jason Lisle and the everlasting fallacy argument

I must have really stung those poor fellows at the Creation “Museum”. They’ve added a new article in the Jason Lisle ouevre which takes a few silly slaps at me, and also perpetuates the image of Lisle as the most boring pedant ever. As usual, his schtick is always the same: he accuses everyone else of committing horrible logical fallacies, therefore, God. This one made me laugh, though. The fallacy du jour is the question-begging epithet, in which someone uses leading or insulting language in addressing a claim to discredit it.

As an example, he uses a quote from me…and I freely admit to having a thoroughly dismissive attitude towards their awful little sideshow (there, again, is the epithet; I won’t shy away from it). Here’s the sentence Lisle uses.

“The Creation ‘Museum’ isn’t about science at all, but is entirely about a peculiar, quirky, very specific interpretation of the Bible.”

The author provided no support for this opinion; it is simply an emotional reaction. He also attempts to deride the Creation Museum by putting the word museum in quotes. His claim is nothing but a fallacious epithet. When people use sarcastic/sardonic statements in place of logic, they commit the fallacy of the question-begging epithet.

That’s not an emotional reaction! That’s a calm statement of fact, and Lisle could have disputed it, but he never will. He can’t. Instead, everything said about his belief system will be instantly slotted into one of his categories of fallacies, so he can ignore it — and ignoring it means he doesn’t have to defend anything by, for instance, saying anything about any credible science behind flood geology, or showing that the fundamentalist Christianity that Answers in Genesis promotes is mainstream, or is independent of a narrow interpretation of biblical literalism. What I wrote is actually entirely factual.

Another common trick of these con-men is to avoid letting anyone see anything in context. He quotes a sentence from me, but doesn’t link to the article. Why would he do that? Because that article quotes directly from the web and publications by Answers in Genesis that shows everything in their view is built around…interpretation of the bible! I even titled the article, Answers in Genesis is proudly Bible-based. Do they dispute that?

Of course they, and especially Jason Lisle, will not ever deal with the substance of an argument. They will instead whine that they’ve been called mean names and run away. That’s what they do.

OK, so far you’re saying this isn’t very funny. Lisle is a drab, boring writer with one rhetorical trick in his book that he plays over and over. Here’s the funny part, though.

They’re claiming that their critics are just noisy brutes who portray the noble creationists, servants of god, in rude and obnoxious terms. They, of course, are entirely above that. They would never, ever stoop to emotional, nasty comments about their opponents. Why, that would be a logical fallacy.

So they chose to illustrate their article with a cartoon. Of me, apparently.


Hypocrisy is a bitch, isn’t it?

I am so stealing that cartoon, though.