The evolution of Darwin

When I was in New York a while back, I got to meet Ben Fry, a clever fellow who has been doing some amazing things with data visualization. One of the things we played with was a a new toy he’d worked out, or rather, a new application of some old tools. One of the things biologists are interested in is change over time, and we compare genomes to see where changes have occurred between two or more species; one of the reasons we’re interested in the chimpanzee genome, for instance, is that it is close to ours, and what scientists are doing is comparing the two, looking for the key differences.

There are other things that change over time that lend themselves to these sorts of analyses. Darwin’s On the Origin of Species went through six editions during his lifetime, and it wasn’t a static document at all — he revised, sometimes extensively, and he added new material, sometimes in response to new data, sometimes in reaction to public and private concerns.

What Fry has done is taken the text of all six editions, compared them, and color-coded the words by when they were added. Then he rendered them in teeny-tiny print and splashed them up on the screen so you can see when and where changes occurred in Darwin’s text. It takes a while to load, since it is loading the full text of six editions of the Origin, plus annotations, but then you can just move your cursor around over the blocks to read and see what he was thinking. For instance, one thing that jumps out at you is the huge block of red in the middle of the document, a whole large section that was added in the sixth edition. Mouse over it, and you’ll see how it starts:

I WILL devote this chapter to the consideration of various miscellaneous objections which have been advanced against my views, as some of the previous discussions may thus be made clearer;

That makes sense; this is a piece of the story that Darwin added late, after the book had drawn a lot of criticism, to address specific problems.

It’s a fun gadget. Go explore the evolving mind of Darwin!

No surprise, you’re all a bunch of mutants

The BBC has an article on the recent direct measurement of human mutation rates, and while it’s not a bad article, it does seem to express the view that the result is something novel. It’s not; it’s a confirmation of a standard measure that scientists have known about for a long, long time. We have estimated the number of novel mutations in newborn human individuals to be somewhere between a hundred and a few hundred (best estimates were on the order of 150) based on a couple of facts.

We’ve had measurements of the fidelity of the enzymes that catalyze replication, and since we know both the per nucleotide rate and the number of nucleotides, it’s straightforward to calculate the average number of errors per replication event. We’ve also had estimates from the measured frequency of spontaneous mutations in human disease genes that have given answers in the same ballpark. The only thing new in this recent study is that they sequenced the Y chromosomes of a group of related men and directly tallied up the new mutations, confirming that the previous calculations were roughly correct.

Like I say, it’s not a bad article, but if you really want the best summary of the work, you should be reading Sandwalk.

It’s useful information for the next time you’re in a debate with a creationist, too. They often assert that all mutations are harmful, but clearly, they can’t be: they’re almost entirely neutral. That creationist is carrying over a hundred new mutations that his parents lacked, and his children will each have over a hundred more, and his grandchildren a hundred yet again. What we have going on is a great churn of frequent change, just change, not a pattern of directional variation that either degrades or elevates us.

Friday Cephalopod: Survivor: Cephalopod!

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Tips for flourishing after a mass extinction. Ceratites nodosus (MCZ-7232) (A), from the Triassic of Germany, was similar to the ceratitid ammonoid species that thrived in the water column in the Early Triassic (1), while bottom-dwelling species languished. Key to the ceratitids’ rapid success after the end-Permian mass extinction were their ecological tolerances, which may be inferred by reference to their closest living relatives, the coleoids (squids, octopuses, and cuttlefish), including the low-oxygen specialist Vampyroteuthis infernalis (B).
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This picture has a little story behind it. Over 250 million years ago, our world experienced the most massive extinction event known, with over 99% of all individuals on the planet dying out abruptly, and diversity was greatly limited for a few million years after that. One possible explanation for the Permian extinction is a correlated series of massive volcanic eruptions that burned through thick coal deposits and drowned the earth in CO2 — global warming on a massive scale. Even cephalopods suffered. The ceratatid ammonoids had been in decline for a long time, but the extinction nearly wiped them out, reducing them to only a few struggling genera.

But then something interesting happened. After the great extinction, the ammonoids exploded in diversity, radiating rapidly. Something about them had made some of them capable of riding out the disaster, and then exploiting the changed world afterwards.

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(Click for larger image)
Total generic richness [Sobs; black bold line,
all ammonoids; gray lines, major ammonoid groups;
Permian dotted line, alternate data from Ammon
(16)] and mean Chao2 estimate of the overall generic
richness with its 95% confidence interval (large circles
with vertical bars) (table S1). PTB, Permian-Triassic
boundary; 1, Kasimovian; 2, Gzhelian; 3, Asselian; 4,
Sakmarian; 5, Artinskian; 6, Kungurian; 7, Roadian; 8,
Wordian; 9, Capitanian; 10, Wuchiapingian; unlabeled
successive intervals, Changhsingian, Griesbachian,
Dienerian, Smithian; 15, Spathian; 16, Early Anisian;
17, Middle Anisian; 18, Late Anisian; 19, Ladinian; 20,
Early Carnian; 21, Late Carnian; 22, Early Norian; 23,
Middle Norian; 24, Late Norian; 25, Rhaetian.

One speculative explanation for the secret of their success is the ability of some members of the cephalopod clade to survive in cold, nearly anoxic conditions, like Vampyroteuthis infernalis. They were able to rebound quickly because of their dismal metabolism and the general fecundity of cephalopods. They restored some ecological webs faster than previously thought and provided an environment for further growth of more severely crippled clades.

It just goes to show you that our current episode of global warming is a relatively minor event. Life will go on. Fast-living organisms with high metabolic demands like, say, humans, might suffer and die from the environmental consequences of a high CO2 atmosphere, but don’t worry — the cephalopods will live on. They might even get a happy surge in numbers from the changes.

Brayard A, Escarguel G, Bucher H, Monnet C, Brühwiler T, Goudemand N, Galfetti T, Guex J (2009) Good Genes and Good Luck: Ammonoid Diversity and the End-Permian Mass Extinction. Science 325(5944):1118-1121.

Marshall CR, Jacobs DK (2009) Flourishing After the End-Permian Mass Extinction. Science 325(5944):1079-1080.

Evolution of the appendix?

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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.

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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.

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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.

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(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]

Darwin and the vermiform appendix

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Last night, I asked 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. J Evol Biol. 2009 Aug 12. [Epub ahead of print]

Yes, millions of years!

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That Answers in Genesis crackpot, Terry Mortenson, is speaking on “Millions of Years” at the Creation “Museum”. Those of us who visited that circus of charlatanry know that this is one of their obsessions — the idea that the earth is more than 6000 years old is one of the wrecking balls atheists use to destroy faith.

He’s right, of course. It’s a very useful tool. When fundamentalists tie their faith absolutely to a claim that is easily refuted, that contradicts the evidence, and that requires them to constantly escalate their denial and delusions in order to sustain their belief, it makes it really easy for atheists to demolish their religion. We don’t even need to attack religion in the classroom at all — we just calmly lay out the facts, let the students work out the conclusions, and sometimes…it’s epiphany time! They realize their pastor lied to them, or was just really ignorant, and suddenly their respect for Christian authority begins to crumble away.

It’s not the atheist’s fault, though. The lesson should be, “Don’t lie to your kids,” not “Silence the people who would reveal that you lied to your kids,” or worse, “Lie harder.”

This is not a lesson that Mortenson has learned. He is apparently planning to babble about revisionist history in his talk, claiming that the evidence for the age of the earth is the product of an atheist conspiracy among geologists.

To really understand what is wrong with belief in millions of years, we need to go back to the early 19th century and study the origin of this idea. This unique and interesting lecture, based on Dr. Mortenson’s PhD research, will clearly show that the idea was not the result of just letting the rocks and fossils “speak for themselves” but rather comes from anti-Biblical worldviews (or philosophical assumptions) being imposed on the geological evidence. The talk explains the key men who helped develop the idea of millions of years, one of the geologically competent Christians who opposed those theories, and the subsequent consequences of the church’s compromise with millions of years. Even non-Christians would find this lecture thought-provoking.

Hah! The only thought it would provoke in me is to wonder where they kept the straitjackets. Looney-tunes revisionist history is not thought-provoking in a good sense.

I actually spend a fair amount of lecture time on the early history of geology in my introductory biology course. One reason is that, if you talk to most people, you will discover this fallacious belief that evolution leapt fully-formed from the brain of Charles Darwin, and there’s an anachronistic idea that ideas about the age of the earth, which are built on independent evidence from geology and astronomy, are somehow rooted in biology. It’s not so! Darwin’s antecedents had already laid the foundations in working out that the earth was old, that life had undergone many transitions, and that maybe species were mutable. Evolution was an inevitable conclusion of the evidence; Darwin and Wallace were just the clever fellows who managed to pull the whole story together.

I find it very useful to give students a quick overview of 18th and 19th century geology before we talk about Darwin, since the creationists in the classroom usually have this image of Darwin as Satan who foisted a false belief on the world because he hated god (hey, sounds like Terry Mortenson!). It’s very useful to be able to show how views of the world evolved, not by ideology, but by the growth of a body of evidence.

Let’s begin with Robert Hooke (1635-1703). He dabbled brilliantly in many things, but one subject of particular interest was the origin of these curious fossils that people kept digging up, which were thought to be either creatures turned to stone by some miraculous process, or were the expression of an intrinsic nature of stone to mimic life. Hooke examined the details of fossils microscopically, and determined that they had once been alive, and also worked out how the transformation had occurred — by the perfusion of minerals into buried or immersed dead organisms. He also examined the distribution of fossils; finding fossilized clams on mountaintops, for instance, says something about the prior state of that environment.

Most of those Inland Places. . . are, or have been heretofore under the Water. . . the Waters have been forc’d away from the Parts formerly cover’d, and many of those surfaces are now raised above the level of the Water’s Surface many scores of Fathoms. It seems not improbable, that the tops of the highest and most considerable Mountains in the World have been under Water, and that they themselves most probably seem to have been the Effects of some very great Earthquake.

These conclusions were evidence-driven. Almost no one in the late 17th century would have been interested in opposing religion, so you can’t pin that heresy on Hooke. He is simply describing the natural world and finding certain conclusions inescapable, including some to which creationists today still can’t adjust — and note that he is writing this more than 300 years ago.

There have been many other Species of Creatures in former Ages, of which we can find none at present; and that ’tis not unlikely also but that there may be divers new kinds now, which have not been from the beginning.

And then there’s Baron Cuvier (1769-1832) and Alexandre Brongniart (1770-1847) who studied the rocks of the Paris Basin. There were many quarries situated around Paris that cut deep into the hills to provide building stone, and they gave these two the opportunity to look into the structure of the rocks. They identified five major layers, and by examining the fossils, worked out what kinds of animals and plants lived there when the layers were deposited. They found that layers with saltwater species were interleaved with layers containing freshwater species — Paris had been under the sea at least twice!

Cuvier was not an atheist. In fact, he was even adamant that the earth was relatively young, but in a way that contradicts what Answers in Genesis would tell you. He had worked out that there were different assemblages of animals in each layer, and proposed an explanation: a series of ages, each very different, with the most recent major catastrophe occurring five or six thousand years ago (to bring it in line with the literal interpretation of the Bible) and sweeping away prior forms to allow for the flourishing of human beings.

It is certain that we are now at least in the fourth succession of terrestrial animals. The age of reptiles was followed by that of the palaeotheres [primitive mammals], then the age of mammoths, mastodons, and megatheria. Finally we arrive at the age of the human species together with domestic animals. It is only in the deposits subsequent to the beginning of this age, in turf-bogs and alluvial deposits, that we find bones all of which belong to animals now existing…None of these remains belong either to the vast deposits of the great catastrophe or to those of the ages preceding that wonderful event.

If you want someone who was willing to assert that the earth was very, very old, we have to look to the Scottish geologist James Hutton (1726-1797), who was accused of atheism for his ideas, but they were backed up entirely by hard-earned evidence. He postulated that the geology we see was created by multiple cycles of sedimentary deposition, volcanic uplift, and erosion, and he mapped and documented complex unconformities and intrusions that demonstrated that the history of the earth was complex and required great time for the formation and distortion of rock. He also found that the evidence of the time was insufficient to even show the history of the beginning of the earth, which is why he closed his book, Theory of the Earth, with the famous line, “The result, therefore, of our present enquiry is, that we find no vestige of a beginning,—no prospect of an end.”

Again, his conclusion was dictated by the evidence, not some atheistic philosophy.

At the same time Cuvier and Brongniart were exploring the Paris Basin, William Smith (1769-1839) was walking all over England, building up his geological map. We know what his motivation was: it was economic. He worked in mines, and was eager to capitalize on the opportunities opened up by the Industrial Revolution. Railroad and canal cuts exposed the strata of English geology all over the place, and being able to assess good locations for coal mines was a profitable skill — much like petroleum geology now. Smith observed consistent features of geology, like the way rocks were layered, and what fossils were present in specific layers, and could see that a layer was a slice of time, and that each slice contained different animals (which led to his Principle of Faunal Succession). He worked out the first geological map of Britain on the basis of his surveying.

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There is a pattern to geology: we can see that the strata are not purely local phenomena, but part of formations that often extend continent-wide. These strata also have a predictable order that reflects the timing of their formation. These observations are not reconcilable with the simplistic dogma of the creationists.

Charles Lyell was also an important geologist, who was also very influential on Charles Darwin. He was not an atheist, but rather, a devout Christian, which caused him considerable discomfort since he was never able to accept the full implications of Darwin’s work. Lyell’s key dictum was that the present is the key to the past, that what you needed to do was work out mechanisms in action right now and use those to explain what must have happened in the past.

Darwin himself applied this principle to estimate a minimum age for the earth. He knew from published observations that a rapid rate of sedimentary deposition was 600 feet in 100,000 years; he also knew that the known strata in England had a depth of over 72,000 feet, which implied that the earth had to be at least 12 million years old.

It’s so widely accepted that even creationists use it — it’s the basis for their arguments that the ocean sediments and moon dust say the earth is young. Unfortunately, the way they accomplish that is by either using the wrong numbers for accumulation or ignoring the multiple processes that affect the rate.

It is simply ludicrous to claim that 18th or 18th century geologists bent their interpretation to fit some imaginary godless worldview — in general, the scholars of that period were more concerned with avoiding conflicts with religion, since the majority of them were doctrinaire church-going Christians themselves. What led them to the conclusion that the earth was millions, and then billions of years old was the evidence, not their ideology.

And now, of course, the evidence is even more overwhelming, and it’s mostly physics at its heart. Trying to salvage Bishop Ussher’s weird numerological and biblical 17th century chronology in the 21st century by invoking the incomplete understanding of 19th century scholars is exactly the kind of inanity we’ve come to expect from creationists.

Arthrodires got penises!

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This is the skull of an arthrodire, an armored placoderm from the Devonian.

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Somehow, 20 foot long predatory fish with a mouth lined with razor-edged bony shears has never made me think of sexy time…until I ran across this comparison image.

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Oh, schwiiing. It really doesn’t take much to get a mammal to associate just about anything with sex. And then, what do you know, the latest Nature has a short article on an interesting fossil: it’s the pelvic region of an arthrodire, Incisoscutum ritchiei, and look what it’s got: an ossified clasper, comparable to the erectile organ of modern sharks. This is a bony rod that would have been the core of an intromittent organ in the living animal, so what we have here is a small relic of the sex life of a big fish from a few hundred million years ago.

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a, Pelvic girdle in dorsal view; b, pelvic girdle restored.

Think about this, you over-sexed apes: what will be left of your manhood 300 million years from now?

Ahlberg P, Trinajstic K, Johanson Z, Long J (2009) Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires. Nature 460:888-889.

Gene regulatory networks and conserved noncoding elements

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We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can’t see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

[Read more…]

The future is roaring your way…

Edge hosted an amazing session that described the looming future of biology — this is for the real futurists. It featured George Church and Craig Venter talking about synthetic genomics — how we’re building new organisms right now and with presentiments for radical prospects in the future.

Brace yourself. There are six hours of video there; I’ve only started wading into it, but what I’ve seen so far also looks like a lot of material that will be very useful for inspiring students about the future of their field. There is also a downloadable book (which is a dead link right now, but I’m sure will be fixed soon) if you don’t want to watch the talks…but the talks are pretty darned good. Somehow, I’m going to have to make time to soak these up. Here’s the overview of the six sessions:

  • Dreams & Nightmares
    Overview, safety/security/policy, nanotechnology, molecular manufacturing

  • Smaller than life
    What is life, origins, in vitro synthetic life, mirror life, computing and DNA, computing with DNA

  • Engineering microbes
    Bio-petrochemicals & pharmaceuticals, accelerated lab evolution

  • Engineering humans
    Electronic-biological interfaces, bioengineered personal stem cells, humanized mice, bringing back extinct species

  • The sorceror
    The diversity of life, constructing life, from Darwin to new fuels

  • The near future, big questions
    Terraforming earth, creating extraterrestrials, the singularity, human nature

There goes your weekend.