My wife and I saw Julie & Julia this weekend — and enjoyed it — but it’s still a little weird to see Julia Child giving lessons on how to make primordial soup.
(via This Blog Contains Caffeine)
There are no more excuses. None.
The defining characteristic of all arguments with creationists is how damned ignorant they are. I’m sure many scientists have been stupefied into stunned silence when they first encounter these people; these advocated of creationism are typically loud and certain and have invested much time and effort into apologetics, but when you sit down and try to have a serious discussion with them, you quickly discover that their knowledge of basic biology is nonexistent. It’s worse than that. We’re used to freshmen entering our classes who don’t know much about the basics, and we can deal with that; these, though, are people with negative knowledge, whose brains are so packed with raging falsehoods that we have to struggle to overcome an unfamiliar hurdle.
For example, last year I got into a radio debate with a Discovery Institute creationist, Geoffrey Simmons. He had written a whole book for creationists arguing that there are no transitional fossils…yet he had never heard of any of the major fossil discoveries in the whale series, and seemed to have gleaned all of his understanding from a garbled misreading of a short Scientific American article.
It’s infuriating. You want to argue against evolution? Then you’d better have some elementary understanding of what evolution actually says. We’ve got the same phenomenon going on right now in one of the comment threads, where a particularly obtuse creationist, Sean Pitman, is raving about the inadequacy of natural selection. I wouldn’t mind, except that he’s a freaking idiot. This goes on day after day — creationists are mired in a pit of ignorance so deep and so black that it takes incredible patience to lead people out of it (and also, some rhetorical boot-stomping against the fools who are trying to drag others even deeper into the darkness).
I have no illusions that we’ll suddenly see a blossoming of enlightenment, but we now have tools to help us, a whole series of recent books that cover the basics. Everyone should read at least one of these, especially if you’re one of those clowns who wants to argue that there is no evidence for evolution. Read and understand, please; we’ve already got enough idiots who claim to have read them and didn’t grasp anything in them.
Read Donald Prothero’s Evolution: What the Fossils Say and Why It Matters(amzn/b&n/abe/pwll). Or Sean Carrol’s The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution(amzn/b&n/abe/pwll). Or Neil Shubin’s Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body (amzn/b&n/abe/pwll). Or Jerry Coyne’s Why Evolution Is True(amzn/b&n/abe/pwll). These are all eminently readable, and are aimed at an audience that knows next to nothing about biology — they will quickly pull you up to a level at which you can at least ask intelligent questions. We even use Carroll’s book here at UMM in our freshman biology course, with the idea that it will introduce them to the concepts they should have gotten in high school, but most didn’t.
Now we have another entry in this collection: Richard Dawkins’ The Greatest Show on Earth: The Evidence for Evolution(amzn/b&n/abe/pwll).
READ IT.
Maybe you already know everything Dawkins writes about in this book, if you’ve got a degree in biology and have done a fair amount of reading in the field; there really aren’t any radical surprises here, just a lovely review of familiar facts. You should read it anyway. Realize that this is the level that you have to operate on if you want to discuss the science of evolution with the public. What this (and the other books I mentioned above) is is a primer on how to communicate the ideas of science to a wider audience. It’s an overview and a synthesis, and it takes each piece of evidence and makes them part of a narrative. This is science plus storytelling — it’s what you have to do.
Or maybe you’re a high school student who is interested in science, but all you’re aware of is that the dumbed-down curriculum in your school has stripped out all of the important content from your courses. Or maybe you’ve got a teacher who is promoting creationism in subtle or not-so-subtle ways in the classroom. Get this book: it will give you the preparation for college that the conservatives on your local school board want to deny you. It’ll also make you ten times smarter than your creationist science teacher, which always feels good.
Hey, and when you graduate, give that science teacher a copy as a parting gift. Or perhaps as a gift to the next class.
Or maybe you’re just a sensible layman who’d like to know more about this subject, but really don’t want to have to get a Master’s degree to understand what the author is talking about. You want something you can read on a quiet Sunday morning, before the football game starts. You want to learn, but you’re not about to invest a lot of sweat in the effort. This is your book. It touches lightly on a lot of lines of evidence, and explains them clearly. You too can become informed painlessly, and for a low, low price!
Like I said, there are no more excuses. If you want to argue for or against evolution, cretins like Ken Ham or Ray Comfort or Carl Baugh or Eric Hovind or any of the thousands of other wandering ranters against the Enlightenment are about to face a big problem: more and more of the people in their audiences are going to have read these books, and are going to be prepared to call them on their bullshit. The enemy of ignorance is education, and the creationists know that; it’s why there is so much effort by the religious conservatives to destroy public education. These are books that provide an end-run around the current deficiencies in science education in this one area, and what they ought to do is help people question the wanna-be theocrats. If they lie about evolution, if they are so transparently wrong about this one subject, maybe more people will wake up to the anti-science agenda so many are peddling in this country.
Dawkins’ new book is very much a grenade thrown right at the heart of the creationists. The God Delusion was a kind of wake-up slap to shake people into attention, and now The Greatest Show on Earth follows on to pound them into the ground with a fusillade of evidence backed up by sound theoretical explanations. It’s all beautifully explained, too, a kind of elegant overview of the various lines of evidence supporting evolutionary theory, with much of the discussion informed by an awareness of the kinds of denial creationists typically make.
Read it, please, please, please.
We need a vocal and informed group of activists in this country who understand the science, but we can’t demand that they all go to grad school. This book and others like it will help us build the intellectual foundation and the network of well-versed literate elites who can can address the rot at the root.
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.
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.
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.
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.
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]
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]
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.
I’m getting a lot of email asking me to talk about the aquatic ape theory, the idea that humans went through a semi-aquatic stage in their evolutionary history. It’s complete nonsense; its proponents spew out a lot of inconsistent and mutually contradictory noise to ‘support’ their claims, and there is no evidence anywhere for such a stage. I don’t need to say more, though, because Jim Moore’s Aquatic Ape page is the definitive web resource for dissecting this fringe theory.
PLoS has recently published a highly speculative but very interesting paper on how a particular signaling pathway, the Hedgehog pathway, might have evolved. It’s at a fairly early stage in hypothesis testing, which is one of the things that makes it interesting — usually all you see published is the product of a great deal of data collection and experiment and testing, which means the scientific literature gives a somewhat skewed view of the process of science, letting the outsider mainly see work that has been hammered and polished, while hiding the rougher drafts that would better allow us to see how the story started and was built. It’s informative in particular for those who follow the creationist “literature”, which often crudely apes the products of actual working science, but lacks the sound methodological underpinnings. In particular, creationism completely misses the process of poking at the real world to develop ideas, since they begin with their conclusion.
So take this description as a work in progress — we’re seeing the dynamic of building up a good working model. As usual, it starts on a sound foundation of confirmed, known evidence, makes a reasonably hypothesis on the basis of the facts, and then proposes a series of research avenues with predicted results that would confirm the idea.
No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It’s actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven’t had thousands of Cambrian explosions.
In case you haven’t been keeping up, miRNAs are a hot topic in molecular genetics: they are short (21-23 nucleotides) pieces of single stranded RNA that are not translated into protein, but have their effect by binding to other strands of messenger RNA (mRNA) to which they complement, effectively down-regulating expression of that messenger. They play an important role in regulating the levels of expression of other genes.
One role for miRNAs seems to be to act as a kind of biological buffer, working to limit the range of effective message that can be operating in the cell at any one time. Some experiments that have knocked out specific miRNAs have had a very interesting effect: the range of expressed phenotypes for the targeted message gene increases. The presence or absence of miRNA doesn’t actually generate a novel phenotype, it simply fine-tunes what other genes do — and without miRNA, some genes become sloppy in their expression.
This talk of buffering expression immediately swivels a developmental biologist’s mind to another term: canalization. Canalization is a process that leads organisms to produce similar phenotypes despite variations in genotype or the environment (within limits, of course). Development is a fairly robust process that overcomes genetic variations and external events to yield a moderately consistent outcome — I can raise fish embryos at 20°C or at 30°C, and despite differences in the overall rate of growth, the resultant adult fish are indistinguishable. This is also true of populations in evolution: stasis is the norm, morphologies don’t swing too widely generation after generation, but still, we can get some rapid (geologically speaking) shifts, as if forms are switching between a couple of stable nodes of attraction.
Where the Cambrian comes into this is that it is the greatest example of a flowering of new forms, which then all began diverging down different evolutionary tracks. The curious thing isn’t their appearance — there is evidence of a diversity of forms before the Cambrian, bacteria had been flourishing for a few billion years, etc., and what happened 500 million years ago is that the forms became visible in the fossil record with the evolution of hard body parts — but that these phyla established body plans that they were then locked into, to varying degrees, right up to the modern day. What the authors are proposing is that miRNAs might be part of the explanation for why these lineages were subsequently channeled into discrete morphological pathways, each distinct from the other as chordates and arthropods and echinoderms and molluscs.
Here’s an interesting use of tweening: take 5 fossil skulls, use the computer to interpolate between them, and animate the results. 3.5 million years just fly by in 5 minutes.
(The sound track is a bit superfluous though—turn the sound down if you’re at work)
