Xiaotingia zhengi

A lovely new dinosaur fossil from China is described in Nature today: it’s named Xiaotingia zhengi, and it was a small chicken-sized, feathered, Archaeopteryx-like beast that lived about 155 million years ago. It shares some features with Archaeopteryx, and also with some other feathered dinosaurs.

i-3933ba25e778e15bba5e605347639ecc-xiaotingia-thumb-400x390-67812.jpeg
(Click for larger image)
a, b, Photograph (a) and line drawing (b). Integumentary structures in b are coloured grey. cav, caudal vertebra; cv, cervical vertebra; dv, dorsal vertebra; fu, furcula; lc, left coracoid; lfe, left femur; lh, left humerus; li, left ilium; lis, left ischium; lm, left manus; lp, left pes; lpu, left pubis; lr, left radius; ls, left scapula; lu, left ulna; md, mandible; rfe, right femur; rfi, right fibula; rh, right humerus; ri, right ilium; rm, right manus; rr, right radius; rt, right tibiotarsus; ru, right ulna; sk, skull; ss, synsacrum.

Now here’s why this particular fossil has some paleontologists in a dither. Systematics uses a set of objective, computer-based tools to objectively build phylogenetic trees: you plug a set of character parameters for a set of organisms into it, and it analyzes them and determines the most likely or most parsimonious tree to describe their relationships. Plugging in data from modern birds, Archaeopteryx, and dromeosaurs, for instance, generates trees in which Archaeopteryx clusters with the birds, and not the dromeosaurs. Archaeopteryx was not a direct ancestor of modern birds, but was thought to be related to the basal avians — so it was a kind of close cousin.

When Xiaotingia‘s data is tossed into the calculation, though, the results change. Xiaotingia doesn’t cluster so tightly with birds; it’s a more distant relative. However, Archaeopteryx shares enough significant features with Xiaotingia that they now cluster together, pulling Archaeopteryx out of the basal Aves and into a new classification. It says that Archaeopteryx is now a kind of second cousin, a little less closely related to the birds than previously thought.

i-ac16f1626601b38b60e444f531cef943-bird_phylo-thumb-500x295-67815.jpeg
(Click for larger image)
Archaeopteryx has historically been regarded as the most basal bird (avialan), but the discovery of the closely related Xiaotingia led Xu et al.1 to pull these archaeopterygids out of avialans (birds) and into deinonychosaurs along with dromaeosaurids and troodontids. This new grouping better accounts for the evolution of feeding strategies among bird-like dinosaurs. Previous research suggested that herbivory was common among this group, as reflected in the tall, boxy skulls of oviraptorosaurs and basal avialans such as Epidexipteryx. The triangular, sharp-toothed skull of Archaeopteryx was incongruous among basal avialans, but fits better among the carnivorous dromaeosaurids and troodontids.

I have to say that I think it’s extremely cool that we have a new fossil from down around the roots of the bird family tree, and it does sharpen our knowledge of what was going on down there in the middle and late Jurassic. There was a whole assortment of delicate-boned, feathered, bipedal dinosaurs that were flourishing and diversifying in that window of time, and we’ve now got enough data that we can distinguish details in the family tree, which is absolutely fabulous.

However, a lot of the fuss over the specimen as somehow radically changing the importance of Archaeopteryx is a bit overblown. The relative status of Archaeopteryx and Xiaotingia is a bit of taxonomic detail — important details in working out the specific history of life — but it’s the equivalent of deciding that a fossil belongs in one pigeonhole rather than the pigeonhole next to it. Its shift in status means that there’s a bigger gap in the early history of the true birds than we thought, and it also means that there was a greater diversity of bird-like forms than we expected in the Jurassic. One other suggestion is that removing the carnivorous Archaeopteryx from the base of the bird family tree opens up the possibility that modern birds might have descended from the vegetarian side of the family — if the last common ancestor of birds was an herbivore, that has interesting implications for the paths evolution took.

But don’t worry, Archaeopteryx still represents a beautiful example of a transitional form. This new fossil is just another transitional form discovered. Creationists cannot take any consolation from it: Archaeopteryx isn’t suddenly gone, it’s become a part of a richer picture of bird evolution.

Xu X,
You H,
Du K
Han F (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475, 465-470.

The greatest science paper ever published in the history of humankind

That’s not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I’m immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there’s pie for dessert. It’s like the authors know me and sat down to concoct a title where every word would push my buttons.

The content is pretty good, too. It’s not perfect; the development part is a little thin, consisting mainly of basic comparative embryology of body plans, with nothing at all really about deployment of and interactions between significant developmental genes. But that’s OK. It’s in the nature of the Greatest Science Papers Ever Written that stuff will have to be revised and some will be shown wrong next month, and next year there will be more Greatest Science Papers Ever Written — it’s part of the dynamic. But I’ll let it be known, now that apparently the scientific community is aware of my obsessions and is pandering to them, that the next instantiation needs more developmental epistasis and some in situs.

This paper, though, is a nice summary of the emerging picture of cephalopod evolution, as determined by the disciplines of paleontology, comparative embryology, and molecular phylogenetics, and that summary is internally consistent and is generating a good rough outline of the story. And here is that story, as determined by a combination of fossils, molecular evidence, and comparative anatomy and embryology.

Cephalopods evolved from monoplacophoran-like ancestors in the Cambrian, about 530 million years ago. Monoplacophorans are simple, limpet-like molluscs; they crawl about on the bottom of the ocean under a cap-like shell, foraging snail-like on a muscular foot. The early cephalopods modified this body plan to rise up off the bottom and become more active: the flattened shell elongated to become a cone-like structure, housing chambers for bouyancy. Movement was no longer by creeping, but used muscular contractions through a siphon to propel the animal horizontally. Freed from its locomotor function, the foot expanded into manipulating tentacles.

i-a4650a364628b045d3f57a3baf0e7529-monoplacophoran.jpeg

These early cephalopods, which have shells common in the fossil record, would have spent their lives bobbing vertically in the water column, bouyed by their shells, and with their tentacles dangling downward to capture prey. They wouldn’t have been particularly mobile — that form of a cone hanging vertically in the water isn’t particularly well-streamlined for horizontal motion — so the next big innovation was a rotation of the body axis, swiveling the body axis 90° to turn a cone into a torpedo. There is evidence that many species did this independently.

i-f8e43ceb7154a2f6b4c1b890e7ac4f64-ceph_rotation-thumb-500x331-67138.jpeg
The tilting of the body axes of extant cephalopods. This was a result of a polyphyletic and repeated trend towards enhanced manoeuverability. The morphological body axes (anterior-posterior, dorso-ventral) are tilted perpendicularly against functional axes in the transition towards extant cephalopods.

We can still see vestiges of this rotation in cephalopod embryology. If you look at early embryos of cephalopods (at the bottom of the diagram below), you see the same pattern: they are roughly disc-shaped, with a shell gland on top and a ring of tentacle buds on the bottom. They subsequently extend and elongage along the embryonic dorsal-ventral axis, which becomes the anterior-posterior axis in the adult.

i-4ad43bc29c4b1d48673f4cd0de6356a5-ceph_comp_embryo-thumb-450x786-67111.jpeg
In extant cephalopods the body axes of the adult stages are tilted perpendicularly versus embryonic stages. As a con- sequence, the morphological anterior-posterior body axis between mouth and anus and the dorso-ventral axis, which is marked by a dorsal shell field, is tilted 908 in the vertical direction in the adult cephalopod. Median section of A: Nautilus, B: Sepia showing the relative position of major organs (Drawings by Brian Roach). C: shared embryonic features in embryos of Nautilus (Nautiloidea) and Idiosepius (Coleoidea) (simplified from Shigeno et al. 2008 [23] Fig. 8). Orientation of the morphological body axes is marked with a compass icon (a, anterior; d, dorsal; p, posterior; v, ventral; dgl, digestive gland; gon, gonad; ngl, nidamental gland).

The next division of the cephalopods occurred in the Silurian/Devonian, about 416 million years ago, and it involved those shells. Shells are great armor, and in the cephalopods were also an organ of bouyancy, but they also greatly limit mobility. At that early Devonian boundary, we see the split into the two groups of extant cephalopods. Some retained the armored shells; those are the nautiloids. Others reduced the shell, internalizing it or even getting rid of it altogether; those are the coleoids, the most successful modern group, which includes the squids, cuttlefish, and octopuses. Presumably, one of the driving forces behind the evolution of the coleoids was competition from that other group of big metazoans, the fish.

The nautiloids…well, the nautiloids weren’t so successful, evolutionarily speaking. Only one genus, Nautilus has survived to the modern day, and all the others followed the stem-group cephalopods into extinction.

The coleoids, on the other hand, have done relatively well. The number of species have fluctuated over time, but currently there are about 800 known species, which is respectable. The fish have clearly done better, with about 30,000 extant species, but that could change — there are signs that cephalopods have been thriving a little better recently in an era of global warming and acute overfishing, so we humans may have been giving mobile molluscs a bit of a tentacle up in the long evolutionary competition.

There was another major event in coleoid history. During the Permian, about 276 million years ago, there was a major radiation event, with many new species flourishing. In particular, there was another split: between the Decabrachia, the ten-armed familiar squid, and the Vampyropoda, a group that includes the eight-armed octopus, the cirroctopodes, and Vampyroteuthis infernalis. The Vampyropoda have had another locomotor shift, away from rapid jet-propelled movement to emphasizing their fins for movement, or in the case of the benthic octopus, increasing their flexibility to allow movement through complex environments like the rocky bottom.

Time for the big picture. Here’s the tree of cephalopod evolution, using dates derived from a combination of the available fossil evidence and primarily molecular clocks. The drawings illustrate the shell shape, or in the case of the coleoids, the shape of the internal shell, or gladius, if they have one.

i-205e51c0850d23812a20e3bd6bf7010f-ceph_lineage-thumb-500x631-67114.jpeg
A molecularly calibrated time-tree of cephalopod evolution. Nodes marked in blue are molecular divergence estimates (see methods in Supplemental Material). The divergence of Spirula from other decabrachiates are from Warnke et al. [43], the remaining divergences are from analyses presented in this paper. Bold lineages indicate the fossil record of extant lineages, stippled lines are tentative relationships between modern coleoids, partly based on previous studies [41, 76, 82] and fossil relationships are based on current consensus and hypoth- eses presented herein. Shells of stem group cephalopods and Spirula in lateral view with functional anterior left. Shells of coleoids in ventral view with anterior down. The Mesozoic divergence of coleoids is relatively poorly resolved compared to the rapid evolution of Cambro- Ordovician stem group cephalopods. Many stem group cephalopod orders not discussed in the text are excluded from the diagram.

The story and the multiple lines of evidence hang together beautifully to make a robust picture of cephalopod evolution. The authors do mention one exception: Nectocaris. Nectocaris is a Cambrian organism that looks a bit like a two-tentacled, finned squid, which doesn’t fit at all into this view of coleoids evolving relatively late. The authors looked at it carefully, and invest a substantial part of the review discussing this problematic species, and decided on the basis of the morphology of its gut and of the putative siphon that there is simply no way the little beast could be ancestral to any cephalopods: it’s a distantly related lophotrochozoan with some morphological convergence. It’s internal bits simply aren’t oriented in the same way as would fit the cephalopod body plan.

So that’s the state of cephalopod evolution today. I shall be looking forward to the Next Great Paper, and in particular, I want to see more about the molecular biology of tentacles — that’s where the insights about the transition from monoplacophoran to cephalopod will come from, I suspect.

Kröger B, Vinther J, Fuchs D (2011) Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators. Bioessays doi: 10.1002/bies.201100001.

Turnabout is fair play

Phil Senter has published the most deviously underhanded, sneaky, subtle undermining of the creationist position I’ve ever seen, and I applaud him for it. What he did was to take them seriously, something I could never do, and treat their various publications that ape the form of the scientific literature as if they actually were real science papers, and apply their methods consistently to an analysis of taxonomy. So on the one hand, it’s bizarre and disturbing to see the like of Ken Ham, Jerry Bergman, and Henry Morris get actual scientific citations, but on the other hand, seeing their claims refuted using their own touted methods is peculiarly satisfying.

Senter has published a paper in the Journal of Evolutionary Biology that takes their claims at face value and analyzes dinosaur morphology using their own methods. ‘Baraminologists’ have published a set of taxonomic tools that use as input a matrix of morphological characters for an array of animals, and then spits out numbers that tell whether they were similar enough to be related. You can guess what the motivation for that is: they want to claim that Noah didn’t have to carry representatives of every dinosaur species on the Ark, but only representatives of each ‘kind’, which then diversified rapidly after the big boat landed to generate all the different species found in the fossil record.

The problem for them is that Senter found that it works far too well. Using creationist techniques, all of the Dinosauria reduce to…eight kinds. That makes the boat haulage problem relatively even easier.

Here is the summary diagram, illustrating the derived creationist tree of common descent. Oops.

i-cf7aed20267bbf27bd8d0565d5df2681-creationisttree.jpeg
Summary of results of taxon correlation analyses across Dinosauria. Each boxed group of silhouettes indicates a group for which taxon correlation found within-group morphological continuity; for silhouette groups in different boxes, taxon correlation found morphological discontinuity between the groups. Dotted lines represent uncertainty as to whether morphological discontinuity is truly present. On the cladogram, triangles indicate paraphyletic groups.

At first, the results of the taxon correlation analyses appear to imply good news for the creationist world view, on several fronts. First, seven major dinosaurian groups (birdlike coelurosaurs, Tazoudasaurus + Eusauropoda, Stegosauria, Ankylosauridae, Neoceratopsia, Hadrosauridae and basal Hadrosauriformes) are separated from the rest of Dinosauria by morphological gaps (Fig. 15). Creationist inferences that variety within Eusauropoda (Morris, 1999) and Ceratopsidae (Ham, 2009) represent diversification within separately created kinds are congruent with these results. Second, each morphologically continuous group found by taxon correlation includes at least some herbivores. This is congruent with the creationist assertion that all carnivorous animals are descendants of originally herbivorous ancestors (Unfred, 1990; Gish, 1992; Ham, 1998, 2006, 2009; Larsen, 2001; McIntosh & Hodge, 2006). Third, although creationists have answered the problem of room on Noah’s ark for multiple pairs of gigantic dinosaurs by asserting that only about 50 ‘created kinds’ of dinosaurs existed (Ham, 1998, 2001, 2006, 2009; Morris, 1999), the problem is solved even better by the results of this study, in which only eight dinosaur ‘kinds’ are found.

Awww. I guess I’m going to have to become a creationist, now that the evidence shows that dinosaurs are related by common descent…oh, hey, wait. Isn’t that what evolution says? And isn’t that easier to accommodate within the idea that they did this over millions of years, rather than the freakishly unrealistic hyper-speciation within a few thousand years that the creationists insist on?

However, a second look reveals that these results are at odds with the creationist view. Whether there were eight dinosaur ‘kinds’ or 50, the diversity within each ‘kind’ is enormous. Acceptance that such diversity arose by natural means in only a few thousand years therefore stretches the imagination. The largest dinosaurian baramin recovered by this study includes Euparkeria, basal ornithodirans (Silesaurus and Marasuchus), basal saurischians, basal ornithischians, basal sauropodomorphs, basal thyreophorans, nodosaurid ankylosaurs, pachycephalosaurs, basal ceratopsians, basal ornithopods and all but the most birdlike theropods in an unbroken spectrum of morphological continuity. The creationist viewpoint allows for diversification within baramins, but the diversity within this morphologically continuous group is extreme. Also, the inclusion of the Middle Triassic non-dinosaurs Euparkeria and Marasuchus within the group is at odds with the creationist claim that fossil representatives of the predinosaurian, ancestral stock from which dinosaurs arose have never been found (DeYoung, 2000; Ham, 2006; Bergman, 2009).

So, effectively, these results, made using the creationists own tools, demonstrate a genetic relationship between a diverse group of animals that evolution predicted, and confronts young earth creationists with the problem of a kind of frantically prolific speciation that is unimaginably rapid. If species are that fluid and can change that rapidly, their own claims of fixity of species are patently wrong.

The final word:

The results of this study indicate that transitional fossils linking at least four major dinosaurian groups to the rest of Dinosauria are yet to be found. Possibly, some creationist authors will hail this finding as evidence of special creation for those four groups. However, such enthusiasm should be tempered by the finding here that the rest of Dinosauria–including basal members of all major lineages–are joined in a continuous morphological spectrum. This confirms the genetic relatedness of a very broad taxonomic collection of animals, as evolutionary theory predicts, ironically by means of a measure endorsed and used by creation science.

This is so wonderfully, evilly devious. Superficially, it seems to support creationist methods—but what it actually is is a grand reductio ad absurdam. Laugh wickedly at it now, but laugh even harder when you see creationists citing this paper in the future, as you know they will.

Senter P (2011) Using creation science to demonstrate evolution 2: morphological continuity within Dinosauria. J Evol Biol. doi: 10.1111/j.1420-9101.2011.02349.x.

Complex eyes in the Cambrian

I got a letter from a creationist today, claiming that “Darwinism is falsified,” based on an article in Nature. It’s kind of amazing; this article was just published today, and the metaphorical digital ink on it is barely metaphorically dry, and creationists are already busily mangling it.

It’s a good article describing some recent fossil discoveries, found in a 515 million year old deposit in South Australia. Matthew Cobb has already summarized the paper, so I’ll be brief on the details, but it’s very cool. What was found was a collection of arthropod eye impressions, probably from cast-off molts. No sign of the bodies of these animals was found, suggesting that perhaps they were not fully sclerotized, or as the authors suggest, that disarticulated eyes were more prone to rapid phosphatization than eyes attached to a decaying body. There is no evidence of biomineralization, so these were animals with a very light armor of chitin alone.

What’s wonderful about the eyes is that they are relatively large and contain numerous ommatidia, the individual facets of a compound eye. They have over 3,000 lenses, and there’s also evidence of regional specialization in the eye. These were highly visual animals that were capable of forming a good image of the world around them.

i-7ab8296f6ca114f363910b5d00636d3b-complexeyes.jpeg
Complex arthropod eyes from the Early Cambrian. a-d, Three fossils of compound eyes from a large arthropod from the Emu Bay Shale, South Australia (a-c), shown in similar hypothesized orientation to the compound eye of a living predatory arthropod, the robberfly Laphria rufifemorata
(d; anterior view of head). All fossil eyes have large central ommatidial lenses forming a light-sensitive bright zone, b, and a sclerotized pedestal, p. Because the fossil eyes are largely symmetrical about the horizontal axis, it is not possible to determine dorsal and ventral surfaces, and thus whether the eyes are left or right. All fossils are oriented as if they are left eyes (medial is to the left of the figure). In b there is a radial tear (white line) with the top portion of the eye displaced downwards to overlie the main part; extensive wrinkling causes some central lenses (arrow) to be preserved almost perpendicular to the bedding plane.

These eyes are also from the early Cambrian, so they appeared in the early stages of large animal evolution. The closest thing to them in ommatidial number are the sophisticated eyes of many trilobites, but even there, these eyes were early and relatively large.

i-1c548b0b7b6021fe20accaedefa965c7-ommatidianumbers.jpeg
Complexity of the Early Cambrian Emu Bay Shale eyes compared to eyes in other early Palaeozoic taxa. a, b, Number of ommatidia (a) and lens size (b) plotted against stratigraphic age for Cambro-Ordovician arthropods. The Emu Bay Shale eyes have many more ommatidia and much larger individual ommatidia than eyes in all other Cambrian taxa. Trilobites are plotted according to eye type: schizochroal eyes have relatively few, large lenses and are optically unusual compared to typical compound eyes.

Where in this is the refutation of evolution? I don’t know. But I did receive a letter from that Canadian idiot, David Buckna, crowing about it, and linking to his very silly creationist article describing it, in which you’ll find the abstract for the paper with curious random spastic boldfacing added which supposedly highlight the parts of the story that contradict evolutionary theory, words like “complexity” and “Cambrian explosion” and “more complex” and “great evolutionary event”. It’s a bit bizarre and like looking at the obsessive activity of a squirrel gathering nuts.

Here’s the creationist summary of the paper, however.

The Cambrian explosion is affirmed; complexity appears suddenly without transitions; Darwinism is falsified; the inference to the best explanation is intelligent design. Let the world know.

Let’s deal with each of these claims one by one.

  1. The “Cambrian explosion” is a term coined by scientists to describe the rapid (in geological terms) appearance of large, complex animals with hard skeletons over the course of a few million years roughly half a billion years ago. There is no creationist gotcha in pointing out the existence of this geological period; scientists have written whole books on the subject.

  2. The sudden appearance of complexity is no surprise, either. We know that the fundamental mechanisms of eye function evolved long before the Cambrian, from the molecular evidence; what happened here was not that, poof, eyes instantly evolved, but that the evolution of body armor gradually increased from the pre-Cambrian through the Cambrian, making the organization of eyes visible in the fossil record.

    It is also the case that the measure of complexity here is determined by a simple meristic trait, the number of ommatidia. This is not radical. The hard part in the evolution of the compound eye was the development of the signal transduction mechanism, followed by the developmental rules that governed the formation of a regular, repeating structure of the eye. The number of ommatidia is a reflection of the degree of commitment of tissues in the head to eye formation, and is a quantitative difference, not a qualitative one.

    And finally, there’s nothing in the data from this paper that implies sudden origins; there can’t be. If it takes a few hundred thousand years for a complex eye to evolve from a simple light sensing organ, there is no way to determine that one sample of a set of fossils was the product of millions of years of evolution, or one day of magical creation. It’s a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously.

  3. “Darwinism” is not falsified. Darwin himself explained in great detail how one should not expect fine-grained fossil series, due to the imperfection of the geological record. Creatonists, read chapter 9 of the Origin; here’s a brief excerpt.

    It should not be forgotten, that at the present day, with perfect specimens for examination, two forms can seldom be connected by intermediate varieties and thus proved to be the same species, until many specimens have been collected from many places; and in the case of fossil species this could rarely be effected by palaeontologists. We shall, perhaps, best perceive the improbability of our being enabled to connect species by numerous, fine, intermediate, fossil links, by asking ourselves whether, for instance, geologists at some future period will be able to prove, that our different breeds of cattle, sheep, horses, and dogs have descended from a single stock or from several aboriginal stocks; or, again, whether certain sea-shells inhabiting the shores of North America, which are ranked by some conchologists as distinct species from their European representatives, and by other conchologists as only varieties, are really varieties or are, as it is called, specifically distinct. This could be effected only by the future geologist discovering in a fossil state numerous intermediate gradations; and such success seems to me improbable in the highest degree.

    Finding a fossil eye with numerous ommatidia a hundred million years after molecular biology tells us that eyes evolved does not in any way falsify the idea of a gradual evolution of the eye.

  4. Given that there is nothing in this story that contradicts the idea of a natural process generating increasing complexity over time, and given that it’s an observation that fits perfectly comfortably within the body of evolutionary theory, there is no reason to leap the utterly unfounded conclusion that an invisible spirit zapped these fossils into existence — an invisible spirit for which there is no evidence. Furthermore, what evidence is in this paper directly contradicts Buckna’s beliefs: he is a young earth creationist, and this is a paper describing organisms that lived 515 million years ago. If you look at the chart I reproduced above, you might also notice that the pattern of complexity (ommatidial numbers) in trilobites shows a trend of increase over 80 million years.

  5. I shall gladly let the world know that David Buckna is an irrational fool who doesn’t know how to read a scientific paper and makes illogical leaps in his arguments.

Lee MSY,
Jago JB,
García-Bellido DC,
Edgecombe GD,
Gehling JG
Paterson JR (2011) Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia. Nature 474: 631-634.

Dyslexic Borat says, “Sexy Mite!”

It’s a real shame. Forty million years ago, this pair of mites, Glaesacarus rhombeus, had just buckled down to a happy grind, when plop, a drop of tree sap fell on them and entombed them in flagrante delicto. Also, coitus interruptus. And as long as we’re slinging around the Latin, Perfututum!.

i-24869be1ee22198325f66be63e3e34a9-ambermites.jpeg

Notice that they mate butt-to-butt. This is probably the preferred position when your partner has a face like an arachnid.

Paleontologists at work

I’m going to break another webcam, aren’t I? While you can, you can actually watch a dinosaur dig in progress in Svalbard, Norway. (Strictly speaking, though, it looks like they’re excavating pliosaurs and ichthyosaurs, not dinosaurs.)

I’m amused that it looks exactly like the the big construction project on the county courthouse in Morris, Minnesota: a lot of people standing around watching one person with an itty-bitty trowel pushing dirt around. Except that these guys are all wearing coats in August.

But seriously, it looks like they’re having a good time — bring the kids around so they can see what the minutia of real science looks like.

There are four cameras — don’t forget to check them all, some are aimed at inactive areas right now.

An unpaleontological lament for lost molecules and shattered cells and the cruelty of time

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

Sometimes, I really hate fossils. I hate them with the passion of a spurned lover, one who is consumed with desire but knows that he will never, ever be satisfied. They drive me mad.

Right now we’re at a point in our technology where we can take a small sample from a living organism and break it down into amazing detail — we can extract every gene, throw them into a computer, and compare them with every other gene that has been similarly sampled. We can look for the scars of evolution, we can analyze and figure out where on the tree of life this cell resides, we can even figure out what local populatons it lived in, who its ancestors bred with, and to a certain extent, what various alleles contributed to its form and physiology. We don’t know everything, but every time someone works out some new detail in a related species, it goes into the databases and presto, the information cascades through every other relative. I’d call it magic, but that would insult the science with cheap understatement.

We can’t do that with most fossils (with some recent exceptions). The cells are gone. Their contents are obliterated — DNA fragmented, dissolved, corrupted, lost. And the farther back in time we go, the less information we have, but the more interesting the problems become.

All organisms are built of cells — they’re like the Lego building blocks of biology, with specific features that snap them together. With Legos, of course, you can build all kinds of different forms: stick them together and build a Lego Triceratops or a Lego T. rex. Different on the outside, different in arrangement, different in pattern, but all fundamentally built of the same kinds of blocks. I can get into the coolness of digging up a Triceratops or a T. rex, but these are all variations on a theme of phylum Chordata, superclass Tetrapoda, and they’re all using the same building blocks, and all the really interesting stuff, the details in the genome that make one morphology different than another, have all been bled out on the sands of time and gnawed by all-devouring bacteria and reduced to at best a non-specific smear of carbon. That makes me frustrated.

Even worse, most familiar fossils are big bony animals — they’re all pretty much the same, deep down. If they’re built of Legos, there are whole other clades of multicellular organisms that are the equivalent of meccano, lincoln logs, Capsela, and tinkertoys. How were they put together? And how did they evolve these different patterns of connections? To know that, we have to go way back into deep time, and look at the unicellular organisms, the cells that first pioneered patterns of interactions and laid down the possible rules of development that enabled big clumsy multicellular to accumulate the bulk that made them more likely to be fossilized. Those pioneers are practically nonexistent in the fossil record.

What prompts my lament for lost cells is this recent amazing discovery: a collection of fossilized multicellular organisms unearthed in Gabon that are 2.1 billion years old. Keep in mind that in comparison, the Cambrian explosion, the event that was the root of familiar animal diversity, was a mere half billion years ago, so these are genuinely ancient. They’re also beautiful.

i-fcc88213964aed91cefd444a1530f14d-gabon_fossils-thumb-400x525-53117.jpg
(Click for larger image)
Samples show a disparity of forms based on: external size and shape characteristics; peripheral radial microfabric (missing in view d); patterns of topographic thickness distribution; general inner structural organization, including occurrence of folds (seen in views b and c) and of a nodular pyrite concretion in the central part of the fossil (absent in views a and b). a, Original specimen. b, Volume rendering in semi-transparency. c, Transverse (axial) two-dimensional section. d, Longitudinal section running close to the estimated central part of the specimen. Scale bars, 5 mm. Specimens from top to bottom: G-FB2-f-mst1.1, G-FB2-f-mst2.1, G-FB2-f-mst3.1, G-FB2-f-mst4.1.

These small, flat, furrowed sheets lived at a kind of temporal boundary, a few hundred million years after a rise in atmospheric oxygen called the Great Oxygenation Event — a crisis in the history of life on earth which occured when the production of oxygen by photosynthetic organisms could no longer be buffered by reacting chemically with minerals, and began to build up in the atmosphere. This was catastrophic for most of the organisms living at that time, which were anaerobic and found oxygen to be a caustic poison. It was an advantage to a subset that adapted to use oxygen as a fuel in chemical reactions, though, so there was also the beginnings of new forms which exploited this newly oxygenated atmosphere. That’s where these mysterious blobs come in; they were found in formations that had a chemical signature indicating the presence of free oxygen.

These were almost certainly colonial organisms that took advantage of the higher concentration of oxygen to build denser mats on top of the sea floor. They probably weren’t true multi-cellular organisms; they were a step up from a colony of bacteria that you might see growing on a petri dish, but with additional molecular features that permitted greater coordination and the development of more elaborate spatial patterning.

We also know that these had to have been very different from organisms that exist now. Those are not animals, they are not plants, they are not fungi — they are something primeval and radically different, organisms that most likely do not have any living descendants. Those are real aliens in the photo above. There is no category in your experience which you can put them into.

It’s what we don’t know that inflames my curiousity. One of the other things that was going on during the Great Oxygenation Event was the steady loss of dissolved iron in the seas — it was all being oxidized, rusted out, and precipitating out, forming geological structures like the banded iron formations. It was also facilitating the preservation of these organisms by pyritizing them — all their soft gooey bits, the whole of creature, were being replaced by fool’s gold, iron pyrite. There are no cells left here. We don’t even know for sure that these are eukaryotic cells; they probably are, indicated by the presence of a sterane chemical signature in the rocks that is characteristic of eukaryotes, but there isn’t even enough fine detail to tell whether there was a nucleus in these cells. It just breaks my heart.

It’s a beautiful tease. We can see that life was exploring the edges of multicellularity over 2 billion years ago, but…the molecular sinews that stitched them together are all gone. The signals and receptors that enabled communication between them are all gone. The genes that drove their growth are all gone. There is nothing left but a blurry crystal-ruptured outline of what once was.

I have to shake an angry fist at you, fossils. I won’t go all Mel Gibson in incoherent rage at you because I like you too much, but still…you taunt me. I want your cells. Nothing less will do.

El Albani A, Bengtson S, Canfield DE, Bekker A, Macchiarelli R, Mazurier A, Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C, Fürsich FT, Gauthier-Lafaye F, Janvier P, Javaux E, Ossa FO, Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D, Whitehouse M, Meunier A. (2010) Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago. Nature 466(7302):100-4.

Chris Nedin, who should know, does not think these fossils represent multicellular organisms at all — they are fossilized, folded microbial mats. Which is fine by me — 2 billion year old microbial mats are also exceedingly cool, and I still want their cells.

You do know that if you want to know more about anything pre-Cambrian, you should be reading Ediacaran, right?

Mother of all squid!

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

Well, more like great-great-many-times-great-aunt of all squid, but it’s still a spectacular fossil. Behold the Cambrian mollusc, Nectocaris pteryx.

i-88d7007c6d86cf755d8ee01fe3b145d6-nectocaris-thumb-450x410-49870.jpeg
(Click for larger image)
Reconstruction of Nectocaris pteryx.

This was one of those confusing, uninterpretable Cambrian animals, represented by only one poorly preserved specimen. Now, 91 new specimens have been dug up and interpreted, and it makes sense to call it a cephalopod. It has two camera eyes — not arthropod-like compound eyes — on stalks, an axial cavity containing paired gills like the mantles of modern cephalopods, and a flexible siphon opening into that cavity. There are also subtle similarities in the structure of the connective tissue in the lateral fins. Obviously, it has a pair of tentacles; no mouthparts have been preserved, but there are hints in the form of dark deposits between the tentacles, which may be all that’s left of the mouthparts — and are in the right place for a cephalopod ancestor.

There are still mysteries. There’s no hint of a shell; previous theories had postulated a shelled common ancestor to squid, nautiloids, and ammonoids, but either this was a specialized branch that lost the shell, or modern cephalopod groups independently re-evolved the structure. It also has only two tentacles! Again, we don’t know whether this was the ancestral condition, or whether Nectocaris is the product of a derived fusion. Known cephalopod Hox genes use a novel combinatorial scheme to encode arm identities, so I guess I wouldn’t be too shocked if the eight- to ten-arm condition is a relatively recent (in geological terms!) innovation.

About that great-aunt remark…here’s where their analysis places the Nectocarids, as a Cambrian side-branch of the group that led to the modern forms.

i-0ea7483a0596ffca6879571a9e380e6d-nectocaris_phylo-thumb-450x188-49873.jpeg
(Click for larger image)
Phylogenetic position of the nectocaridids. Arrows indicate the crown groups of 1, molluscs; 2, conchifera; 3, cephalopods. Stars represent the earliest record of mineralization in each lineage. Clade divergence times (dotted lines) are unconstrained. Early branches follow previous phylogeny.

Note the dotted lines everywhere — those are lineages that we haven’t found in the fossil record yet. Nectocaris is small (about 4cm long) and softbodied, and it required excellent preservation for any trace of them to survive. Specimens from the beginning of the Cambrian, representative of the groups indicated by the red arrows at 1 and 2, would be wonderful to have…but they’re also going to be forms that wouldn’t have been ideal for fossilization. Clearly, we need to fund more paleontology.

Ed Yong has more to say at Not Exactly Rocket Science.

Smith MR, Caron J-B (2010) Primitive soft-bodied cephalopods from the Cambrian. Nature http://dx.doi.org/10.1038/nature09068.

Casey Luskin embarrasses himself again

Once again, the Discovery Institute stumbles all over itself to crow victory over evolution, led by the inspiring figure of that squeaking incompetent, Casey Luskin. This time, what has them declaring the bankruptcy of evolution is the discovery of tetrapod trackways in Poland dating back 395 million years. I know, it’s peculiar; every time a scientist finds something new and exciting about our evolutionary history, the bozos at the DI rush in to announce that it means the demise of Darwinism. Luskin has become the Baghdad Bob of creationism.

The grounds for this announcement is the bizarre idea that somehow, older footprints invalidate the status of Tiktaalik as a transitional form, making all the excitement about that fossil erroneous. As we’ve come to expect, though, all it really tells us is that Casey Luskin didn’t comprehend the original announcement about Tiktaalik, and still doesn’t understand what was discovered in Poland.

The fossil tetrapod footprints indicate Tiktaalik came over 10 million years after the existence of the first known true tetrapod. Tiktaalik, of course, is not a tetrapod but a fish, and these footprints make it very difficult to presently argue that Tiktaalik is a transitional link between fish and tetrapods. It’s not a “snapshot of fish evolving into land animals,” because if this transition ever took place it seems to have occurred millions of years before Tiktaalik.

Errm, no. Shubin and Daeschler are smart guys who understand what fossils tell us, and they never, ever argued that Tiktaalik‘s status as a transitional form depended on slotting it in precisely in a specific chronological time period as a ‘link’ between two stages in the evolution of a lineage. A fossil is representative of a range of individuals that existed over a window of time; a window that might be quite wide. They would never express the kind of simplistic, naive view of the relationship of a fossil that the DI clowns seem to have. For instance, here’s a picture of the relationship between various fossils, as published in Nature when Tiktaalik was announced.

i-317070f4db90df3b55f8534f268e8dad-tiktaalik_phylo.jpg
The lineage leading to modern tetrapods includes several fossil animals that form a morphological bridge between fishes and tetrapods. Five of the most completely known are the osteolepiform Eusthenopteron; the transitional forms Panderichthys and Tiktaalik; and the primitive tetrapods Acanthostega and Ichthyostega. The vertebral column of Panderichthys is poorly known and not shown. The skull roofs (left) show the loss of the gill cover (blue), reduction in size of the postparietal bones (green) and gradual reshaping of the skull. The transitional zone (red) bounded by Panderichthys and Tiktaalik can now be characterized in detail. These drawings are not to scale, but all animals are between 75 cm and 1.5 m in length. They are all Middle–Late Devonian in age, ranging from 385 million years (Panderichthys) to 365 million years (Acanthostega, Ichthyostega). The Devonian–Carboniferous boundary is dated to 359 million years ago.

Notice what you don’t see? They didn’t publish this as a direct, linear relationship that could be disrupted by a minor anachronism. It does not look like this:

Ichthyostega
↑
Acanthostega
↑
Tiktaalik
↑
Panderichthys
↑
Eusthenopteron
↑

These are all cousins branching off the main stem that led to modern tetrapods. Tiktaalik was almost certainly not our direct ancestor, but a distant cousin that was representative of a transitional state in the branching cloud of species that emerged out of the Devonian. And the authors of these papers knew that all along, weren’t shy about stating it, and if they made an error about anything, it would be in assuming that a gang of self-styled scholars who claim to be presenting a serious rebuttal to evolutionary ideas would actually already understand a basic concept in paleontology.

You would think Luskin would have also read the Niedzwiedzki paper that describes this new trackway, which rather clearly describes the implications of the discovery. It does not declare Tiktaalik to be uninteresting, irrelevant to understanding the transition between fish and tetrapods, or that Tiktaalik is no longer a transitional form. It clearly is.

No, here’s the new picture of tetrapod evolution that Niedzwiedzki and others have drawn. At the top is a diagram of the relationships as understood before the discovery, at the bottom is the new order.

i-1077993faea342c8477ca4d12095d8c4-clad1.jpegi-91c210e6965144049a9a049f28db61fb-clad2.jpeg
Phylogenetic implications of tracks. a, Phylogeny of selected elpistostegids and stem tetrapods fitted to Devonian stratigraphy. The grey bar indicates replacement of elpistostegids by tetrapods in body fossil record. b, Effect of adding the Zachełmie tracks to the phylogeny: the ghost ranges of tetrapods and elpistostegids are greatly extended and the ‘changeover’ is revealed to be an artefact. Pan, Panderichthys; Tik, Tiktaalik; Elp, Elpistostege; Liv, Livoniana; Elg, Elginerpeton; Ven, Ventastega; Met, Metaxygnathus; Aca, Acanthostega; Ich, Ichthyostega; Tul, Tulerpeton. ANSP 21350 is an unnamed humerus described in ref 17. The bars are approximate measures of the uncertainty of dating. These are not statistical error bars but an attempt to reflect ongoing debate.

Look closely.

Hey, the branches are the same! The relationships are unchanged! What has changed is that the branches of the tree go back deeper in time, and rather than a sharp changeover, there was a more prolonged period of history in which, clearly, fish, fishapods, and tetrapods coexisted, which isn’t surprising at all. Tetrapod evolution was spread out over a longer period of time than was previously thought, but this is simply a quantitative shift, not a qualitative change in our understanding of the relationships of these animals. It also says that there is the potential for many more fossils out there over a bigger spread of time than was expected, which is something we can look forward to in future research. Not research from the Discovery Institute, of course. Research from real scientists.

Now also, please look at the b phylogeny above, and tell me where the evidence for Intelligent Design creationism in this new figure lies. Perhaps you can see how a cladogram illustrating the evolutionary relationships between a number of fossils challenges our understanding of evolutionary history, because I don’t see it. If anything, it affirms the evolution, not the Sudden Appearance by Divine Fiat, of tetrapods.

For extra credit, explain where in diagram b of the Niedzwiedzki paper it shows that Tiktaalik has been “blown out of the water,” as Luskin puts it. Should they have scribbled in a frowny face or a skull and dagger next to the Tiktaalik bar, or perhaps have drawn a big red “X” over it? Because I can guarantee you that Niedzwiedzki and coauthors still consider Tiktaalik a transitional form that is part of the story of tetrapod evolution. All they’ve done is put it on the end of a longer branch. Nothing has changed; Tiktaalik is still a revealing fossil that shows how certain vertebrates switched from fins to limbs.

Finally, just for fun, maybe you can try to explain how the “Big Tent” of Intelligent Design creationism is going to explain how the Young Earth creationists in their camp — you know, the ones that think the planet is less than ten thousand years old — are going to find it heartening that a fossil discovery has pushed one stage in tetrapod evolution back farther by another 20 million years. That’s 2 x 103 times greater than the entire span of time they allow for the existence of the universe, all spent in shaping a fin into a foot. There ought to be some feeble expression of cognitive dissonance out of that crowd, but I suspect they won’t even notice; as Luskin shows, they aren’t particularly deep thinkers.

Ahlberg PE, Clack JA (2006) A firm step from water to land. Nature 440:747-749.

Daeschler EB, Shubin NH, Jenkins FA (2006) A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440:757-763.

Niedzwiedzki G, Szrek P, Narkiewicz K, Narkiewicz M, Ahlberg PE (2010) Tetrapod trackways from the early Middle Devonian period of Poland. Nature 463(7277): 43-48.

Shubin NH, Daeschler EB, Jenkins FA (2006) The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440:764-771.

Tetrapods are older than we thought!

Some stunning fossil trackways have been discovered in Poland. The remarkable thing about them is that they’re very old, about 395 million years old, and they are clearly the tracks of tetrapods. Just to put that in perspective, Tiktaalik, probably the most famous specimen illustrating an early stage of the transition to land, is younger at 375 million years, but is more primitive in having less developed, more fin-like limbs. So what we’ve got is a set of footprints that tell us the actual age of the transition by vertebrates from water to land had to be much, much earlier than was expected, by tens of millions of years.

Here are the trackways. Note that what they show is distinct footprints from both the front and hind limbs, not drag marks, and all that that implies: these creatures had jointed limbs with knees and elbows and lifted them and swung them forward to plant in the mud. They were real walkers.

i-7c534308c9f00e73cf31353a1066764b-trackway1.jpegi-55a13b4b3a79452858e68be0cd01fa4f-trackway2.jpeg
Trackways. a, Muz. PGI 1728.II.16. (Geological Museum of the Polish Geological Institute). Trackway showing manus and pes prints in diagonal stride pattern, presumed direction of travel from bottom to top. A larger print (vertical hatching) may represent a swimming animal moving from top to bottom. b, On the left is a generic Devonian tetrapod based on Ichthyostega and Acanthostega fitted to the trackway. On the right, Tiktaalik (with tail reconstructed from Panderichthys) is drawn to the same shoulder-hip length. Positions of pectoral fins show approximate maximum ‘stride length’. c, Muz. PGI 1728.II.15. Trackway showing alternating diagonal and parallel stride patterns. In a and c, photographs are on the left, interpretative drawings are on the right. Thin lines linking prints indicate stride pattern. Dotted outlines indicate indistinct margins and wavy lines show the edge of the displacement rim. Scale bars, 10 cm.

They were also big, approximately 2 meters long. What you see here is a detailed scan of one of the footprints of this beast; no fossils of the animal itself have been found, so it’s being compared to the feet of Ichthyostega and Acanthostega, two later tetrapods. There are definite similarities, with the biggest obvious difference being how much larger the newly-discovered animal is. Per Ahlberg makes an appearance in a video to talk about the size and significance of the mystery tetrapod.

i-7f4600fb6e10f03a446adb1e20fde705-foot.jpeg
Foot morphologies. a, Laser surface scan of Muz. PGI 1728.II.1, left pes. b, Complete articulated left hind limb skeleton of Ichthyostega, MGUH f.n. 1349, with reconstructed soft tissue outline. c, Left hind limb of Acanthostega, reconstructed soft tissue outline based on skeletal reconstruction in ref. 8. We note the large size of the print compared to the limbs of Ichthyostega and Acanthostega, and that the print appears to represent not just the foot but the whole limb as far as the knee. d, digit; fe, femur; ti, tibia; fi, fibula; fib, fibulare. Scale bars, 10 mm.

What’s it all mean? Well, there’s the obvious implication that if you want to find earlier examples of the tetrapod transition, you should look in rocks that are about 400 million years old or older. However, it’s a little more complicated than that, because the mix of existing fossils tells us that there were viable, long-lasting niches for a diversity of fish, fishapods, and tetrapods that temporally coexisted for a long period of time; the evolution of these animals was not about a constant linear churn, replacing the old model with the new model every year. Comparing them to cars, it’s like there was a prolonged window of time in which horse-drawn buggies, Stanley Steamers, Model Ts, Studebakers, Ford Mustangs, and the Honda Civic were all being manufactured simultaneously and were all competitive with each other in specific markets…and that window lasted for 50 million years. Paleontologists are simply sampling bits and pieces of the model line-up and trying to sort out the relationships and timing of their origin.

The other phenomenon here is a demonstration of the spottiness of the fossil record. The Polish animal has left us no direct fossil remains; the rocks where its footprints were found formed in an ancient tide flat or lagoon, which is not a good location for the preservation of bones. This suggests that tetrapods may have first evolved in these kinds of marine environments, and only later expanded their ranges to live in the vegetated margins of rivers, where the flow of sediments is much more conducive to burial and preservation of animal remains. That complicates the story, too; not only do we have diverse stages of the tetrapod transition happily living together in time, but there may be a bit of selective fossilization going on, that only preserves some of the more derived forms living in taphonomically favorable environments.

Niedzwiedzki G, Szrek P, Narkiewicz K, Narkiewicz M, Ahlberg PE (2010) Tetrapod trackways from the early Middle Devonian period of Poland. Nature 463(7277): 43-48.