Embryonic similarities in the structure of vertebrate brains

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I’ve been doing it wrong. I was looking over creationist responses to my arguments that Haeckel’s embryos are being misused by the ID cretins, and I realized something: they don’t give a damn about Haeckel. They don’t know a thing about the history of embryology. They are utterly ignorant of modern developmental biology. Let me reduce it down for you, showing you the logic of science and creationism in the order they developed.

Here’s how the scientific and creationist thought about the embryological evidence evolves:

i-0fbb95c437feb7bb89110acb6f8e6326-brcorner.gifScientific thinking

An observation: vertebrate embryos show striking resemblances to one another.

An explanation: the similarities are a consequence of shared ancestry.

Ongoing confirmation: Examine more embryos and look more deeply at the molecules involved.

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Creationist thinking

A premise: all life was created by a designer.

An implication: vertebrate embryos do not share a common ancestor.

A conclusion: therefore, vertebrate embryos do not show striking resemblances to one another.



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Puijila darwini

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It’s yet another transitional fossil, everyone! Oooh and aaah over it, and laugh when the creationists scramble to pave it over with excuses.

What we have is a 23 million year old mammal from the Canadian arctic that would have looked rather like a seal in life…with a prominent exception. No flippers, instead having very large feet that were probably webbed. This is a walking seal.

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a, Palatal view of skull; b, lateral view of skull and mandible, left side; c, occlusal view of left mandible. Stippling represents matrix, hatching represents broken bone surface. The images are of three-dimensional scans. The brain case was scanned using computed tomography, whereas all other elements were surface scanned.

What it tells us is that marine pinnipeds almost certainly had an origin in the arctic, derived from terrestrial and semi-aquatic forms — these were more otter-like animals.

You’ll want to learn more about this beautiful creature. There is a website all about Puijila (in English, French, and Inuktitut) where you can find all kinds of images…and you can also find out how to pronounce “Puijila“, something we’re all going to have to practice. Who knew paleontology was going to lead us all into learning a few words of Inuktitut?

Rybczynski N, Dawson MR, Tedford RH (2009) A semi-aquatic Arctic mammalian carnivore from the
Miocene epoch and origin of Pinnipedia. Nature 458:1021-1024.

Jerry Coyne lobs another bomb at the accommodationists…to the barricades!

It’s another one of those long traveling days for me today. I’m on my way to Oregon (I’m at the airport already, so don’t worry about any more accidents!), so I may be a bit quiet for a while. Which means I should put something here to keep everyone in a busy uproar for a while.

My job is done, and Jerry Coyne has done the dirty work for me. He has put up a long post criticizing the accommodationist stance of several pro-evolution organizations, particularly the NCSE.

Among professional organizations that defend the teaching of evolution, perhaps the biggest offender in endorsing the harmony of science and faith is The National Center for Science Education.  Although one of their officers told me that their official position on faith was only that “we will not criticize religions,” a perusal of their website shows that this is untrue.  Not only does the NCSE not criticize religion, but it cuddles up to it, kisses it, and tells it that everything will be all right.

In the rest of this post I’d like to explore the ways that, I think, the NCSE has made accommodationism not only its philosophy, but its official philosophy. This, along with their endorsement and affiliation with supernaturalist scientists, philosophers, and theologians, inevitably corrupts their mission.

Let me first affirm that I enormously admire the work of the NCSE and of its director, Eugenie Scott and its president, Kevin Padian.  They have worked tirelessly to keep evolution in the schools and creationism out, most visibly in the Dover trial.  But they’re also active at school-board hearings and other venues throughout the country, as well as providing extensive resources for the rest of us in the battle for Darwin.   They are the good guys.

I give it ten enthusiastic thumbs up, not just for the deserved criticism but also for the praise given to the NCSE’s efforts. As Coyne explains, they are trying to have it both ways, arguing that science is a secular enterprise, but at the same time leaning over backwards to incorporate theological arguments, an act of political pragmatism that compromises their mission. It’s a failed strategy that is leading us down a dangerous path — I already feel that there is an unfortunate atmosphere that favors scientists with religious leanings over the more sensible majority.

He also includes a marvelous quote from Charles Darwin. As I’ve said many times, Darwin was not an atheist, but an agnostic, and that he refused to engage in conflict with religion…a sentiment that I think is fair and a personal choice, and one that I think the NCSE wants to follow as well (which I would think is also a reasonable strategy). However, by favoring theism as much as they have, they have broken away from the spirit of that plan.

I entirely reject, as in my judgment quite unnecessary, any subsequent addition ‘of new powers and attributes and forces,’ or of any ‘principle of improvement, except in so far as every character which is naturally selected or preserved is in some way an advantage or improvement, otherwise it would not have been selected. If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish. . . I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent.

Note that what Darwin is rejecting in that statement is what we now call theistic evolution.

I freely admit to being anti-religious myself, and I would agree that an organization trying to represent all of science and promoting science education does not have to be on the same page with me (and maybe even ought not to be), but the NCSE, NAS, and AAAS have all been erring in the opposite direction, jumping merrily into bed with every evangelical god-botherer who blows them a kiss. If they are going to snub the raging new atheists in the name of religious neutrality, they should be similarly divorcing themselves from Christian apologetics.

Richard Dawkins has weighed in…and asks whether we should take the gloves off in dealing with the accommodationist position. Too late! They’re off!

Larry Moran shares a similar view.

Many people seem to be misinterpreting Coyne’s article — it actually makes much the same point I have in talks over the last year. The science classroom must remain secular — that is, it is not a place to endorse atheism or theism, or for those conflicts to take place. We should be teaching about science and science only, and let the implications of that science on culture be discussed freely outside. Organizations like the NCSE and the NAS and AAAS are supposed to be defenders of that secularism. Nobody is asking them to promote atheism. What we’re objecting to is that they have gone too far in mollycoddling theistic views, and have falsely represented science as being congenial to religious interpretations, to the point where godless explanations are being actively excluded.

I know they have a very narrow path they have to walk to be diplomatic and try to gather popular support for science education. The point is that they are wobbling off the tightrope to court the faithful — and the science they are trying to encourage is looking less and less secular.

The impeccable logic of evolutionary psychology: spit or swallow?

Jerry Coyne carries out an amusing exercise in reasoning like an evolutionary psychologist: why does human semen taste bad? It turns out that it is really easy to invent all kinds of entirely reasonable rationalizations for it: in particular, it’s to promote ejaculation in the orifice that is more likely to result in pregnancy, since women can’t get pregnant by way of their stomach. It’s all deductively logical, but built on premises floating in thin air, with no empirical foundation at all…the usual flaw on which evolutionary psychology fails.

It does open up all kinds of angels-dancing-upon-pins sorts of questions. By the same logic, shouldn’t most women find anal sex extremely distasteful and unpleasurable (there’s another subject for Coyne to use in an informal poll — or maybe not, unless he really wants a reputation as a perv). Would the unusual anatomical arrangement in Deep Throat be evidence against evolution? And say…shouldn’t there be selection against male interest in fruitless pornography? There’s potential for a whole industry to flower around the pursuit of these questions. With illustrations.

Crank science is as crank science does

I was sent this story about genes and IQ, and right from the beginning, my alarm bells were ringing. This is crank pseudoscience.

Gregory Cochran has always been drawn to puzzles. This one had been gnawing at him for several years: Why are European Jews prone to so many deadly genetic diseases?

Tay-Sachs disease. Canavan disease. More than a dozen more.

It offended Cochran’s sense of logic. Natural selection, the self-taught genetics buff knew, should flush dangerous DNA from the gene pool. Perhaps the mutations causing these diseases had some other, beneficial purpose. But what?

At 3:17 one morning, after a long night searching a database of scientific journals from his disheveled home office in Albuquerque, Cochran fired off an e-mail to his collaborator Henry Harpending, a distinguished professor of anthropology at the University of Utah in Salt Lake City and a member of the National Academy of Sciences.

“I’ve figured it out, I think,” Cochran typed. “Pardon my crazed excitement.”

The “faulty” genes, Cochran concluded, make Jews smarter.

Why are European Jews prone to certain genetic diseases? My first answer would be to consider that they are a sub-group isolated by a history of bigotry from the outside, and strong cultural mores from the inside that promote inbreeding. These are variations amplified by chance and history.

I would not be offended by this. It’s logic, too. Natural selection is important, but it’s not everything — but so often, “self-taught genetics buffs” get the emphasis all wrong, and think of evolution as a machine that churns out generations that are relentlessly optimized for the best of all possible solutions, and these are the people who are also unsatisfied that evolution also churns out mistakes that are perpetuated over and over again. Errors happen, and their existence does not need an explanation; there is also no tendency by a benign nature to balance every individual’s shortcomings with a beneficial mutation.

Mr Cochran’s flaw is in his premise. There is no reason to assume that the frequency of every allele in a population must be the product of a selective advantage. The mathematics was worked out in the last century, and we know that even deleterious alleles can go to fixation in a population. His frenzied scribblings and off-the-wall database searches were driven by a need to reconcile the facts with his naïve and erroneous vision of evolution, and are not very convincing.

Here’s another explanation: this isolated subgroup of Ashkenazi Jews also had a culture with a deep historical respect for scholarship, and emphasized and supported education and learning to a greater degree than the larger culture surrounding them. Their children therefore begin life with a leg-up on intellectual pursuits. We don’t need a genetic explanation for their better performance (on average) on academic tests. Note also that this does not exclude a genetic component, but now at least we’re talking about an environmental factor that favors selection for intelligence. Again, though, I haven’t seen any convincing evidence for such a thing; personally, I think our intelligence is built on a shared genetic/development core that enables a wide range of kinds and degrees of intelligence to be expressed in response to environmental conditions.

But here’s the final confirming evidence that Cochran is a crank and a non-scientist.

It would be easy to test the theory, said Steven Pinker, a Harvard cognition researcher: “See if carriers of the Ashkenazi-typical genetic mutations score higher on IQ tests than their noncarrier siblings.”

Cochran and Harpending readily acknowledge the need for such experiments. But they have no plans to do them. They say their role as theorists is to generate hypotheses that others can test.

“One criticism about our paper is ‘It can’t mean anything because they didn’t do any new experiments,’ ” Cochran said. “OK, then I guess Einstein’s papers didn’t mean anything either.”

I don’t agree with Pinker that it would be easy — there’s going to be a lot of individual variation in performance, and I think it’s very hard to split the variables of culture and genetics apart in these kinds of tests. But at least he’s offering a positive approach to the problem, and that would be a good starting point.

But Cochran isn’t interested in doing them? He’s just a theorist? That’s where he begins to sound exactly like an intelligent design creationist.

Snails have nodal!

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My first column in the Guardian science blog will be coming out soon, and it’s about a recent discovery that I found very exciting…but that some people may find strange and uninteresting. It’s all about the identification of nodal in snails.

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Why should we care? Well, nodal is a rather important — it’s a gene involved in the specification of left/right asymmetry in us chordates. You’re internally asymmetric in some important ways, with, for instance, a heart that is larger on the left than on the right. This is essential for robust physiological function — you’d be dead if you were internally symmetrical. It’s also consistent, with a few rare exceptions, that everyone has a stronger left ventricle than right. The way this is set up is by the activation of the cell signaling gene nodal on one side, the left. Nodal then activates other genes (like Pitx2) farther downstream, that leads to a bias in how development proceeds on the left vs. the right.

In us mammals, the way this asymmetry in gene expression seems to hinge on the way cilia rotate to set up a net leftward flow of extraembryonic fluids. This flow activates sensors on the left rather than the right, that upregulate nodal expression. So nodal is central to differential gene expression on left vs. right sides.

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What about snails? Snails are cool because their asymmetries are just hanging out there visibly, easy to see without taking a scalpel to their torsos (there are also internal asymmetries that we’d need to do a dissection to see, but the external markers are easier). The assymetries also appear very early in the embryo, in a process called spiral cleavage, and in the adult, they are obvious in the handedness of shell coiling. We can see shells with either a left-handed or right-handed spiral.

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Chirality in snails. a, Species with different chirality: sinistral
Busycon pulleyi (left) and dextral Fusinus salisbury (right). b, Sinistral (left)
and dextral (right) shells of Amphidromus perversus, a species with chiral
dimorphism. c, Early cleavage in dextral and sinistral species (based on ref.
27). In sinistral species, the third cleavage is in a counterclockwise direction,
but is clockwise in dextral species. In the next divisions the four quadrants
(A, B, C and D) are oriented as indicated. Cells coloured in yellow have an
endodermal fate and those in red have an endomesodermal fate in P. vulgata
(dextral)15 and B. glabrata (sinistral)28. L and R indicate left and right sides,
respectively. d, B. glabrata possesses a sinistral shell and sinistral cleavage
and internal organ organization. e, L. gigantea displays a dextral cleavage
pattern and internal organ organization, and a relatively flat shell
characteristic of limpets. Scale bars: a, 2.0 cm; b, 1.0 cm; d, 0.5 cm; e, 1.0 cm.

Until now, the only organisms thought to use nodal in setting up left/right asymmetries were us deuterostomes — chordates and echinoderms. In the other big (all right, bigger) branch of the animals, the protostomes, nodal seemed to be lacking. Little jellies, the cnidaria, didn’t have it, and one could argue that with radial symmetry it isn’t useful. The ecdysozoans, animals like insects and crustaceans and nematodes, which do show asymmetries, don’t use nodal for that function. This suggests that maybe nodal was a deuterostome innovation, something that was not used in setting up left and right in the last common ancestor of us animals.

That’s why this is interesting news. If a major protostome group, the lophotrochozoa (which includes the snails) use nodal to set up left and right, that implies that the ecdysozoans are the odd group — they secondarily lost nodal function. That would suggest then that our last common ancestor, a distant pre-Cambrian worm, used this molecule in the same way.

Look in the very early mollusc embryo, and there’s nodal (in red, below) switched on in one or a few cells on one side of the embryo, the right. It’s asymmetrical gene expression!

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Early expression of nodal and Pitx in snails. a, 32-cell stage L.
gigantea expressing nodal in a single cell. b, Group of cells expressing Pitx in
L. gigantea. c, Onset of nodal expression in B. glabrata. d, A group of cells
expressing Pitx in B. glabrata. e, 32-cell L. gigantea expressing nodal (red) in
a single cell (2c) and brachyury (black) in two cells (3D and 3c).
f-h, brachyury (black) is expressed in a symmetrical manner in progeny of 3c
and 3d blastomeres (blue triangles in g), thus marking the bilateral axis, and
nodal (red) is expressed on the right side of L. gigantea in the progeny of 2c
and 1c blastomeres, as seen from the lateral (f) and posterior (g, h) views of
the same embryo. i, A group of cells expressing nodal (red) in the C quadrant
and Pitx (black) in the D quadrant of the 120-cell-stage embryo of L.
gigantea. j, nodal (red) and Pitx (black) expression in adjacent areas of the
right lateral ectoderm in L. gigantea. L and R indicate the left and right sides
of the embryo, respectively. The black triangle in b and i, the green, yellow
and pink arrows in f and i, and the black and pink arrows in f and h point to
the equivalent cells. Scale bars: 50µm.

Seeing it expressed is tantalizing, but the next question is whether it actually does anything in these embryos. The test is to interfere with the nodal-Pitx2 pathway and see if the asymmetry goes away…and it does, in a dramatic way. There is a chemical inhibitor called SB-431542 that disrupts this pathway, and exposing embryos to it does interesting things to the formation of the shell. In the photos below, the animal on the left is a control, and what you’re seeing is a coiled shell (opening to the right). The other two views are of an animal treated with SB-431542…and look! Its shell doesn’t have either a left- or right-handed twist, and instead extends as a straight tube.

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Wild-type coiled and drug-treated non-coiled shells of B.
glabrata. Control animals
(e) display the normal sinistral shell morphology. Drug-treated animals
(f, g, exposed to SB-431542 from the 2-cell stage onwards) have straight
shells. f and g show an
individual, ethanol-fixed, and shown from the side (f) and slightly rotated
(g).

What this all means is that we’ve got a slightly better picture of what genes were present in the ancestral bilaterian animal. It probably had both nodal and Pitx2, and used them to build up handedness specializations. Grande and Patel spell this out:

Although Pitx orthologues have also been identified in non-deuterostomes such as Drosophila melanogaster and
Caenorhabditis elegans, in these species Pitx has not been reported in
asymmetrical expression patterns. Our results suggest that asymmetrical expression of Pitx might be an ancestral feature of the bilaterians.
Furthermore, our data suggest that nodal was present in the common
ancestor of all bilaterians and that it too may have been expressed
asymmetrically. Various lines of evidence indicate that the last common ancestor of all snails had a dextral body. If this is true, then our
data would suggest that this animal expressed both nodal and Pitx on
the right side. Combined with the fact that nodal and Pitx are also
expressed on the right side in sea urchins, this raises the possibility
that the bilaterian ancestor had left-right asymmetry controlled by
nodal and Pitx expressed on the right side of the body. Although
independent co-option is always a possibility, the hypotheses we present can be tested by examining nodal and Pitx expression and function in a variety of additional invertebrates.

It’s also, of course, more evidence for the unity of life. We are related to molluscs, and share key genes between us.

Grande C, Patel NH (2009) Nodal signalling is involved in left-right asymmetry in snails. Nature 457(7232):1007-11.

Guiyu oneiros

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A fish is a fish, right? They’re just a blur of aquatic beasties that most people distinguish by flavor, rather than morphology or descent. But fish are incredibly diverse, far more diverse than terrestrial vertebrates, and there are significant divisions within the group. Most people know of one big distinction, between the Chondrichthyes (fish with cartilaginous skeletons, like sharks and rays) and the Osteichthyes (fish with bony skeletons), but there’s another particularly interesting split within the Osteichthyes: the distinction between Sarcopterygians (the word means “fleshy fins”, and we call them lobe-finned fishes colloquially) and the Actinopterygians, the ray-finned fishes. The lobe-finned fishes most distinctive feature is the muscular and bony central core of their fins — extant forms are the coelacanth and lungfish. It is this lineage that led to us terrestrial tetrapods, but other than that successful invasion of the land, the sarcops were something of an aquatic failure, with only a few genera surviving. The ray-finned fishes, on the other hand, are a major success story, with more than 28,000 species today. To put that in context, there are only about 5,500 species of mammals.

The Sarcopterygii and the Actinopterygii must have begun diverging a long time ago, and a couple of questions of interest are a) when did the last common ancestor of both groups live, and b) what did it look like? We don’t have a good and specific answer yet, because Osteichthyes origins are lost far, far back in time, over 400 million years ago, but every new discovery edges us a little closer. What we now have is a well-preserved fossil of a fish that has been determined to be an early sarcopterygian, and it tells us that a) the last common ancestor had to have lived over 419 million years ago, the age of this fossil, and the divergence probably occurred deep in the Silurian, and b) this animal has a mosaic of primitive Osteichthyan features, which tells us that that last common ancestor may well have shared some of these elements. It is another transitional fossil that reveals much about the gradual separation of two great vertebrate groups.

And here it is:

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a, b, A near-complete fish in part and counterpart. c, Close-up view of the anterior portion of the trunk shield in dorsal view, showing MD1 and MD2 flanked by rhomboid scales. d, Close-up view of the dorsal fin spine. MD1, first median dorsal plate; MD2, second median dorsal plate. Scale bar, 1 cm.

That may be a bit disappointing at first — it looks like Silurian road-kill — but really, that’s a remarkable good and useful specimen. The animal was covered with thick bony scales, and the skull was built of thick bony plates, and so while it was squashed flat by pitiless geology, the pieces are all there, and it can be reassembled into a much more fishy state. This drawing may be more satisfying:

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a, Restoration of the entire fish in lateral view. b, Interpretive drawing of the holotype V15541. Areas shaded in grey are unknown, and are reconstructed from other early osteichthyans. ano, anterior nostril; br, branchiostegal ray; cla, clavicle; cle, cleithrum; drs, dorsal ridge scale; dsp, dorsal fin spine; et, extratemporal; eta, accessory extratemporal; f.add, adductor fossa; f.gl, glenoid fossa; gu, gular; ju, jugal; l.ext, lateral extrascapular; lj, lower jaw; m.ext, median extrascapular; mx, maxillary; n.sp., spiracular notch; op, opercular; pa, parietal shield; pcl, postcleithrum; pop, preopercular; ppa, postparietal shield; psc, presupracleithrum; pt, post-temporal; scl, supracleithrum; sop, subopercular; sp., pectoral spine; tr, lepidotrichia; vrs, ventral ridge scale.

Now it looks like a kind of armored, spiky salmon with a thick muscular body (and yes, I too wonder about flavor, and would like to taste a slab of that). It’s definitely not a salmon, though — the bony structure is a curious set of compromises where some features are distinctly sarcopterygian, some look like they belong on a primitive actinopterygian, and others are unique or show affinities to characters of ancient extinct fishes, like rhipidistians. This is very cool. What we see here are relics of an ancient common osteichthyan ancestor, which are being honed into the specific characteristics of the Sarcopterygii. The analysis of the totality of the animal’s features, though, place it more in the lobe-finned than the ray-finned clade. That places it on a branch of the line leading to us…a very, very old branch, making this your many-times-great grand uncle, or cousin only a few million times removed. Now my curiosity about a taste-test is making me feel mildly cannibalistic.

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(Click for larger image)
The topology is the most parsimonious tree arising from a matrix of 23 taxa coded for 153 morphological characters (tree length = 292, consistency index = 0.572, retention index = 0.737, rescaled consistency index = 0.421). The numbers at nodes indicate bootstrap support (where the value is greater than 50%) and Bremer decay index (bottom and top numbers, respectively). Eif., Eifelian; Ems., Emsian; Fam., Famennian; Fras., Frasnian; Giv., Givetian; Gor., Gorstian; Loch., Lochkovian; Lud., Ludfordian; Prag., Pragian.

When you look at that diagram, what should jump out at you is all the diversity in the Devonian, the so-called Age of Fishes, and the paucity of representative fossils from the Silurian…which is exactly where all the interesting branch points in the fish family tree are located. Once again, paleontology is a predictive science, and this tells us where to look for the next batch of exciting and informative fossils.

Zhu M, Zhao W, Jia L, Lu J, Qiao T, Qu Q (2009) The oldest articulated osteichthyan reveals mosaic gnathostome characters. Nature 458:469-474.

Tianyulong

I’m not going to say much about this since Ed Yong has an excellent write-up, but a new feathered dinosaur has been discovered, called Tianyulong. As you can see in this image of the fossil, it was bristling with a fuzz of thin fibers — proto-feathers.

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a, Main slab of the holotype (STMN 26-3). b, Broken slab. The scale bar in b refers also to a. c, Close-up of skull and mandible. d, Interpretive drawing of skull and mandible. e, Close-up of dentition. Abbreviations: a, angular; aof, antorbital fossa; ca, caudal vertebrae; cv, cervical vertebrae; d, dentary; dv, dorsal vertebrae; emf, external mandibular fenestra; en, external naris; f, femur; h, humerus; isc, ischium; j, jugal; l, lacrimal; m, maxilla; n, nasal; pd, predentary; pf, prefrontal; pm, premaxilla; po, postorbital; pub, pubis; q, quadrate; qj, quadratojugal; scaco, scapulocoracoid; sa, surangular; tf, tibia and fibula.

There are a couple of noteworthy features in this creature. One is apparent: feathers just didn’t bloom suddenly in evolution, but appeared in steps. This animal has ‘feathers’ that don’t branch like those of modern birds, but instead form more of a furry coat than a set of flat blades.

The other cool thing is that this is an ornithischian dinosaur; most of the other dinosaurs that have been discovered to have feathers were saurischian. What that means might be made more clear by this diagram:

Feathered-dinos.jpg

It implies that just maybe the last common ancestor of the saurischia and ornithischia were also covered with proto-feathers, which means that feathers may be a primitive state in this lineage.

Zheng X-T, You H-L, Xu X, Dong Z-M (2009) An Early Cretaceous heterodontosaurid dinosaur with filamentous integumentary structures. Nature 458:333-336.

Octopods from the Cretaceous!

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Several new and spectacular cephalopod fossils from 95 million years ago have been found in Lebanon. “Spectacular” is not hyperbole — these specimens have wonderfully well-preserved soft parts, mineralized in fine-grained calcium phosphate, and you can see…well, take a look.

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Keuppia levante sp. nov. from the Upper Cenomanian (Metoicoceras geslinianum Zone) of Hâdjoula (Lebanon). A,
holotype, MSNM i26320a. B, sketch of the holotype.

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