Friday, September 29, 2006

Whence life began

Ooh! This is fun! An entire issue of Philosophical Transactions of the Royal Society dedicated to research on the origin of life. It covers everything from the prebiotic earth to the chemistry of replicators. I'm going to see how much of it I can read today and over the weekend and try to post some summaries. I'm no biochemist, so don't expect too much critical analysis, but origin of life stuff is a bit of a side hobby of mine. So hopefully I can say something meaningful. In the meantime, if you're keen enough to slog through some of this stuff, check it out!

01/10/06: Not going to get around to posting any summaries soon. There's a couple of conferences coming up, so preparing my talks and finishing a manuscript have taken priority. I'll try to get on it before I leave.
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Sunday, September 24, 2006

And now for something completely different

Since I've been really busy and this site has recently been devoid of much content of a biological character, I'm going to continue the trend. Here's an interesting homepage for an artist who examines the interface of advertising and western media and politics. I like it. I think his stuff has guts, humour, and isn't (in my opinion) overly pretentious. He's also my cousin and so I should plug his stuff. I particularly like this piece and this one.

Check out the site and enjoy!
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Anti-science vs. anti-evolution

I've grown to disapprove of the term "anti-evolution" to refer to the efforts of creationists to undermine education about evolution. I find it too vague a term, as it could also imply being against the actual process of evolution itself. Moreover, it masks the fact that the fundamental problem with creationism is not the fact that it is counter to a particular scientific theory (in this case evolution). Rather, the problem with the modern creationist movement is that it attempts to erode the honest, questioning, and disinterested process of investigation that gives us the best and most meaningful view of the world. There is no need for me to re-iterate the number of ways in which creationism is anti-scientific.

Because of this, I prefer to characterize this contemporary movement against evolution as that which it is: anti-science.

Creationists will frequently argue that it is not their facts that are different but merely their interpretation. Whereas the evolutionist assumes there is no god, the creationist assumes that there is and we just get a different result. This kind of thinking exemplifies the creationist misunderstanding of science. For they have no concept simply not assuming anything about god. For them, the fact that this independent and freely-thinking method of reasoning cannot discover gods and mysticism is a threat, because the world that it can discover did not discover one in agreement with their favourite scriptures.

For this reason, religious bodies have attacked science at nearly major turn in its history. Evolution is only the latest victim. But reproductive biology is already under heavy fire and it won't be long before the neurosciences and psychology are victims, too. The attack on evolution is only part of a larger pandemic of superstitious unreason. The people who attack evolutionary science fear it because it has been one of the most stark reminders that a literal reading of Genesis is incompatible with science. It is doubly unnerving for these people since it presents an altogether more convincing case, thoroughly modern in its expression, and based on the same principles of reasoning that have given us vaccines and rockets. People who oppose the teaching of evolution and who are disputing based on their egregious misunderstandings of the theory and deep-running ignorance of the facts are not simply opposed to evolution but to science in general.

However, as a minor semantic point alluded to at the beginning of this entry, the creationists aren't preventing evolution as a phenomenon (except socially). I would say they are trying to stymie that phenomenon known as science. Because of this, I think the semantic difference becomes important and the creationists are best referred to as "anti-scientists" and their activities as "anti-science". While their particular beef is with evolutionary theory, I'd say that referring to them as "anti-evolutionists" is too restrictive.

My problem is not their problem with evolution, it's with their bad methods, bad logic, bad evidence, and dishonest tactics. For that reason, I prefer not to call them anti-evolutionists but anti-scientists.
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Friday, August 11, 2006

Perfect neighbors

I saw this on Whyte Avenue in Edmonton... (click for a larger view).

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Wednesday, August 09, 2006

Fieldwork Pt II: Miguasha

There was once a time when there were very few animals living on the land. Vertebrates are pretty much the last animals to march onto land. The time before tetrapods is one of the most interesting for paleontologists and evolutionary biologists because it represents a time when the basic evolution of vertebrates is happening -- from their very origins to their two largest radiations: sarcopterygians ('lobe fins' - including ourselves) and ray-fins (all the most common fish we recognize today. Together, these two groups contain the vast majority of vertebrate diversity. It is also during this time that jaws originated and all kinds of appendages evolve into a diverse array of forms. If we are to single out the most significant site in helping us understand this time it is the greenish coloured cliffs of the Escuminac Formation at Miguasha, Quebec.

Located on the Baie des Chaleurs on the Gaspé Peninsula, the Parc Nationale de Miguasha preserves unbelievably beautiful and complete vertebrate fossils. The most famous of these is probably Eusthenopteron, the icon of children's books on prehistoric life as that fish that crawled from the water. While it is doubtful that Eusthenopteron crawled around on land, it certainly had much in common with the first tetrapods.

These are the cliffs from which it and many other extremely important fossil fishes were found.

I spent at least a few hours of every day, or sometimes the better part of a day out prospecting on the beach and the cliffs. Even with constant patrolling and daily visits by tourists, there are still important specimens to be found -- even lying on the beach. The most common fossil out there is probably the placoderm (or "armored fish") known as Bothriolepis. It's initial discovery was a serious case of "mistaken identity", as it was thought to be a turtle! However, later specimens from Miguasha showed preservation of its soft, unarmored body and tail demonstrating that it was a fish. Recently, a specimen was discovered showing stains on the inside of the ventral shield where the blood vessels had been!

This same locality is also the place where Elpistostege, Tiktaalik's sister-taxon was first recovered. Elpistostege was really the first so-called "fishapod" to be found. Initially, only a partial skull roof was known and was described by T.S. Westoll in 1938. Since then, some more of the skull and body, seen below, have been found and described.

This is the beautiful museum which stands at the top of the cliffs. In my opinion, it probably has one of the finest displays of any museum in all of Canada -- and it's very small. The display is very pedagogical, in a good way. It uses the finest examples of each type of fish that is found at Miguasha to give the visitor a sense of the diversity that exists there. It uses a lot of pictures, specimens and cleverly organized displays to teach the history of the site: both geologically and in terms of the discovery, exploitation and research of the site. Sorry, I haven't got pictures of the displays handy.

In short, this bit of fieldwork was more like a holiday for me. In fact, it wasn't much in the way of fieldwork, since I got more work done in the collections. I really would like to encourage people to check the place out if they ever get the chance. It's a bit out of the way, but if you're at all interested in palaeontology, evolution, or just pretty places, it's well worth the visit.
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Monday, July 31, 2006

Fieldwork Pt I

Alas, an internet connection and a bit of time to explain my inexcusable absence from the blogging world! As some of you may know, my absence has been due to extended fieldwork missions in eastern Canada. My first project was in southern New Brunswick, collecting fossil fishes from the earliest part of the Carboniferous. The goal is to study the fish faunas that existed at that time and to understand how the vertebrate fauna turned over after the end of the Devonian. Of course, there is always the hope that one will find a tetrapod.

The site is relatively accessible and I'm not keen to inspire private collectors to poach the site, so my details will be limited. Most of the material is not really the envy of collectors as it is generally disarticulated, broken open in section, and ridiculously difficult to prepare. The fossils are found in shale beds that crop out in various parts of southern New Brunswick.

An outcrop of Carboniferous shale that is quite typical of the region. Fossil vertebrates appear to come from only a few restricted horizons in the formation.

The site is relatively rich and surprisingly more diversity is found here than we had previously expected from this fauna. Sadly, the tetrapod continues to elude us.

The partially articulated skeleton of an undetermined genus of lobe-finned fish is seen in section on the side of a large boulder.

Hopefully, the data from this work will help us understand both the diversity and paleoecology of vertebrates that lived shortly after the Devonian. This site has equivalent age counterparts all over the Atlantic provinces of Canada, each of which has different kinds of animals living in it. This could provide some information on how animals are distributed across different environments during this time which should be crucial in understanding what these ancient communities were like.
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Thursday, July 20, 2006


In case you've been visiting and wondering why I haven't posted in so long, I've been in the field collecting fossils -- lots of fossils. I've had a very successful field season working on Early Carboniferous rocks in Atlantic Canada. I've been less successful with the Late Devonian outcrops, sadly, since there are so few of them. Since I've been camped out in what is essentially a cow pasture, I haven't had much time to post anything, but there will obviously be much coming up!
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Thursday, June 22, 2006

World's science academies against creationism

A lot of buzz about this. I didn't pay it much mind at first because a lot of scientific societies (even non-biological ones) have issued their statements against ID/creationism and for teaching evolution. But this one unites scientific societies from all over the world and has one of the single best statements I have seen:

"Scientific knowledge derives from a mode of inquiry into the nature of the universe that has been successful and of great consequence. Science focuses on (i) observing the natural world and (ii) formulating testable and refutable hypotheses to derive deeper explanations for observable phenomena. When evidence is sufficiently compelling, scientific theories are developed that account for and explain that evidence, and predict the likely structure or process of still unobserved phenomena."

-- IAP Statement on the Teaching of Evolution

That one elegant paragraph beautifully encompasses what is and what is not science, and cuts through to the very nature of science. The common creationist/IDist whine is that "macroevolution hasn't been observed, bla bla bla". Well, of course this is nonsense. This statement was evidently written by a people with their finger on the pulse of this issue. Well done!
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Wednesday, June 21, 2006

Mesomyzon, a Cretaceous lamprey

Fossil lampreys are exceedingly rare. The oldest are known from Early Carboniferous and that's about it. These fossils are recorded in limestones, suggesting that they were marine, while modern forms are known to inhabit marine and freshwater environments where they make their living parasitizing fish.

Today in Nature, Mee-mann Chang and colleagues report on a fossil lamprey from the same beds that have yielded feathered dinosaurs. Mesomyzon, figured below, is very similar to modern lampreys in many respects and helps bridge the, albeit rather small, morphological gap between the Carboniferous forms and modern forms. It also tells us that by the Early Cretaceous, lampreys had invaded freshwater habitats.

a, A complete fish (IVPP V14718A) in left view. b, Holotype (IVPP V14719) in right view. c, Drawing of the holotype, with the dorsal fin and caudal region reconstructed on the basis of IVPP V14718A. d, Photograph of head and anterior part of body of the holotype. e, Drawing of the same part as in d. Scale bars, 10 mm (a–c) and 5 mm (d, e). Abbreviations: a., anus; br.b., branchial basket; c.f., caudal fin; d.f., dorsal fin; d.t.?, possible digestive tract; g., gonads; g.a., gill arches; g.f., gill filaments; l., liver; l.e., left eye; l.ot., left otic capsule; ms., myosepta; nc., notochord; or.d., oral disk; p.c.?, possible piston cartilage; pc.c., pericardial cartilage; r.e., right eye; r.ot., right otic capsule. From Chang et al. 2006.

More about lampreys to come.

Chang, M.-m. et al. 2006. A lamprey from the Cretaceous Jehol biota of China. Nature 441: 972-974. <link>
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Friday, June 09, 2006

The pygmy giant: Europasaurus holgeri

Europasaurus holgeri is a pretty extraordinary animal. It is a sauropod dinosaur that would've barely stood taller than a man -- as an adult!. What's interesting about the discovery of this animal, is that the investigators decided to try to explain the size of this animal. Head over to the Palaeoblog and check it out.

There were a number of interesting papers in this week's Nature and I simply haven't had time to cover them or use them in some way. I'm on it! I'm on it! Just give me some time!
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Thursday, June 08, 2006

A little something about scientific publishing

Manuscripts sent to journals get rejected all the time. It's no surprise, since it's unlikely that journals could even publish everything that's sent to them... okay, maybe some could. However, I just had a really frustrating experience: an editor who decided to make up his own reasons for rejecting the paper.

Despite favourable reviews from two referees, this editor claimed that our manuscript had previously been submitted to and rejected by another journal and that we didn't even bother to send a clean copy, just a re-formatted manuscript! Of course, my co-author and I have never submitted anything in our careers to that other journal! Thus, it does not appear that this editor even bothered sending any emails to check his facts, as there should've been no ambiguity.

I'm expecting an apology from the editors any day now. I don't care if they can reject it on scientific grounds, but to make up such an offensive charge is academically irresponsible and shows brazen indifference. I'm not even expecting them to re-consider the manuscript, as I'm not sure I want to publish in that journal anymore. This has left me seriously dismayed with the quality of editorship there. If they don't apologize to us, I may well fill in the blanks here with names.
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Wednesday, June 07, 2006

Oh crap...

I don't cover a lot of politics, mainly because I'm Canadian and a lot of my readers are from elsewhere. However, this burns my ass. How does one manage to accidentally pass a budget? A conservative budget at that! This is going to be a scary year, folks!

(Hat tip to Orange Juice -- who is now appearing in my blogroll, by the way. If you're up on Canuck politics, go say 'hi'.)
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Thursday, May 11, 2006

A little more Tiktaalik...

...just for good measure.

Neil Shubin, one of the discoverers of Tiktaalik roseae has an essay online about the discovery, a bit about its history and why it's significant.

Tiktaalik would appear to be the only fossil with its own homepage, check it out.
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Sunday, May 07, 2006

My letter to The Dispatch.

I responded to Mark Looy's (of AiG) letter to the Columbus Dispatch, it was published today. Many thanks goes to the editors of the Dispatch for having the integrity to publish a response to the misinformation spread by Looy.
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Just entertainment?

"Psychics" really are scum. Onegoodmove has the video.

These so-called psychics are a bunch of bozos that prey on the emotional fragility that each and every one of us has to face at some point in our lives.
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Thursday, May 04, 2006

The "other end" of the fish-tetrapod transition

I guess one can't really talk about an evolution transition having 'ends', since one might even consider the origin of vertebrates as a whole to be part of the origin of tetrapods story. However, we focus a lot on the transformation from sarcopterygian (lobe-finned) fishes to the earliest tetrapods like Acanthostega and Ichthyostega. Lest we forget the origin of the sarcopterygians themselves. This is a murky and poorly understood part of vertebrate evolution where the fossils are limited to what we affectionately call "thumbnail skulls". These are usually braincases and associated snouts that aren't much bigger than, well, your thumbnail (and kind of shaped like them too).

In recent years, we have seen the publication of a number of really peculiar thumbnail skulls from China, nearly all of which belong to some kind of sarcopterygian. One of the defining features of the sarcopterygian skull is a joint that runs right through the braincase. The only living sarcopt to retain such a feature is the modern coelacanth. However, once upon a time in the Devonian, most sarcopterygians were built this way. We know these skulls are sarcopterygian because of this division of the skull and braincase, as well as the histology of the dermal bone. Sarcopterygians are unique in having had a system of pores and canals running through an enamel-like layer on the outside. This tissue matrix is called cosmine. One will often hear of "cosmine-covered osteolepiforms" or "cosmine covered sarcopterygians", to distinguish these forms from taxa that later lose cosmine (for instance, the loss of cosmine is a character that Tiktaalik shares with tetrapods).

But apart from these defining features of sarcopterygians, the thumbnail skulls from China also have a strange mélange of characters from all kinds of other fish groups: actinopterygian (ray-finned) fishes, sharks, placoderms, and acanthodians. For instance, it was recently noted that several of these taxa had the bony facet for the attachment of an eyestalk -- a cartilage rod found in some modern sharks that supports the eyeball. Similar facets have been seen in fossil shark braincases and later in ray-finned fish braincases. Psarolepis, for instance, was shown to have a cheek very similar to that of an actinopterygian and it even had a spine on a shoulder girdle that was associated with the skull. The actual identity of some of these parts, however, may be disputed because we still haven't got whole skeletons of these fishes.

Today in Nature a new piece is added to this puzzle: Meemannia eos. This new taxon is peculiar as far as sarcopts go. It has something sort of like cosmine, but somewhat more rudimentary. However, another interesting aspect is the absence of an intracranial joint, like the one described above.

This 405-Myr-old fish shows a mixture of basal actinopterygian and sarcopterygian features. a, b, Dorsal view of skull roof (a, holotype, V14536.1; b, V14536.2). e, f, Ventral view of posterior portion of the skull roof with incompletely preserved oto-occipital structures (e, V14536.4; f, illustrative drawing). c, d, g, h, Reconstruction of skull roof (c) compared with two actinopterygians, Dialipina (d) and Cheirolepis (g), and one sarcopterygian, Powichthys (h). Abbreviations: am.a, am.e, anterior and external ampullae;, cranial cavity;, supraotic cavity; Dsp, dermosphenotic; It, intertemporal; lc, otic portion of the main lateral line canal; lcc, lateral cranial canal; P, parietal; pdf, posterior dorsal fontanelle; pl.m, pl.p, middle and posterior pit-lines; Pp, postparietal; re.u, utricular recess; sac, sacculus; sca, anterior semicircular canal; soc, supraorbital canal; St, supratemporal; T, tabular; IX, exit of the ninth cranial nerve. Open arrow in c, g and h indicates the position of the orbit. Scale bar, 5 mm (a, b, e, f). From Zhu et al. 2006.

Immediately, one is faced with two options: was the joint lost or was it simply primtive? The answer appears to be the latter, and that Meemannia is the most primitive sarcopterygian known to date. The skull roofing bones of Meemannia are curiously similar to those of primitive ray-finned fishes. In fact, the authors note, the snout appears to have been loosely attached to the rest of the skull, a feature also seen in placoderms. The weight of the evidence appears to support the conclusion that Meemannia is a rather 'primitive' animal.

The figure is based on two most parsimonious trees that differ in the positions of Ligulalepis. Bremer support values are shown at nodes. Tree length 222, consistency index 0.6216, homoplasy index 0.3784, retention index 0.7807, rescaled consistency index 0.4853. See Supplementary Information for details. Insets compare the histological features of Meemannia (b) with those found in actinopterygians (Andreolepis, a) and crown-group sarcopterygians (Porolepis, c). From Zhu et al. 2006

Furthermore, I mentioned that it had cosmine or something very much like it. The authors note that what we see in Meemannia the cosmine structure is unique among sarcopterygians and offers some clues about its natural history. In previous decades, the pore-canals have been suggested to represent a system something like the ampullae of Lorenzini in sharks. This is a network of electrosensory organs that sharks have spread over their faces, and the networks of the ampullae are quite similar to that seen in cosmine. Of course, cosmine-covered sarcopterygians are all extinct and we have no way of knowing what the function of the cosmine canals and pores were for. However, the new fossil suggests a rather different function: growth. Unlike the cosmine of other sarcopterygians, but somewhat like the enamel tissue of actinopterygians, the cosmine of Meemannia grew by the addition and expansion of layers. This suggests that Meemannia's cosmine growth is more primitive. Furthermore, this unique mode of growth suggests that he pore-canals may be a vascular system that supprted this, and may not necessarily have been for sensory purposes. However, I don't see these options as neccessarily exclusive, so I'm not sure if we can really rule out a sensory function just yet.

Meemannia is another addition to the story of the early evolution of bony vertebrates. It's another clue about how this event proceeded and how the two major lineages of bony vertebrates emerged. We still need a lot more clues and a lot more work to figure out the details, but the fossils from China are (once again) helping to disperse the fog.

Also worth a mention here is that Meemannia eos is named after the renowned vertebrate palaeontologist Chang Mee-mann for her enormous contribution to vertebrate palaeontology, especially in China. Her influence on palaeoichthyology has been enormous and she is easily one of the most respected contributers to the field of early vertebrate and early fish evolution.

Zhu, M. et al. 2006. A primitive fish provides key characters bearing on deep osteichthyan phylogeny. Nature 441: 77-80. <link>

See also:

Basden, A.M. et al. 2000. The most primitive osteichthyan braincase? Nature 403: 185-188. <link>

Zhu, M. et al. 1999. A primitive fossil fish sheds light on the origin of bony fishes. Nature 397: 607–610. <link>

Zhu, M. et al. 2001. A primitive sarcopterygian fish with an eyestalk. Nature 410: 81–84. <link>
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Thursday, April 20, 2006

The serpent beguiles?

More blasted intermediates to deny today. This hasn't been a good month to be a creationist. Najash rionegrina from the Late Cretaceous of Patagonia is no ordinary snake: it has legs.

This is not the first fossil snake with legs to be found. Previously, there had been Pachyrhachis, Haasiophis and Eupodophis. What's especially interesting about Najash is the presence of a sacrum: usually a modified rib that forms a strut between the vertebral column and the pelvis and helps support the body on land. This is a feature that is found even in the earliest tetrapods and tends only to be lost when limbs are lost or when tetrapods become more fully acquatic.

The authors analyzed the characters of various snakes (fossil and living) and generated the following tree:

The interesting thing to note is that Najash is the most primitive snake. However, the other three legged snakes find themselves deep inside snakes. In fact, they're what are known as the Macrostomata, the group that includes the things you most commonly refer to as modern snakes: boas, pythons, as well as the more derived vipers and the elapids (cobras and their kin).

Now, the last thing I want to get myself into is the sordid debate on snake origins. This new hypothesis will not go without contention since it requires several independent losses of limbs or even the independent re-development of limbs in order to account for the distribution. The debate on snake origins is a hot topic and the key players show no mercy with each other! So, I'll try to ride the fence here.

This phylogeny lies at the heart of the debate on snake origins. One issue here centers on whether or not the mosasauroids (large, extinct marine lizards) are the sister group of snakes and whether or not snakes have a marine origin. The mosasauroids (which includes the mosasaurs proper, as well as the smaller aigialosaurs) are not likely to include the ancestor of snakes, but they share a lot of features in common, such as body elongation and the way the teeth fit into sockets in the jaws -- a condition called "thecodonty" (tooth in hole). In other varanoid lizards (like the Komodo Dragon), the base of the tooth is sort of "squished" to the inside of the jaw, a condition called "pleurodonty" (see a diagram of these tooth types here).

Interestingly, however, a lower jaw referred to Najash apprears to present a pleurodont type condition, or something very similar. This means that the pleurodont condition might actually be ancestral for snakes, and therefore the condition seen in mosasauroids might have nothing to do with the condition seen in snakes.

A matter of outgroup:

The dichotomy that arises between a mosasauroid vs. 'other' sister-group hypothesis is also one between a terrestrial origin for snakes and a marine or aquatic origin. Najash is apparently a terrestrial snake and, in its position as the most 'primitive' snake of all would suggest that terrestriality is ancestral for snakes. But all of this is dependent on how we interpret their tree. This, of course, is further dependent on how the authors treat the data.

One of the potential problems with this new work is that it doesn't actually test the question of who is most closely related to the snakes. If you look at the tree they've obtained, one can see the most deeply stemming branch is labeled "Varanoid root". This is the outgroup, the taxon in the analysis against which allows the analysis to infer the "direction" of evolution inside the tree. The authors constructed a hypothetical varanoid from observations of different varanoids, including mosasauroids. However, since it's only a single terminal taxon, it is impossible for snakes as a total group to "move around" in the analysis. They're stuck there next to a hypothetical taxon. So, the question of mosasauroid relationships is unaddressed. Furthermore, the different outgroup will have different characters, resulting in

The other (and somewhat related) argument that may fall under contention is the inference of the ancestral condition for snakes as a whole based on the environment of Najash. This may be somewhat problematic, especially where they have the other snakes with legs higher up in the tree. If, instead, the other snakes with legs are more primitive (as one would initially think), and one were to test whether or not there is a marine outgroup, then terrestriality might be a specilaization of Najash rather than an ancestral feature. The placement of the legged snakes within the macrostomatans has been contested int he past and will continue to be, so watch for that!

The take-home message here is actually me 'busting down' the sacrosanctitiy of the concept of 'transitional forms'. Najash is almost certainly intermediate and, at this time, I hardly doubt that it is the most primitive snake. As such, it tells us about the early origins of snakes. But it is not an ancestor, and even as an approximation of an ancestor, it is still specialized in its own way. The same could be said for Tiktaalik which has its own specializations that are not necessarily intermediate between other fishes and tetrapods.

The other thing to bear in mind is that perhaps our problem with the re-elaboration of limbs is fraught with 'common sense' thinking -- often a danger in science. It is difficult to imagine how snakes could simple re-evolve their legs, but it would be unwise to use such an argument. The development of an embryo is a hierarchical process and all or most of the genes used in 'leg-making' in snakes probably never disappear (though perhaps somebody more up to speed on this could comment here). A few or a single 'up-stream' switch in the hierarchy of development could perhaps turn the whole leg on or off. Our personal preference or bias that snakes should not 'grow back' their legs must not be an argument. More robust phylogenetic arguments as well as developmental biology should be looked to for clues.

The goal of the study of phylogeny is to sort out between three different kinds of characters: those that are ancestral and therefore ancient and general (plesiomorphy), those that are specialized and unique to a taxon (autapomorphy), and those that are the characteristics unique to a group that shares a unique common ancestor (synapomorphy). When we have sorted out the best and most heavily tested solution to this trichotomy, we can then infer what is the ancestral state. The data on the fish-tetrapod transition are so unequivocal that it is pretty easy to sort this out for Tiktaalik. The same can't yet be said for the origin of snakes, and Najash is by no means the last word. We'll be hearing a lot more about this soon.

Other blogs:

Apesteguía, S. and Zaher, H. 2006. A Cretaceous terrestrial snake with robust hindlimbs and a sacrum. Nature 440: 1037-1040. <link>
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Sunday, April 09, 2006

The squirming continues...

Creationists haven't said a lot about Tiktaalik, and it's no surprise. However, a few responses have trickled out and they more or less run in the same vein.

I thought this was a rather telling remark on Tiktaalik posted over on Dembski's blog. We're treated to an excerpt of the pre-transformation version of the DI's original response that goes:
I especially like Crowther’s last sentence which I present in its original form (bold type included): “There’s a problem with the Darwinist position that runs even deeper than this, however: If Darwinian evolution is an undisputed fact, as its chief defenders routinely claim, why is this fossil find being billed as such an crucial piece of evidence?”
Icing on the cake! I love it!!!
What I love even more is all this rhetoric and absolutely no reference to the actual fossil material. So, I'll take that as meaning that these guys have nothing to say about its transitional status. The real icing on the cake is all this puff and no real substance.

Unfortunately, the media's response to the discovery is not quite the same as the palaeontological community's interpretation of it. Therefore, by responding to these articles, creationists and their ilk are just blowing smoke. The importance of Tiktaalik has nothing to do with proving the fish-tetrapod transition. That's pretty much taken care of by a wealth of data from the past 100 years.

I would support this with a longer statement or references, but creationists are kindly providing the background for this fact by talking about Acanthostega and Ichthyostega as though we used to believe that were transitional forms and now somehow don't. All these clowns are doing is neatly summarizing growing list of "transitional forms" and making themselves look like asses in the process. These taxa are all still very much there, playing a critical role at the forefront of these reports on Tiktaalik:

From Daeschler et al. 2006
Most of the features used to support this grouping, however, are also seen in early tetrapods such as Acanthostega, Ichthyostega and Ventastega.


Tiktaalik retains primitive tetrapodomorph features such as dorsal scale cover, paired fins with lepidotrichia, a generalized lower jaw, and separated entopterygoids in the palate, but also possesses a number of derived features of the skull, pectoral girdle and fin, and ribs that are shared with stem tetrapods such as Acanthostega and Ichthyostega.

From Shubin et al. 2006
The glenoid [shoulder joint] is oriented posteroventrolaterally and partially exposed in lateral view, which is intermediate between the posterior orientation of the glenoid in Eusthenopteron and the lateral orientation of Acanthostega and other basal tetrapods


In both Acanthostega and Tiktaalik the appendage projects ventrolaterally from the body wall.


The endochondral bones [internal bones] of the pectoral fin of Tiktaalik combine features of Eusthenopteron and Acanthostega, and in some aspects are intermediate.

Need I continue?

If these folks had actually read the papers, they would've seen how comparisons with these early tetrapods figure so prominently in how we actually recognize what Tiktaalik is.
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Saturday, April 08, 2006

The DI's orwellian take on Tiktaalik

Young-Earth Creationists (YECs) have certainly been at this longer than the clowns over at the Discovery Institute. The DI has a remarkable statement on Tiktaalik that doesn't even require a rebuttal. They've just managed to do it themselves.
These fish are not neccesarily intermediates, explain Discovery Institute scientists I queried about the find. Tiktaalik roseae is one of a set of lobe-finned fishes that include very curious mosaics--these fishes have advanced fully formed characteristics of several different groups. They are not intermediates in the sense that have half-fish/half-tetrapod characteristics. Rather, they have a combination of tetrapod-like features and fish-like features. Paleontologists refer to such organisms as mosaics rather than intermediates.
I wonder if they could explain how an animal with tetrapod-like features and fish-like features is not an intermediate. This is followed by
What is clear is that forms like Tiktaalik are a melange of primitive and more developed features.
My word, this circus act just keeps getting better!
According to DI Fellows a number of these fishes—Ichthyostega, Elpistostege, Panderichthys—have been hailed in the past as the “missing link.” Maybe one is a missing link; maybe none are.
Once again, these guys have rather nicely pointed out their own ignorance and a few extra transitional forms, to boot! Nobody hails anything as "the missing link". "Missing link" is a term that scientists don't use and we even try to ask that the media does not use the term, but they do anyway. We can't stop them.

It was nice to see that they tossed in a mention of Elpistostege. As you can see, Elpistostege is a lot like Tiktaalik, which is why Tiktaalik is dubbed an "elpistostegalian". Elpistostege is known only very incomplete remains, the limbs have been entirely unknown. However, it's tetrapod affinities have been recognized since its discovery in 1938, when T.S. Westoll actually called it the earliest known tetrapod! In 1985, Hans-Peter Schultze and Marius Arsenault recognized it for what it was, a very tetrapod-like fish, similar to Panderichthys. In 1996, Schultze described a short pice of the trunk that has rhomboid-shaped schales and a few vertebrae. What little is known of its skull and trunk of Elpistostege is scarcely different from Tiktaalik. However, after decades of searching no new data on Elpistostege ever came to light. Shubin and Daeschler wanted more of this animal, but knew that the original locality wasn't going to give up its secrets. So, they went looking in similar-aged rocks elsewhere in the world. Their discovery of Tiktaalik essentially confirms the prediction of what we have long thought Elpistostege to be (and shows that Westoll was not too far off!)

Again, like AiG's response, the DI is simply responding to the media and not the original material itself.
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Friday, April 07, 2006

AiG tries to respond to Tiktaalik

So, Answers in Genesis (AiG), one of America's leading creationism ministries, has now issued a (preliminary) response to Tiktaalik.

It's sort of amusing and sad, all at the same time. This is no surprise, as the response is co-authored by Dr. David Menton, a captial clown. He and co-author Mark Looy have produced a terrible mess: all their basic facts are wrong, dead-wrong. There is the clear impression that they have not even looked at the original reports (a point further evidenced by the fact that they cite only one of the two back-to-back articles published in the same issue).

Most of the article discusses the report in the NY Times rather than the original reports in Nature. This has the clear implication that the authors are more interested in the public's perception of the matter and have no scientific interest in the actual fossil material itself. As if that needed to be said. It is another manifistation of that odd species of thought that is creationist solipsism.

Their opening shot is the fact that the discoverers, when interviewed, used tentative wording to describe their interpretations. This is a rather alien concept for creationists: the idea of proceeding cautiously towards conclusions, rather than brazenly starting with immutable revealed Truth.

Here's the pinnacle of dishonesty, though. Menton and Looy write: "[the use of tentative language implies that] the find is not as firm as evolutionists would lead you to believe". You only wish. I'm not sure how the use of tentative language could result in Daeschler and Shubin overblowing the implications of their discoveries. Creationists are no strangers to contradiction.

But as I said, they've got their facts dead-wrong, to the point of outright dishonesty. So, let me back that up. Here's the breakdown (break-down?) of some of their thoughts. I've taken some bits out of order.

There is the coelacanth fish, found in the same geological system (Devonian it is called) as this Tiktaalik discovery, that also has lobed fins. These lobed fins were once thought to enable the coelacanth to walk on the ocean floor
Thanks for that careful bit of analysis there, guys. You should get a prize for that. Sorry that we didn't circulate a memo beforehand to point out that tetrapods are widely regarded to have desceded from lobe-finned fishes for maybe the past 50 years. Somehow, I think it might be odd if a bona fide fish-tetrapod intermediate were not allied with the lobe-finned fishes. If it had been anything else, it would have been a problem! But I'm glad these gentlement have conceded the point on behalf of AiG.

However, this business with the coelacanth is a pretty nasty equivocation: 'coelacanths are lobe-fins, Tiktaalik is a lobe-fin'. Hmm... I'm not sure if that really captures all the details, so perhaps a little comparison might help us evaluate this claim:

The authors' cluelessness takes them to previously unexplored depths of hoplessly impotent arguments. But these intrepid crusaders in the name of ignorance soldier on!
(in fact it was, like “Tiklaalik,” once considered by evolutionists to be a type of transitional form). Later, it was determined that the coelacanth fins were used for better maneuvering through the water, and not for walking.
These guys have their own wild and weird theory of evolution that has no basis in reality. Coelacanths are still considered a plesion (branch) on the tetrapod tree. Coelacanths, as demonstrated by a large amount of molecular and morphological data, are closely related to tetrapods. What happened was, J.L.B. Smith who was an ichthyologist and not a palaeontologist or evolutionary biologist, took the accepted relationships of coelacanths and tetrapods to infer that coelacanths might walk around on the bottom. He was shown to be wrong. Science moved on. This is quite different from how the authors of the Tiktaalik papers reached their conclusions.

Please consider for a moment the fin of an extant (i.e. living) coelacanth, on the left; and the fin skeleton of Tiktaalik on the right.
The fin skeleton of Tiktaalik is much more robust and has a number of prominent ridges and scars for muscle insertions. The joints have surfaces that permit a range of motion in the fin elements suggesting flexibility and even elbow joint movement. The shoulder bones (not shown -- I'll try to get an image up soon) are like a tetrapod's: it has a robust, plate like region where the limb attaches. It has grooves and passages for more muscle attachments and suggests that there was a very sturdy shoulder region. All of these are features that set Tiktaalik apart from a coelacanth or any other lobe-finned fish and ally it closely with tetrapods. Moreover, the distinct structure of the two types of fin implies radically different functions, nonetheless. Whatever functional argument you want to make for that is immaterial, the fact remains that the equivocation of Tiktaalik's fin skeleton with that of a modern coelacanths is pretty absurd. But you guys looked pretty funny doing it! Nice try!

This hopelessly optimistic appraisal kind of made me feel sad on the inside:
The new creature uncovered in the Arctic might be something similar.
If only they knew how wrong they were, 'maybe, just maybe the editors of Nature were having a slow newsday and decided to publish two back-to-back articles on another generic lobe-finned fish!'. I hate to break your heart, Tiny Tim, but it ain't similar to a coelacanth -- that's why it's newsworthy!

After completely embarassing themselves in the domain of diversity, they move on to anatomy, the area where Menton is supposed to be an expert. In the process, they manage to discover the nexus of pathetic and hilarious:
[T]he bones for Panderichthys, Tiktaalik and the coelacanth are imbedded in the muscle, and are not attached to the axial skeleton, which you would find in a reptile or amphibian (and which would be necessary for weight-bearing appendages). [emphasis added - MB]
Presumably this is about how the shoulder girdle lacks a direct structural connection to the vertebral column. In fishes, the front fins attach to the shoulder girdle which is embedded in the tissues and muscles of the body. Well, guess what? It's exactly the same way in almost all primitive tetrapods, including Ichthyostega and Acanthostega, the taxa widely held to be the next plesions up from Tiktaalik. In fact, this is general for most tetrapods, where a bony structural link to the ribs or vertebral column is the exception, not the rule. Do we laugh or cry here? I'm not sure.

On the other hand, if they're talking about the pelvic limbs, then Menton and Looy are just blowing smoke, because there is no report on the pelvic girdle here.

Also, there are other creatures (e.g., the Panderichthys) that are thought to be fish and yet appear to be similar in lobe and fin structure to Tiktaalik.
Panderichthys is widely regarded as a close relative of tetrapods and it is only one node below Tiktaalik in the evolutionary tree presented by the authors of the Tiktaalik papers. It would, in fact, be somewhat of a problem if these two animals were not similar. Thanks for pointing this out, guys! It's amazing that these are the same people who say there aren't any transitional forms, but they've nicely admitted that both Panderichthys and Tiktaalik are transitional.

As we often state on this website, keep in mind that evolutionists and creationists have the same facts (e.g., fossils), but interpret the facts uncovered today differently in regard to the past.
Well, apparently you don't have all the same facts. According to your "facts", the shoulder girdles of tetrapods generally have a bony connection to the vertebral column. Apparently your "facts" did not include the facts of tetrapod anatomy and diversity at all. Your "facts" are convenient selections of observations, untruths, and equivocation of terms like "lobe-fin". These are not facts at all, but the framework of a deceptive fantasy that helps insulate you from reality.
Because evolutionists want to discover transitional forms, when they find a very old fish with leg-bone-like bones in its fins, they want to interpret this as evidence that it is some sort of transitional creature. However, other fish seem to have the same sort of structure as stated above, and these bones are not constructed as one would expect for weight-bearing legs.
So, there we have it again, further evidence that the authors have not read the paper. What appears to be more important than reality to these men is the term "lobe-fin", a term of convenience used to describe a general condition for a certain type of fish: the sarcopterygians. However, fin morphology is radically diverse in this group, and there are many ways of being a "lobe-finned fish". To deny the tetrapod-like nature of the fins of Tiktaalik on the basis of the fact that it happens to be a lobe-finned fish as well as is a coelacanth is a shameful advertisement of one's ignorance.

This is my favourite:
For the moment, we can confidently state that evolutionists have no examples of mutations or evolutionary processes that can lead to an increase in genetic information in a creature that would, for example, develop the appendage of a land animal from the fin of a fish
Here are two men, claiming that they will be able to provide a scientific opinion on this discovery, and they haven't the foggiest clue about anything they're talking about. One of the most remarkable things about limb and fin development is the extraordinary conservation of molecular genetic mechanisms. For the most part, fins and limbs employ exactly the same set of genes to make their structure. The main difference is the timing, level, and position of the deployment of these genes. Until AiG specifies exactly what they mean by "new information" whenever they say this, it'll be uncertain as to what "new genetic information" is that they're talking about. Presumably, they've somehow measured "information" in fishes and tetrapods and found that tetrapods had "novel information"? I thought not.

The interesting thing about all this is that the Menton and Looy are simply pointing out that Tiktaalik has attributes of a fish, but doing nothing to dispute the observed similarities with tetrapods. Has it ever dawned on them that an animal somewhere between fishes and tetrapods might actually have some attributes of a fish? What makes me wonder is why AiG didn't post a picture of the specimen. There are, by now, tons of pictures on media websites all over the place. A Google image search for "tiktaalik" turns out four pages of results. Here's why: they're scared, deathly scared. The implications of Tiktaalik are so bloody obvious that they have a lot of work to do in order to deal with this one.
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Thursday, April 06, 2006

More paddlin'

A creationist has decided to start commenting on Tiktaalik over at the Panda's Thumb as though he actually knew something about it. I decided to wade in
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Let the ass-paddling begin!

I was searching around looking to see if any of the creationists have started to comment on Tiktaalik. I haven't seen anything yet, and I'm really wondering how they're going to spin it. It should be rather hilarious.

However, I did find ´this. It's a Q&A from John Morris at the Institute for Creation "Research", answering the question "what's a missing link?"

With almost prophetic timeliness, Morris gives the following example:
If some type of fish evolved into some type of amphibian, there should have been distinct steps along the way of 90% fish/10% amphibian; then 80% fish/20% amphibian; etc., leading to the 100% amphibians we have today.


does this count:

a, Left lateral view; b, dorsal view with enlargement of scales; and c, ventral view with enlargement of anterior ribs. See Fig. 3 for labelled drawing of skull in dorsal view. Abbreviations: an, anocleithrum; bb, basibranchial; co, coracoid; clav, clavicle; clth, cleithrum; cbr, ceratobranchial; ent, entopterygoid; hu, humerus; lep, lepidotrichia; mand, mandible; nar, naris; or, orbit; psp, parasphenoid; ra, radius; suc, supracleithrum; ul, ulna; uln, ulnare. Scale bar equals 5 cm. From Daeschler et al. 2006


Hee hee, just wanted to do that one more time.

Apart from that, however, Morris is still making a ridiculous caricature of evolution that's couched in his own typological thinking. In other words, as opposed to recognizing that there are probably about 35,000 species of things we call "fish", all of them quite different from one another in many ways, he thinks there's a "fish kind" and an "amphibian kind" and one should morph into the other, with something that's an "average of all fish" and an "average of amphibians". The reality is that some lineages of fish, very distinct in their own right, ought to acquire progressively more tetrapod-like features, as we see presented in an animal like Tiktaalik.

So, I'll wrap it up with this little prediction from Dr. John
Creation says they never existed, and agree that we have no record of them.

Well, does that settle it then?

Somehow, I think I can hear the sounds of distant goalposts scraping...
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Wednesday, April 05, 2006

Tiktaalik rosae

Well, here it is in all it's beautiful glory, another piece in the tetrapod origins story has just arrived in two articles in Nature today. I'll give you the chance to oggle at some of the beautifal specimens before I get into the details of what, apart from the obvious makes this thing so interesting.

a, Left lateral view; b, dorsal view with enlargement of scales; and c, ventral view with enlargement of anterior ribs. See Fig. 3 for labelled drawing of skull in dorsal view. Abbreviations: an, anocleithrum; bb, basibranchial; co, coracoid; clav, clavicle; clth, cleithrum; cbr, ceratobranchial; ent, entopterygoid; hu, humerus; lep, lepidotrichia; mand, mandible; nar, naris; or, orbit; psp, parasphenoid; ra, radius; suc, supracleithrum; ul, ulna; uln, ulnare. Scale bar equals 5 cm. From Daeschler et al. 2006

This is Tiktaalik roseae, a lobe-finned fish from the Late Devonian Fram Formation of Arctic Canada. The key features that make this animal a lobe-finned fish are the limbs which clearly have a humerus that branches out to a radius and ulna, like our own limbs. But Tiktaalik is clearly different. It has foregone a lot of the other lobe-finned fish conditions for characteristics that are much more like a tetrapod. In fact, Tiktaalik is without question the most tetrapod-like sarcopterygian known to date, and it fills an important gap in the fossil record. Clearly, it's can no longer be safely jammed into that "fish" category.

Here's the fin skeleton and a picture of one of the specimens to go with. The important thing to note is that the dashed lines are not inferred elements. There are several specimens of the fin and shoulder skeleton (I've seen them personally), and the dahsed lines represent gaps that are filled by an overlapping specimen. The authors were able to study the specimens in articulation as well as prepare them 'in the round'

a, Dorsal view; b, ventral view. Elements with stipple shading were preserved in articulation in NUFV 109 and prepared in the round. Elements with a dashed outline are reconstructed based on their presence in the articulated distal fin of NUFV 110. It is not known how many radials lie distal to the first, second and fourth in the proximal series. Note the dorsal expansion of the distal articular facets on the ulnare and third distal radial/mesomere. The dorsal expansion of these facets would have facilitated extension of the distal fin.

a, Stereo pair of left pectoral fin of NUFV 108 in dorsal view showing disparity in size and position of anterior (alp) and posterior (plp) unjointed lepidotrichia and the relative position of dermal girdle elements. b, Right pectoral fin of NUFV 110 in anterior view showing preservation of anterior lepidotrichia (alp), clavicle (cl), scales (sc) and endochondral bones in articulation (H, humerus; U, ulna; u, ulnare; r, radials). The anterior lepidotrichia terminate at the elbow, thus allowing a full range of flexion at that joint. c, Right pectoral fin of NUFV 110 in ventral view showing positions of coracoid (co) and endochondral and dermal fin elements. an, anocleithrum; cb, ceratobranchial; clth, cleithrum; int, intermedium; ri, rib; suc, supracleithrum. Both images from Shubin et al. 2006.

Now, recall the story I posted a few days ago. Well, this new material is the result of that expedition that went up to the arctic looking for this type of stuff. Earlier, I posted this image which was from a book published in 1997, documenting the gap in the fossil record between fishes and tetrapods.

The authors put the fish into the context of the following phylogeny, or 'evolutionary tree', using a computer-based analysis.

Tiktaalik is the sister group of Acanthostega + Ichthyostega in one of the two most parsimonious trees, and clades with Elpistostege as sister to the tetrapods in the other. Tree length = 149, consistency index = 0.8389, consistency index excluding uninformative characters = 0.7966, retention index = 0.8140, and rescaled consistency index = 0.6828. The characters list and data matrix are available as Supplementary Information. From Daeschler et al. 2006

As you can see, Tiktaalik fits squarely in the gap between Panderichthys and other tetrapods -- a precise confirmation of the predictions made by the existing theory and geological knowledge.

The important point here is to ask why this animal fits there. Isn't this somewhat arbitrary? Well, no. We already know a lot about what sets tetrapods and fishes apart. Moreover, we've got some really important details from Tiktaalik that allows the authors to place it in the tree where it is.

The skull is remarkably tetrapod like. Compare here and here. The resemblances are striking. Most notably, is the lengthened snout of Tiktaalik, where even in very tetrapod-like fishes such as Panderichthys, the snout is relatively short and the skull roof behind the eyes is longer. The conditions are opposite in Tiktaalik and early tetrapods.

Tetrapods all lack a bony gill cover, while primitive ones (and modern amphibians) retain gills but no bony gill cover. The result is a moveable neck. Unlike even the most tetrapod-like fishes known previously, Tiktaalik has a neck and no bony gill cover. The propotions and shape of the head are a lot more like Acanthostega or other early tetrapod than like any known fish, even (in my opinion), Panderichthys.

Another interesting aspect of both Tiktaalik and Panderichthys is their shoulder girdle. What's great about Tiktaalik however, is that we have more, better, and more accessible specimens. The shoulders bone where the limbs attach, is rather puny in most fishes. On the other hand, tetrapods have a rather beefy affair that really helps support the weight of the animal. Tiktaalik shows something much more like the tetrapod condition, with a very beefy shoulder bone.

The fin, as illustrated above, is quite interesting. Not only is it fragmented into a bunch of little bones called radials (which are strikingly similar to digits), but there are apparently moveable joints between the units of the fins. When looked at closely, there are evident "roller surfaces" on the bones that permit the neighboring elements to flex, sort of like a primitive wrist.

The ear region shows a marked advance on the condition myself and Per Ahlberg described for a similar fish, Panderichthys. Unlike this latter form, however, Tiktaalik has a much broader spiracle and an even shorter hyomandibular bone -- the "gill arch" bone that eventually becomes the "stirrup" bone of the middle ear. In the earliest tetrapods, this bone looks neither like a fish nor like that of modern tetrapods. It's a short nubbin of bone that pokes out from the side of the braincase. The hyomandibula of Tiktaalik, if we can call it that, was a stubby little nubbin, too. However, it was still oriented in the spiracle like a hyomandibular bone.

More news will certainly come about this interesting animal. The publications in Nature are generally only preliminary reports and a much more complete description awaits. It is usually during this process that the really interesting comparisons come out and we find out how similar/different Tiktaalik is when compared with tetrapods and other lobe-finned fishes.

Tiktaalik presents a sort of classic 'transitional form', y'know the kind that creationists say doesn't exist. I can't wait to see how they're going to spin this. I wonder if it will be "just a fish" or if it will attack the integrity of the authors. We'll see. In the meantime, science marches on.

EDIT: Pharyngula has it too, with more pics.

Ahlberg, P.E. and Clack, J.A. 2006. Palaeontology: A firm step from water to land. Nature 440: 747-749.<link>

Daeschler, E.B. et al. 2006. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440: 757-763. <link>

Shubin, N.H. et al. 2006. The pectoral fin of Tiktaalik rosae and the origin of the tetrapod limb. Nature 440:764-771. <link>
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Professor denied federal research funds for assuming evolution to be scientific fact!

What happened to Canada since I left? Ignorant troglodytes have penetrated the federal funding level, denying a grant to a social science professor for the alleged assuption that the theory of evolution was correct!

A good friend of mine from back home in Ottawa sends me the story.

I'm about to go ballistic!

The Social Sciences and Humanities Research Council (SSHRC) denied funding McGill professor Brian Alters on the following grounds:

"The committee found that the candidates were qualified. However, it judged the proposal did not adequately substantiate the premise that the popularizing of Intelligent Design Theory had detrimental effects on Canadian students, teachers, parents and policymakers. Nor did the committee consider that there was adequate justification for the assumption in the proposal that the theory of Evolution, and not Intelligent Design theory, was correct. It was not convinced, therefore, that research based on these assumptions would yield objective results. In addition, the committee found that the research plans were insufficiently elaborated to allow for an informed evaluation of their merit. In view of its reservations the committee recommended that no award be made." [my emphasis]

It appears there are other grounds for the decision, but the very fact that the emphasized claim was made makes the whole thing stink of "creationist agenda". Never does a researcher have to justify an "assumption" that is, in fact, a recapitulation of the prevailing scientific opinion. Let's even give them the benefit of the doubt: I'll go so far as to pretend that evolution is wrong. It is still the established scientific principle and Prof. Alters doesn't have to justify it any more than we have to cite "Darwin (1859)" every time we want to talk about evolution!

The article quotes Janet Halliwell (a chemist, and SSHRC's executive vice-president) who justified the decision:
Ms. Halliwell added there are phenomena that "may not be easily explained by current theories of evolution," and the scientific world's understanding of life "is not static. There's an evolution in the theory of evolution."
Sounds like we have our classic "closet creationist" who uses the fact that science progresses as evidence that current science may be bogus. How did this person ever get a chemistry degree? Should we pan applications that make presumptive appeals to atomic theory simply because we 'don't know everything about the structure of an atom' and that 'there's an evolution in the theory of the atom'? Of course not, because we don't think atoms conflict with our previously conceived viewpoint.

This is a disgrace to academia in Canada. It's ironic that we pronounce the acronym "SSHRC" as "shirk", isn't it?
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Tuesday, April 04, 2006

Take a hike, wiseguy

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How to pickle an embryo for more than half a billion years

Check out this great post on some experimental studies show the conditions favourable to preserving embryos in the fossil record.
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Thursday, March 30, 2006

A blurb about prediction in historical science

Let's call this 'Part I' of a series I'll finish on Thursday.

The origin of tetrapods is one of the most important and remarkable events in the history of animal life. It is, after all, part of the story of our own origins. According to the fossil record, this event appears to have taken place in the Late Devonian period, between 375 and 365 million years ago. This event gave rise to the lineages that ultimately became humans, dinosaurs, birds, whales, and any other vertebrate that makes a living on land (or had an ancestor that did).

That is to say, the earliest tetrapods we have are known (from complete remains, anyway) from the very latest Devonain, a stage called the Famennian (see the diagram below). We already know that some very fish-like tetrapods called 'elpistostegalians' have been discovered in the earliest part of the Late Devonian, an interval called the Frasnian. Somewhere in the intervening Frasnian and Famennian rocks should be more tetrapods or elpistostegalians.

The diagram below shows some of the most completely known forms surrounding the origin of tetrapods and their distribution in time. The large pink band shows the approximately 10-million-year interval where very few fossils are known. Admittedly, the gap is somewhat exaggerated, there are some fragmentary animals known from this interval.

Modified from Carroll, 1997 Patterns and Processes of Vertebrate Evolution

One can see quite easily that finding more intermediates will involve finding more fossils in Late Devonian rocks. For instance, in the early part of the Frasnian, the elpistostegalian Panderichthys is present and is already very tetrapod-like, but still recognizably a 'fish'. Presumably, more tetrapod-like fishes will be found in rocks of similar date. A prediction is furnished.

To try to bear out this prediction, two intrepid palaeontologists set their sights on some new rock outcrops. Instead of going back to localities that have already been known and worked for decades, Ted Daeschler and Neil Shubin set their sites on a massive band of Devonian rocks in the Canadian Arctic.

An article dating back to 1999 quotes Shubin:
"A place like this that’s so vast and so clearly in the right time period is a great opportunity for us."
Daeschler adds:
"the earliest of the limbed animals. Or at the other end, fish that are just beginning to develop limblike structures."
As you can see, before Shubin and Daeschler ever set foot in the arctic, they already knew where they were going to look. All the following parameters need to be correct and established independently in order to make the prediction: the age of the rocks, the type of sediment, and the estimation of when the even took place. Then you should be able predict where you will find the fossils you want. In this case, the scientists knew from previous work (done by geologists, independently of they) that there was a huge section of the righ age and type of rocks in the Canadian Arctic.

I'm telling this story for a number of reasons. One, is that it's because I found this article some time ago, but that the results of six years of work in the arctic have not yet come to light. The artcile was written seven years ago when this expedition was being planned and the first year of several years work by Shubin and Daeschler. It's now quite dated and written quite some time before the authors ever went up. It provides perfect evidence for a 'case study' of how palaeontologists work. I'm often asked how palaeontologists know where to dig to find fossils, and this article helps give some insight as to how palaeontologists plan their expeditions.

The key is that the object of the Daeschler and Shubin mission is very rare. To pinpoint where one might find such rare fossils, a lot of things have to go right: the age of the rock formation needs to be known (and correct). The type of environment it was deposited in needs to be correct. Marine-type sediments very rarely have tetrapods or their nearest relatives. Thirdly, your prediction based on the evolutionary sequence seen in the rest of the fossil record has to be accurate. In essence, multiple independent lines of historical evidence are being put to the test. Each one converges to pinpoint where the right fossils of the right type and age will be found.

I'll leave the reader with those thoughts to contemplate and investigate. I'll finish this up later this week.
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Tuesday, March 28, 2006

Centipede eats mouse

In the tradition of the Octopus eats shark video that was so wildly popular, I give you Centipede eats mouse. Believe me, this video is not pleasant if you are faint of heart -- the audio captures exactly how unpleasant the mouse is finding this...

Edit: By the way, the centipede is Scolopendra

(Via Pharyngula)
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Wednesday, March 22, 2006

My last exam...

I've just finished what is my last (written) exam ever. If all goes well, I should never have to write another. There is, however, that little thing called my defense, however.
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Sunday, March 19, 2006

Randi speaks!

James "The Amazing" Randi, stage magician and investigator (=debunker) of claims of the paranormal, has recently undergone a major bypass operation. He has been recovering for the past few weeks, and friends have been filling in his weekly commentaries. According to the JREF website (Randi's outreach organization), he has been making considerable progress.

Randi has left an audio message for all his readers. He sounds a little weak, but it's good to hear that he will be back to kick some 'paranormal' butt soon!

I wish him well, soon!
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Thursday, March 16, 2006

Good Math, Bad Math

There's a new blog about math, this one that tackles the particularly bad math of creationists. It should be informative, and the author writes in a very clear style (no equations, if you're not into that). Check out Good Math, Bad Math.

(Via Pharyngula)
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Juravenator and the complex pattern of feather evolution

I normally like to post news here, but since this is a science and natural history blog (plus, apparently, random ramblings about other things) I'll post something that isn't very novel: a new theropod dinosaur published in Nature this week. The big news about Juravenator starki is what it doesn't have: for once, Nature is running an article about a dinosaur that doesn't have feathers.

Type specimen of Juravenator starki from the Late Jurassic of Germany. From Göhlich and Chiappe 2006

Ultraviolet and normal light photographs of the tail, showing patch of scales. From Göhlich and Chiappe 2006

The reason this is of interest to some palaeontologist is the fact that the authors' analysis suggested that it "should" have had feathers. That is, it was a type of theropod dinosaur that nested in the tree where feathers are predicted for the common ancestor.

Phylogeny showing the relationships of Juravenator with other theropod dinosaurs. From Göhlich and Chiappe 2006

Birds have scales and feathers needn't always cover the remainder of the body. The preservation of feathers in Juravenator's nearest relative known to have feathers, Sinosauropteryx is apparently limited to a mindline "mane" of filaments, an may not necessarily have covered the bodies. Whether or not this was the true condition in life could, potentially, be disputed. However, it follows from the enormous diversity of theropod dinosaurs that their feather distributions (both within and among taxa) were considerably more varied than previously though.

Tyrannosaurs are known to have patches of scaly skin, but recent discoveries show that their ancestors probably had feather-like structures. Thus, at some point, feathers must have been either incompletely covering the animal or lost and gained over varying degrees. Moreover, it appears that estimates of feather covering in dromaeosaurs were dramatically underestimated It would appear that our interpretation of feather evolution paints, perhaps too conservatively rather broad coating of feathers on just about anything descended from the common ancestor of all coelurosaurian dinosaurs.

Xing Xu, who has described many of the Chinese feathered dinosaurs, wrote a News and Views piece which raised some interesting cautions about these results: For one, we don't know that Juravenator did not have feathers. All we know is that parts of its body had scales. Fossilization is biased against feather preservation and those few records we have are remarkably rare. The specimen is apparently a juvenile and may, in fact, create a false signal pulling the animal to a particular part of the tree. Normally, this would be the other way around: juvenile characters tend to make you look more 'primitive'. However, Juravenator clumps with a group of small theropod dinosaurs which may share character similarities simply related to the fact that they're small, and not any real common ancestry. It's possible that this animal is more primitive, but unites with these other animals due to bias.

Göhlich, U.B. & Chiappe, L.M. 2006. A new carnivorous dinosaur from the Late Jurassic Solnhofen archipelago. Nature 440: 329–332.

Xu, X. 2006. Palaeontology: Scales, feathers and dinosaurs Nature 440: 287-288.
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Will they be controlled by a collective overmind?

I'm still not sure if this is some kind of joke. I don't suppose that trying to engineer a battalion of cyber-insects is entirely out of the question.

The article has some anecdotes of past attempts at animal-based warfare:
WWII: Attach a bomb to a cat and drop it from a dive-bomber on to Nazi ships. The cat, hating water, will "wrangle" itself on to enemy ship's deck. In tests cats became unconscious in mid-air
It looks like the U.S. military's Tierekrieg strategies have a poor track record.

EDIT: Predictably, there's some great commentary over at Pharyngula.
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Tuesday, March 14, 2006

I bet they won't be calling Randi

The Catholic Church, that harbinger of critical thought and objective reasoning, is said to be "investigating an alleged miracle that, if proven true, could be crucial in naming John Paul II a saint." Oh, how our mortal intellects can only guess at what truth will be discovered.

According to the article:
John Paul... has been credited with curing a French nun of Parkinson's disease.
Conveniently, however
The woman's name, age and place of residence have not been disclosed.
No surprises. If you read the article you'll see that we're fed the same old B.S. that we see from the Peter Popoff's and Oral Roberts's. We've got the anecdotal evidence from 'honest people', the claim that 'science can't explain it', and the media failing to pass any critical judgement. The big difference is that it's the Catholic Church, so it's dressed up in white robes, rubies, and over a thousand years of gullible credulity so that a billion people are going to believe it simply because they will have been told to.

Rest assured, the hard-nosed team conducting the investigation has no interest in pursuading you of "miracles" or "saints":
Msgr. Slawomir Oder, a Pole who is leading the case for John Paul's sainthood, said he is asking the French bishop in whose jurisdiction the alleged miracle took place to start investigating what happened.
Of course, the candidate saint performs these miracles after they die. But, of course, if a miracle happens after a pope dies, then I mean, c'mon, who else could have done it, right? I mean, the miracle practically proves itself, let's not beat around the bush here.

Here is the rigorous water-tight methodology that will be used to objectively ascertain whether or not a miracle had in fact occurred:
All of the testimony gathered will be sent to the Vatican. After that, a team of experts appointed by the Vatican's Congregation for the Causes of Saints will determine whether a miracle happened.

Something tells me that they won't be calling in James Randi to conduct the "investigation". After all, we know what he might find out, and wouldn't that upset this little pageant? Randi's still has his unclaimed million-dollar prize for anybody who can prove their claimed miracle. And, I'm guessing, with all those collection plates that get passed around on Sundays, the Catholic Church could really use a million bucks, right?
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Monday, March 13, 2006

More Tommy

There's some more interesting stuff and links about Tommy Douglas over at Chandrasutra. Check it out!
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Tommy Douglas: The Greatest Canadian

Attention Canadians! Be sure to tune in to CBC's Prairie Giant: The Tommy Douglas Story tonight at 8PM E.T. Douglas is the man responsible for bringing us health care in Canada (in the same capacity that King Ralph may well bring it down). Douglas is also the founding father of the NDP a socially conscious left-wing party in Canada.

Tonight is apparently the second part of the series, meaning that I missed plugging part one. I obviously can't view it over here in Sweden, but I'd appreciate hearing from anyone who's seen the series. Please post a review in the comments section here -- I would be most grateful!
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Saturday, March 11, 2006

Spreading the word: arsonists' attack on Holocaust History Project

Arsonists have attempted to burn down an office for the Holocaust History Project (THHP), an organization that publishes and distributes educational material about the holocaust. See Orac's post for details and a press release. THHP has been a vocal opponent of holocaust denial efforts, making it a prime target for radical anti-semetist movements--the likely perpetrators of these attacks. The attacks targeted a distribution

If so, then the attacks are an effort to silence THHP and further an anti-semetic agenda. In response, bloggers have been linking to the site and raising awareness about the attacks that have escaped considerable media attention.

I'm deeply ashamed of my delay in posting this and sorry that I missed this post earlier in the week. Please, spread the word and visit the THHP website.
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Friday, March 10, 2006

When it doesn't contradict your previously conceived view...

Sorry I haven't been posting much recently. I've been up to my eyeballs in a full-time course balanced with my research responsibilities (=major overtime!). I still haven't got much time to write anything substantial these days, but I can't resist pointing out when creationists are caught with their pants down.

I love how blatantly creationists are willing to accept facts when they are (seemingly) not contradictory to their worldview, even when accepting that same fact is contrary to arguments they've already made against evolution. Creationists have been quite adamant in their disputation of feathered dinosaurs. Groups like the multi-million-dollar organization Answers in Genesis have gotten a lot of mileage out of the "Archaeoraptor" incident, despite the fact that it is irrelevant to the question of dinosaurs with feathers. "Archaeoraptor" was a dinosaur rear-end stuck on a bird's upper torso. However, both taxa involved are known to have feathers. What's funny is how much effort they've expended in trying to dispute the feathers and other lame efforts to try to explain them away as plant matter or accidentally associated bird feathers.

Generally speaking, these creationist articles refrain from publishing any pictures of the actual fossils. They prefer instead to lure in unsuspecting children with images of the big, colourful, and goofy-looking dinosaur models and then abuse their minds with the senseless tripe in the articles.

However, AiG has published this twadle about a recently described Jurassic fossil mammal from China, Castorocauda. Here, we see no question of the preservation of integumentary structures (i.e. hair, in this case).
The fossil is in good enough shape to preserve hair

What? What about all those fantastic theories about ginko leaves or wildly improbable chance association of bird feathers and dinosaur bones? Isn't this another prime example of evil-atheist-evolutionist-commie-paleo brainwashing? Oh wait! There's nothing about the presence of hair on a mammal fossil that challenges AiG's preconceived view of the world, so might as well let it slide. Just because we know that mammals have hair, it doesn't mean that we can just go making such wild-ass conclusions about this grubby-looking fuzz around a mammal fossil! C'mon, guys (and they are all guys), you could at least be consistent in your challenges to the preservation of keratinized structures!

How does AiG fit Castorocauda into their worldview? Why, by fitting facts to fairy-tales, of course!
One interesting question in the creation model is where these mammaliaform organisms fit ecologically into the pre-Flood world. Modern groups of placental mammals are not found among the dinosaurs—only mammaliaforms and some marsupials. This suggests that placental mammals may not have lived with dinosaurs [i.e., shared the same habitat] before the Flood—only mammaliaform animals and some marsupials. The destruction of that entire ecosystem might explain why not only the dinosaurs, but also the mammaliaform animals, are not found on the earth today.

Yes, the fact that several thousand species of modern mammal are known from (or around) all continents and that dinosaur fossils are known from all continents (even Antarctica) sure sounds like a good indication that they would not have lived together in the pre-flood world. You mean to say that with dinosaurs roaming the entire planet not one happened to cross into the general neighborhood of a wildebeest, or a buffalo, or a kangaroo, or a cat, or a bear, or a squirrel, or a cow, or a sheep, or a pig, or a...

Too bad creationists are serious. You can't write comedy like this.
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Saturday, February 25, 2006

Thursday, February 23, 2006

The Bearded Man Conundrum

Over at the Panda's Thumb there is a rather lively discussion about who is the bearded man in the picture.

The picture purports to be from and signed by Charles Darwin. While it is a man with a white beard (not nearly as impressive as Darwin's), the picture sure doesn't look like him!

Anyway, I'm somewhat interested in knowing what comes out of this, so I thought I should spread it around a bit more.
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Old icons will die hard

It would be grossly inappropriate for a blog called The Lancelet to avoid discussing some of the interesting findings reported in today's issue of Nature. The new study, puts an interesting twist on our deep ancestry. In what is almost prototypical for science, it seriously challenges the common sense perceptions that have led us to our traditional classification. That is, science is almost at odds with how our subjective impressions tell us things ought to be. In this case, the authors have challenged a prevailing idea of how vertebrates are related to our neares invertebrate relatives.

Lancelets, or Branchiostoma, or amphioxus, (seen in the header of this site) are almost iconic in their status as the protovertebrate. There is even a song about our kinship with the lancelet. Lancelets have a notochord (a firm rod of tissue that underlies the dorsal hollow nerve chord -- one of the unique features that unites chordates, the group that includes tunicates, lancelets, and vertebrates), an elongate row of gill slits, and segmented muscle blocks.

A debate has raged among biologists as to who is more closely related to vertebrates: lancelets or tunicates. Tunicates (or sea squirts) are sessile animals that live kind of like a sponge, rather than like a fish. As was noticed by the early 19th C. embryologist, Karl Ernst von Baer, they have a free-swimming larval stage that has gill slits and a notochord and looks a lot like a lancelet. The ongoing debate (especially in recent years with the advent of molecular phylogenies) has been who is more closely related to whom: are lancelets more closely related to vertebrates? Are tunicates? Or are tunicates and lancelets closer to each other than either is to vertebrates?

The new study tested tested the interrelationships of the deuterostomes: the branch of the animal family tree that includes vertebrates, the various chordates, and echinoderms (sea stars & co.). The researchers used 146 nuclear genes of 36 different animals and two fungi. Their results were rather unorthodox. They recovered a tree that placed the tunicates as the sister group of the vertebrates. But what was more striking was the placement of lancelets with an echinoderm lineage.

The results, if correct, imply that the last common ancestor of vertebrates and echinoderms was an animal very much like the lancelet and that sessile filter feeders are more closely related to us than is a particularly vertebrate-like swimmer. A common, but fallacious, interpretation of such a phylogeny is that it implies we evolved from a sessile filter-feeder or, in this case, a tunicate. But it makes no such implication, since all the tunicates converge to a single unique node in the tree (the red branches marked "Tunicata"). What the tree actually implies is that their condition evolved along the "trunk" of that cluster of branches. This in itself partly explains why tunicates have a free-swimming, lancelet-like larval stage.

Common sense would make us want to lump lancelets with vertebrates. After all, lancelets look most like fishes. However, the question raised by this analysis is more along the lines of: what if tunicates split from the tree after lancelets split from vertebrates? This is an entirely possible scenario, but one that is not accounted for by a classification that focuses on overall similarity. The way evolution works is not necessarily reflective of the way we think it should work.

The reality is that looking back at evolutionary history from the present can be as biased as observing the solar system from here on earth. Appearances can be deceptive. The reason why we share so much in common with lancelets may not be because we have a special common ancestor with them. Instead, it may in fact be because lancelets haven't changed much since the common ancestor of vertebrates and echinoderms. Instead, it may be that tunicates and echinoderms are the ones that have diverged the greatest. This is certainly what the new result implies.

However, this phylogeny is far from being the last word on the interrelationships of our deepest ancestors. The authors themselves call for the need to test the grouping of lancelets with echinoderms. One of the potential problems here may be that each is represented by a single taxon. In the case of lancelets, we haven't got much choice. However, more echinoderms will be needed. A single, ancient lineage in an analysis can cause problems due to a phenomenon that systematic biologists call "long branch attraction". In simple terms, this just means that the longer and more rapidly evolving your lineage is, the greater the chances that parts of your genetic sequence will happen to match that of another ancient lineage, just by chance. When this happens, two unrelated branches can "snap together" implying recent common ancestry, when there is in fact none.

One of the strengths of this study is that they tried to circumvent this and other potential problems as much as possible. They concentrated on what were considered to be slowly evolving lineages. One of the problems that happens when a gene evolves too quickly is that it changes too much and, consequently, looks a lot less like the ancestral gene would have looked like. The result is that fast-evolving genese amount to a lot of "noisy" data over very long periods of time. The old information gets overprinted by new information and confuses the analysis and also confuses the analysis process.

There will certainly will be a number of researchers who will dispute this analysis. People who know their molecular evolution far better than I do will probably have much to say about it. In the meantime, it serves as a welcome challenge to the prevailing "dogma". This is not the first analysis to cast doubt on the status of lancelets, and certainly won't be the last.

EDIT: Predictably, Carl Zimmer has written another summary with an interesting twist. Check it out.

Delsuc, F., Brinkmann, H., Chourrout, D., and Philippe, H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-968. link.

Gee, H. 2006. Careful with that amphioxus. Nature 439: 923-924. link.
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