On the use of the stem group concept.

The notion of a 'stem group' is indespensible for a palaeontologist. Much used and abused, it is simply not possible to talk about the relationships of fossils to modern life without the use of the crown and stem group concepts. The crown group is a clade which is delimited by its living (extant) members. The stem group comprises those fossils which are closer to the crown group than to any other extant clade, but do not fall within the crown group. As a result, the stem group is paraphyletic, and thus not really a group at all. It is perhaps more useful to talk about a 'stem assemblage' than a 'stem group'.

While at this year's SVP (and at previous meetings), I was struck by some of the terminological abuses of the term 'stem group'. In various instances, it was used either to refer to the nearest sister taxa of an extinct clade, or it appealed to essentialist nomenclature. I comment further on these below the fold.

'Stem groups' of extinct clades:
When a clade is extinct is has neither a crown nor a stem. If we did not distinguish between extant and extinct clades when applying the crown group concept, then crown groups could be arbitrarily small and stem groups arbitrarily deep. Because nodes in a cladogram are rotatable, we could use any taxon (fossil or living) to be a stem taxon.

We already have a set of terms for this: sister group relationships. This is also what the crown group concept conveys. However, it's purpose is to convey the relationship of fossils to a particular living group. When we talk about fossil or extant clades, we can talk about the nearest sister taxa. When talking about fossils in relation to an extant clade, only then do we apply the crown group concept.

Arbitrarily deep stem groups
One abstract title at this year's meeting struck me, because it referred to the fossil Morganucodon as the earliest stem-mammal. This taxon is almost certainly a stem-mammal. Is it the earliest? Take a look at this figure (from Angielczyk, 2009) (you may have to click on it to see the full image):


Notice the placement of the node "Mammalia". It's a full two internodes displaced from the node that subtends the extant mammalian branches: monotremes, marsupials, and placentals. You'll also notice that the Triassic fossil Morganucodon is the nearest fossil sister group of the three extant mammal lineages. In other words, it's the nearest sister taxon (in this tree) of the mammalian crown group (which, strangely, is unnamed!).

This is a peculiar trait among palaeontologists: give the standard crown group name (i.e Mammalia, Aves, etc.) to some arbitrary node within the group's stem. For instance, Aves (birds) is often considered to be the clade delimited by the last common ancestor of all extant birds + Archaeopteryx.

What you should also notice in the diagram above is that the root node of this tree is called "Synapsida". This means it entire run of taxa in this tree from the Synapsida node up to (but not including) the unnamed mammalian crown group nodes are part of the mammalian stem assemblage. Yes, Dimetrodon is a stem mammal, as well as Morganucodon. This means that a host of Permian (and potentially earlier) forms are also stem mammals, leaving Morganucodon appearing fairly late in the game.

The utility of the stem/crown group concept comes in placing fossils in relation to living groups. When we do this, fossils can be used to build up knowledge of the sequence of acquisition of homologies where living forms provide no clues. Fossils can, in turn, help test hypotheses of homology by providing unexpected combinations of characters, as well as precluding or 'predicting' certain character combinations. It is important that these concepts are applied in the correct fashion, or else they (and fossils) will lose their meaning.

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Angielczyk, K. 2009. Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution. Evolution: Education & Outreach 2:257–271.


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Oops!

"A treasured piece at the Dutch national museum - a supposed moon rock from the first manned lunar landing - is nothing more than petrified wood, curators say." Full story
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A dubious honour...

It seems that my latest paper has been nominated for a dubious honour. That is, I've been singled out as having committed a cardinal sin of systematics: appeals to the reality or significance of paraphyletic groups.

This post was some time ago, and I have not had time to address it. And, I'll mostly not address it in detail here as it is not terribly worth it. Mostly, it is a kind of juvenile stunt, rather than a serious academic undertaking. However, since the authors Williams & Ebach (with whom I actually agree about much, even with respect to fossils), have ascribed to me ideas I do not actually subscribe to: namely a belief in paraphyletic groups, I'll post a little response here. In fact the point of Brazeau (2009) is to demonstrate that a group that is commonly appealed to in the literature, the "Acanthodii" is, in fact, a non-real group.

Most of Williams & Ebach's gripe with my paper is derived from either a BBC report or a non-specialist, non-technical, non-peer-reviewed interview piece in Nature. I have never used the term "missing link" in my article, nor did I use it in discussions with journalists. In fact, I try as much as possible to disabuse journalists of such popular misconceptions.

No, what is most surprising are the factual errors about my work that Williams and Ebach have made:

What any systemtist should do - re-classify the osteichthyans and chondrichthyans in light of this new evidence. Brazeau is naive to suggest that this discovery will "...not overturn a general consensus about gnathostome interrelationships" If Ptomacanthus is more closely related to chondrichthyans then bang goes the acanthodians. They need to be reclassified along with the chondrichthyans.

This contains several patently wrong statements. The monophyly of the Chondrichthyes and Osteichthyes remains after my analysis, as did their status as each other's extant sister group (which my analysis could hardly have contradicted apart from finding if their respective monophyly is not challenged). That general consensus is not changed by my result, so there is no need to re-classify either osteichthyans or chondrichthyans.

The acanthodians do not all get re-classified with chondrichthyans because, as my results showed, some "acanthodians" are members of the osteichthyan stem. So, we have to reclassify some as chondrichthyans and some as osteichthyans. Something I entirely agree with. Figure 3 of my paper clearly shows where I have placed Ptomacanthus in the group Chondrichthyes and a bunch of other "acanthodians" under Osteichthyes and highlighted in bright colours so that you could see that this is what I already did!

Figure caption: a, Strict consensus trees of the 2,904 shortest trees from the global analysis (left; treelength: 318 steps; consistency index: 0.44; retention index: 0.76; rescaled consistency index: 0.34) and the 30 most parsimonious trees from the endocranial data set (right; treelength: 83 steps; consistency index: 0.64; retention index: 0.85; rescaled consistency index: 0.54). b, Bothriolepis. c, Buchanosteus. d, Tetanopsyrus. e, Ptomacanthus. f, Cladodoides. g, Acanthodes. h, Mimia. Vertical arrow shows position of palatoquadrate-braincase articulation that corresponds to the basipterygoid articulation shown in Fig. 2. Double digits indicate percentage bootstrap support; single digits show Bremer decay indices (when greater than 1). Illustrations are modified from refs 5 and 18 (also see Supplementary Information).

Continuing, Williams & Ebach write:

But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic!

I did state the obvious. It's in the figure. Look at it. I did not "descend into evolutionary explanation". The nested series of monophyletic groups that imply acanthodian paraphyly actually do provide sequences of character acquisition along the chondrichthyan and osteichthyan stem segments. As Williams & Ebach know well, each monophyletic group is supported by synapomorphies, and those nested groups synapomorphies are simply synonymous with what we call 'sequences of character acquisition'. This is how we make sense of fossils (or any other newly discovered taxon) and the implications fossils have, if any, on further hypotheses of synapomorphy (homology). If it's not the sequences of nested homologies that define monophyletic groups (the groups that matter) then what does? I'm perplexed as to why Williams & Ebach, of all people, would challenge this, since this seems to be their own view. I thought we had accepted and moved beyond disputing the idea that "evolution", when talking about fossils and the unrepeatable past, was only reducible to our best systematic hypotheses. In the quoted statement, that is all it is to me. It seems, perhaps, I wasn't careful enough and Williams & Ebach saw what they wanted to see in it. If so, then I'll take responsibility for my error, but note that my critics are playing fast and loose ascribing ideas to me which I have not explicitly stated.

Finally, they raise the following gripe:

"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (BBC Online, 19 January 2009).
This is false and misleading - the study shows quite the opposite.

Mostly, Williams & Ebach are just being pedantic and annoying, but this is infuriating bullshit. Those are not my words!

My words in the BBC article were:

"This figures in nicely with the emerging idea that acanthodians don't form a group of fishes that are all closely related to each other. Some of these fossils are primitive sharks while others are primitive bony fishes."

Even in the BBC article I state clearly that some are chondrichthyans (though I used the term "sharks" as a shorthand) and others are osteichthyans.

I believe my primary sin in that paper is to refer to terminal taxa as "basal". As I will cover here in another post, this is a problematic use of the term "basal", and one that is infectiously used amongst people who apply systematic methods. Maybe that could net me a Pewter Leprechaun, but if you nominate me on that basis you have to nominate just about anybody who talks about trees these days.

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Nice fossil, shame about the name...

Poor Darwinius, getting all this attention that it can never possibly live up to. Thankfully, a number of blogs out there are offering good summaries and the straight dope on the significance of the fossil. Just to add another fly in the ointment, I must sadly report that the name may become a problem due to it's being published in an online-only journal.

According to the International Code of Zoological Nomenclature:

Article 8.6 Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.

I see no evidence in the original paper that this condition has been met. Thus, under the rules of the ICZN, the name Darwinius may not be considered considered "published".
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Being wrong for all the right reasons.

Just a bit of a ramble with some totally unresearched ideas here. Well, not totally unresearched, but impressions and the like, but without explicit references.

Working with fossils can be as frustrating as it is rewarding. It's a lot of fun, but each fossil only tells you so little. In fact, a fossil might be said to really tell you nothing. By themselves, fossils are dry bones, unanimated. Everything we know about fossils depends on our interpretations of them. This seems a little nihilistic, not to mention ripe for creationist misquotation. I'll warn now that there is nothing of use to the creationist here. I'm not talking about the big picture about evolution. I'm talking about the finer points. The crossed t's and dotted i's. Creationists might claim that there are no transitional fossils and try to use my words as a way of showing that even I, the palaeontology graduate student, thinks there's a problem. However, I'm not only predicating this post on the reality that there are many transitional fossils, but that our human frailties might even be preventing us from recognizing more transitional fossils than we have. I believe that we can cut the story of early vertebrate evolution even more finely than most palaeontologists are willing to admit.

When studying the fossil record, we need to recognize patterns. Humans recognizing patterns is tricky business -- we're pattern-seeking animals. We see shapes in the clouds or in random scattering of pebbles in a riverbed. We are often very prone to error, as our common sense thinking can fail us when more arcane matters are in question. We have confirmation bias, where we easily remember the confirming instances for our pet hypothesis but ignore, discard, reject, or rationalise any contradictory observations.

But this is why we have science. The idealised scientist aims to eliminate bias, tries to suspend wishful thinking, and (most importantly) challenges conventional wisdom and common sense thinking. The greatest discoveries in science were not the confirmations of things we already believed, but the revelation the startling facts that were totally inaccessible to our naked perceptions--often demonstrating how wrong we actually were.

There is apparently a world that exists independently of our ability to perceive it. And so, there are necessarily truths about the world that we may not be comfortable with. The point is that science can only tell us something new if it doesn't exist to support those comforting narratives we tell ourselves about how the world works. It is an "unnatural way of thinking" as the embryologist Lewis Wolpert put it:

[T]o do science it is necessary to be rigorous and to break out of many of the modes of thought imposed by the natural thinking associated with ‘common sense’. p. xiii-xiv. Wolpert, L. 1993. The Unnatural Nature of Science. Faber & Faber, Ltd. London

What Wolpert is saying is that science is almost like an affront to a very sacred sense of understanding the world: common sense. It forces us to think in ways that sometimes feel counterproductive, uncomfortable, and even revealing conclusions that do not look like they make sense. The conclusions might be very difficult (or even impossible) to understand.

Palaeontology has, for a long time, been a discipline of narratives. Stories, of whatever sort, tied to fossils in order to explain the patterns observed. The tradition has often been one of very elegant, if not fanciful, speculation that has, in some way, been tied to peculiar observations about fossils. No one can count the speculative hypotheses on dinosaur behaviour, for instance. Some have proven more testable than others, of course. The stories of evolutionary relationships between fossil species, as well as between fossil and living species, were at one time unverfiable just-so stories. At least this was the case in terms of their expression as narratives. We understood two things to be related because they bore homologous structures, but we also knew two things to be homologous because they were borne in related creatures. The cladistic revolution changed that and allowed us to express homology in terms of the nested distribution of similarities. It be came an explicit way of uncovering the patterns in our observations about fossils.

Palaeontology is still experiencing its growing pains in becoming a mature, accountable, rigorous science. The tools, like cladistics and related methods, are there and so is the ambition to use them. However, the steps towards Wolpert's vision of a science are not complete.

Cladistics, when treated with care and in an honest attempt to eliminate your bias, can be very helpful. However, it can just as easily be used to come up with a tree that makes you feel comfortable. It's just an algorithm. You can shove whatever you want in to make whatever you want happen. The point is what the algorithm does, and the logic behind choosing to apply it.

I won't go into the details of it, because I don't think that's what this rant is about. The point is that it acts like a filter for our observations. We can record apparent similarities between a bunch of fossil, or living, or fossil and living things and interpret, in our own minds, what that means. Or, we can subject it to a particular type of analysis that might not give us what our brain tells us it should be. What it will (hopefully) give us is a result of the kind we want, based on logical principles that we have worked out beforehand. These arguments are, themselves, worked out based on some general principles.

Methods like cladistics might not give us the right result. Methods will, at one time or another and however frequently or infrequently fail. Usually for some reason (the method is bad, we used it improperly, or just pure randomness).

The point, interestingly, isn't even about the right answer. It's actually about the wrong answer. We can and will be wrong when trying to explain the world. But we can be wrong for two reasons: the right reasons and the wrong reasons. It's like anything else, you can have all the calculations and the protocols and experimental controls right, and still Nature can throw you a curveball. Or it can be impossible to collect all the neccessary data, or simply impossible to know how much to collect. Nevertheless, we have to try. This can lead to us being wrong, but we will be wrong at no fault of our own. Alternatively, we can be too caught up with getting a result -- especially the result we want. This leads to us being wrong for all the wrong reasons.

So, for those of us working with fossils, I think we can be wrong for the righ reasons and wrong for the wrong reasons. I think honest attempts to challenge received wisdom, to upset old taxonomies, and question the authority of old is a good thing. It may lead us to stronger hypotheses, if not simply to a more honest evaluation of our data. It might be that we simply don't have the evidence to say all the things we're saying. We might, for the time being, only have the evidence for a very coarse picture of interrelationships of some fossil organisms. But the more we strive for a result, and the more we strive for a result that makes us feel comfortable, the farther our thinking get from Wolpert's description of true scientific thinking.
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The origin of whales and "missing links"

The remains of a very basal member of the whale lineage was described this week in Nature. Carl Zimmer's got the gist of it, and you can see pics at Pharyngula. In short, this new fossil material suggests that an aquatic mode of life evolved in the whale lineage at some considerably earlier stage than their predatory mode. The finding is interesting because it illuminates some of the earliest stages in whale evolution.

But at times like this, the term "missing link" likes to fly around in the popular media (but certainly not in Carl Zimmer's writing!). "Missing link" has a certain seductive quality in that it's a familiar concept and can be used to easily grab the interest of lay readership. But therein lies the problem: this does nothing to dispel the misleading notions carried with the term "missing link", and instead only perpetuates them.

As others have pointed out, I'm sure, evolution is not viewed as a chain or a ladder, and concepts that apply such linearity are definitely misleading. However, one could defend the term by nothing that, often times, a fossil might alter the grouping we make and thus "link" one group to another group -- something we didn't know before. But even if that is the case (and it rarely is), no single fossil holds a privileged place in illuminating the tree of life. We understand the importance of a fossil, such as Indohyus, because of what it shares in common (or doesn't share in common) with other fossil forms and other living taxa as well.

Indeed, these forms to which we often apply the label "missing link" do demonstrate structures and charicter combinations that are in some sense intermediate between groups as we recognise them, but that is somewhat misleading as well. For instance, Tiktaalik is widely regarded as a "fish-tetrapod intermediate". In a sense this is true, but it implies the reality of fish as distinct from tetrapods and that one animal somehow bridges this otherwise un-crossable boundary between types. Instead, we understand tetrapods as nested within the bony fishes, with the lobe-finned fishes sharing a special common grouping with them. Among these lobe-finned fishes exists a range of forms that are either more or less like tetrapods than others.

It is within this comparative context that transitions are understood. Sequences of character change are built up be recognizing the common features shared among groups in a hierarchy. It is thus a branching picture, rather than a straight chain with some missing links. The so-called "missing links" get portrayed as somehow essential to the whole story, the last piece of evidence required to prove some otherwise incomplete notion. In reality what they do is quite often to fit neatly into a picture that we already understand very well and serve instead to make the details much clearer.

In the case of Indohyus, it adds important new information in understanding the origin of whales, both from a phylogenetic perspective, but mostly from a functional and ecological perspective. It's not so much a "missing link" no longer missing, as a piece of the puzzle that helps us decide between competing solutions.
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Science as a process: placoderm muscles revisited

You might recall the discovery of fossil placoderms with preserved muscle tissue from earlier this year. I posted on it here, but noted that there was a problem with the analysis, but I didn't say exactly what. This week, the journal Biology Letters published a comment on this paper by a colleague and myself, along with the response from the authors of the original paper.

It's tempting to write a counter rebuttal here, but I'll just let you read the papers if you have access to them. The point is, this is how science works: we depend on other workers being willing and able to criticise our work when they think there is reason to do so. Because of this, science maintains its credibility and its integrity. A case example for your edification. Enjoy.
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Dr. David Menton is a liar.

(Jasper is out! It's time for a paddlin'! This post is in two sections. Recognizing the potential for it to drag on into lengthy details and scare readers away, I have chosen to put the main points up front and add a supplementary section at the end for those of you who are interested in some of the additional details of biology related to this post)

Dr. David Menton of Answers in Genesis has written the latest reaction to Tiktaalik roseae. Interestingly, the article makes almost no reference to the Tiktaalik fossils themselves, except where facts are made up.

In the article, Menton's only claims about the anatomy of Tiktaalik relate to the pelvic fins and girdles (i.e. the hips and legs) of Tiktaalik. There is no disucssion of the skull or shoulder girdle, and only tacit reference to the fin skeleton. Menton explains in relation to fishes and tetrapods that:

[t]he hind limbs [of tetrapods] in particular have a robust pelvic girdle securely attached to the vertebral column. This differs radically from that of any fish including Tiktaalik. Essentially all fish (including Tiktaalik) have small pelvic fins relative to their pectoral fins.

Menton is a liar. He cannot possibly know anything about the pelvic fins of Tiktaalik. The two papers describing Tiktaalik offer absolutely no descriptions of the pelvic fin skeletons or girdle. I've seen the material first-hand and there are no such details of the pelvic fin.

I took the time to go one step further. I emailed Ted Daeschler (of Colbert Report fame) who is one of the authors of the papers to drive this point home. Here's his reply which I got this morning [emphasis added]:

Regarding Tiktaalik pelvic fins . . . no pelvic fin material has been reported. Less for him to misrepresent!

I know this is like taking a whizz in the ocean, but chalk up another lie for AiG.

The article is replete with misinformation, and I will only take up a few of them here. There is a "supplement" below for those who are interested in the finer details of biology or the particularly vapid claims that Menton makes. The article has some subtle ways of using definitions as though they were arguments. For instance, Menton claims that "no fish (including Tiktaalik) has true finger or toe bones." This is a "truth by definition". Tetrapods, by definition, have digited limbs. In other words, only tetrapods have true finger or toe bones by definition. If it has fingers, it ain't a fish! Menton's claim isn't even an argument, but it sure is misleading.

Edited to add. It gets worse and I can't believe I forgot to add it. Nevermind the rhetoric, Menton (who is an anatomy professor! states: "Finally, no fish (including Tiktaalik) has true finger or toe bones. Instead, fish have slender bony fin rays, which even evolutionists concede are not homologous or related in any way to digits". Rays are not in the place of digits. Rays are dermal bone, they develop in the skin like scales and skull bones. Thus, they are in the skin and form a "sandwich" over the internal, or endochonrdral/cartilage, skeleton. Digits are part of this internal skeleton. You cannot have "rays instead of digits". You may have one and not the other, but neither takes the other's anatomical place. Coming from an anatomist, this statement demonstrates first-rate incompetence. Tiktaalik does have jointed radials, a feature which is typically only in lobe-finned fishes. These are endochondral bones. Whether or not they are homologous to digits is a question of ongoing investigation which will require more fossils and involves gene expression work in lungishes.End of edit

The real problem is not even whether or not Tiktaalik has a tetrapod-like pelvic girdle. It's that Menton's attempt to discredit the claims of the authors is based on listing the fish-like aspects of Tiktaalik and ignoring the tetrapod-like aspects. An animal that is a fish-tetrapod transitional would be expected to have some properties of a fish, no?

Menton's use of quotations is also appallingly dishonest. In a section titled "So Is Tiktaalik a Missing Link?", he quotes the News and Views article by Ahlberg and Clack and states that it concedes a point he is trying to make.

In their review article on Tiktaalik, Ahlberg and Clack (Nature 440(7085):747–749) tell us that “the concept of ‘missing links’ has a powerful grasp on the imagination: the rare transitional fossils that apparently capture the origins of major groups of organisms are uniquely evocative.” The authors concede that the whole concept of “missing links” has been loaded with “unfounded notions of evolutionary ‘progress’ and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transition.”

But the whole quote reveals that Menton's own choice of word's ("missing link") is a loaded question (a particularly dishonest rhetorical trick such as asking somebody "Have you stopped beating your wife yet?").

The concept of 'missing links' has a powerful grasp on the imagination: the rare transitional fossils that apparently capture the origins of major groups of organisms are uniquely evocative. But the concept has become freighted with unfounded notions of evolutionary 'progress' and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transitions. Much of the importance of transitional fossils actually lies in how they resemble and differ from their nearest neighbours in the phylogenetic tree, and in the picture of change that emerges from this pattern.

Ahlberg and Clack were saying nothing like Menton's implication.

What I don't understand is why this article had to be written by a professor of anatomy. There is no cogent discussion of anatomy that is relevant to the issue of Tiktaalik. There's a heck of a lot of really bad zoology (see the supplementary section), but not even a discussion of the anatomy of of Tiktaalik. Instead, the attack is a shameful distortion of definitions, quote mining, and outright lies. To give you an impression of what Ahlberg and Clack actually think about Tiktaalik here is the figure from their article. Compare especially the skull roofs along the left-hand side of the figure, an aspect which Menton completely ignores.

Figure caption: The lineage leading to modern tetrapods includes several fossil animals that form a morphological bridge between fishes and tetrapods. Five of the most completely known are the osteolepiform Eusthenopteron16; the transitional forms Panderichthys17 and Tiktaalik1; and the primitive tetrapods Acanthostega and Ichthyostega. The vertebral column of Panderichthys is poorly known and not shown. The skull roofs (left) show the loss of the gill cover (blue), reduction in size of the postparietal bones (green) and gradual reshaping of the skull. The transitional zone (red) bounded by Panderichthys and Tiktaalik can now be characterized in detail. These drawings are not to scale, but all animals are between 75 cm and 1.5 m in length. They are all Middle–Late Devonian in age, ranging from 385 million years (Panderichthys) to 365 million years (Acanthostega, Ichthyostega). The Devonian–Carboniferous boundary is dated to 359 million years ago18.

I suspect I know why this article was written and where these comments stem from. When Tiktaalik was first reported in Nature nearly a year prior to this writing, Answers in Genesis published a screed co-authored by Menton. In response, I called out the authors for botching Vertebrate Anatomy 101. They seem to be clarifying their mistake, but I already covered that base:

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.

The problem that the creationists are facing here, and what Menton's reaction is symptomatic of, is that fossils like Tiktaalik are stunningly beautiful, articulated, their implications immediately obvious even at a glance, and information about them can be disseminated widely through the world wide web. Anybody with a computer can get high-res pictures of Tikaalik and see it for themselves. In response, big-money creationists like AiG have to go through extraordinary rhetorical acrobatics to keep fleecing the flock.

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"Supplementary section"

Here I outline some detailed responses to claims in Menton's article but aren't necessarily related to Tiktaalik.

Part I: Fish breathing and circulation

Menton briefly discusses a number of teleost fishes that have specialized types of air breathing: mudskippers and climbing perch. Teleosts are ray-finned fishes and to put things in creationists terms: "Evolutionists" believe that all ray-finned fishes are more closely related to than they are to tetrapods. In other words, they form a clade. Conversely, there are lobe-finned or sarcopterygian fishes which "evolutionists" believe are closer to tetrapods than they are to any other fishes. Thus, they are said to form a clade with tetrapods. (Digression: It makes sense that Tikaalik is a bona fide lobe-finned fish. If it had been a teleost, that would have been a problem.) In discssing air-breathing teleosts, Menton concludes:

none of these curious fish are considered by evolutionists to be ancestors of tetrapods—they are simply interesting and specialized fish.

Isn't there a glaring omission here? Has Menton not heard of lungfishes? Lungfishes are, indeed, sarcopterygian fishes. They breathe air (hence lungfishes). In fact, not only do they breath air, but their circulatory system is connected to their lung in the same way as it is in amphibians. A review of vertebrate circulatory systems can be found here, and a particular reference to the lungfishes can be found here.

Here's a little review. Vertebrates have two main types of circulation: single and double (or undivided and divided). Fishes have the single (undivided) system, and the heart is relatively simple: it's basically a muscular series of chambers. Blood is pumped through the gills where it is oxygenated and passed through the body, collected back to a major vein (common cardinal vein) and delivered back to the heart. Repeat. In tetrapods, it gets complicated where the system is double or divided. In reptiles, birds, and mammals, the blood is first sent to the lungs where it is oxygenated, then back to the heart where it goes out to the body and back. Repeat.



Amphibians and lungfishes have a system that is somewhere in between. A pulmonary artery is linked to the lung from the systemic (or gill) arches and leads to the lung where it is oxygenated. A pulmonary vein then carries blood from the lung to the heart and it is pumped back to the body. However, the heart remains largely a simple structure like in fishes. The key difference is that the atrium, the chamber that receives the blood, is partly divided to separate the flows of oxygenated blood from the lung and deoxygenated blood from the body coming back to the heart (i.e. there is some mixing, but this is also controlled a bit). This partly divided system is lacking the air-breathing fishes he talked about. It is only known in lungfishes and amphibians.

Why was this information not important enough to be included and discussed by Menton?

Part II: Air breathing "crossopterygians"?":

It gets even more deceptive where Menton notes:

Most evolutionists look to crossopterygian fish for the ancestors of tetrapods—even though unlike many living fish, none of these fish are known to be capable of either walking or breathing out of water. [Original emphasis]

Very clever. "Crossopterygian" is a dated term showing that Menton has read nothing about the study of tetrapod origins or lobe-finned fish systematics from the past 20 years. Although I have a particular affection for the term, nobody uses "crossopterygian" anymore. It's Menton's convenient use of an outdated typological term that excludes lungfishes by it's definition that is particularly misleading. The term "crossopterygian" referes to a sub-group of lobe-finned fishes that included coelacanths and "osteolepiforms", the latter including the iconic Eusthenopteron frequently seen crawling out of the water in children's dinosaur books (though few scientists think it actually did this). The term is largely discarded today because it assumes that lungfishes and tetrapods are not simply modified "crossopterygians". By using this term, Menton can safely ignore lungfishes, even though most palaeontologists (and a significant number of molecular biologists) now think lungfishes are a closer living cousin than is the only living "crossopterygian", the coelacanth Latimeria. I hesitate to comment as to whether this was done on purpose by Menton, but it is rather convenient that he should choose to dig up such an old term that specifically excludes lungfishes whilst simultaneously neglecting them in a discussion of air-breathing fishes.

However, let's accept Menton's use of "crossopterygian" for the moment. Coelacanths are the only living crossopterygians. They do not have a lung, but rather an oily swim bladder. This swim bladder has a little trachea (the tube that connects the lung to the throat) and a very small version of a vein that corresponds to the pulmonary vein.

What's even more deceptive is Menton's comment that there are no crossopterygians known to breathe air when, in fact, most things that are called "crossopterygians" are extinct. While there is one living genus of coelacanth, hundreds of other genera of "crossopterygian" are extinct. Rhizodontids, "osteolepiforms", porolepiforms, onychodonts, are all "crossopterygians" and have very distinct from coelacanths and may have anywhere from half a dozen to hundreds of sub-taxa with different adaptations and, presumably, different modes of life. Of these, it is impossible to observe air-breathing. At best, some functional and/or bone histological studies might give clues to different respiratory physiology. But, at best, conclusions about air-breathing would be inferential, and thus excluded from phylogenetic analysis (i.e. interpretations of how organisms are related to each other). That said, it is yet another truism that Menton should claim that no crossopterygians are known to breathe air.
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Placoderm soft tissue preservation

The Late Devonian Gogo Formation is noteworthy for its exceptional preservation of fossils in limestone nodules -- particularly vertebrates. Amazing examples of nearly three-dimensional fossil fishes have been collected, showing life-like articulation. These fossil fishes have been exceptionally influential in our understanding of early vertebrate evolution, since they reveal such exceptional details. Now, Gogo is revealing new, unexpected details: the oldest soft tissue preservation in jawed vertebrates.

A recently published paper by Trinajstic et al. in the journal Biology Letters presents the details of muscles, blood vessels and individual neurons in an extinct type of early jawed fish, the placoderms. Unfortunately, the figures are, for the most part, less than dazzling. Nevertheless, here are some examples for your edification.


a) Shows an individual muscle fiber; b) individual neuron connecting to a muscle fibre; c) capillaries (blood vessels); d) calcium phosphate crystals that make up the preserved tissues.

One of the important discoveries in this paper helps us understand how the placoderms are related to modern fishes. Over the decades, numerous hypotheses have been offered for how all the various groups of jawed vertebrates were related to each other, particularly how the fossils fit in. Fossils, of course, give us essential clues to how evolutionary transformations have taken place, but it is first important to know how they are related to each other and modern forms. Placoderms have been proposed as the sister group of sharks and their kin, of bony vertebrates, or as the most "primitive" of the jawed vertebrates.

What some of these partially articulated placoderms show is the morphology of the actual muscle blocks of the body axis.



These will add much to the debate on how placoderms may be related to modern lineages of jawed fishes. The authors of the paper note certain similarities to lamprey in these muscle blocks, suggesting that placoderms were the most primitive jawed vertebrates. However, I'm going to leave my discussion of it there and leave it to the reader to investigate this question more fully.

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Update 19/02/2007: As somebody in the comments asked: how did these tissues get preserved. Yes, of course! These days, I'm so wrapped up in phylogenetic analsysi work of my own that I totally forgot about other interesting science! Yes, how are these soft tissues actually preserved.

Well, the important thing to point out is that they've been phosphatized, just like the Doushanto embryos. No these are not "fresh meat" as Karl in the comments says. So this is this really analogous to the preserved dinosaur soft tissue, either.

The authors of the paper rely on palaeoenvironmental information about the site to infer that the conditions were in fact anoxic at the immediate site of tissue preservation. In the absence of oxygen, the calcium precipitated in the local environment would've preferentially been calcium phosphate rather than calcium carbonate (limestone). The presence of microbes on the surfaces of the cells served to concentrate the calcium phosphate precipipation in the place of the tissues. Remember, bacterial cells are much, much smaller than differentiated animal cells and so an entire colony of bacteria encasing an animal cell can effectively create a facsimilie of the original thing! However, my competence of the geochemistry involved in this type of preservation is quite limited and if you're interested in knowing more, I suggest looking into the process of soft tissue phosphatization for yourself.

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Trinajstic, K. et al. (in press) Exceptional preservation of nerve and muscle tissues in Late Devonian placoderm fish and their evolutionary implications. Biology Letters. link
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Where the fossils are

Today I had a rare opportunity to see something that gets most palaentologists excited. First, a little introduction. If you're not very familiar with finding fossils, you'll first need to know that fossils are found in sedimentary rock: the type of rock that is formed by deposited sediments (ie. sand, mud, or chemical precipitates). However, as any palaeontologist or amateur fossil collector will recount, you can search through vast amounts of sedimentary rock without ever finding a fossil. One can sift through tons of rock in some places and not find a single scrap of bone, or shell, or leaf of plant. On the other hand, there are places where one cannot take two steps without walking on fossils.

Fossil preservation can be a very selective thing. Some environments are more conducive to finding fossils than others. This week, I am in Wales where I had the oppotunity to visit some Early Devonian fossil sites (about 410 million years old) that are worked by a local amateur palaeontologist. At one of his sites, I pointed out some geological structure that explains the high quality of the material collected there, and the promise for more fossils. If you're out looking for fossils, this is where you want to look.

Take a look at the image below. It shows a sequence of sedimentary rock layers and shows a classic type of structure known as a channel form. Notice the two different rock types. The upper rock is a coarse material, with heavy bedding. It's base is tapered to the left forming what's normally called a "lense" or a "lenticular bed". Below it is a noticably different-textured rock. It's heavily cracked and broken up. It is mudstone.



Here's the same image with some guides.



In the mudstone below the massively bedded (typically coarse-grained, but not greatly in this case) is where the fossils are. This is one of the best types of sequences for finding fossils and, in large part, is where articulated fossil animals are to be found. It should be no surprise then, that this friend of mine has actually recovered quite a few articulated fossils from there. He became quite excited when I remarked that this is the ideal type of sedimentary sequence in which to find articulated fossils. So, let's hope, some exciting discoveries will come from this site.

Why do fossils preserve so well in these sequences? What are they? These deposits form in a river channel, and the image below shows quite nicely the lenticular shape of the channel.



What you can see is that there is deposition of sediments in one direction that partly causes the channel to migrate (concomitant erosion of the opposite bank is the other cause). In such settings, bodies of animals are buried very rapidly. Moreover, they are quite prone to flooding and the rapid deposition of sediments (that is often why the bedding above is massive, as it was filled in rapidly, rather than in progressive layering).

This is where the fossils are.
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