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".
Read full post

Evolutionary gems

Nature is running a little online feature 15 Evolutionary Gems that have been published on its pages over the past 10 years.

One of the interesting things you'll note is the amount of molecular biology appearing in the section on the fossil record. Nevertheless, fossils have given us next to zero molecular data (even what is known is a infinitesimally small proportion of fossils in the fossil record). The reason this is possible is because of the way in which fossils fit into the tree of life: they intercalate into the branches between living branches. Thus, they act as a sort of "control" on how we propose hypotheses of morphological change -- in fact they often tell us all we can know about morphological change.

But there's more to this than just fossils: stories from population-level studies show us how the mechanisms of evolution act. Fossils and gene expression data tell us about patterns, but population studies tell us about evolution at the level of process. How natural selection and other forces act to shape the morphology, physiology, and behaviour of organisms can only be studied in real time, using population-based analyses. The work highlighted by Nature tackles important topics such as the role of natural selection in speciation, co-evolution, and the contingent nature of evolution -- the necessary consideration of phylogenetic history in studying adaptation.

Finally, we marry these two through the study of molecular processes. Mutation, gene regulation, epigenetics, these are all forces that influence the possibilities of evolution. These are the driving forces of diversification, but also the conservative nature of descent with modification. It is a slow and stumbling processes. Nature illuminates these issues by covering gene regulation studies in Galapagos finches, insects, among other worthwhile reads.

My main problem with this piece, however, is the way in which item #13 suggests that there is a fundamentally different macroevolution and microevolution. It attributes perceived large steps in evolution as real and refers to them as "macroevolutionary". This reads to me like saltationism, which seems to be bore strictly out of the argument from ignorance or the assumption that gaps in the fossil record are real. Nevertheless, it's a nice summary and worth checking out.
Read full post

The end of the long road. A new beginning.

Friday, 21 November, 2008, I successfully defended my doctoral thesis: "Endocranial Morphology and Phylogeny of Palaeozoic Gnathostomes". I'm no longer a student, I'm now a doctor of philosophy. It's a strange feeling being done, but now you know a bit about why I've been conspicuously absent from posting much in the past year. I've had a lot to do!

My next stop will be a postdoctoral fellowship at the Museum für Naturkunde in Berlin. Hopefully, I'll be able to pick up more blogging in the next few weeks. But first, I think I'm going to have a little holiday. Maybe somewhere sunnier than Sweden, for a change...
Read full post

Except was no such fella as Noah...

The problem I have is that I'm sure this isn't a metaphor to him.
Read full post

Homology: what's evolution got to do with it?

British palaeontologist Colin Patterson became an unwitting friend of creationism during his career. That misbegotten legacy continues to this day, in misquotations that continue to pop up in creationist literature. Patterson has been widely cited by creationists as some sort of closet creationist who though evolution was a speculative farce. Unfortunately, what has become lost in the maelstrom of attack and counter-attack in the world of creation/evolution apologetics are lessons for both evolutionists and creationists.

If anybody was a skeptic, Patterson was. In the forward to his posthumous second edition of his textbook Evolution, two of his close colleagues wrote: "His favourite critical internalised question was 'how do we know that?': to which he often got the answer 'authority or tradition'--something he respected only after he had explored the evidence for himself". He was notorious for a need to figure things out for himself and endeavoured like no other to never let preconceptions get in the way. Indeed, based on anecdotes of people who knew him, I have learned that "how do you know that?" was not merely internalised, but frequently vocalised in a deep Oxford English from the back of the room.

As a result of Patterson's take-no-prisoners approach to belief and science, he became the champion of some unpopular ideas. Patterson questioned every authority and, in the end, challenged (and I believe overturned) some deeply held beliefs about evolution. More importantly, he overturned some ideas about how we know what we know about evolution. For instance, even as a palaeontologist, he argued strongly that fossils themselves play little (if any) role in the establishment of species relationships. That belief emerged from beliefs about fossils revealing ancestor-descendent relationships, and from prior commitments about transformation.

This is where the creationist and evolutionist misunderstandings commence. Patterson argued that evolutionary theory had no role to play in systematics. To creationists, this is touted as evidence that the theory of evolution has no practical applications and is, indeed, unnecessary in biology. To evolutionists, this is often either ignored, disagreed with, or misunderstood.

But what Patterson showed was that a lot of the pre-Darwinian basis for evolutionary theory had been co-opted or subsumed into evolutionary theory. Ideas that had a pre-evolutionary basis had become drenched in evolutionary pre-conceptions and language. Homology, for instance, had become (and still is for most): shared similarity due to common ancestry. However, if homology is explained by common ancestry, then what is the basis for the inference of common ancestry? Well, as it turns out, homology! Patterson recognized the problem and iterated a definition of homology that took into account the way in which homologies define nested groupings. That is, homology is the relation that defines the ranks in a nested hierarchy.

Homologies are homologies because they define nested groups. They are sets of characters that fall into a series of congruent groupings. Similarity alone isn't enough to justify statements of homology, otherwise, we have no way to distinguish convergence from homology. Many will cite examples such as bird, bad, and pterosaur wings as examples where "fundamental differences" allow us to distinguish homology from non-homology.

But, the reality is that we already know these structures are non-homologous because they appear in distantly related groups. We know they're not homologous because of the distribution of other characters which act as a test of homology. If there were ample character evidence that birds, pterosaurs, and bats were all a tightly related group, we might then explain the differences as specializations of a common ancestral wing. The test, ultimately, is whether these taxa share other important characters in common.

The consequence of Patterson's definition of homology--the relation that defines a monophyletic group--is that evolutionary preconceptions are not necessary. Many evolutionists are uncomfortable with this. There is a sort of pluralistic approach (what I call a 'holistic' approach) to homology assessment that many biologists subscribe to. People argue that as many lines of evidence as possible should be considered. I agree, but the question is, through what filter do we analyze this evidence? Patterson would have answered: "tradition, authority, convenience, or assumptions about evolution". There is actually no need to be uncomfortable with Patterson's approach, which I'm surprised has not become more widely embraced.

The problem, as others had pointed out before Patterson, was that we need a knowledge of phylogeny (or interrelationships) in order to know anything about evolutionary history. In order to make generalizations about how evolution works, we need to know the pattern of descent. However, if our assumptions about evolution feed into our inferences about the pattern of descent, these assumptions become untestable. As a result, Patterson argued that our beliefs about evolution played no role in systematics. It was the task of systematists to uncover the patterns that exist in nature which we choose to explain by evolution and common descent. Patterson's rejection of the role of evolutionary theory in systematics was an attempt to keep the enterprise from decaying into circular argumentation.

So, the lesson for evolutionists should be kept in mind as we are deep into a new age in comparative biology. Genes and proteins can now be sequenced, we can map gene expression to embryos, and study the fate of populations of cells in developing embryos. We must ask ourselves: what beliefs about evolution that we developed before these wonderful advances have we carried with us to the present? And for each of these beliefs have we asked: how do we know that?.
Read full post

Open thread: are genes really a guide to homology?

I have been putting this question to some of my colleagues:

What is the value of gene expression data in determining homology of morphological features?

Are genes really important in determining if two structures in two different animals are homologous? If so, why? If not, then what does really matter?

Discuss.
Read full post

"It will have been more than worth it"

A nice article in the National Post about the fallout from the rumours that Stephen Hawking might move to the Perimiter Institute in Canada. It winds its way to a nice conclusion about the value of supporting basic research and the careers of promising youn scientists. Although it's clearly written by somebody with some first-hand (or otherwise close) experience with science and academia, I can't find the name of the author on the piece.
Read full post

Reader comments: Learning about evolution

A question in the comments prompted me to give a response up here:

[I]s there anyway I could learn about evolution without having an upper level education in biology and whatnot, (I'm a senior in High School)?

Yes! The "catch" (if there is one) is that you will develop an upper level education in biology on the way. You just have to do a lot of reading. Thankfully, there are a number of good books out there that can introduce you to the topic. It is, however, a good idea to have a basic familiarity with biology, particularly genetics and a bit of molecular biology. But, to begin with, the material covered in a high school biology class (or equivalent level of textbook) is a good start. It's important to know, for instance, what an allele is, or the base-pairing of DNA. Also, it's important to understand the relationship between DNA and proteins.

The study of evolution is pretty varied. We can break it down into two major parts:

1) The study of the mechanisms and principles that cause evolutionary change
2) The history of life: the historical record and inferred pattern of changes/transformation

It's important to understand both of these things and they will come from different sources. For instance, basic texts on evolution are pretty weak on paleontology. But paleontology texts will be pretty weak on aspects of evolutionary mechanisms. They're needed to complement each other.

The most important thing, beyond anything, is to understand the evidence for any proposition about evolution. Always ask if the evidence is convincing. If so, why? If not, why not?

Some book recommendations:

A few lay-reader type of books that are really good:

Weiner, J. 1995. The Beak of the Finch. Vintage.

Carroll, S.B. 2005. Endless Forms Most Beautiful. Norton.

Zimmer, C. 1998. At the Water's Edge. Free Press.

Texts on biology and evolutionary biology are always a good and obvious place to start. But my preferred way to do things is to get some basic knowledge set up and start looking at evidence (that's how I learn). Books of any type, age, or scope on zoology, botany, anatomy, palaeontology, are very good because they're extremely visual and give you an understanding of the diversity of living form. If you're a very visual learning, as I am, then these can really be helpful. But they're also useful because a lot of texts on evolution or biology talk about things as though they're somewhat divorced from the actual organism to which they might be relevant. A good background in zoology, botany, as well as palaeontology will be extremely helpful.

The short answer is: yes, there are a lot of readily available resources for self-educating in evolutionary biology. Have fun!
Read full post

Define evolution in one sentence!

Here's my stab at the challenge:

Evolution is the accumulation of changes over generations in a self-replicating system caused by heritable biases in the probability of self-replication.

Read full post

Episode IV: A New Pope

This made my day...


Read full post

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.
Read full post

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.
Read full post

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.
Read full post

Dinosaurs and Devonian fish: A field trip through Victoria

Last week, I attended the CAVEPS conference in Melbourne (I gave my talk on Tuesday, and I'll say more on that later). The previous weekend was the pre-conference field trip which took 25 or so conference delegates to a number of interesting fossil sites around the state of Victoria. We headed out on the morning of Friday the 9th of April.

A brief coffee break at the town of Yea. Delegates enjoy hot cross buns, given that it was Easter weekend.

The first of our stops was a site near Yea where the Silurian beds have produced the articulated remains of a single fish, Yealepis, described by Carole Burrow and Gavin Young in 1997. Yealepis looks like an acanthodian-type fish, but has no fin spines. Fancy that.

John Long holds a specimen of Yealepis and directs our attention to the Silurian beds exposed along a road cut. This photo was taken near the site where Yealepis was recovered. Sadly, the exact locality is not known.

The evening of the 9th was spent at the Mansfield Backpacker's Inn (which I recommend). We headed out to a site on a farm in the Mansfield district where some Carboniferous sand- and siltstones were cropping out in a field and along a river. Sadly, we didn't see a platypus or any snakes.

The fossils here are very rare and and the rock exposures are rather limited. However, in these beds, a number of important fossil fishes have been discovered, including early actinopterygians and some of the first-known rhizodontid material. More recently, a large and disarticulated skull and articulated fin of the rhizodontid Barameda was discovered here. It represents one of the most anatomically informative rhizodontid specimens and is to be published in the next issue of Journal of Vertebrate Paleontology. I will say no more until that time.

Conference delegates dig in to the Carboniferous sand and siltstones at Mansfield.

Beautiful vistas seen from the outcrops.

Anne Warren (La Trobe University) points out unusual sedimentary structures in the rock exposed in the creek bed. In this area, numerous spines of gyracanth fishes have been found.

The site has been well picked over, but a lot of exposed rock remains. In the relatively distant future, more great discoveries may be made here, once the rock has had more time to erode.

We visited a family of Cunningham skinks tucked between layers of Carboniferous rocks.

On the 11th, we visited a Devonian fish site atop the hills of the South Blue Range. The fossils here are also scattered and rather rare. Moreover, there are not really any articulated remains but mainly isolated head and shoulder plates from placoderm fishes. Moreover, to even find those scattered fossils, one needs to find the few restricted layers that are yielding them. However, with about two dozen conference delegates scouring the hillside, we ended up doing pretty well.

Making our way to the top of the South Blue Range

The incline was steep. Don't drop your water bottle, it would almost certainly roll to the bottom of the hill. We had to be careful not to send rocks tumbling down on the people below us! Kangaroos and wallabies were spotted darting though the forest.

Damn! A centipede absconds before I can get my macro function set!

Zhu Min (IVPP) examines some placoderm bits recovered at the top of the hill.

More fish are found. More placoderms, but a few other diverse bits are showing up too. Here, John Long (Melbourne), Robert Gess (Witwatersrand), and Daniel Goujet (Paris) zoom in on some placoderm plates.

The effects of bush fires can be seen over the region. As devastating as such events may be, the forests here dominated by eucalypts depends on long, intense fires for growth and regeneration. Without fire, eucalypts will not sprout new buds and seed germination will not occur. It also bodes well for palaeontologists in that it can clear out plant cover and reveal new rock exposures! Unfortunately, the aftermath can create hazards and one of the field trip sites at Mt. Howitt had to be cancelled.

Over the hills and through the spectacular Yarra Ranges National Forest.

We travelled next to the south coast of Victoria to a Mesozoic-aged sea cliff at a site called Flat Rocks, near Inverloch. In these cliffs dinosaurs and mammal fossils have been recovered following decades of dedicated and painstaking prospecting, quarrying, and even tunnelling. The sand- and siltstones here preserve coalified wood and tree trunks. A sharp eye is needed to spot the often similar-coloured bones in the blue-ish gray rocks.

Theropod dinosaur teeth recovered from the site.

An isolated dinosaur footprint. Rare occurrences of dinosaur footprints happen here. This one is a bit beat up, but it is believed that there are two prints, one inside the other. I only see one.

One of our guides on this part of the trip, Mike Cleeland, points out a large, fallen petrified tree.

The site is particularly special, for the researchers working there believe that it represents a polar dinosaur fauna. A number of lines of evidence have been cited to suggest this. The most important has been the geophysical evidence of permafrost. A layer of intermixed mud and siltstones showing a distinctive pattern known as cryoturbation is typical and, apparently, indicative of permanent ground freezing.

The palaeogeography of this part of Australia has been considered to have been polar in the Early Cretaceous when these beds were laid down. Thus, it seems to have been the case that these dinosaurs were living in a polar climate for at least some part of the year.

Mike again, pointing out the cryoturbation. It's difficult to see, so don't squint too hard. We couldn't get close due to the hazard of falling rock.

The field trip concluded at a second, related Mesozoic fossil site near San Remo. While we didn't find any additional fossils, I think it was easy to be distracted by the spectacular beach and gorgeous sunny day! However, this site was the provenance of what is probably the latest-occurring temnospondyl amphibian, Koolasuchus. This type of amphibian occurs very early in the fossil record, during the Carboniferous not very long after the first appearance of land-living tetrapods. However, the group persists well into the Triassic period. Koolasuchus thus represents a very late survivor of this lineage.

Mike poiting out the geology near the Koolasuchus site.

---

Edit: Plenty more pictures can be seen at the CAVEPS site. Including this picture of yours truly taking flight! Enjoy!
Read full post

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.

---

"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.
Read full post

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.

---

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.

---

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
Read full post

Not bad for only having read bits and pieces...

You know the Bible 56%!

 

Congratulations! You know a lot about the Bible - the books, the characters, the events. You are able to remember a lot of what you have heard and read!

Ultimate Bible Quiz
Create MySpace Quizzes

...but, perhaps I'll have to do a bit more reading. Perhaps not. I'd really like to see how my score stacks up to a lot of believers'. Zeno (score: 100%!) points out that a lot of non-believers know their bible as well or better than many believers. Granted, many non-believers are often 'de-converted' fundies who eventually emerged from their benighted state.

(Via Pharyngula.)
Read full post

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.
Read full post

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.
Read full post

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!
Read full post