The Lancelet

Simon Singh (and science) WIN!

2010-04-01T20:17:00.003+02:00

Simon Singh has won his libel appeal.

This is an enormous victory for freedom of speech and science in the UK. British libel laws strongly favour the plaintiff, having a potential (or, in this case, very real) stymying effect on public scientific discourse—which may often be very critical.

Deepak Chopra Fail

2010-03-28T21:47:00.002+02:00

It's fun to see somebody with both a knowledge of physics and a sense of humour take on Deepak the Woo-Meister.

Cancelling Coulter:the U of O's shame

2010-03-24T09:44:00.004+01:00

I was much dismayed to learn that Ann Coulter was going to speak at the University of Ottawa. I was even more dismayed to find that the U of O provost sent her a letter warning her of the consequences of hate speech. However, I'm shocked and ashamed that her talk has been cancelled citing "security reasons". The real reason seems to be a response to the 2,000 angry protesters on campus. I support the protesters, but I also support Ann Coulter's right to speak—even if I find what she has to say bigoted, vile, and contemptible.

In the first instance, I don't think she should have been invited to speak at the U of O at all. While I'm not a conservative, I grant that there are probably countless other conservatives with far more scholarly and worthwhile opinions than Coulter. Coulter is the Howard Stern of political punditry, and the more shocking and offensive her remarks the more she thrives. After all, each time she spouts one of her racist, homophobic, or xenophobic slurs, her name rockets up to the top of the headlines. There is all of zero intellectual content in what she has to say. Nonetheless, she had been invited to speak and the attempt to un-do the mistake is simply a farce.

On a university campus, the way to handle cases like Ann Coulter is pretty simple: pack the audience and ask questions at the end. The stage is as much a platform for her to speak as it is one for her to receive the brunt of criticism and questioning of her dispicable views. Universities are marketplaces of ideas, and there's no doubt that there are enough well-informed, intelligent people there who can handle Coulter's hateful rhetoric.

UPDATE: The news now is that it was the organizers themselves, not the university who pulled the plug on this event. Like several other bloggers and columnists, I was quick to pour scorn on the U of O.

Here's the University's statement on the event:

Dear Alumni and Friends,

On Tuesday, March 23, an appearance by Ann Coulter was scheduled on our campus, organized by the International Free Press Society Canada and the Clare Boothe Luce Policy Institute.

The University of Ottawa has always promoted and defended freedom of expression. For that reason, we did not at any time oppose Ann Coulter’s appearance. Whether it is Ann Coulter or any other speaker, diverse views have always been and continue to be welcome on our campus.

Last night, the organizers themselves decided at 7:50 p.m. to cancel the event and so informed the University’s Protection Services staff on site. At that time, a crowd of about one thousand people had peacefully gathered at Marion Hall.

"Freedom of expression is a core value that the University of Ottawa has always promoted," said Allan Rock, President of the University. "We have a long history of hosting contentious and controversial speakers on our campus. Last night was no exception, as people gathered here to listen to and debate Ann Coulter’s opinions.

I encourage our students, faculty and other members of our community to maintain our University as an open forum for diverse opinions. Ours is a safe and democratic environment for the expression of views, and we will keep it that way."

Nevertheless, Coulter is still playing her martyr card, and Faux News, I'm sure, is crowing right along with her.

h/t to tom for pointing this out in the comments. Thanks!

Rotting the tree of life

2010-02-10T20:30:00.006+01:00

There are good papers, great papers, and those clever little papers that make you say "I wish I'd thought of that!". Before I get to that, a little preamble:

Taphonomy is the branch of research that is interested in describing what happens to an organism between dying and ending up as a fossil (or even why it won't end up as a fossil). A lot can happen to an organism in that period of time, as the earth is a dynamic spheroid. The older a fossil, the more possible disturbances it can experience. Taphonomy can tell us a lot about the environment an organism was deposited in and it can provide important controls on the inferences we make about the environment we think a fossil organism once lived in. But taphonomy is also an important consideration in considering what an organism is. That is, the 'life' of a fossil after death, might have a profound impact on how we place that fossil in the tree of life.

Enter the experiments of Rob Sansom and colleague's experiments on lamprey larvae and the title organism of this blog, reported in this week's issue of Nature. Sansom et al. wanted to examine what happens to 'primitive' vertebrates that lack hard, mineralized tissues, the type of tissues that normally fossilize. I say "normally", because there are some 'abnormal' cases in which soft-bodied creatures with no bones, teeth, or hard cuticles actually form as fossils. Some such fossils have played an important role in understanding the timing and early origin of vertebrate animals.

For instance, this species known as Yunnanozoon (Chen et al. 1999) from the Cambrian of China. It represents one of the earliest known vertebrates or vertebrate-like forms.

Yunnanozoon is remarkably well preserved, but other Cambrian chordates can be even more incomplete. The problem with such fossils is that they're difficult to interpret because they're squished, and they're made of soft parts. We have no idea how much they might have decayed, apart from the fact that they seem to be an exception to the rule that soft parts don't fossilize. This usually implies some sort of exceptional conditions favouring preservation, but doesn't necessarily rule out decay or other types of disruption.

Sansom et al. let larval lamprey and lancelets rot in buckets of sea water and recorded the progress of the decay over the period of several months.

The impressive and startling results of watching fish decay are below the fold:

As the animals rotted away, Sansom et al. recorded details of their anatomy. Not just general features, but the types of characters that would be used to score an organism for a phylogenetic analysis. These include classically important features, like the gill filaments, cartilages of the gill arches, the type of heart, the shape of the body muscles, the dorsal rod known as a notochord, and so on. These are characters that have normally played a significant role in establishing the relationships of vertebrates and their nearest non-vertebrate relatives, such as the lancelet.

What this figure shows is the length of time each character survived as the animal rotted. What's striking is that the characters that lasted longer all tend to be characters that we consider phylogenetically more primitive. Characters such as a notochord and segmented axial musculature are all considered to be primitive features shared by the last common ancestor of lancelets and lamprey. On the other hand, features such as eyes, or a chambered heart are more derived features found in modern vertebrates.

This figure shows nicely how the decay features plot out in phylogenetic history. If you go back to figure above, there is a graph showing the relationship between phylogenetic rank and decay stage.

What we see is that the level of decay would lead one to think that the taxon was signicantly more distantly related to the vertebrates, much like the early chordates we find in the Cambrian.

Not only do these results provide a caution against how we interpret soft-bodied Cambrian chordates, but it illustrates a framework for studying the phylogenetic effects of decay. As decay is studied across a wider phylogenetic scope, the more we can determine about the generality of these types of patterns. That will have a profound effect on how we study and interpret the exceptional cases of soft-tissue preservation in fossils.

Chen, Y.-J., Huang, D.-Y., and Li, C.-W. 1999. An early Cambrian craniate-like chordate. Nature 402:518-522 link

Sansom, R.S., Gabbott, S.E., and Purnell. M.A.2010. Non-random decay of chordate characters causes bias in fossil interpretation. Nature 463:797-800 link

Briggs, D.E.G. 2010. Palaeontology: Decay distorts ancestry. Nature 463:741-743 link

Maybe some redemption can be found in parody.

2010-01-11T15:02:00.002+01:00

This review, and all seven subsequent parts made my day.

Early tetrapod footprints from Poland: what changes and what doesn't.

2010-01-07T14:10:00.005+01:00

A few years ago, I wrote a post about prediction in the historical sciences. This post came in anticipation of the publication of Tiktaalik roseae, a remarkably well-preserved fossil of an aquatic animal very closely related to the first tetrapods. I offered this figure to illustrate the position of a gap in the fossil record as a predicate for how/where we might look for fossils that would fit within those 'gaps' in phylogeny.

Yesterday, this picture got a lot more complicated. With the publication of tetrapod footprints some 18 million years in advance of this gap by Niedźwiedzki et al., the nice congruence between the node order of the tree and stratigraphy no longer appears so nice.

Here's a picture of the trackways (click for the full view):

[More below the fold]

This news has already broken, and I'm usually the last person to blog about it these days. Naturally, Ed Young has a good take on it. As noted by Jenny Clack in Ed's piece, the individual footprints are more convincing than the trackways in terms of their identity. Here's one from the supplementary information file (which is free to access).

[Picture deleted: I made a mistake, reading too fast and posted an image of Triassic temnospondyl footprints! A better image is this digital surface rendering from the main paper posted below]

But how "bad" is the record now that we know this? Well, bear in mind that lungfishes and tetrapods are considered (at least by the phylogenies in question) to be sister groups. That is, they split from their last common ancestor at exactly the same time. The earliest 'true' lungfishes (i.e. lungfishes with toothplates, and upper jaws fused to the braincase, etc.) are Emsian in age, roughly the same age as these new footprints. Recognizable close relatives of lungfishes, such as Diabolepis, Youngolepis and Powichthys, however, are considerably older. Do, we can set a minimum age for the origin of the tetrapod stem lineage down in very earliest part of the Devonian even if we do not have the fossils.

So, not surprisingly, the record is pretty bad. It's certainly 'gappy'. But we should not be too surprised that tetrapods emerged long before the time when we find their first actual fossils.

MAJOR news about early tetrapods today.

2010-01-06T19:01:00.002+01:00

Okay, I've exaggerated by putting MAJOR in all-caps, but here it is:

Tetrapod trackways from the early Middle Devonian period of Poland

The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways. The earliest body fossils of tetrapods date to the Late Devonian period (late Frasnian stage) and are preceded by transitional elpistostegids such as Panderichthys and Tiktaalik that still have paired fins. Claims of tetrapod trackways predating these body fossils have remained controversial with regard to both age and the identity of the track makers. Here we present well-preserved and securely dated tetrapod tracks from Polish marine tidal flat sediments of early Middle Devonian (Eifelian stage) age that are approximately 18 million years older than the earliest tetrapod body fossils and 10 million years earlier than the oldest elpistostegids. They force a radical reassessment of the timing, ecology and environmental setting of the fish–tetrapod transition, as well as the completeness of the body fossil record.

I'll update with a detailed explanation soon.

Interesting a reasoned takes on "Climate gate"

2009-12-19T23:46:00.002+01:00

Just a couple of articles worth reading:

"Climategate, global warming, and the tree rings divergence problem"

"A 2,000-page epic of science and skepticism" Part I of a series that continues on Monday, apparently.

Enjoy.

Carl Gans (1923-2009)

2009-12-10T16:08:00.002+01:00

Carl Gans, a giant in the field of comparative and functional morphology, has died at 86.

Dr. Gans has left a profound and lasting impact on vertebrate anatomy and evolution. His work with Glenn Northcutt laid foundations for modern ideas on the role of neural crest in the evolution of the vertebrate head. He was the editor of the 23-volume Biology of the Reptilia, a remarkable source of ideas and data on reptile biology and evolution.

Obituaries: NY Times; CNAH

Tip to Palaeoblog

I never thought of science as a sausage before...

2009-12-09T18:06:00.005+01:00

...but maybe that's because I'm a scientist who happens to be a vegetarian.*

Anyway, John Wilkins has a nice little comment on the CRU emails fiasco. This will definitely be useful for those civilized discussions you're planning on having with that global warming denier in your family over the holidays.

Enjoy!

* and thus, by default, my socialist overlords have decided that I must also believe that global warming is human-caused. Easy enough, because I do.

I'm a disillusioned Mac user today.

2009-11-11T20:35:00.005+01:00

This was a frustrating and disappointing part of my day:

After lunch, I opened my year-old MacBook Pro from its slumber to find a nice set of off-center racing stripes down my screen. Turns out, they go away if I jostle the monitor panel a bit, but that's not going to cut it. The vertical lines will reappear and continue to remind me of the cheap and overrated engineering.

I'm very disappointed by this. My options right now are either to pay to get it fixed or pay to get a new computer. I can't stand the thought of going back to Windows, really. However, the thought of giving Apple another cent of my money is really putting me off. This one forum thread alone can regale you with 12 pages of anecdotes about this same problem with MacBook Pros. Even while under warranty, some folks have gone through three or more new computers—or so the stories say.

UPDATE: Apple has kindly offered to cover the costs of the repair. It's still rather disappointing though.

Stop the closure of the MSU geology department!

2009-11-10T08:59:00.003+01:00

I received the following message recently, via the Society of Vertebrate Paleontology. Please sign the petition.

The Department of Geological Sciences at Michigan State University is home to a nationally and internationally prominent, vibrant group of students, faculty and staff. As a response to current budget distress, the Board of Trustees and Provost Kim A. Wilcox are considering a proposal to close the Department, along with all of the graduate and undergraduate programs offered by the Department. The immediate effect will be the loss of three tenure-track untenured faculty positions and one technical and three office staff support positions. Longer term effects of such a closure would include the loss of formal geosciences as a fundamental part of undergraduate and graduate training, and would impair Michigan State University’s service to students, the local community, and the global scientific community.

To offer your support to geosciences at MSU and oppose closing the department, please add your signature to the petition located at:
http://new.ipetitions.com/petition/savegeosciencesatmsu/

Please also consider passing the petition along to others who would offer their support.

More unfortunate fallout from celebrities vs. science

2009-10-24T11:51:00.004+02:00

It looks like the anti-vaccination crowd is starting to have the effect they want on public opinion. This article is not very encouraging.

"I don't believe in the flu shot," said a typical posting on a Canadian news website this week, which went on to suggest the vaccine could have the same effects on pregnant women as Thalidomide. "I refuse to be a guinea pig."

An Ipsos Reid survey for Canwest News Service released yesterday suggested that barely half of Canadians were even somewhat likely to get the shot.

At the same time, I'm a bit encouraged by the reporting in that article. I does not give any credible space to antivax lunatics. It does look to the 'other side' of the question of the H1N1 vaccines (or flu vaccines in general), by considering the opinions given by a team of university-based researchers—not Bill Maher, Jenny McCarthy, or Jim Carrey.

The opinions of these wack-o Hollywood types are winning the battle of public opinion, however, and more of this type of reporting is going to be needed. The article also has a list of figures at the end which, I think, also helps mitigate some of the over-the-top media hype about this flu, while providing evidence against the unfounded claims about the dangers of this new vaccine.

What's been going on? Some academic musings.

2009-10-22T17:26:00.005+02:00

So, what's been happening in the past few days (weeks?) since I last posted? Well, autumn is setting in here, so it's not like I'm spending a lot of time outside right now. I've been focused pretty much on a few things: writing a manuscript, updating a dataset, writing a job application, and learning some programming skills.

One of the nice things about being a postdoc is the flexibility of your time. It is an important period in the life of a researcher where you not only apply those skills you already learned towards being productive, but you have the opportunity to learn new ones. I'm picking up where I left off early in my postgraduate education, learning new tools and tricks for the software environment R. This really is an indispensable tool for biologists, or anyone who applies statistics. I would hope that in the near future, R will become an integral part of undergraduate biology curricula. It combines the ability to analyze data with a programming environment.

As much fun as being a postdoc is, I really want a permanent job—a good one, with lots of interaction with enthusiastic and creative students. Being a postdoc can be limiting, too. There are lots of small cash funds for Ph.D. research projects from various scientific societies, institutions, or funding agencies. I've had a lot of success with these as a Ph.D. student, and I really think they are important in helping students b. On the other hand, faculty tend to operating grants: a fund that supports their research throughout the year or several years. Somewhere in the middle is the postdoc, who has to rely either on his host's grant (allusions to parasitism here may or may not be intended), or the very few small (and therefore competitive) external sources. Thankfully, my current project can make use of a lot of published data, as well as data existing within our collections at this museum. However, I certainly feel the need to grow and develop something much larger and sustained.

Dawkins on O'Reilly

2009-10-10T19:11:00.002+02:00

Bill O'Reilly is a dunce, but Dawkins could've done a lot better.

Sometimes, it takes comedians to communicate science more effectively than scientists themselves:

O'Brien has every answer that Dawkins needed for this debate against O'Reilly.

"The moon is a huge water balloon" and other wisdom.

2009-10-09T16:51:00.002+02:00

NASA sure does know how to drag out the kooks. NASA's innovative new project for studying the Moon's chemistry and attempting to detect water involves effectively slamming a projectile into the Moon's surface and analyzing the resulting ejecta. The Register reports on the crazies who are concerned about the US government's latest 'bombing campaign':

He wasn't alone, either, with various observers backing the surrealists' possible belief that NASA might inadvertently cause major havoc with their crater strike. This might seem to be impossible given the bigness of the Moon, the smallness of the LCROSS, and the laws of physics - but there were those who disagreed. Commentard Greenstar perhaps summed up this point of view best:
Think of the planets in terms of forming a sentence. The Earth is a noun. The moon is a verb. Its very existance creates action in the tides, the weather, and possibly human mood. It's perfection of rotation sets into play all the components that make it possible for life here to exist and yet no life exists there. How is that possible? Wouldn't it seem logical for the earth to have a reciprocal effect on the moon - but it doesn't. The laws of symbiosis don't apply. If the moon is nothing more than a big rock then it can be cleaved like a big rock. Laws of mass and density don't apply nor do they offer us protection from the idiots at NASA who have never watched a diamond cutter. They are big boys with BIG toys and brains the size of a TRex AND are running the risk of making us all extinct.

In the meantime. The reality-based community can follow the LCROSS project at NASA's LCROSS website

Larry Moran on Ardipithecus

2009-10-04T16:25:00.003+02:00

Larry Moran has a good piece about the newest fossil hominid find, Ardipithecus ramidus. He goes after some of the irresponsible reportage from both the journalists and scientists alike. Having dealt with the sometimes difficult task of explaining the significance of certain new fossils to journalists, I can understand that sometimes things would get lost in translation. However, here we have an example of highly problematic statements coming from both scientists and the media.

I've got a lot on my plate this week, but I would like to write a comment or two about Ardipithecus this week. Hopefully I'll have that up soon.

Primordial soup with Julia Child

2009-10-03T13:38:00.002+02:00

Seriously.

(Via onegoodmove)

On the use of the stem group concept.

2009-10-02T11:00:00.002+02:00

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.

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.

The return from SVP

2009-10-02T06:30:00.002+02:00

I returned from the UK on Tuesday after attending the SVP meeting and then visiting a friend in Oxford. Sorry I've not been posting. My talk went well, and I hope to be able to post a summary with some slides here. The meeting was quite productive, at least in terms of making some contacts and plotting some plots, etc.

"We have a village idiot in this country; it's called Fundamentalist Christianity"

2009-09-17T11:12:00.004+02:00

Wise words from Frank Schaeffer.

Visit msnbc.com for Breaking News, World News, and News about the Economy

The video is well worth a watch, if you like to see a former Christian fundamentalist use some damning rhetoric against the batshit crazy group he used to be part of.

(Via Evolving Thoughts)

That snake with a leg...?

2009-09-16T18:10:00.005+02:00

There's been a report of a snake with a legs and toes in the media recently. The blogosphere has some interesting comments on it, too. Most notably, there is skepticism. Take a look at our snake in question here:

In a comment on Pharyngula, Jerry Coyne notes:

I suspect that this snake ingested a lizard, and that the lizard's limb simply burst through the side of the snake. I may be wrong, and I hope so, because this is great evidence for evolution.

Some graphic images below the fold illustrate why this is not unreasonable speculation.

Snakes sometimes consider their prey choices poorly. Here's a snake with legs and two tails:

(Hat tip to Febble)

Oops! I sort of skipped the first comment at Pharyngula. This commenter noted first that it was probably something the snake ate. Moreover, they note a fact I forgot to mention in my haste: the limb is quite far from where we'd expect the hindlimb to be, if one were to show up. It would be much closer to the tail, not at mid-length of the body. It should be at approximately the same level as the cloaca. There's the unlikely case that it's an atavistic forelimb however, which would raise the issue of where a snake's neck begins or ends.

Rampant paraphyly on Wikipedia

2009-09-16T17:51:00.006+02:00

I've just been having a look at some of the Wikipedia pages about certain bony fish groups, particularly Sarcopterygii and Rhipidistia. These need some serious fixing. There's a lot of stuff out there about 'ancestral groups'. That is to say, describing a group as the ancestor of another group.

"Tetrapods — four legged[sic] vertebrates were the terapodomorphs'[sic] descendants."

"Rhipidistia is now understood to be an ancestr for the whole of Tetrapoda."

The notion that a group is 'ancestral' is a bit misleading, especially if we accept that groups (i.e. clades) are actually the descendents of a single common ancestor. That's not really the problem, though.

Let's look at each of the quotations below the fold.

The first one claims that tetrapods descended from tetrapodomorphs. The actual meaning of 'Tetrapodomorpha' is the tetrapod total group (Ahlberg, 1991). By definition, this group includes all tetrapods, and any and all fossil taxa that are more closely related to tetrapods than to any other extant group (in this case, probably lungfishes: the Dipnomorpha). Tetrapods are a subset of Tetrapodomorpha, not descendents of them.

The second quotation is similar. Ahlberg (1991) also re-defined 'Rhipidistia' cladistically as the Dipnomorpha + Tetrapodomorpha. In this sense, Rhipidistia is monophyletic. However, the Rhipidistia was a pre-cladistic grouping meant to encompass porolepiforms and 'osteolepiforms'. Porolepiforms (probably a real clade) and the 'osteolepiforms' (not a real clade) represent an assemblage of lobe-finned fishes that would look quite similar to an 'untrained observer'. This similarity is mostly just shared primitiveness. That is, it does not unite them to the exclusion of other taxa (namely lungfishes in the case of porolepiforms; and tetrapods in teh case of 'osteolepiforms').

Figure 1. Some 'rhipidistian fishes'. Top: Holoptychius. Bottom: Eusthenopteron along with an illustration of its pelvic and pectoral fin endoskeletons.

What is significant about 'rhipidistians' in the classical sense (i.e. before Ahlberg's 1991 paper) is that they lack synapomorphies or homologies. They have to be defined on the basis of a set of characters and character absences, implicit and explicit, that is hand picked to exclude other groups. They are 'fishes', meaning they have fins (not digits) with lepidotricia, bony dermal rays. But these are also found in the early tetrapods Ichthyostega and Acanthostega. However, these latter taxa lack an intracranial joint, a division of the front part of the braincase from the back part that contains the ear capsules. Coelacanths also have this division, but they are not rhipidistians. However, coelacanths lack the dermal skull bone characters, such as a maxilla, that are found in 'rhipdidistians' such as Eustheonopteron and Holoptychius showing in Figure 1., above.

As you can see, it quickly becomes obvious how the defining characters are arbitrary, in some sense. They are picked to justify a group of taxa that share some overall similarity. It does not reflect an attempt to discover the hierarchical relationships among characters. This latter process is the discovery of homology: the characters that unite monophyletic groups. It is in this way that real evolutionary relationships are discovered; not through the nomination of "ancestral groups".

Ahlberg, P.E. 1991. A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes. Zoological Journal of the Linnean Society 103: 241-287.

Brief update

2009-09-16T17:04:00.002+02:00

This week, I've been working on my presentation for this year's Society of Vertebrate Paleontology meeting in Bristol. The conference is next week and I've got my own talk, plus contributions to another talk and a poster. Unfortunately, I can't post details of my talk until after the meeting, because the abstract is embargoed. This year looks somewhat promising. There was a record number of abstract submissions, so a lot of the papers that focused on strict descriptive alpha taxonomy did not make the cut. I'm quite happy with that, to be honest. I don't really need to travel a long way to see talks on descriptions of new animals when, in a few months, I can read and use the paper. I'm a bit more interested in seeing progress on sorting out the relationships of problematic taxa, and maybe learning about novel uses for fossils. There's some promising stuff this year.

Spent part of last week on holiday in Prague. One of the great things about living in Europe is the short distance to all these great places.

First reactions to The Greatest Show On Earth

2009-09-07T23:02:00.002+02:00

The Guardian has run a review by Richard Fortey of Richard Dawkins' upcoming book The Greatest Show On Earth. I won't get a free review copy, I'm sure... so I'm probably not going to spend time reviewing it myself. However, it looks like it's a feed of standard fare. I'm a bit comforted by this video, as it sounds like Dawkins doesn't waste much time with fossil apologetics. However, I'm wondering to what extent concepts such as homology, palaeontology, biogeography, and embryology are disjoined in their presentation. I wonder when someone is going to write a book about that for general consumption.

Anyway, here's the video plug:

Anyway, I'm off to Prague until Friday. Probably won't have much of a chance to blog again before that. Consider this an open thread.

Oh no! Silence again?

2009-09-04T12:57:00.002+02:00

No. I just have family visiting this week and haven't spent much time close to the computer. Instead, I've been guiding half-assed historical tours of Berlin, visiting museums and the aquarium, etc. etc.

I was unaware before yesterday that the Berlin Zoo actuall has a live, captive Tuatara. These poor beasts are on the verge of extinction, something they are often credited with dodging for over 220 million years. That's not exactly true, of course, because modern Sphenodon are not identical to fossil ones, but nevertheless they are the last surviving representatives of that extinct clade.

"Merck published fake journal"

2009-08-31T13:00:00.002+02:00

I've been wanting to blog about this for a while, and it's a story that I don't think should die. Merck is a major pharmaceutical manufacturer who requires no introduction. Elsevier probably requires no introduction to most readers of this blog, but if you are not familiar it is a publishing company that owns an enormous swathe of scientific journals, including top-ranked titles such as Cell and The Lancet. Chances are, if you've done research in science you've linked through the Elsevier or ScienceDirect sites.

According to an article in The Scientist:

Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles--most of which presented data favorable to Merck products--that appeared to act solely as marketing tools with no disclosure of company sponsorship.

From the Nature News article

In a statement released on 7 May, Michael Hansen, chief executive officer of Elsevier's Health Sciences Division, acknowledged that, between 2000 and 2005, an Australian office of Elsevier had distributed promotional periodicals that were packaged as journals, without disclaimers clearly marking them as industry-sponsored products.

[...]

During the trial, George Jelinek, a member of the World Association of Medical Editors, testified that the publication would be commonly mistaken for a peer-reviewed journal, even though it was sponsored by Merck and contained only articles that drew positive conclusions about Merck products.

Additionally, the publication listed an "honorary editorial board." One of the listed members, Australian arthritis specialist James Bertouch, reportedly testified that, until recently, he did not know of the journal's existence.

This sort of thing is rather disturbing. To me, it speaks of the dangers of letting a small number of corporations own the bulk of scientific publications. What is equally disturbing is the relative lack of press this story got. This story first appeared in The Scientist and Nature following the report of a lawsuit against Merck. I've seen remarkably little about this elsewhere and it would be a shame if the story died. I'd be interested if anyone could post their own or links to further commentaries about this.

Oops!

2009-08-28T15:08:00.002+02:00

"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

Coming soon...

2009-08-27T17:59:00.003+02:00

Here's an interesting project: The Science and Entertainment Exchange. Okay, this is already here, but it will be interesting to know what long-term impact this has on the quality of science portrayal in popular media. Basically, the US National Academy of Sciences is proposing an agency through which to advise entertainment media on portrayal of scientists and scientific matters. An interesting and hopefully fruitful endeavor.

My only concern is that it might end up causing science, as portrayed in the media, to represent the minority of some particular scientists, even if they are members of the National Academy, or are considered 'top' in their field. Oh well, if it can prevent another Mission to Mars disasterpic, then that will right any injustice caused by a mere biased perspective.

(Via Pharyngula)

"Inferred justification": how we support our false beliefs

2009-08-27T17:46:00.002+02:00

A recent study in the journal Sociological Inquiry investigates how we support false beliefs.

Abstract:

One of the most curious aspects of the 2004 presidential election was the strength and resilience of the belief among many Americans that Saddam Hussein was linked to the terrorist attacks of September 11. Scholars have suggested that this belief was the result of a campaign of false information and innuendo from the Bush administration. We call this the information environment explanation. Using a technique of "challenge interviews" on a sample of voters who reported believing in a link between Saddam and 9/11, we propose instead a social psychological explanation for the belief in this link. We identify a number of social psychological mechanisms voters use to maintain false beliefs in the face of disconfirming information, and we show that for a subset of voters the main reason to believe in the link was that it made sense of the administration's decision to go to war against Iraq. We call this inferred justification: for these voters, the fact of the war led to a search for a justification for it, which led them to infer the existence of ties between Iraq and 9/11.

The authors introduce a new term: "inferred justification", as one of several mechanisms for how we support beliefs which are unsupported or even contradicted by evidence. The authors describe inferred justification as (in this particular case): "recursively inventing the causal links necessary to justify a favored politician’s action." What the authors found in many interviews with people who were in favour of the current Iraq war was that, in spite of evidence against a link between 9/11 and Saddam Hussein's regime there 'had to be a reason why we were over there'. Naturally it followed, in the minds of the respondents, that Saddam must have been responsible for the 9/11 attacks.

While the authors focused this particular study on the Saddam-9/11 question, I would imagine that this phenomenon is pervasive throughout life, and even much of science.

The Twat-O-Tron

2009-08-26T17:46:00.005+02:00

If, like me, you're (not) a fan of the comments on news articles that usually devolve into the rubes wanting to reincarnate dead conservative icons and reinstating the death penalty, you'll love the Twat-O-Tron, developed after the BBC's "Have Your Say" (HYS) feature. It will (almost) randomly generate a reactionary right-winger comment.

Here are some wonderful examples:

[Courtesy of the Twat-O-Tron] In my opinion non-taxpayers are banning nursery rhymes because they are foreign and its what they do. The only solution is to bring back flogging and the death penalty i say. FACT!!!!

[Courtesy of the Twat-O-Tron] The bbc pretends its not true but Asylum seekers are helping their scottish comrades because they've allowed immigration to go unchecked!. Come on send them back where they came from. Hell in a handcart!!!

[Courtesy of the Twat-O-Tron] this post will probably be deletde. . the media wont admit that French farmers are building mosks on every corner. It's time we send the mback where they came from. It could only get worse if the french start coming over!!!!!!

It's hard to tell them from the real thing. Don't get ahead of yourself, however. The Turing test is for artificial intelligence. We already know that robots exist.

Bill Maher--New Rules

2009-08-26T14:09:00.001+02:00

This is one of the best ones I've seen in a while.

A couple of re-posts

2009-08-26T01:06:00.002+02:00

Since I've been trying to inject some new life into this blog, I figured I'd link back to some of the few posts that tricked out over the past year or so that might be worth revisiting.

Here are a couple on homology:
Open thread: are genes really a guide homology?

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

A dubious honour...

2009-08-25T20:08:00.009+02:00

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.

Blogging back to life

2009-08-25T18:40:00.002+02:00

I keep trying to revive this thing, and I keep getting distracted. Just shows you something. I believe in communicating science to the public, but I guess my heart is in doing research... especially right now and this early in my career. Nevertheless, I hope to have a few posts up on what I've been working on and what I've been thinking.

Mostly, however, I've just moved to Berlin where I've taken up a postdoctoral fellowship at the Museum für Naturkunde. Slowly, I learn little bits and pieces of German, too... and enjoy the cheap and tasty beer that can be found here.

The Society of Vertebrate Paleontology Annual Meeting is coming up in September. It will be in Bristol, UK. I'm giving a talk. I think the abstracts are embargoed, so I don't think I can publish details of my talk here, unfortunately. But I'll do so as soon as I can.

I'm in the process of writing a review about a topic that has been done to death. Why write a review, you say? Because, in spite of the number of times it's been done to death, the side that is wrong still hasn't died, apparently. Eek! This is taking up a bit of my time because, as you might expect, it's stalling and stalling... kind of like this blog!

In the meantime, I'm CT-scanning lizards*, legless lizards, and snakes at a micro-CT scanning facility here in Berlin. I'm also in the midst of setting up a breeding colony for geckos. Perhaps as things develop more, I will write a bit more about my current project which (as you might have guessed) is somewhat removed from my previous work on fossil fish.

*OH NO! I just use a paraphyletic group! More on that later.

Nice fossil, shame about the name...

2009-05-20T16:21:00.002+02:00

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".

Evolutionary gems

2009-01-08T22:52:00.003+01:00

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.

LOL!

2009-01-08T22:47:00.003+01:00

A colleague of mine who works on fossil sharks just received an interesting request. He was asked by a woman in Florida to confirm that, indeed, the image of Christ on the cross appears in her father's fossil shark tooth necklace. You know, some people should not go advertising their gullibility under such potentially compromising situations. I wonder if he should take a fee for this service... I'm sure he could probably fund part of his research by using this as a sideline.

Anyway, I thought I just had to share.

SPAMMED!

2008-12-01T11:12:00.003+01:00

I'm getting a major, major spam attack on this blog. Unfortunately, I'm going to have to turn on regristration and moderation... at least until the attack subsides. Sorry! But, since activity is very low these days, it won't inconvenience too many people, I hope.

The end of the long road. A new beginning.

2008-11-27T19:05:00.003+01:00

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...

Except was no such fella as Noah...

2008-10-08T11:25:00.002+02:00

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

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

2008-09-19T11:02:00.009+02:00

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?.

Open thread: are genes really a guide to homology?

2008-09-18T23:23:00.002+02:00

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.

"It will have been more than worth it"

2008-07-20T23:08:00.002+02:00

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.

Reader comments: Learning about evolution

2008-03-06T08:41:00.005+01:00

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!

Define evolution in one sentence!

2008-03-05T16:18:00.003+01:00

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.

Episode IV: A New Pope

2008-03-03T20:39:00.000+01:00

This made my day...

Being wrong for all the right reasons.

2008-03-02T11:58:00.005+01:00

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.

Oh Canada. Our home and emergent theocracy.

2008-03-01T19:13:00.003+01:00

This disturbing news item came through via Pharyngula. I especially like PZ's analysis of this story, so please give it a read. If the government can deny funding for artistic projects it deems offensive, then what's next for other government-subsidized human enterprises? I dunno, like science?

Notwithstanding the apalling injection of religious piety into public policy, this is a classic example of conservative hypocrisy: "The Government is a bad thing, and it should stay as far from intervening in your life as possible... except when we're The Government. Don't let the government and its endless reams of bureaucracy take away your freedom and right to choose. But, we sure as hell know what types of movies and television you should watch!"

Beyond anything, however, is the most dispicable equation of homosexuality with "graphic violence":

Charles McVety, president of the Canada Family Action Coalition, said his lobbying efforts included discussions with Public Safety Minister Stockwell Day and Justice Minister Rob Nicholson, and "numerous" meetings with officials in the Prime Minister's Office.

"We're thankful that someone's finally listening," he said yesterday. "It's fitting with conservative values, and I think that's why Canadians voted for a Conservative government."

Mr. McVety said films promoting homosexuality, graphic sex or violence should not receive tax dollarsEmphasis added, MDB

People didn't like Brian Mulroney, but I don't think that even he as a conservative would have ever promoted measures such as these. The Conservative Party of Canada is not the old product, folks. It's a relabeling of a much more sinister enterprise with a familiar label. Stop voting for these people like they are the party led by Brian Mulroney, or Joe Clark, or even John Diefenbaker.

Canada phases out PM science advisor office

2008-01-27T22:29:00.000+01:00

Well, I'd say "holy shit", right now, but that would express some kind of surprise. I remember when the position of science advisor to the Prime Minister was created by Paul Martin. I thought this was a great step forward: a lawyer asking a scientist for advice. Oh how we Canadians are so enlightened. Well, it appears as though His Holiness Stephen Harper has decided to phase out the position when it's current (and only ever) holder retires at the end of March.

So, there it is folks, the leader of one of the richest industrialised nations in the world doesn't need someone to advise him on science. No, of course not. Science has too many facts, is far too self-critical, and requires rigorous thought to permit oppotunistic conservative expedience. This would be more dismaying if I had even the slightest admission that Harper ever even considered consulting this office.

See this editorial by one of Canada's leading science journalists.

(via Pharyngula)

The Story of Stuff

2007-12-20T13:43:00.000+01:00

If you've ever wondered where all our consumer goods came from, and where they go when we're done with them (or when we never sell, buy, or use them in the first place), then here's an interesting video. It's called The Story of Stuff.

Albeit it's quite dramatic. A bit too much for my tastes and is perhaps a bit thin on details (it is only 20-minutes long, though). But I think the overarching message is quite important: our numerous gadgets and goods come at a cost that is not borne by us. More importantly, however, the fallacy that "consumerism is good for the economy" is challenged here by the argument that consumerism is good for a particular type of economy. There are other types of economies than the massive free-market capitalistic economy that is consuming nations and livelihoods globally, as the video shows.

The origin of whales and "missing links"

2007-12-20T13:01:00.000+01:00

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.

Science as a process: placoderm muscles revisited

2007-12-06T20:42:00.000+01:00

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.

Look out for Expelled

2007-11-26T08:46:00.000+01:00

Although the amount of creationism I tackle is supposed to be diminishing, come February that won't be possible. When this new creationist propaganda reel, Expelled, hits theaters the bullshit is going to hit the fan and we're going to have one mighty mess on our hands.

Here's the cringe-worthy preview:

These guys just don't get it, do they? Yes your ideas are being discriminated against. That's how science works. Other scientists have looked at your ideas and shown them for what they are: vacuous bullshit. Responsible scientists discard such ideas. Unfortunately, when a person clings to discarded and discredited notions, they discard their own credibility too. Oh yes, and poor Sternberg. Of course, violating editorial procedures to do your friends a favour is such a laudable and noble thing to do, after all. Hello? We'd can anybody for that.

The clip is only a preview, and they're already quote-mining Richard Dawkins, who's seen saying something to the effect of: "As a scientist, I'm pretty hostile to rival doctrines...". This clip is inserted at a convenient time, but that's the last we hear from Dawkins. I suspect that Dawkins was explaining the checks and balances within science. What promotes good science is that there are other scientists out there who are going to take shots at new and rival scientific ideas. Scientists tend to be good at this. Alternatively, he explains why the supposed rival, in this case "intelligent design", is utter bollocks.

But this is clearly something the folks at the Discovery Institute and other ID proponents don't get: this is how science works and their ideas have been discarded. Clinging to them is, and ought to be, career suicide. Instead, they are choosing to legislate, litigate, and propagandize their way into equal standing. They couldn't come up with the scientific goods, so they came up with a lot of money and a movie.

(Via Pharyngula.)

Buy Nothing Day!

2007-11-21T22:16:00.000+01:00

Buy Nothing Day, a day where you . . . buy nothing!

Put a lid on excessive consumerism during one of the year's biggest shopping days.

In North America: 23 November, all day.

International: 24 November, also all day.

"Our beloved corporate gods who claimed they created rock video", MTV, have dug deep into their bag of excuses for not running the official BND ad from Adbusters: The ad "goes further than we are willing to accept on our channels".

Yes, because a burping pig is way below the standards of MTV...

The BND site also explains Buy Nothing Christmas:

"Buy Nothing Christmas is not really about refusing to spend a dime over the holiday season. It’s about taking a deep breath and deciding to opt out of the hype‚ the overcrowded malls‚ and the stressful to–do lists. It’s about reminding ourselves to really think about what we are buying‚ why we are buying it‚ and whether we really need it at all."

Actually, in my family, we've taken to not buying gifts at all. We did it for the first time last year and only exchanged cards. I think it was one of the best Christmases in recent memory. Instead of panicking in jammed parking lots, dodging slow-walking, bag-loaded, bleary-eyed shop zombies, I spent the time with my family, who I hardly see since I moved out of the country three years ago.

JREF site re-design

2007-11-19T14:09:00.000+01:00

The James Randi Educational Foundation has undergone a massive site re-design. It's high time. They've now got lots of media, including videos that are well worth watching. As usual, Randi continues his weekly newsletter and his relentless battle against pseudoscience.

PBS Judgment Day online and short review.

2007-11-19T13:50:00.000+01:00

The PBS documentary, Judgment Day is not available for viewing online (Safari users: the video might give you problems. Try a different browser if you have problems).

I agree with most of the other science bloggers out there that it was a really good program. I have a gripe, though. I think they missed a key point about why the statement is a bad idea. They did allude to the fact that the statement read to the students singled out "Darwinism" (read: evolution). However, they did not cover Brian Alters's testimony which, to my mind, was particularly important on this issue. Alters pointed out that by singling out evolution for particular critical analysis, it misleads students about the rest of science. As Ken Million said as well, all theories in science are tentative and provisional, so why single out evolution.

The Dover board members who advocated for the statement on intelligent design were not simply trying to "make students aware of another theory". It was systematic way of discrediting evolution with an underhanded tactic: single out a truism about all scientific theories (that they are provisional), but only mention it in relation to evolutionary theory. I think that could have driven the point home.

There are also some other minor gripes, but those have been taken up elsewhere.

Alan Alda undermines himself to good effect.

2007-11-19T11:53:00.000+01:00

Alan Alda has long been a champion of critical thought and good science education. His public lectures and hosting Scientific American TV. Check out his appearance on CBC's The Hour. As always, he's funny an articulate and tells us his reasons for not talking publicly about politics: "We don't need one more person telling us what to think who doesn't necessarily have qualifications, but he believes in it... If we just keep putting people up because people will listen to them, then I think we get out of the habit of asking people to come up with evidence for why they're saying what they're saying".

Ironically, I think it's great that Alda says these things. In a sense, he undermines his own point by bringing that argument to an attentive and young audience. Sorry Mr. Alda, but you're going to have to keep saying intelligent things!

Back to life...

2007-11-19T11:42:00.000+01:00

It's time to bring this blog back to life. It's had a lot of visitorship despite the inactivity over the past few months. I'll not list my excuses for my absence here. I'll try to post something of value at least once a week!

A few new things you'll see (or won't see):

-Blogging peer review. I hope to be introducing these new icons in relation to summaries of refereed papers.

- Less about creationism. Yes, less. I have only one major riposte planned for AiG, and a "think piece" about godlessness and morality, and after that I will try to stay away from it. They provide easy substance, but I feel that polemics about creation vs. evolution get in the way of talking about real science in an engaging, but still disinterested way. No amount of counter argument is going to convince a creationist. Reliable, responsible science writing, however, will inform those who wish to be informed. The creationists who infiltrate school boards and try to put their crap into the curriculum don't give a shit about science. They couldn't care less if Pluto is a planet or why, or if we all come from fish. What they care about is the moral ramifications of what they see as secular materialism. I'll cover that later.

- More about critical thinking in general. Though, ironically, I won't always be putting up my own material. In addition to my own thoughts, will try to be more active in giving out some "link love".

- Frequency. I'll try. I promise. I have to admit that I put my own research and career ahead of the blogging business. I believe that blogging is a small and effective thing I can do to make myself and my science accessible to a general audience. But I have no intentions of ever giving up research for a career in science writing.

Something fishy at YouTube

2007-09-11T19:14:00.000+02:00

Apparently, videos critical of his Criminalness Kent Hovind are being taken down from YouTube. This has popped up in the comments on this blog in a few places. I'm not sure what the deal is or how they're getting away with it. My guess is that they're claiming copyright over the material in which Hovind appears and that the use of that material is in violation of that copyright. In my opinion, everything that I have seen is in agreement with fair use practices.

My guess is that it's thuggery. Of course we won't see the non-critical vids being taken down, only those critical ones, I'm sure. Of course, until that starts to cut into CSE profits.

There's more at Pharyngula.

Reasonable people can be pursuaded by reasoned argument

2007-08-31T00:18:00.000+02:00

I travel a lot, and I meet a lot of people, and I'm happy to harbour fellow travellers in my home (this isn't an invitation, I note.). I recently had a guest who is on a six-month trip around Europe, and who is a veteran of the current wars in Iraq and Afghanistan. We had many enjoyable discussions over a few beers and good food. A frequent and obvious topic of discussion were the current wars and the subject of terrorism. We were, of course, of two very different worlds of experience and, despite my disagreements with current policies, remained humble and interested in knowing his opinion.

In our discussions about terrorism and the impact it has on western values and society, my guest proffered the sentiment that many people sympathize with. Essentially it is that 'I am willing to sacrifice a few personal freedoms to guarantee or increase my security against this threat'. This sentiment is frequently (and was in this case) backed by the statement that those who complain about these measures might very well sing a different tune if something bad ever happened to them.

I explained that the reaction to these measures is driven by something greater. Those who drafted the constitution of the United States of America knew full well of the threat of despotism and dictatorship. The document was drafted with the view that it should protect the freedom of people from these threats. Throughout history, we can see that democracies have crumbled through the peoples' willingness to curtail a few freedoms here and there to allow their government to protect them from some threat, external or internal, real or perceived. The actions of the current administration appear to be drawn directly from this playbook and people with a sense of history and knowledge of their constitutional freedoms are weary and suspicious.

There is a balance of threats here. One is the (apparently) imminent danger of attack by terrorists. But the other is of a despotic regime who will threaten peoples' right to gather peacefully and challenge the decisions of their government. The latter threatens everybody's right to live in freedom and to decide who shall lead their government.

I explained that those who oppose the measures being taken in the name of security are aware of their gambit, but choose instead to protect those things that are sacred to all living and future generations.

"I never really thought of it that way" said my guest.

That was enough for me. Reasonable people can be reached by reasoned argument. Sometimes, it's worth it.

Where was the blood? The guts? The horror?

2007-04-26T19:02:00.000+02:00

I didn't see O'Reilly's guts on the floor (either by evisceration or by massively aggravated expulsion). Neverthelss Dawkins did okay but don't get your hopes up. You're dealing with Dawkins vs. a man who referred to the "physiology" of the universe. And by that I mean, yes, a retarded individual who has his own cable program. Sometimes there's an audience for such programming...

As usual, onegoodmove has the clip. That site is like my only TV. I do not own one at home, I simply depend on 1gm to supply the goods. It's a daily stop, make it yours.

Oh. My. Dog!

2007-04-20T00:11:00.000+02:00

Richard Dawkins will be on Bill O'Reilly's program. I thought Dawkins didn't grant interviews with total numbskull crank idiots. I wonder if it could possibly be as good as the Geraldo incident.

(via onegoodmove)

Dinosaurs and Devonian fish: A field trip through Victoria

2007-04-18T00:33:00.000+02:00

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!

Melbourne Pt. I

2007-04-05T00:25:00.000+02:00

Now that I've had a few days to adjust, here's a few pics of what I've seen so far. I've been working at the Melbourne Museum (Museum Victoria). Nothing really of substance to say here, just a few pics of the environs I've been working in.

Here are the grounds of the museum, with the Royal Exhibition Building (REB) on the left and the Melbourne Museum, the modern glass wall building on the right.

A fossil of the Devonian placoderm fish Bothriolepis from Gogo, West Australia. The specimen shows the awesome three-dimensional type of preservation that can often be recovered from the site. Sadly, the model of the body attached to it is wrong: Bothriolepis only had one dorsal fin and no pelvic fins. The model makers are making a new one, however.

The palaeontology laboratory below REB.

Fossil fish palaeontologist John Long and a fossil fish from Gogo.

A little bit about what John is doing: No, he's not making crystal meth. He's applying ammonium chloride sublimate to the specimen. this technique is used to increase contrast and give a matte finish to specimens to acheive better photographic results. Powdered ammonium chloride is heated in a glass cylinder and a thick white smoke (sublimate) is produced and blown over the specimen. Unfortunately, ammonium chloride reacts very slowly with airborne water vapour to produce hydrochloric acid. If it is not removed soon enough after application, it can damage specimens and this technique is viewed by some as a conservation risk. However, it is very easily removed with luke warm running water and if you're thorough, it shouldn't be a problem (just don't do it all the time!).

The REB in the evening:

That's all for now. Fieldtrip on Friday and over the weekend, conference next week. More of substance to say then, and I'll be able to recount all the details of the skewering I will be getting after my talk.

Oz 2007; First Lancelet Open Thread

2007-04-02T01:05:00.000+02:00

Well, I'm sitting in the airport in Kuala Lumpur, in transit to Melbourne. They have free wifi here! I'll be spending the next two months in Australia, attending a conference, doing a little bit of fieldwork, and hitting all the museum collections I possibly can whilst still making time to try surfing. I just completed the first, 10-hour leg of this journey and so I'm pretty stunned right now. It was a good trip though. I like flying in 747s, especially as their massiveness sails them through turbulence with hardly a bump. I will update this post later once I get to Melbourne.

In the meantime, consider this the first open thread at The Lancelet (I know, I should have had more long ago!) I'd really appreciate hearing from Australian readers (and experienced Australian travellers) about places to hit, cheap transportation, etc. etc. Otherwise, just go nuts in the comments section.

Well, it's 1:20 AM in Melbourne, but I made it more or less in one piece and alive, I think... It's now a question of how well I will sleep. So far, I have hardly any impressions of the place as it was dark when I got here. Will write more with pictures later. In the meantime, start posting in the open thread!

Dr. David Menton is a liar.

2007-03-13T15:47:00.000+01:00

(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.

Hovind and Haeckel's embryos

2007-02-17T22:10:00.000+01:00

If you've been following the news surrounding Randy Olson's documentary Flock of Dodos, you've probably caught a whiff off the stink that the Discovery Institute has been raising, claiming that Olson is essentially lying about Haeckel's embryos in biology textbooks. PZ Myers has put up a post consolidating his responses (a blogrpahy?) of his responses to the DI claptrap.

As my thesis work relates specifically to the pharyngeal arches of early fossil vertebrates, the creationist nonsense about Haeckel, embryonic "gill arches", and evolution naturally gets me all bent out of shape as well. I once called up Kent Hovind in his radio show to challenge him on the matter. Well, somebody made a YouTube video with a segment of the call!

It seems to be a rather popular clip and has raised some controversy in the comments section of that video. I, for one, felt that whole telephone call could have gone a lot better, but apparently I did OK.

I should point out that while the neural crest tissue that I talk about in that vid does form part of the pharyngeal arches, it's important to note that all the germ layers of the embryo (mesoderm, enoderm, and ectoderm) are involved in their construction. They are not merely "folds of skin" as Hovind frequently claims.

More cool geology

2007-02-17T21:58:00.000+01:00

I figured I should say a little more about the fiedlwork I was up to in January. This latter effort was, admittedly, a little half-hearted and done off the cuff, but I got to see some really cool geology. After I arrived in Edinburgh a few weeks ago, I did some touristy things, I went out to North Berwick to try to relocate a fossil locality. I am currently describing some scrappy Early Carboniferous tetrapod material that comes from this region, but I'm not certain of the exact locality data. I found the fossil last time I was in Edinburgh. It is a tetrapod partial lower jaw that was shoved into a drawer marked "rhizodont indet." and forgotten since 1977. Drawers marked "rhizodont indet." are actually a good place to look for tetrapod fossils. Rhizodontids and early tetrapods can be so similar that they have a long history of being confused with one another. But that is another story for another time.

It turned out to be a beautiful sunny day for a walk on the beach, so even though I never ended up finding the original site, it wasn't a complete waste of time!

The sequence of rocks that crop out along the beach are primarily conglomerate. You've probably seen conglomerates before, they are a type of sedimentary rock with very large, irrectular chunks of rock in them. Usually, they indicate very high energy environments that were very close to the source material for the sediments. For instance, in streams close to large mountains, the water is often very fast moving and the bed tends to be made of very large (often very rounded) rocks. Such environments, when preserved in the geological record, form conglomerates. The picture below shows that this particular conglomerate has large, squarish chunks of layered sandstone within it. These layered sandstones were formed before the formation of the conglomerate and later included within it. These appear to be from the older "Old Red Sandstone" rocks which are Devonian in age. However, I can't be sure because there are also sandstone beds in these Carboniferous rocks.

Here is some of that sandstone. A nice arty shot of some cross-bedding. These features are typical of channel deposits as I mentioned in a previous post, but also of sand dunes (both under water and on land).

As I moved further to the east, the major rock type was a sort of volcaniclastic sediment. That is, the rocks were composed of chunks of volcanic rock, typically basalt. But it was getting dark, I had a quick view of Tantallon Castle and had to make my way back to North Berwick and catch my train in to Edinburgh.

Okay, that's enough of my Gonzo geology.

Placoderm soft tissue preservation

2007-02-13T22:30:00.000+01:00

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

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

2007-02-03T20:31:00.000+01:00

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.)

Edinburgh

2007-01-28T21:40:00.000+01:00

I'm in Edinburgh now, with a crappy internet connection. Will post more later with some nice pictures once I get to a decent connection.

Frilled shark caught on video

2007-01-24T18:15:00.000+01:00

Chlamydoselachus anguineus is an icon of vertebrate anatomy textbooks. A truly remarkable-looking animal, though it has only rarely been seen alive. Now, it's been caught on video in what can hardly be called alive... but okay, we'll take it just like we took the giant squid video.

It's being billed as the "prehistoric shark" because it has a number of strange and plesiomorphic (ie. "primitive") features. One of the coolest things is its teeth which have multiple cusps. This characterizes a lot of fossil shark teeth, especially the oldest known shark teeth.

Cardiff to Manchester via Ludlow

2007-01-24T17:35:00.000+01:00

I'm in Manchester today until Friday. I'm quickly making my way up to Edinburgh, where I will spend a good week raiding the collections of the National Museum of Scotland which has a huge collection of fossil fishes. For now, however, I'm in the Manchester Museum looking at a few acanthodians and also some coal-measures fishes in two unrelated projects (except in that they deal with old fish).

Here are the collections. My days on the road are usually spent in rooms like this, going through drawer after drawer of fossils. It might seem boring, but when I've got my nose to the grindstone, I don't really think of anything else. Each drawer can yield a world of surprses or an empty box of disappointment.

Most often, you go to a museum and you know which specimens you're going to see, as they've likely already been published in the literature. But most museums often have a large collection of unpublished, unfigured, and often unprepared specimens. The only way to find them, often times, is just to go through one drawer after another. By far my favourite drawers are the ones marked "indet". Often times, fossils are deposited in museums and neither the collector nor the curator knows the exact significance. You often just have to follow leads here and there and visit collections to see what you can find.

On my way here yesterday, I stopped in Ludlow (to the right). I visited a relatively small museum there, but did not find much of use or interest. Not at the moment, anyhow. But that's often how it goes. The city was quite beautiful, though with a medieval town centre. If you're in the neighborhood, I think it's well worth a visit if you really like historic architecture.

That's all for now.

Technology: My new digital camera

2007-01-22T20:10:00.000+01:00

Okay, so this blog has been dead as Elvis for a while. Now I'm bringing it back to life. My main excuses are lack of enthusiasm, no time, and lack of a digital camera. Well, I bought my first* digital camera -- the Canon Powershot G7. Here it is in all its glory.

[The host for this image also has a review.]

So far, I'm quite satisfied with this camera's performance. Some features were lost from the original line of Powershot cameras however. One is the RAW image format, but I rarely used that anyways. I usually shoot high-resolution JPEGs for most of the stuff I want to publish. However, the option would be nice to have.

The second drawback that I find is the amount of peripheral lense distortion. However, this is hard to avoid with cameras as compact as this. For specimen photography I usually have the camera mounted anyway. Simply by zooming in from a distance will mitigate lense distortion. It also helps mitigate the effects of parallax when the camera is placed to close to the subject and is therefore a method I prefer to use anyway, especially for scientific work.

Nevertheless, I quite like this camera. It's extremely fast shooting and has image stabilization. These two features really improve photographs in low-light conditions. This is very helpful for when you don't want to take overexposed pictures or ones that are too "flashy" (i.e. shadows cast by the flash, subject over-illuminated). It's compact, relatively lightweight, and has a nice 2.5" LCD screen. For work, I had previously been using a Nikon Coolpix with a flip/twist screen. It's much smaller but thicker, making the whole camera rather clunky and cumbersome. The Powershot G7 is much more streamlined, fits easily in your pocket or under your coat and so works well when I get out to see some of the cities I get to visit.

It's built very robustly. I haven't dropped it yet, and I don't plan on testing its ability to withstand impact. However, it has a very sturdy metal case. I'll take the word of other reviews which have described it as "built like a tank".

It's probably a bit pricey if you're not seriously into photography or don't use it for work. However, given my needs as a palaoentologist who works on typically small fossils, and likes to be a bit of a tourist it is ideal. It serves both manual functions that you need while working indoors and in collections, and for when I want to experiment with my photography "skills".

*I've had other cameras: one was a gift that broke within a year of its purchase (I dropped it back in the day when you couldn't drop a camera on a linoleum floor), my second was a crappy freebee I got with an internet company. I miss the first one, whic was one of those tiny pocket-sized Canon camera's. No doubt today's cameras put it to shame, but it was handy and very compact! It was also a gift from my dad. So, I mourn its loss.

I like this guy's message

2007-01-22T18:16:00.000+01:00

Say what you want about the content of this guy's t-shirt, but I think Qantas was way out of line preventing him from flying. His t-shirt was not indicative of a security risk in any way shape or form. This type of move will further erode the ever-diminishing right to free expression in favour of the new "right not to be offended". Sorry, but people are going to hold views that are different from yours. They're also going to express them and they should be allowed to express them. If you don't like it, you do not have a right to be protected from it. Sorry.

This guy has effectively brought the erosion of free speech to international media attention. While I'm amazed at the incredible expense such a move would cost him, I can only say kudos! I wouldn't have the stones to do it, but he sure did.

If you're as apalled as I am by this move by Qantas, feel free to drop them a line and let them know. It only takes a few seconds and a few lines to say that you're apalled by this decision.

A sawbuck and change for Hovind

2007-01-21T23:48:00.000+01:00

As you're probably already aware, convicted tax fraud and professional child deceiver Kent Hovind has been sentenced to 10 years in prison, two years parole, and a hefty swack fo fines. Oh yes, Hovind is a professional bullshit-peddler (=evangelical creationist).

My thoughts on the matter:

I'm not really sure what to think, actually. I'm glad Hovind will not be travelling around peddling his bullshit to countless families who do not know better. He is a severely deluded man, whom I believe sincerely believes what he tells people. Even about his taxes. But I do believe that he knows he broke the law. He violated two of the agreements he makes while living in (what is supposed to be) a civilized and just society: obey the law and pay your taxes.

I think his actions are a very serious crime and that he has robbed his fellow citizens and spit in the eye of democratic principles. There are many ways to protest taxation, and I think Joe Meert states it best:

I don't much care for taxes, but the law states that I must pay taxes so I do. I am fighting to change the tax laws, legally. I write my congressman, I support fair tax legislation and I push for change via legal methods. Hovind could have done the same. Instead he flaunted the laws and taunted the IRS. Hovind spits in the face of the very freedoms that allow him to peddle his nonsense across the country and make a buck doing it. Hovind did the crime, now he must face the time.

Even as I might not agree with Joe's views on taxes, Joe and I both agree on how best to deal with aspects of our society that we do not like. I think Hovind got what he deserved as his crime is more than simply not paying his taxes.

Hovind's religious views are part of the very delusional mental state that led him to these crimes. He sees the world in such simplistic terms. Having watched many of his tapes and debates, listened to his radio program, and debated him 'on air' several times, one oft-repeated phrase sums up his thinking: "I'm right; they're wrong". This is how he characterises all his disagreements with just about anybody -- even fellow creationists, such as Answers in Genesis! In having such a juvenile and righteous view of the world, Hovind fails to grasp the far-reaching consequences of his words and actions. He is now paying for them.

Where the fossils are

2007-01-21T22:18:00.000+01:00

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.

From Cardiff

2007-01-20T21:32:00.000+01:00

Okay, time to brin this puppy bck to life.

Instead of using travel as an excuse for not blogging, I've decided I would do more of what the rest of the reasonable world does: blog on the road. No, I'm not talking about what you do in the wee hours of Saturday morning after the Friday night before. I'm here in Cardiff as I begin a two week journey through the UK. From here it's on to Manchester and finally Edinburgh.

My plans in Wales include visiting the collection of a private fossil collector who has some fish material that may be of interest to me. By the way, at this time I should update my profile which is rather taxonomically restricted. I've moved on to look more intently at early jawed fishes, particularly acanthodians and placoderms. That's what I hope to see tomorrow.

Private collectors can be a boon and a bane of scientific research. Those who share their material and even, ultimately, donate it to museums have the potential to greatly advance and enrich our science. The trophy hunters who hoard material, on the other hand, may end up doing more harm than good. Nevertheless, my own experiences with private and amateur collectors has been quite good.

I'm right now sitting at one of the terminals in a Cardiff youth hostel. I won't tell you which one, because I'm not keen to advertise for them, in light of the crappy set-up they have for internet access. It's basically running one of these staight-jacket operatin systems that prevents you from doing anything other than visiting specific web-based email services (hotmail, gmail, etc.) but won't let me access my work's webmail. Ugh! Oh well. Maybe it's better that way and I can forget about email and blog instead! But, by far the worst aspect of the internet experience here is the keyboard! You wouldn't believe this thing - I'll try to post a picture! It's like typing on your late-1980s model telephone keypad!

Okay, enough bitching. What little I've seen of Wales so far is very pretty. I haven't been able to explore much of Cardiff yet, so everything I've seen so far is kind of drab. Hopefully, beween coop-ups in museums I'll be able to get out and see things a bit.

Comment from a creationist crank

2006-12-15T14:01:00.000+01:00

Despite all my posts about evolution, rebuttals to creationists, and the odd comment on religion here and there, I get surprisingly few comments from creationists. In fact, I don't think I get any. Today, I got one on a post from a while back where I decided to take up some funny contradictions in an AiG article. The post was more about the fact that AiG has no dispute with the preservation of hair in a fossil mammal from China. In fact, they didn't even question it. Why is that odd? Because, for some reason, they need to question the veracity of the feathers on feathered dinosaur fossils as even structures of the skin, let alone feathers.

But what was the truly offending paragraph? It was this:

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

Let's see what he had to say. Normally, I'd try to answer in a polite, informative way. But it appears as though this person dismisses the need for this right off the bat:

How moronic can you become while claiming wisdom?

I don't know. I wasn't making any claims of wisdom. But you seem to claim to know better, so let's find out.

The quote made plain that they felt that some mammals and dinosaurs did not share the "same habitat."

Right. I happened to notice that and also happened to think it was a particularly uninformed and stupid kind of argument to make. At least some dinosaurs and some extant mammal species should be found together. Especially if there had been a great flood that wiped out the face of the earth, as AiG claims.

This is true today. If we had a great flood today and dug up the fossils, how many bear fossils would be found with alligators?

Quite likely none. But this is isn't a very good argument, as it instead reveals your profound ignorance of the topics on which you write.

The term "dinosaur" refers to about 300 hundred different genera of animals from represented in sedimentary rocks from every single continent. The term "alligator" refers to a single genus with two species found in a particular corners of the world. Do you honestly think this is a fair comparison? If so, you should probably pick up a copy of the The Golden Book of Dinosaurs and find out what most elementary school children know: that there were many, many kinds of dinosaur. Then, perhaps, move on to some more advanced reading to find out that they didn't all live together at the same time and place. You could probably afford to do the same for mammals. There's about 4500 of them; from nearly every continent.

A better counter example would be that the fossil record of the Recent fauna would show some mammals and some crocodilians in the same deposits. And you know what? We do. Why? Because they actually do live together in time (and space). By contrast, none of the 4500 living mammal species has been found in the same deposits as dinosaurs. These deposits can, in many cases, span large tracts of an entire continent, and possibly a range of different habitats. So, it's not so much about finding them together, as it is about finding them in the same beds, or even intercalated beds. There really are a host of ways this could go wrong for the story of evolution. It does not.

In fact, most reports of dinosaurs for the past 2000 years are in some way associated with swamps and/or water, but not streams.

Ah, yes. Fantasies of the benighted. "I think others must be at least as ignorant as I am, so I can just make up stuff to secure my point". I'm going to give our commenter the benefit of the doubt and assume they meant past 200 years -- which is still an overestimate for how long western science has known anything about dinosaurs. Studying dinosaurs in their geological/environmental context is actually a relatively recent phenomenon. But I'm wondering why this is relevant, and where the commenter draws a distinction between "streams" and "water".

I happen to have collected dinosaur fossils in western Canada over three summers and, one occasion, in the Canadian high arctic. By and large, in one of the richest dinosaur sites in North America, the most complete and well preserved skeletons tend to be found in channel deposits (i.e. rivers and streams). Typically these beds where the point-bar or overbank deposits buried the skeleton rapidly after it was deposited in a meandering stream. You can see the physical boundaries of the channel in the quarry where the bones are being excavated. Swamps tend to give rise to coal beds. When I was in the arctic, we found vast tracts of unfossiliferous sadstones that were dominated by coal beds. Why? Because the acids in the decaying plant matter tend to destroy biomineralized tissues.

Therefore, there is sound reason for at least suggesting that dinosaurs may not have shared habitat with horses and bears.

Therefore? Therefore? This word is usually reserved for a conclusion that follows logically from a set of premises. Your conclusions are based on your confusion of an uninformed fantasy world with reality. Could you remind us what it was you said about morons and wisdom at the beginning of your comment?

A little correspondence with Nature...

2006-11-29T18:36:00.000+01:00

...that didn't go through.

You might recall the letter of Dr. Maciej Giertych published by Nature that

Myself and fellow infidel Joe Meert sent in a reply. Found out today that it wasn't selected for publication. The beauty of a blog is that it allows you to self-publish your own crackpot claims. So, here it is for your enjoyment:

Sir:

Thank you for publishing the letter of Dr. Giertych concerning his creationist leanings. If for no other reason than to counter the claims that there is an editorial bias against creationists, it serves as a useful example to all.

Dr. Giertych complains that his views have been unfairly characterized as religiously derived. This is amusing, since he proceeds to defend his complaint with a creationist boilerplate so uninspired that it could as well have been skimmed off the “Answers in Genesis” website .. Dinosaurs and people lived together? Really? What evidence? We’re sure that Nature would gladly publish such a revolutionary find!

And why is it always about dinosaurs and humans anyway? As if that would be the first sign that something’s wrong with our global stratigraphic column. How about finding any one of the 25,000 extant species of teleost fishes in the Cambrian-aged Burgess Shale? Wouldn’t we expect that (and a host of other unlikely combinations) before finding evidence of dinosaurs and people together?

So, we must ask Dr. Giertych to forgive us if we are now too branding his views as ‘religiously inspired’. However, without sources or references (as is often the limitation of letters and newspaper articles), we are left guessing about the origins of his myriad claims. Taken at face value, they remind us of similar pseudoscientific arguments forwarded by young earth creationists.

Martin D. Brazeau (Uppsala University, Sweden)
Joe Meert (University of Florida, USA)

That's all for now! Hey, that was easy! Watch this week's Nature which will presumably have the "winners".

The hiatus continues

2006-11-26T19:45:00.000+01:00

I'm on a hiatus from blogging. Too many things on my plate at once and these other things have to take priority. No certain details about when I will get things rolling here again, but I suspect that the Christmas holidays might give me the necessary down-time for writing all the little projects I wanted to put up here.

See you soon!

Myers? Meyers? Miers? PZ's got nothing on Brusseau!

2006-11-04T01:05:00.000+01:00

PZ Myers, our friend of Pharyngula fame, probably sees his last name misspelled more often than anybody I know of. The culprits are frequently creationists. I, on the other hand, probably have my last name (Brazeau) mispronounced more than anyone ('Bra-zoo', 'Braz-ee-ow', 'Braz-ee-awe'. It should be 'braz-o', just as you would pronounce the '-eau' in 'bureau'). The culprits are usualy well-meaning, unsuspecting folks who haven't seen that many vowels in a string before. However, this is the first time I've ever seen my name misspelled for no apparent reason -- Brusseau! Beat that, PZ!

One would suspect that the creationists who are citing me actually read my paper. However, misspelling my name "Brusseau" suggests to me like they got their information over the phone. Love it.

I'll get around to dealing with this article in full at a later time (once I've had a chance to post something meaningful about the original paper). Most of article is baseless innuendo and aspersions, something we've all come to be familiar with from creationists.

Verdict: Guilty!

2006-11-03T01:19:00.000+01:00

Kent Hovind, the infamously unscrupulous creationist evangelist is getting put on ice!. Good bye "Dr." Dino! He and his wife could face over 200 years in prison!

Is Ken Lay still alive?

2006-11-02T14:12:00.000+01:00

To paraphrase Michael Shermer: smart people are really good at finding reasons to defend things they came to believe for non-smart reasons. My friend has a suspicion that Ken Lay (of Enron scandal fame) who died of a heart attack just following his conviction is actually still alive and hiding somewhere.

Now, this friend is a clever guy, as he's currently a master's student working on the genetics of heart disease. He's well-read and generally has very informed opinions. So, it made me really surprised to have this exchange with him. He doesn't believe in UFOs, ghosts, psychics, or gods -- but it was interesting to see him make the same arguments as people who do, just on a different subject matter.

[13:37:45] Friend says:
I think he's not dead

[13:37:53] Martin says:
really?

[13:38:05] Martin says:
what's the evidence?

[13:39:14] Friend says:
a dirty lying cheating snake of a person who was about to go to jail suddenly dies, and then almost immediately his conviction is overturned because he's dead so nobody can touch his ill-begotten estate

[13:39:50] Friend says:
I think it's more parsimonious to assume he paid someone off and is living in the bahamas

[13:44:31] Martin says:
Well, one might easily suspect, yes. But sadly none of that is actual evidence.

[13:45:15] Martin says:
It could just as well have been stress.

[13:45:34] Martin says:
No doubt it's suspicious, but evidence would be nice.

[13:46:22] Friend says:
his personal history suggests this is the kind of thing he would do

[13:46:34] Martin says:
certainly wouldn't put it past him

[13:46:39] Martin says:
still no evidence, though

[13:46:50] Friend says:
no, I don't have a postcard from the bahamas, but in this case I don't think one is required

[13:47:00] Martin says:
I think some evidence is [required]

[13:48:40] Friend says:
I think if he was stupid enough to leave evidence he would still be in a cell right now

[13:49:02] Martin says:
Ah yes, and if we found a body in the tomb that would've proven that Jesus didn't exist.

[13:49:15] Martin says:
Same thing. No evidence.

[13:49:20] Friend says:
that's not the same argument at all

[13:49:24] Martin says:
Actually it is.

[13:49:37] Martin says:
You're actually making a case based on an absence of evidence.

[13:49:45] Martin says:
or stating a belief, at least

[13:50:39] Friend says:
the religious argument asks one to believe in a supreme improbability of a divine being/creator. the ken lay argument asks one to believe that an evil old man who has always hurt other people to protect and grow his material wealth has continued to do so in a new situation.

[13:50:59] Martin says:
No, the issue of Jesus and the tomb isn't a religious argument.

[13:51:27] Martin says:
at least not one in the capacity that you have given

[13:51:47] Martin says:
Your argument was of the form: "If there were evidence my statement wouldn't be true"

[13:51:51] Friend says:
experience teaches rich people cheat when given the oppurtunity

[13:52:29] Martin says:
Okay, I'm sold on that one.

[13:53:29] Friend says:
my argument was *it isn't a long leap to assume that* this particular one continued to do so rather than go to jail and in doing so, it is suspicious that his assets and estate were protected

[13:53:59] Martin says:
Right, that's actually your belief, but I wouldn't really admit it as an argument, since it isn't a very good one.

[13:54:20] Friend says:
define 'good'

[13:54:54] Martin says:
One that involves some sort of interpretation of some observations that are best understood if Ken Lay is alive.

[13:54:55] Friend says:
I would posit that understanding that this is how the world works makes me much more fit to survive, nay flourish within it.

[13:55:07] Martin says:
Right.

[13:55:08] Friend says:
whatever

[13:55:13] Friend says:
I have a lab meeting to get to

[13:55:21] Martin says:
Alrighty. Have fun with that

[13:55:31] Martin says:
Don't forget to read your tea leaves

[13:55:32] Martin says:
hehe

Ah yes, all the same airy-fairy intuition and arguments from coincidence. "I just know it's true". "My understanding tells me it's true". "When I can't produce evidence, I will denigrate your understanding of the world". The point is, this person has no argument. They are merely re-stating their speculation. Evidence, as I noted, would be something that is best explained by Ken Lay still being alive. As I said, I wouldn't put it past him, but his is far different from evidence that he actually is.

We can speculate about these kinds of things all we want, but I don't agree that coincidences and "just makes sense" arguments are very good. Nor is blatant "parsimony abuse" an acceptable way of trying to reverse the burden of proof.

Smart people can believe things for reasons that aren't very good. If you're alert and pay careful attention, you'll catch these arguments, even by some of the very brightest people you may know.

Bush approval ratings chart

2006-11-01T10:38:00.000+01:00

What impresses me the most is how steady the decline is!

Check out the spike after September 11 and the long, steady crapulence of that emotionally inflated approval rating.

From BBC

Highlights from SVP

2006-10-31T18:56:00.000+01:00

As mentioned previously, I was attending this year's Society of Vertebrate Paleontology (SVP) meeting in Ottawa. As usual, it's four days of more talks than you can possibly attend at once. Some days of the meeting have up to three parallel sessions! So, you're often stuck missing talks you want to see because it's on at the same time as another you want to see, or you miss your buddy's talk because you're giving your own! One particular highlight of the meeting was the reception held at the Canadian Museum of Nature (CMN) where we were witness to their new fossil gallery.

The new gallery boasts an impressive display of mounted dinosaur and early mammal skeletons. We're treated to dinosaurs of the Late Cretaceous from Canada and selected parts of the world. There is a life-size diorama of a pair of Daspletosaurus attacking a herd of Chasmosaurus. Following a walk through the Cretaceous-Tertiary extinction, the visitor is led upstairs to a gallery displaying various specimens and dioramas exhibiting the radiation of large mammals during the early Tertiary, including an impressive display of early whales (which I will come back to shortly).

Yes, the gallery is impressive, very aesthetic and tasteful. I found it lacking pedagogically. It starts off with a relatively unstructured "rogues gallery" of dinosaurs and leaves much to be desired in terms of what visitors actually learn by being exposed to these skeletons.

I wasn't the only one unimpressed by the display. Philip Gingerich (who described a number of the archaeocetes or early whales) was similarly unimpressed by the pedagogic value of the displays. He made his concerns public during his talk that week and castigaed the CMN and Research Casting International, the company that manufactured most of the skeletal mounts and dioramas for the museum.

What's got Phil all tied up in knots? Well, take a look here and here. The skeletons that RCI sells and museums display are effectively mounts of disarticulated and often even disassociated skeletons. Many of the skeletons are ridiculously incomplete, but the resulting mounts by RCI and displayed by CMN give visitors no indication of this. The problem? Well, as he put it in his talk: you might not care, RCI might not care, and the average visitor might not care -- but the creationists care. They jump at any opportunity to undermine the credibility of scientists and these types of displays are perfect ammunition.

Okay, so that's really just one highlight. Pretty much all I can say, since I'm not at liberty to report on peoples' talks or preliminary results.

However, one final note, I'd like to congratulate, once again, Nadia Fröbisch a friend and former colleague from my McGill days on winning the Romer Prize for best student presentation. For those not familiar, the Romer Prize is a very presitigious award given annually to doctoral-level students. It recognizes the outstanding scientific merits of the work as well as the quality of presentation. Nadia's prize was in recognition of her talk entitled 'The evolution of preaxial dominance in tetrapod limb development'. Congrats Nadia!

The re-appearing act, again

2006-10-31T16:18:00.000+01:00

I've returned to Uppsala today after having attended this year's Society of Vertebrate Paleontology meeting in my hometown of Ottawa. It was a good meeting and, as usual, a lot of good contacts were made along with getting to see some interesting talks. We also got to see the Canadian Museum of Nature's new fossil gallery, a few days before it opened to the public. So, if I find time this week I'll try to get around to some updates on those things.

I've also been missing out on some interesting fishy news in the last couple issues of Nature, one on the relationships of Gogonasus and early tetrapods; and another on a very early lamprey fossil. I'll try to get around to these too, as I especially have things to say about the Gogonasus paper.

Now I must go and try to keep myself upright in an effort to combat jetlag! It's always worse going east...

You'd think all this travelling would be fun

2006-10-11T20:22:00.000+02:00

I'm off again -- back to Canada. Gee, it seems like I was just there not, oh, two months ago. I'm headed off to two conferences: the Canadian Palaeontology Conference in Montreal on the weekend and next week's Society of Vertebrate Paleontology meeting in my home town of Ottawa. In the unlikely event that I'm diligent enough, I'll try to post some pictures and give some updates. For now, however, it seems that my other preoccupations are leading to the slow, agonizing death of this site. Perhaps after the conference, there will be some wiping clean of my plate of duties and this site will come back to life.

Never fear, more responsibilities will be sure to emerge! Welcome to academia!

Fair-Vote Canada

2006-10-08T00:20:00.000+02:00

Here's a worthwile cause for my fellow Canadians: proportional representation. I think it is high time that we Canadians, of whatever political stripe, demand a proportional representation system. For now our parliament does not represent actual voting proportions. For instance, we have elected majority governments where the victor did not receive a majority of the vote. This is because our voting system is representational, which means voters in particular regions elect representatives to parliament according to those regions. However, the regions are not of equal sizes and there are more than two parties. This kind of system severely mangles the total vote count, producing a parliament which may have, at best,

We have it simply because it's the status quo. It was developed in a time when vote counts had to be reported by messengers on horseback and it made counting more efficient. It also "worked" in very large countries such as Canada and the U.S. simply because the sheer vastness of the

We don't have these limitations anymore. We have more voices, more parties, and more diversity. We know the math is bad in our current system. We know it disenfranchises voters of any political alignment. We need to get into proprtional representation.

Born on this day: Erik Andersson Stensiö

2006-10-02T16:33:00.000+02:00

Erik Andersson Stensiö was born (b. Erik Andersson) on October 2nd, 1891, in the village of Stensjö, Kalmars Län, Sweden. He made prolific contributions to the study of vertebrate palaeontology through his extremely detailed studies of Triassic and Palaeozoic coelacanths, cephalaspid (jawless fishes), and placoderms. He trained other noted vertebrate palaeontologists such as Erik Jarvik, Gunnar Säve-Söderberg, Eigil Nielsen, and Hans Bjerring (known collectively as the "Stockholm School"). His technical contributions included improvements to Sollas's grinding method which permitted him to build larger-than-life wax models of the internal structures of fossil vertebrate heads. The results of these investigations have been published in his many detailed treatises and followed by his students, especially Jarvik.

Below: Stensiö (left) and Jarvik in their elder years.

A little known fact is that during 1930s and '40s, Stensiö was a vocal opponent of the Nazi movement, which had a strong following in Nordic countries. This occurred during a time when Sweden declared neutrality and was either sympathetic will or unwilling to antagonize the Nazi regime for fear of repercussions.

Stensiö died January 11, 1984, at the age of 92. His contributions to science have been long-lasting and continue to influence vertebrate palaeontology today.

Whence life began

2006-09-29T09:33:00.000+02:00

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.

Harper, Here we go...

2006-09-26T00:34:00.000+02:00

Conservative is as conservative does: cut, cuts, and cutting. Now, let's be fair here, conservatives tend to cut very selectively, for instance things they've already decided won't be fruitful. For instance, nonsense research on the medicinal uses of marijuana. Ah yes, it appears as though the Tories are keen to put their "value for money" strategy into effect after all. This is really bad news... very bad. I'm sure that if the Tories aren't afraid to cut research into medicinal marijuana, basic research will be next.

Well, it looks like Canada will no longer be such a hot place to do science after all. Here we go...

And now for something completely different

2006-09-24T23:33:00.000+02:00

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!

Anti-science vs. anti-evolution

2006-09-24T17:40:00.000+02:00

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

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

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

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

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

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

Welcome back, Palaeos!

2006-09-22T13:52:00.000+02:00

Palaeos has been restored as a Wiki! The site will soon incorporate the material from the original Palaeos and then be continually updated in Wiki format. It might not look like much yet, but there is a dedicated, hard-working, and very talented group of people behind all of this. Believe me, as I've been following the efforts to restore Palaeos, these good folks wasted no time and got things up and running in a matter of weeks.

More to come!

That's right, you stinkin' turd from the bowels of the Dark Ages!

2006-09-08T22:42:00.000+02:00

For those of you who are not familiar with the concept of a pope here is a refresher: they are undead entities raised to ensure the vitality of bronze-age wisdom. It remains a mystery why media outlets continue to pay attention to them and report their supersitious bullshit as though we should give a damn. Nevertheless, it sounds like Pope Ratzi has censured Canada for allowing both gay marriage and abortion:

"In the name of tolerance, your country has had to endure the folly of the redefinition of spouse," the Pope told a group of bishops from Ontario. "In the name of freedom of choice, it is confronted with the daily destruction of unborn children."

Such laws, Benedict said, are the result of "the exclusion of God from the public sphere."

In the name of a superstition started by pre-literate goat-herders your establishment has through corruption, delusion, violent force, intimidation, and torture committed some of the most hainous crimes against human-kind. Why the hell should we take you seriously on matters of tolerance and freedom? Why should we take seriously any establishment who has only recognized the acheivements of Galileo and Darwin in the very final years of the 20th Century? Why should we trust the supposed "wisdom" of a consortium of "celibate" men regarding the bodies of women and the rights of homosexuals?

No, there is not an "exclusion of God from the public sphere". Rather, there was an exclusion of bullshit superstition from that rational discourse on the agreement of society called democracy. Sadly, that threatened ol' Raisin Nuts in Robes' monopoly on the bodies of women and he didn't like that.

Isn't it about time we started treating popes like the senile old bags that they are? If he were just a guy on a street corner in downtown Ottawa yelling this at Stephen Harper himself, he wouldn't even make a column note on page A19. In fact, he would've been dragged off to the R.O. Give him robes, rubies and 2,000 of intolerant superstition he's front-page stuff.

Dipnogate: vital studies on lungfish survival suppressed, ordered destroyed

2006-08-24T15:46:00.000+02:00

The Queensland Government has issued the destruction of a vital report on the Australian lungfish, reports the Noosa Journal. As you may (=should) be aware, this unique animal is threatened with extinction by the building of a dam in the Mary River in Queensland. The previous construction of a small weir in one of the rivers was not stopped in time, but the government agreed to conduct a study on the effect of the weir on the lungfish's numbers. The study showed that following the construction of the small weir, some 20% of the spawning sites were wiped out. Now, consider the construction of a dam! This doesn't jive with the Queensland Government's plans for a dam. So, what do morally bankrupt, intellectually retarded people do about it? Suppress it, of course!

Thankfully, there are some copies of the report that have circulated to hands outside the government, and now these clowns look like the donkey's arses that they are. I think that PZ puts it best:

You know the other side is completely in the wrong when they're reduced to hiding reality. The Queensland government seems to have adopted the American Republican style of policy making.

A reminder: please get out and sign the petition, pass it on to friends and get them to sign it!

A big loss from the WWW: Farewell to Palaeos

2006-08-17T06:24:00.000+02:00

Palaeos has gone offline, apparently for good. This is a bad thing. It was one of the most extensive, well-researched, well-illustrated online resources for anyone interested in things palaeontological. I've linked to the site so many times that a lot of my posts will now become almost irrelevant without it! Hopefully we can find out what's going on and, if it's a money/time issue, perhaps there will be ways to bring it back to life. I for one would be more than willing to fork up a bit of cash to keep it going. I would certainly be willing to contribute to parts of it that are relevant to my research. If only I had known before this happened.