Thursday, October 22, 2009

What's been going on? Some academic musings.

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.
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Friday, October 02, 2009

On the use of the stem group concept.

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

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

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

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

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


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

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

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

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



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


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Wednesday, September 16, 2009

That snake with a leg...?

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.
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Rampant paraphyly on Wikipedia

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.

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Brief update

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.


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Friday, September 04, 2009

Oh no! Silence again?

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.
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Monday, August 31, 2009

"Merck published fake journal"

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.
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Friday, August 28, 2009

Oops!

"A treasured piece at the Dutch national museum - a supposed moon rock from the first manned lunar landing - is nothing more than petrified wood, curators say." Full story
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Thursday, August 27, 2009

Coming soon...

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)
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Wednesday, August 26, 2009

A couple of re-posts

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?
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Tuesday, August 25, 2009

A dubious honour...

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

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

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

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

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

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

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

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


Continuing, Williams & Ebach write:
But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic!
I did state the obvious. It's in the figure. Look at it. I did not "descend into evolutionary explanation". The nested series of monophyletic groups that imply acanthodian paraphyly actually do provide sequences of character acquisition along the chondrichthyan and osteichthyan stem segments. As Williams & Ebach know well, each monophyletic group is supported by synapomorphies, and those nested groups synapomorphies are simply synonymous with what we call 'sequences of character acquisition'. This is how we make sense of fossils (or any other newly discovered taxon) and the implications fossils have, if any, on further hypotheses of synapomorphy (homology). If it's not the sequences of nested homologies that define monophyletic groups (the groups that matter) then what does? I'm perplexed as to why Williams & Ebach, of all people, would challenge this, since this seems to be their own view. I thought we had accepted and moved beyond disputing the idea that "evolution", when talking about fossils and the unrepeatable past, was only reducible to our best systematic hypotheses. In the quoted statement, that is all it is to me. It seems, perhaps, I wasn't careful enough and Williams & Ebach saw what they wanted to see in it. If so, then I'll take responsibility for my error, but note that my critics are playing fast and loose ascribing ideas to me which I have not explicitly stated.

Finally, they raise the following gripe:
"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (BBC Online, 19 January 2009).
This is false and misleading - the study shows quite the opposite.
Mostly, Williams & Ebach are just being pedantic and annoying, but this is infuriating bullshit. Those are not my words!

My words in the BBC article were:
"This figures in nicely with the emerging idea that acanthodians don't form a group of fishes that are all closely related to each other. Some of these fossils are primitive sharks while others are primitive bony fishes."
Even in the BBC article I state clearly that some are chondrichthyans (though I used the term "sharks" as a shorthand) and others are osteichthyans.

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

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Blogging back to life

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.
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Wednesday, May 20, 2009

Nice fossil, shame about the name...

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

According to the International Code of Zoological Nomenclature:

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

I see no evidence in the original paper that this condition has been met. Thus, under the rules of the ICZN, the name Darwinius may not be considered considered "published".
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Thursday, January 08, 2009

Evolutionary gems

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

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

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

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

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