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.

LOL!

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.

Monday, December 01, 2008

SPAMMED!

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.

Thursday, November 27, 2008

The end of the long road. A new beginning.

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

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

Wednesday, October 08, 2008

Except was no such fella as Noah...

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

Friday, September 19, 2008

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

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

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

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

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

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

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

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

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

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

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

Thursday, September 18, 2008

Open thread: are genes really a guide to homology?

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

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

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

Discuss.