Darwinius masillae

The news sites and blogs have reports of a new fossil found in Germany, a 47 million year old primate, named Darwinius masillae.  The quality of preservation of this fossil is extraordinary, and even reveals what its last meal was.  PZ Myers gives the lowdown at Pharyngula (Darwinius masillae).

Of course, there’s a major PR job going on about this – check out Ed Yong’s blog (Not Just Rocket Science – Darwinius changes everything) for a refreshing view.  John Wilkins (Evolving Thoughts –No, it’s not an ancestor either (probably)) questions statements that it’s the ancestor of all primates (he cites Science Daily).

The blogosphere’s pretty full of writing about Darwinius – some buys into the hype, others question it.  one thing’s for sure, it’s a damn fine fossil.  On the downside is the confusion the news coverage may engender in the public, with buzz-words/phrases like “missing link” and “oldest ancestor of humans” flying around.

I think the BBC News website (Scientists hail stunning fossil) strikes the correct balance with comments such as:

Dr Henry Gee, a senior editor at the journal Nature, said the term itself was misleading and that the scientific community would need to evaluate its significance.

The publication is accompanied by a David Attenborough fronted BBC TV programme!  (Makes my YouTube press release via the BBSRC look really rather puny!). If you’d like to read the paper, it is publishe din the open access journal PLoS One:

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, et al. 2009 Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723.doi:10.1371/journal.pone.0005723

“Why Evolution is True” by Jerry Coyne

I recently picked up a copy of Jerry Coyne’s new book, Why Evolution is True.  You can also visit Jerry Coyne’s blog of the same

cover image
cover image

name, Why Evolution is True.  This book review is being written as I make my way through the book – the first thing I need to point out is that I am a biologist, and like the vast majority of biologists I happen to consider that evolution is indeed true.  That being said, I’m also a little dismayed by the outpourings of religiously motivated twaddle-merchants who seek to place creationism on an equal footing.  It is these kind of anti-science arguments that the book is aimed at.

Coyne sets the scene in the preface: the ruling in the 2005 Harrisburg trial (Kitzmiller vs Dover Area School District).  This was a resounding defeat for a group attempting to manoeuvre creationism into the science curriculum.  Despite this, similar shenanigans keeop cropping up across the USA.  And indeed, at least one UK state-funded school has gone down the same route (The Guardian – Top school’s creationists preach value of biblical story over evolution).  The brief introduction continues the theme of religious belief versus acceptance of evolutionary theory.

The first chapter proper is entitled “What is Evolution?”, and presents six “parts” or concepts that are important to evolutionary theory.  Firstly, the idea of evolution itself – that over time species undergo genetic change, and that this need not happen at the same rate (examples of horseshoe crabs and the ginkgo are given for slow-changing taxa).  The second part is that of gradualism – the notion that evolutionary change is slow, so slow that long periods of time are required.  In fact this can be one of the stumbling blocks for many people, for whom the short human lifespan doesn’t necessarily equip them to grasp deep time.  The third idea is of speciation – that lineages split to yield new species.  As Coyne observes, this is intimately tied to the fourth part, common ancestry, which can be seen at different levels, from molecular to anatomical.  The fifth part is the most significant element of Darwin’s theory – natural selection.  It does seem to me that this subsumes a number of concepts, including notions of variation and heritability, and so is the major Darwinian innovation here.  Finally, the sixth part is that of processes other than natural selection can cause evolutionary change – genetic drift for example.

Chapter one also deals with the issue of the word theory – possibly the most abused weapon of the creationists, who generally take the tack of using colloquial definitions of “theory” to suggest that supporting proof or evidence is lacking – as the book goes on to show, this is so far from the truth that the title of the book is most definitely not mistaken.  In fact, despite the study of evolution largely being a historical kind of science, evolutionary theory enables us to make predictions about what we might expect to see in the geological/palaeontological record or in the genomes of different species: these predictions are invariably confirmed.

The second chapter “Written in the Rocks” deals with the palaeontological record of past species.  It clarifies issues to do with the so-called “missing links” so beloved of creationists.  Documented examples of gradual change found in the fossil record include several invertebrates: transitional series demonstrating the evolution of birds, the evolution of amphibians and the transitions to the terrestrial habit and the evolution of whales are all given as examples where evolutionary theory has enabled scientists to make predictions of what the fossil record would show, predictions fully supported by later discoveries.  The ability of evolutionary theory to make testable (and disprovable) predictions is a recurrent theme in the book, and is really a good indicator of its superiority over creationist explanations.

Chapter 3, “Remnants: Vestiges, Embryos, and Bad Design” shows how evolution leaves its mark in occasional atavisms, in patterns of embryonic development and in the “molecular legacy” revealed by the large scale genome sequencing projects.  Interestingly, I can recall being taken to task at a conference in around 1989 by Richard Lewontin, Coyne’s PhD supervisor, over our then non-existent plans to sequence the Drosophila melanogaster genome (he was concerned by what would be chosen as the standard “wild type” genome).  Now we have the sequence of 12 different Drosophila species (see my post on the polytene chromosomes and genome sequences of the Drosophilids over at Flies & Bikes).  It’s also worth looking at my recent article on the Genome Sequence-based Tee of Life).

Biogeography is the subject of the fourth chapter, “The Geography of Life”, which shows how the evidence of both extant and fossil taxa across continents, continental islands and oceanic islands clearly argues against creation, and instead makes a logical fit to evolutionary theory.  Patterns of distrbution of animals and plants across the world were something that puzzled Victorian naturalists – ideas of plate tectonics had not been formulated.  Clearer perhaps were the explanations of diverse species on recent oceanic islands, such as Hawaii and the Galapagos.  The theme of testable predictions is raised again here, with the nice example of Glossopteris, a fossil tree found in the southern hemisphere, and which was predicted would be found in Antarctica.  It was, and indeed 30 odd pounds of Glossopteris fossils were carted back by Scott’s ill-fated polar expedition. Chapter 5, “The Engine of Evolution” includes a clear statement of why “Intelligent Design” fails as an explanation of the world around us: “Since ID itself makes no testable scientific claims, but offers only half-baked criticisms of Darwinism, its credibility slowly melts away with each advance in our understanding”.  Unfortunately, this is probably untrue of the religiously-blinkered.

Darwin was possibly more troubled by peculiar (and on the face of it inexplicable) structures auch as the peacock’s tail than he was by the mechanisms by which eyes evolved.  He did of course invoke sexual selection as a mechanism, and the sixth chapter, “How Sex Drives Evolution” deals with this.  And convincingly.  I was particularly interested to see mention of an experiment that my colleague Tim Halliday and colleagues conducted using the peacocks at Whipsnade Zoo in Bedfordshire, which demonstrated the sexual selection pressure on peacock tails.  Interestingly this settled a matter that had been discussed by both Wallace and Darwin: an experimental demonstration of  sexual selection.

The Origin of Species is, perhaps surprisingly, not really covered at length by Darwin in On the Origin of Species – here, Coyne devotes an entire chapter to the subject, and covers the issue well.  Good examples are given, which clearly provide evidence of how speciation processes operate, including experimental recapitulation of a polyploidy-related speciation event in plants: that of Welsh groundsel, in which it’s origin as polyploid hybrid of two other species was confirmed by laboratory crosses between those two species in which the hybrid species was synthesised.   Human origins are covered in the eighth chapter, “What About Us?”, and the question of whether human races reflect a meaningful biological reality is dealt with.

Why Evolution is True is an excellent little book – it clearly states why the author, and indeed the vast majority of biologists, accept evolutionary theory as true.  It takes an excellent strategy of illustarting the deifference between the scientific and colloquial use of the word “theory”.  In particular I felt the running theme of how evolutionary theory makes testable predictions makes celar distinctions between this scientific explanation for the diverstiy of life over archaic supernatural explanations was particularly effective.  But of course in this reader, Coyne is preaching to someone with a pretty good grasp of the biology.  And while I was particularly interested in comparing the material covered in this book with the kind of arguments advanced by the creationist in The Big Question TV programme (see this recent article –The Big Question – The Bible and Evolution), what kind of impact is this going to have on the evolution vs creationism debate?  I worry that the creationist side is so undereducated in science, and unlikely to read beyond a cover (witness the recent furore over the dreadful “Darwin was Wrong” New Scientist cover – Darwin was right), and certainly aren’t going to be swayed from their religious “truth”.  Still, the book does offer clear arguments against many of the lies and misrepresentations proffered by the creationists.  And it’s an enjoyable read.

Mary Midgley on the limits of Darwinian explanations

Mary Midgley made a contribution to The Guardian’s Comment is Free section last week (February 9th, 2009), Selectionism can only take us so far -Darwin made it clear that he never meant to exalt selection into a kind of ‘universal acid‘. This is in the series concerning the limits of Darwinian explanations.

I have to confess that, having read her article, I cannot understand what it is she is trying convey, and in fact much of what she writes seems to betray a lack of understanding of evolutionary biology.

Natural selection can’t possibly account for everything in evolution any more than human selection can account for everything in a chihuahua.

I suppose my response would be that no-one in their right mind would make such an assertion in the first place.  The reasonable biologist would say that the first dogs were products of natural selection, but that human intervention by dog breeders is what has moulded their descendants into the myriad of forms we see today.

Selection only works where there is a given range of candidates. Selectionist theorists take this range for granted, treating the selectees as if they were indefinite, passive objects with no natural tendencies of their own. But (as helpful scientists have lately pointed out) at every stage, from the initial molecules to the most complex living organisms, these participants are themselves specific, active entities.

This is just a hopelessly incorrect understanding of evolutionary theory, I think.  I am uncertain what Midgley means by the first sentence of that quotation.  I don’t know what Midgley means by “Selectionist theorists”, nor do I know what she means by “helpful scientists”!

[…] a particularly enterprising mouse which suddenly decides to move into a new valley can defeat the best-laid plans of its former evolutionary pressures. And we can see that an alien observer might well suppose that it would be quite easy to turn a person into a kangaroo or a chihuahua into a slug. But in fact no amount of selection will achieve these feats. The moral is that the tendencies of the materials present are every bit as important in evolution as the selective forces.

Evolutionary pressures (presumably this means natural selection) don’t have “plans”, best-laid or otherwise.  And as a commenter at the Guardian page pointed out, an alien observer who had the scientific and technological wherewithal to reach our planet would probably have a better understanding of biology than Midgley.

But he made it clear that he was always unhappy about the apparent inadequacy of this cause to explain the whole range of actual effects. When he said that thinking about the problem of the peacock’s tail made him feel positively sick he was clearly expressing this deep uneasiness – this sense that the change was too large to be explained in such a way.

I have always understood his uneasiness was due to the fact that biological observation might not always be easy to explain, and indeed, they are often exploited by the ignorant as weapons to bring the evolutionary edifice down.  The “problem” of the peacock’s tail seems to me to not be a problem at all, and is explicable by sexual selection.

In the final two paragraphs, Midgley wanders off into odd territory, analogising the influences that lead to evolutionary change to the Hindu trinity of Shiva, the destroyer, Brahma the creator and Vishnu the preserver (she ascribes this to Lyell).  This I don’t get at all, and I think I need that to be explained.  My personal view is that in these closing paragraphs, Midgley merely reveals that she just doesn’t like the scientific explanation for how life got to be the way it is – the Wonderful Life that I see around me.  One final comment: isn’t it time the commentators who seem so keen to pick at evolutionary theory realised that evolutionary biology has moved on in the last 150 years?

Genome sequence-based Tree of Life

A tree of life derived from completely sequenced genomes
A tree of life derived from completely sequenced genomes

I came across this rather excellent variation of the “tree of life”, which is derived from an analysis of completely sequenced genomes.  If you click on the diagram, you’ll get the full version in its considerable glory.

This really demonstrates quite neatly the ancestry of life on Earth, and how the growing quantity of genome data supports the origins of, and relationships between, different taxa.

It’s interesting to compare this with Darwin’s notebook sketches, his published figure from The Origin of Species, and Haeckel’s famous “tree illustration”.

Here’s Darwin’s first tree of life, from his notebooks:

Darwin's first tree of life
Darwin's first tree of life

It’s interesting to see “triple branching” events in this tree, and also his scribbled notes.  By the publication of the Origin of Species, the diagram had metamorphosed into a somewhat more geometrical plan.  This is the only illustration in The Origin!

Darwin's tree of life, from "On the Origin of Species", 1859
Darwin's tree of life, from "On the Origin of Species", 1859

Haeckel’s version, complete with Humans at the top, is perhaps the most decorative.

Haeckel's ornately drawn tree of life.
Haeckel's ornately drawn tree of life.

See also the Wikipedia pages on Cladistics and the Tree of Life.

Another intermediate “proto-whale” fossil – complete with foetus

Ed Yong, over at his excellent blog Not Exactly Rocket Science has posted about the fetus found within the fossilised remains of Maiacetus inuus (Fossil foetus shows that early whales gave birth on land).  It’s another case of the so-called “missing links”, really.  In this case an intermediate between terrestrial vertebrates and fully aquatic cetaceans.  What’s particularly neat here is the presence of a fossilised foetus within the larger animal’s remains.  This clearly indicates that Maiacetus was amphibious, as the foetus is oriented so as the born head-first.  Head-first birth is never found in modern cetaceans, as the newborn animal would likely drown.

Other reports include the following blogs:

Greg Laden’s Blog
The Questionable Authority
You can also read the paper at PLoS ONE (freely available, as it’s Open Access)