Way back in 2008 I wrote a brief blog article about the sequencing of the genome of a rather poorly unusual organism, Trichoplax adhaerens (What the heck is a Placozoan, anyway?).  The interest there was that the genome had a variety of genes associated with organisms with a more 'complex' structure (Trichoplax looks rather like a flattened blob of cells), while no-one really knew much about the biology of the animal.A paper describing sexual reproduction in Trichoplax has just been published in PLoS One (Eitel M, Guidi L, Hadrys H, Balsamo M, Schierwater B, 2011 New Insights into Placozoan Sexual Reproduction and Development. PLoS ONE 6(5): e19639. doi:10.1371/journal.pone.0019639).  Here's an excerpt from the abstract:

[...] Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. [...] Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction.

After a bit of teasing in the blogosphere that the draft sequence of the Neanderthal genome would be released in time for Charles Darwin's birthday this week, I was eagerly looking for a paper.  Instead what I find are three news articles in Science, one describing some of the outcomes of the work, and two setting it in context. Some quotes:

Initial comparisons with our own 3 billion bases indicate that a mere 1000 to 2000 amino acid differences, as well as a yet-unknown number of non-coding changes, do that job. For comparison, about 50,000 amino acid differences separate us and chimpanzees. 

The journal Current Biology invited a number of prominent biologists from a number of disciplines to re-read Darwin's On the Origin of Species, and to write commentaries - they can be found at (Re)Reading The Origin.

Charles Darwin's 1859 book On the Origin of Species is much referenced, especially in this double anniversary year. But, does anyone still read it? And, if so, what is the book itself like as a text? We have asked biologists from a range of fields evolutionary biologists, but also geneticists, ecologists, paleontologists and molecular biologists to re-read (or read) The Origin for Current Biology. Below are the responses, contributed by: Andrew Berry, Matthew Cobb, Simon Conway Morris, Jerry Coyne, Hopi Hoekstra, Peter Lawrence, Robert May, Christiane Nüsslein-Volhard, Mark Ptashne, Matt Ridley and Marlene Zuk.

There's been a bit of a rumpus echoing through the blogosphere following a series of pop sci articles about Darwin and his legacy (see for example this review of recent stories).  Generally, and presumably to attract readers, many make some kind of provocative claim in the title, such as "Was Darwin wrong?" or similar.

In contrast, the February 2009 edition of National Geographic features a rather excellent article by Matt Ridley: Darwin's Legacy. In a refreshing change from the tabloid-style hatchet jobs often seen in the press, this is a measured view of how modern biology has built on Darwin's foundations, and quite responsibly points out that Darwin, for all his breadth of knowledge never knew the physical basis for inheritance.

The new Peguin Books' edition of Darwin's On the Origin of Species... features a cover by celebrated/reviled (dependent on one's opinion!) modern artist Damian Hirst. Now, while I quite like some (but not all) of Hirst's work - and recall I am no art aficionado, this cover seems a little odd to my tender eyes - a little like a cross between Francis Bacon's Pope paintings and something from Tim Burton's ghoulish animations. Still, it makes a nice change from pictures of heavily bearded Charles Darwin, or of finches etc.

A short article at the Guardian (Damien Hirst salutes Darwin's 'courage' in On the Origin of Species painting) initially passed me by.  It's by Hirst himself, and he says nice things about Darwin.  Apparently the painting is called ""Human skull in space", but while I quite like it, it's still not clear to me how it relates to the book.  Even after reading what Hirst has to say about it!

Quite a few of the bloggers at ScienceBlogs have been writing about an exciting new fossil find: a newly discovered fossil ancestor of whales.  The exciting thing here is that the fossil contains the remains of foetal whales.  Here's the University of Michigan podcast.

The fossil confirms that Maiacetus inuus was amphibious, or at least gave birth on land, as the foetus is oriented to emerge head-first (clearly not adaptive for aquatic birth, and something not seen in present-day cetaceans).

A paper in the current issue of Nature [Love et al (2009) Nature 457; 718-722] suggests that multicellular life existed about 100 million years before the explosion of bilaterian animals in the Cambrian. The evidence comes from analysis of rocks from the Arabian peninsula, in which geologically preserved derivatives of characteristic chemicals have been detected. Now, this paper interested me because of its message concerning the dating of the origins of multicellular life; I am not a geologist or a chemist, so many of the details escape me.

Identification of the presence of soft bodied animal in the fossil record is always difficult: it's generally the hard parts of the animal that are preserved by fossilisation (there are exceptions). The Cambrian explosion (see timeline diagram- click on it to link to the interactive Wikipedia diagram) resulted in a wide variety of animal forms: what's less clear is from where this abundance of diverse forms arose. This paper takes chemical approach to establishing the presence of animal remains in rock samples.

There's been a profusion of articles in the popular press as he big Darwin anniversary swings into top gear.  Many of these make over-stated cases that Darwin's theory of evolution by natural selection has been "shaken up", or "over-thrown" (see for example this blog post).

There's another at the Daily Telegraph today: Charles Darwin's tree of life is 'wrong and misleading', claim scientists. Setting aside the obvious point that Darwin couldn't have got all the details right given the scientific knowledge of the time, the article seems to restate the popular myth of the big icon of evolution - the diagram of evolutionary relationship as an oak tree:

I was interested to know more about Stephen Green, the man who has filed a complaint with the Advertising Standards Authority against the Atheist Bus ad campaign.  The blog site mediawatchwatch has an interview with Stephen Green, dating from June 2005.  In it, he demonstrates an astonishing lack of understanding of biology and evolution by natural selection.  For example, on one of the classic examples of sexual selection, the peacock's tail:

Why does the peacock have such a magnificent tail? ‘So he can attract a mate', the evolutionist replies. So how does the hedge-sparrow do it? 

The journal Science has launched a new blog to celebrate the Darwin 200 anniversary, entitled Origins. There's an rss feed.

In the current issue of the journal are articles by Peter Bowler on Darwin's Originality and by Carl Zimmer entitled On the Origin of Life on Earth. [subscription may be required].

I picked up on this new blog at ScienceBlogs - "Blogging the Origin" via Science's Origins blog.  In this blog, science writer and evolutionist John Whitfield, who bravely admits to never having read The Origin of Species before, is conducting a book club cum blog as he reads the text, chapter by chapter in this anniversary year.  As I write, he's covered the Introduction and Chapters 1 and 2, with the next instalment due on Friday.  He plans to finish in time to celebrate Darwin's 200th birthday.

I haven't read The Origins since I was a teenager (which is an upsettingly long time ago), and this has inspired me to read it again.  But which version?   The old Pelican paperback edition I read all those years ago is a later edition of the tome, while the edition reprinted in the compilation From So Simple a Beginning", edited by E. O. Wilson, is I think the first edition (but lacks a certain portability - the volume also has Voyage of the Beagle, Descent of Man and The Expression of Emotions, all in a hardback binding).  Perhaps I should limit myself to the 1858 pair of papers by Darwin and Wallace?

Via the excellent Pharyngula blog, I came across this ridiculous article by Bryan Appleyard in The Times:  For God's sake, have Charles Darwin's theories made any difference to our lives? - published on 11th January (so I got to it a little late - I'm more of a Guardian reader!).

Yes, Bryan, they have made a difference, and not the spurious negative ones you build up to in your article.  To be charitable, one must suppose the point of Appleyard's article is to point out that many (usually from the under-educated religious wing) do not accept evolution by natural selection (and I come back to the difference between comment and reportage later).

The Royal Mail has issued (or will issue) stamps to celebrate the upcoming Darwin anniversary.  There's also a miniature sheet, depicting the Galapagos Islands, and a variety of the specialised fauna found there.

I think they are particularly attractive, and it's good to see the profile of this most important of anniversaries maintained.  For more information, visit Norvic Philatelics - there is a much more information on the design, background information, and how to buy first day covers etc (and I also linked to their images).  I have to say, I never thought I'd blog about postage stamps, but there you go!

[Post edited to remove direct links to the images]

The Open University is hosting a web page devoted to the upcoming Darwin 200 anniversary.  Usefully, it's also the 150th anniversary of the publication of the Origin of Species (free e-book, web book), possibly the most influential work in science ever (your starter for '10'!).

Of course, I can be accused of a little bias since the site is the work of my colleagues at the OU, but it's a more graphically pleasing route to finding courses such as Darwin and Evolution than the standard OU website!  The course is one of a number of Science Short Courses that expect no prior qualification, but which reflect topical issues in science - the courses are very popular, and offer a relatively low commitment introduction to distance learning via the Open University.

Yet another palaeontology blog post!  This story roared round the internet just before Christmas (for example the BBC News story), but I found it interesting as a non-specialist in arachnid evolution or palaeontology, partly because of the methods used for extracting fossil arthropod material from the substrate, and partly because it tells a tale of re-examination and reanalysis of specimens with a quite different interpretation. Oh, and there's a tale of the evolution of silk use by spiders!

Production and use of silk is the defining characteristic of spiders - modern advanced spiders use silk for a quite astonishing array of purposes (from taking flight to encasing eggs; from capturing prey to constructing shelters), and a single individual may produce silk of several types with distinct properties.  Spider silk is produced from specialised structures called spigots, which are in turn located on modified appendages called spinnerets (see picture on the right, from the arachnology website, where there's a description of silk production). 

In this year of not only the 200th anniversary of Charles Darwin's birth, but the 150th anniversary of the publication of The Origin of Species, we can expect the major celebratory events to be countered by the usual mediaevally-minded creationist suspects.  The journal Nature has published a useful document with the aim of highlighting an publicising why (the vast majoroty of) scientists regard evolution by natural selection as a fact -  "15 Evolutionary Gems"- the contents are as follows:

Gems from the fossil record
   1 Land-living ancestors of whales
   2 From water to land
   3 The origin of feathers
   4 The evolutionary history of teeth
   5 The origin of the vertebrate skeleton
Gems from habitats
   6 Natural selection in speciation
   7 Natural selection in lizards
   8 A case of co-evolution
   9 Differential dispersal in wild birds
  10 Selective survival in wild guppies
  11 Evolutionary history matters
Gems from molecular processes
  12 Darwin's Galapagos finches
  13 Microevolution meets macroevolution
  14 Toxin resistance in snakes and clams
  15 Variation versus stability 

The Natural History Museum has a packed programme of events to celebrate the big Darwin anniversary in 2009.   I'm not sure why they've chosen the image on the left as par tof the logo - it seems to suggest Darwin is swearing us to secrecy!  (I wonder if it's a photoshopped image...).  In any event, this is a big deal in public understanding of science, and my university, The Open University, is a significant contributor:

The Open University is working with the BBC to co-produce four TV series that consider the impact and legacy of Darwin's theories and ideas in an attempt to engage the public to take their interest in Darwin further. The four series are: Tree of Life (BBC ONE) where Sir David Attenborough argues the case for the importance of the science of evolution; Life (BBC ONE) which will capture the most extraordinary and awe-inspiring animal survival behaviours ever shown on TV; Andrew Marr on Darwin's Legacy (working title, BBC TWO) which will explore the impact of Darwin's theory in science, society, political movement and religion; and A Year in Darwin's Garden (working title, BBC TWO) in which entomologist and farmer, Jimmy Doherty, recreates many of Darwin's ground-breaking experiments with plants.

Once again, I find myself interested in a paper about the analysis of a fossil! This time the point of interest is origin of the tetrapod limb digits. The origins of the proximal elements of the tetrapod limb are well understood, and can be seen as homologues of elements of the fins of sarcopterygian (lobe-finned fish). The origins of the digits may have been fin rays, or possibly evolutionary novelties. The latter explanation was supported by developmental genetic studies and analysis of fossils (including the subject of this paper, the transitional fish/tetrapod Panderichthys). In this paper, CT scanning was used to generate 3D images of Panderichthys limbs, demonstrating the presence of distal radials, and correcting a mistaken reconstruction.
The figure below shows the skeletal structure of the limb, coloured to show homologies to the elements of the tetrapod limb. 

This interesting paper investigates whether there is a relationship between polyandry and selfish genetic elements, in the fruit fly Drosophila pseudoobscura. 

Polyandry - where females have multiple mating partners - is widespread in animals, but despite its frequency, little is known of the costs and benefits of this reproductive strategy (though this paper cites evidence that the costs of multiple mating appear to outweigh the benefits.  It is likely that the benefits lie in that polyandry gives the female a greater degree of control over paternity, via sperm competition.  There is also a possibility that selfish genetic elements may promote polyandry by correlating male fitness with sperm competition.