Uncategorised

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).

Read the bloggers at

Not exactly Rocket Science

Greg Laden's Blog

Laelaps

The Questionable Authority

Read the paper at PLoS ONE (freely available)

Just as I finish reading (or rather, re-reading) chapters concerning the fate of Easter Island (Rapanui) and of Henderson and Pitcairn Islands in Collapse: How Societies Choose to Fail or Survive by Jared Diamond, the 23rd January issue of Science arrives, bearing two articles on the spread of humans (Austronesians) from Taiwan and onwards across Micronesia to Polynesia.  One of these papers, by Gray and colleagues, presents a linguistic analysis of langauages across this region.  The second, by Moodley et al looks at the variation of the human pathogen Helicobacter pylori in these same peoples.  Both strands of evidence documenting this population spread are in striking agreement.

I have no experience in the kind of linguistic analysis carried out by Gray and colleagues, so my understanding is informed by Colin Renfrew's Perspectives article in this issue of Science.There are over 1000 polynesian languages, making it one of the largest language families.  Ultimately, the populations that eventually colonised even the most remote islands such as Easter were ultimately derived from a migration that can (at least in one theory) be traced back to origins in Taiwan (upper panel in the figure below).  Other possibilities include origins in island Southeast Asia.  Genetic evidence (such as that provided by mitochondrial DNA sequences) has been ahrd to interpret, and may not support the Taiwan origin of the Austronesian speaking people.  On the other hand, such evidence may be complicated by post-colonial gene flow.

Gray et al have applied computer analysis to languages across the Pacific diaspora. They have analysed a large database of 210 basic vocabulary (basic in the sense that they are words representing basic activities, and which are the words/concepts that tend to be conserved as languages evolve), and plotted the time course of the Austronesian languages.  It seems that their analysis indicates a pause-pulse mode, in which there were two pauses in expansion.  The first coincides with the crossing of350km Bashi channel between Taiwan and the Phillipines, and the second between the colonisation of  Western Polynesia and that of the remoter Eastern Polynesian islands.  Both the pauses are thought to have ended with technological advances the the sea canoe technology (for example the development of outriggers, improved navigational  techniques, and double hulled canoes.  In the lower panel of the figure below, the related-ness of the languages is tied to the map above by colour coding, and the pauses are indicated.

In the second paper, Moodley et al have analysed 212 H. pylori samples taken from Taiwanese aboriginals, New Guinean highlanders, Melanesians and Polynesians.  Seven genomic fragments were sequenced, revealing 196 haplotypes, which were compared with haplotypes from Europeans in Australia and other haplotypes derived from populations across Asia and the Pacific.

From my position of ignorance about linguistics, it would seem that sequence-based phylogeny reconstruction must be the easier of the two analyses (though I'm happy to be corrected on this).  The figure below shows the phylogenetic relationships between the H. pylori haplotypes (in B) and the geographic spread of samples (in A).

In addition, the global spread of H. pylori is assessed, clearly showing that the New Guinea and Australian colonisation was distinct from the much later colonisation of the Pacific.  What's quite striking is the correspondence between the two trees, as presented in the accompanying Perspectives article, which concludes with the hope that a sysnthesis of linguistic and genetic approaches may be possible on a global scale.

R. D. Gray, A. J. Drummond, S. J. Greenhill (2009). Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement Science, 323 (5913), 479-483 DOI: 10.1126/science.1166858 Y. Moodley, B. Linz, Y. Yamaoka, H. M. Windsor, S. Breurec, J.-Y. Wu, A. Maady, S. Bernhoft, J.-M. Thiberge, S. Phuanukoonnon, G. Jobb, P. Siba, D. Y. Graham, B. J. Marshall, M. Achtman (2009). The Peopling of the Pacific from a Bacterial Perspective Science, 323 (5913), 527-530 DOI: 10.1126/science.1166083 C. Renfrew (2009). ANTHROPOLOGY: Where Bacteria and Languages Concur Science, 323 (5913), 467-468 DOI: 10.1126/science.1168953

A recurring theme in this blog is not just that the Government seems determined to trample over the data protection rights of the UK population, but that they are singularly inept at ensuring that the state machinery treats various data sources in a careful and secure manner.

From databases left on trains, to stolen laptops contaning databases of personal data, I (and I guess many others) view Wacky Jacqui's upcoming Uber-database that will be made possible by a combination of databases (including the vile IMP comms database and that of the ridiculous ID card scheme) using the "interesting" clause 152 of the Coroners and Justice Bill Part 8 - Data Protection Act 1998 (c. 29).  This empowers Ministers to direct the linkage of diferent databases.

Now we hear that the files of over 17,000 asylum seekers have been lost (The Guardian).  It's not clear from this report whether these are digital files or hard copy, but it's just another illustration of the laxity with which he civil service seems to treat personal data.  As the articles says:

This follows a series of high-profile losses of data, including an Inland Revenue CD with the details of 25 million child-benefit claimants, four CDs with the names of dozens of magistrate court defendants and witnesses, and a Ministry of Defence laptop containing details of 620,000 recruits and potential recruits. 

The startling ineptitude is the tip of the iceberg: apparently the  UK Border Agency has a backlog of about 200,000 cases asylum cases to deal with.  One wonders if the principal strategy is to encourage asylum seekers to experience such glacial progress in their claims that they lose heart and try another country.  Or perhaps just die of old age.

According to the Daily Telegraph, a team of scientists (we're always "teams") have cloned an extinct Spanish mountain goat from DNA contained in frozen skin samples from the last known specimen, aand using domestic goat eggs.

The article, Extinct ibex is resurrected by cloning,saysthat

The Pyrenean ibex, a form of wild mountain goat, was officially declared extinct in 2000 when the last-known animal of its kind was found dead in northern Spain.

Shortly before its death, scientists preserved skin samples of the goat, a subspecies of the Spanish ibex that live in mountain ranges across the country, in liquid nitrogen.

Using DNA taken from these skin samples, the scientists were able to replace the genetic material in eggs from domestic goats, to clone a female Pyrenean ibex, or bucardo as they are known. It is the first time an extinct animal has been cloned.

Sadly, the newborn ibex kid died shortly after birth due to physical defects in its lungs.

There's a slight hitch here, though isn't there?  I mean, aside from the fact the poor wee died shortly after birth, aren't we only going to be able to generate specimens of one sex?

Perhaps the plan is to mate the resurrected Pyrenean Ibex with a closely related species and try to breed from the progeny?  Sounds like a  lot of work!