Wednesday, April 26, 2006

Vindolanda tablets online

The famous birthday party initation from Claudia Severa to Lepidina

Just found this via ABZU: Vindolanda tablets online, This is a collection of the texts found on wooden tablets at the vindolanda roman fort on hadrian's wall. These have been voted the greatest archaeological treasure in britain, with some justification - they give such rare and amazing details of the people of roman britain. There is all the information you could possibly want - images of the tablets, the latin text, a translation and notes. A treasure trove of information and a great example of providing public access to data.

Chernobyl: 20 years on

The Chernobyl reactor today, from Daniel Cuthbert

Today is the 20th anniversary of the Chernobyl disaster . There is alot of research on the consequences of this disaster . The health consequnces to people are well known although there is some controversy about the magnitude of these effects but there is also research on the effects on wildlife. The animals did not have the opportunity to flee so provide a fascinating place to study the effects of radiation on various organisms. Tim Mousseau’s Lab has lots of information about Chernobyl and several interesting papers to download:

Biological consequences of Chernobyl: 20 years after the disaster (PDF) - an excellent recent review.

Albinism and phenotype of barn swallows Hirundo rustica from Chernobyl (PDF)

Mutation and sexual selection: A test using barn swallows from Chernobyl (PDF)

Condition, reproduction and survival of barn swallows from Chernobyl (PDF)

See also:

In Focus : Chernobyl (IAEA)

Chernobyl's continuing hazards (BBC)

The Chernobyl disaster (BBC)

Chernobyl's lost city, Daniel Cuthbert, the abandoned city of Pripyat, Ghost Town, (photos)

Sunday, April 23, 2006

Pygmy Elephantids

Illustration showing the size of a dwarf elephant

It seems to be common theme that when populations of large mammals are isolated on islands they tend to evolve a dwarfed stature. This is particularly noticeable in elephantids where many have been among the largest species of land animal.

This Island dwarfing has occurred several times in many places and with many different elephantid species, including mammoths on Californian islands, on Wrangel Island in Russia and on the islands of the Mediterranean.

The islands of the Mediterranean have been searched for these the animals and remains have been found on many islands: Sardinia, Sicily, Malta and the Egad Islands, Crete, Cyclades, Dodecanese, Cyprus. They were clearly fairly common in the Mediterranean.

They roamed these islands from the middle Pleistocene (approx ) to about 10,000 years ago. Some people have suggested that they survived into historic times and were depicted on the walls of Egyptian tombs. Sadly, they are all extinct now. One important feature of these elephants is their cuteness. Judging by how many times this dwarfing has happened it shouldn’t be too hard to recreate, a worthy project for someone. I wonder if anyone could get funding for such a project.

There is a theory that the discovery of skulls of pygmy elephants led to the legend of the Cyclops as the skulls have a large hole in the middle (associated with the trunk) that looks a bit like a single large eye socket. The geography origin of the story and occurrence of the pygmies certainly coincide making this theory plausible.

It used to be thought that all of these species were quite closely related and descendants of Elephas antiquus although the polygenetic position derived from their morphology was never particularly clear. There has now been DNA analysis carried out on bones from several different islands and it turns out that these elephantids probably have at least two separate ancestoral species with the eastern and western parts of the Mediterranean being colonized at different times. The ones in the eastern Mediterranean seem to be descended chiefly from Elephas during the Late Pleistocene and those in the eastern from Mammuthus during the Middle Pleistocene.

This research is remarkable because some of the DNA recovered is around 800,000 years old. This represents one of the oldest DNA fragments ever recovered, this opens up the possibility of further analysis of other organisms of this age.


Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids.
Biology letters, in press, published online: 21 April, 2006. DOI: 10.1098/rsbl.2006.0467
Nikos Poulakakis, Aris Parmakelis, Petros Lymberakis, et al.

Dwarf elephants (Wikipedia)

Adalgisa Caccone lab

Dwarf elephants: evolutionary patterns (12 papers can be downloaded here)

Cyclops Myth Spurred by "One-Eyed" Fossils?

Did endemic dwarf elephants survive on Mediterranean islands up to protohistorical times? (PDF)

Thursday, April 20, 2006

Pro research petition

Some good news from the BBC:

"An online petition has been launched allowing the UK public to back medical research using animals.

The Coalition for Medical Progress, which includes drug companies and research agencies, started it at the suggestion of a member of the public.

It says the petition will give voice to the "silent majority" who accept the need for animal studies. "

Here it is:

See also: Pro-test

The Research Defence Society

Friday, April 14, 2006

Plant Cellular Anatomy

Found via Pruned beautiful pictures of fluorescent stained plant cells, more pictures can be found Here , part of Jim Haseloff's Laboratory website - lots of other interesting stuff there too.

Positive selection on gene expression in the human brain

There has been a fair bit of recent research on the role of positive selection on the evolution of the human brain with the discovery that genes such as FOXP2, ASPM and Microcephalin had undergone rapid evolution on the lineage leading to humans.

A new piece is added to this picture with the publication of a new paper in Current Biology on the evolution of gene expression (1) rather than changes in protein sequence, although the two are not mutually exclusive.

This research compared the amount of linkage disequilibrium (LD) which is expected to be high around genes that have experienced recent positive selection with the amount of expression divergence in four tissues (brain, heart, kidney and liver). There was found to be a positive correlation between LD and genes expression divergence in the brain but no the other three tissues. This indicates that the divergence in gene expression is most likely partly due to positive selection rather than another factor like the relaxation of selective constraint. These results show once again that the human brain which is arguably on of our most unique characteristics is clearly the product of evolution.

Other results include:

"Interestingly, the top 5% of gene orthology groups with the highest expression divergence as well as the highest LD contain many genes involved in metabolism (Supplemental data). These genes, most noticeably the ones involved in electron transport and energy pathways, increased significantly in expression in the human versus the chimpanzee brain. It has been argued that amino acid changes in proteins involved in these pathways might have been positively selected for, due to changes in brain size and lifespan."

"Because we observe correlation between LD and expression changes at the level of functional groups rather than individual genes, some or many of the expression changes selected for in the human lineage may have occurred more than to 200,000 years ago. Consequently, our results do not show that all of the expression changes in brain observed in the human lineage can be explained by events within the last 200,000 years. However, a detectable proportion of these events is recent and potentially associated with the origin of modern humans prior to their spread out of Africa."

This seems to agree with other recent research that there has been alot of selection acting on many genes in the human genome 10,000–40,000 years ago (2) and more recently (3). This type of research has the potential to reveal alot about the genetic basis of humanness and proces of human evolution, although as always there is plenty more to discover.

1) Positive selection on gene expression in the human brain
Philipp Khaitovich, Kun Tang, Henriette Franz, Janet Kelso, Ines Hellmann, Wolfgang Enard, Michael Lachmann, and Svante Pääbo. Current biology (in press)
(LINK) full text seems to be available for free at the moment

2) Wang ET, Kodama G, Baldi P, Moyzis RK.
Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):135-40. Epub 2005 Dec 21.
Global landscape of recent inferred Darwinian selection for Homo sapiens.

3) Voight BF, Kudaravalli S, Wen X, Pritchard JK.
PLoS Biol. 2006 Mar;4(3):e72. Epub 2006 Mar 7.
A map of recent positive selection in the human genome.

Sunday, April 09, 2006

More Sharovipteryx

The Hairy Museum of Natural History has a nice post on Sharovipteryx mirabilis with some more information and an excellent drawing of the beast in flight.

Friday, April 07, 2006

Sauropod tracks

I love these dinosaur tracks, it looks almost as if the giant sauropods had just walked past:

Detail of Sauropod tracks, Large scale bar 50 cm, small scale bar, 20 cm.Plan of the tracks. theropod (white arrows, T1-6), sauropod (black arrows, S1-5), and pterosaur (stippled arrows, P).

Diverse dinosaur-, pterosaur-, and bird-track assemblages from the Hakou Formation, Lower Cretaceous of Gansu Province, northwest China
Jianping Zhang, Daqing Lib, Minglu Li, Martin G. Lockley, Z. Bai.
Cretaceous Research
Volume 27, Issue 1 , February 2006, Pages 44-55 (free full text as part of sample issue - lots of other interesting stuff)

DNA sequencing revolution?

This press releass via Eurekalert:

Nanopore method could revolutionize genome sequencing

"A team led by physicists at the University of California, San Diego has shown the feasibility of a fast, inexpensive technique to sequence DNA as it passes through tiny pores. The advance brings personalized, genome-based medicine closer to reality.

The paper, published in the April issue of the journal Nano Letters, describes a method to sequence a human genome in a matter of hours at a potentially low cost, by measuring the electrical perturbations generated by a single strand of DNA as it passes through a pore more than a thousand times smaller than the diameter of a human hair. Because sequencing a person's genome would take several months and millions of dollars with current DNA sequencing technology, the researchers say that the new method has the potential to usher in a revolution in medicine."

This is really interesting research, lets hope it can be implemented effectively and cheap genomes become a reality.

Fast DNA Sequencing via Transverse Electronic Transport
Johan Lagerqvist, Michael Zwolak, and Massimiliano Di Ventra
Nano Letters.

Full text Here

Thursday, April 06, 2006

The end of light pollution?

Well hopefully the beginning of the end, here in Britain at least.

New rules have been introduced today which amoung other things will hopefully help reduce light pollution. The 'Clean Neighbourhoods and Environment Act 2005' will bring in fines of up to £5000 for individuals and £20,000 for businesses for light that is 'prejudicial to health or a nuisance'.

It would be amazing if this would lead to me getting to see anything other than the brightest stars and planets.

International Dark-Sky Association
Light pollution soon to be criminal

Wednesday, April 05, 2006

New fossil between fish and tetrapods

A fantastic new fossil documenting the evolutionary transition of vertebrates from the sea to the land has been published in the current issue of nature. It's been called Tiktaalik roseae and seems to be a very important fossil.

There are posts about it in greater detail on Pharyngula , The Lancelet , The Loom , Palaeoblog and The Hairy Museum of Natural History .

The fungi from space

"Swift as the shooting star, that gilds the night
With rapid transient Blaze, she runs, she flies;
Sudden she stops nor longer can endure
The painful course, but drooping sinks away,
And like that falling Meteor, there she lyes
A jelly cold on earth" - William Somerville.

While browsing the Mycologist I found this interesting article on the old idea that fungi came from space and some meteorites contained fungi. This is in some ways logical, fungi often appear very suddenly almost as if they fell from the sky and various fungi can resemble genuine meteorites:

A meteorite

A fungus

Strangely this idea seems to have been resurrected in the age of UFOs where fungi and fairy ring are again mistaken for extra-terrestrial traces.

There are various names for these celestial fungi including ‘star jelly’, ‘rot of the stars’ or ‘star shot’ and ‘pwdre ser’ in welsh. These probably refer to fungi such as Tremella lutescens.

The Idea of space fungi put me in mind of HP lovecraft’s ‘fungi from yuggoth’ and also this illustration of the peculiar ancient fungus Prototaxites:

Prototaxites - Click for larger version

This painting is very evocative of an alien world which in many ways the Devonian was. Its strange how the ancient world can look stranger than people’s imaginary concepts of alien worlds.


Ethnomycological notes. II. Meteorites and fungus lore
Mycologist, Volume 20, Issue 1 , February 2006, Pages 22-25
Á.M. Nieves-Rivera and D.A. White. (free full text)

Star jelly - Wikipedia

Pwdre Ser or 'Star Jelly' - The Edinburgh Geologist

Pwdre Ser - Space Blobs

Rotted wood–alga–fungus: the history and life of Prototaxites Dawson 1859
Review of Palaeobotany and Palynology
Volume 116, Issues 1-2 , August 2001, Pages 123-158
Francis M. Hueber

Tuesday, April 04, 2006

Fake eggs in China!

This is totally unbelievable but apparently the notorious fakers of China are no longer content just to pirate medicines, cars, aircraft parts and designer goods and are now creating artificial eggs that they can sell for half the price of real eggs [Via].

These eggs can cause serious health problems if you eat them as they are made from things like Alum, Calcium chloride paraffin wax, gelatine, lactone, carboxymethyl cellulose, sodium alga acid, sodium benzoate, lysine etc. - yuk.

A photo of the final stage in the process of making fake eggs, from Here

See also:

Faked Eggs The World's Most Unbelievable Invention (The Internet Journal of Toxicology)

Egg Piracy in China (news report in chinese - pics of real and fake eggs)