Sunday, September 24, 2006

3d Rock art scanning update

I have mentioned using 3d laser scanning technology to record rock art before. Now the archaeology data service has made the archive of the project: Breaking Through Rock Art Recording: 3D laser scanning of megalithic rock art available. There are lots of nice images and renderings of the scans available and it is even possible to get hold of the 3d data if you ask for it and pay a fee as the files are quite big. The sites scanned for the project were Long meg, Castlerigg, Copt Howe and Horseshoe rock.

See also: Project page at the University of Durham

Castlerigg - the spiral that vanished at the Rock art blog

The mighty Phallus

I was alerted to the presence of the world’s most obscene fungus – the stinkhorn Phallus impudicus in the garden by the terrible stench that could be detected from a considerable distance.

The Stinkhorn Phallus impudicus

The stinkhorns are a fascinating fungi noted for their rapid growth, smell and unusual appearance.

“This is a fowl-smelling fungus that attracts flies to its spore-laden, slimy body, thus increasing the odds of its spores being dispersed to new habitats. The fruiting body can appear almost overnight, and may "scent" your entire back yard. ....This fungus begins as an egglike body beneath the soil. An erect phallus-like stalk breaks through the "egg," forming a cuplike basal volva as the stalk rapidly elongates. The swollen "head" or cap is coated with a black, putrid, musilaginous mass of spore slime.” (3) Mmm nice

The speed of growth is remarkable with a speed of 10-15cm per hour (1).

Phallus impudicus breaking through a pavement from ref. 1

The growing fungus can also exert a considerable amount of force being able to break a glass bottle if the ‘egg’ is allowed to grow inside and even break through tarmac with a force calculated to be 1,33 kN/m^2 so theoretically, one mushroom could lift a person weighing 133kg (1).

The smell that serves to attract flies that spread the fungal spores is astonishingly pungent and seems to do a good job (see pic.). The chemicals responsible seem to be: dimethyl disulphide, dimethyl trisulphide, Linalool, trans-ocimene, and phenylacetaldehyde (2). Interestingly dimethyl sulphide and trisulphide are important chemicals responsible for the bad smell of human flatulence, and seems to be a very effective attractant of various flies.

Because of its unusual shape, the fungus has unsurprisingly gained the reputation of being an aphrodisiac. It may be of some use is treating other medical conditions including epilepsy, gout and rheumatism. Apparently, it can also be eaten and is considered a delicacy in China and is sometimes mistaken for Morels by (presumably nose-less) fungus hunters. I doubt if I could stomach this particular delicacy.


1) Is Phallus impudicus a mycological giant?
Mycologist, Volume 18, Part 1 February 2004
DOI: 10.1017/S0269915X04001041

2) Dimethyl oligosulphides, major volatiles released from Sauromatum guttatum and Phallus impudicus
Phytochemistry, 1994, vol. 35, no2, pp. 321-323.

3) Wayne's World amazing fungi:

Friday, September 01, 2006

Fake medicines given seal of approval

There is sad news for people who care about good science and effective medicines: Homeopathic 'medicines' will be allowed to make medical claims on their packaging here in the UK by the Medicines and Healthcare products Regulatory Agency. It is unbelievable that instead of being prosecuted for fraud the hucksters that flog expensive water/sugar pills are being encouraged. Clearly quackery is highly rewarded here - if you want to make a quick buck flog false hope to the sick.

See also:

Friends In High Places & Homeopathy Packaging And Flu from Badscience

New regulations on licensing of homeopathy from Sense about Science see also: Malaria & homeopathy

A Quack's Charter (Lock & Load)

Reminder: things arenÂ’t so great in the UK, eitherÂ… (Memoirs of a Skepchick)

Water Torture (Holmes Report Blog)

Tuesday, August 29, 2006

Tetrahymena genome published

I have written before about the very unusual genome of the ciliate Tetrahymena thermophila, now its genome has been published in PLOS biology. The paper is free so everyone can read it for themselves. Tetrahymena has lead to many important discoveries in molecular biology such as catalytic RNA, telomeric repeats, telomerase and the function of histone acetylation. Lets hope the genome provides more insights into this fascinating organism and lead to more discoveries.

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, et al. (2006)
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4(9): e286

What's shaped like a pear and has two genomes? Check the pond (press release, Eurekalert)

Tetrahymena Genome Database

Tetrahymena Genome Project

Tetrahymena thermophila Genome Project

Thursday, August 24, 2006

Electrical Walks

Yesterday I went on an unusual art type thing in Birmingham. It was called 'Electrical Walks' by the artist Christina Kubisch and was based at the Ikon Gallery Basically you wore a pair of silly looking headphone things (see picture) that converted the radio waves generated by electrical devices into sound. It was extremely interesting and gave a completely new perspective on the city with things like security barriers suddenly becoming very prominent where usually they are passed by unnoticed. The most prominent sound though was the almost constant hum of Alternating current becoming overwhelming in places but fading to silence in a few places that were far from buildings. Other noisy things included cash machines, some lights sounded like a large and annoying insect flying aroud a large outdoor television buzzed and chittered in a very strange way and wandering past a taxi rank i could hear the drivers talking. It should theoretically be quite easy to make your own so you can experince this strange new world from the comfort of your own corner of this planet.

Saturday, July 29, 2006

New fossil spiders

In the latest issue of the journal Palaeontology some beautifully preserved fossil spiders are described:

Cretadiplura ceara - Carapace length = 4.95mm

Dinodiplura ambulacra - Carapace length = 12.80mm

They come from the lower Creataceous Crato member of the Santana Formation In Brazil that contains many other amazingly well preserved fossils.

This reminded me that I had found the website of Paul Selden where he has kindly made available many of his publications on fossil spiders available:


Palaeontology Volume 49 Page 817 - July 2006

Abstract: The first mygalomorph spiders from the Lower Cretaceous Crato Lagerstätte of Cearà Province, north-east Brazil, are described, from adult males and females, in two new genera and species: Cretadiplura ceara Selden, gen. et sp. nov. and Dinodiplura ambulacra Selden, gen. et sp. nov. They belong to the extant family Dipluridae, hitherto known as fossils only from Tertiary strata; thus this occurrence extends the family record by some 90 myr.

See also: Santana Formation Fossils and my post: oldest orb weaving spider discovered

Friday, July 14, 2006

Moths in decline

Or rather moths join the club of declining species. I have mentioned butterflies and beetles before and now there is long term data on moths. I found this article in the Guardian:

Moths' decline may herald crisis in UK biodiversity

"Conservationists are warning of an impending crisis in British biodiversity after recording dramatic countrywide declines in some of the most common moth species. Records spanning nearly four decades show two-thirds of the country's most popular moths are declining, amounting to about 220 separate species. Numbers of 71 species, more than a fifth of the total, have plummeted by a third in the past decade.

Ecologists at the government's agricultural institute, Rothamsted Research, in Hertfordshire, said the figures added to an already gloomy picture of British biodiversity, which has seen sharp declines in bumble bees and butterflies. Fears have now taken hold that the seemingly relentless loss of insects will have a knock-on effect on birdlife.

Researchers used a network of 95 light traps, most of which have been in place since 1968, to study populations of insects drawn to the glow of the traps' lamps.

The records show that some species, including the dusk thorn and hedge rustic, have declined by more than 90% in the past 35 years.A graph showing the decline in British moths (33%). This is an average, there was no significant change in the 'north' but a greater decline in the 'south' (44%) from (1).

"The thought that these species are declining so severely is shocking. You have to remember these are, or were, common species - they're not considered rare," said Kelvin Conrad, a population ecologist who led the study, which is due to appear in the journal Biological Conservation.

The researchers divided Britain into three sections by first drawing a horizontal line across the country at the level of the Humber river. They then split the southern regions with a line running down from the Pennines.

The scientists discovered that moths local to the south-east fared worst, suffering the most species declines.

In the north, far fewer species were threatened, but the populations of those that were fell spectacularly. The south-west, including Wales, Cornwall and Devon, had the most stable populations of moths.

Dr Conrad blames a general and widespread degradation of the moths' natural habitat for the bulk of the losses, but added that climate change, light pollution and farming practices had all taken their toll.

Studies of the garden tiger moth found that climate change, in the guise of warmer, wetter winters, had gradually forced the moths to retreat from the south-east to cooler territories.

Light pollution, a term used to describe night-time lighting from office blocks and roadside lamps, is thought to disrupt moths' behaviour, either by attracting them or by fooling them into thinking it is daytime.

The findings add to recent reports that nearly three-quarters of butterfly populations in Britain have crashed as their habitats have become damaged and fragmented.

"We have now got good data on moths and butterflies, and we know bumble bees are in trouble. All the studies now point to the same thing, that we are losing many of our insect species in Britain," said Dr Conrad.

Ecologists fear that if the decline in insects is widespread, bird populations will be next to be hit. In the past 100 years, three breeding bird species have disappeared from Britain, the Kentish plover, wryneck, and red-backed shrike.

A recent study from Stanford University concluded that some 10% of the world's bird population will have become extinct by the end of the century, with a further 15% close to the brink."


1) Rapid declines of common, widespread British moths provide evidence of an insect biodiversity crisis
Kelvin F. Conrad, Martin S. Warren, Richard Fox, Mark S. Parsons and Ian P. Woiwod
Biological Conservation
Volume 132, Issue 3 , October 2006, Pages 279-291

The State of Britain's Moths

Large-Scale Temporal Changes in Spatial Pattern During Declines of Abundance and Occupancy in a Common Moth
Kelvin F. Conrad Contact Information, Joe N. Perry, Ian P. Woiwod and Colin J. Alexander
Journal of Insect Conservation, Volume 10, Number 1, March 2006

Update: bootstrap-analysis has a post on extictions that mentions the moth study: 'sunday times: extinction, coming soon to a planet near you'

Thursday, July 13, 2006

Odontogriphus omalus and Kimberella

In my previous post on Odontogriphus omalus I mentioned that Kimberella is considered to be it's early molluscan relative. Since I have found a nice picture of feeding traces called Radulichnus probably produced by Kimberella that indicate that it had a radula and rasped away at microbial mats during the Ediacaran:

The Ichnofossil Radulichnus

This links Kimberella very clearly to Odontogriphus and to later molluscs.


Trace fossils in the Ediacaran–Cambrian transition: Behavioral diversification, ecological turnover and environmental shift
Adolf Seilachera, Luis A. Buatoisb, and M. Gabriela Mángano
Palaeogeography, Palaeoclimatology, Palaeoecology Volume 227, Issue 4 , 10 November 2005, Pages 323-356

Odontogriphus omalus and the Ediacarans

In this week’s nature there is a report on the Cambrian fossil Odontogriphus omalus (1). P.Z. has a nice write up at Pharyngula but I want to discuss the relationship between Odontogriphus and earlier Ediacaran fossils. It is mentioned in the article that Kimberella may be an ancestor of Odontogriphus but it seems that many of the bilaterian fossils of the Ediacaran have greater similarities particularly Dickinsonia type organisms (2). If that is the case Spriggina, Yorgia and Chondroplon may also have similarities to Odontogriphus although they are probabaly more distant relative than Dickinsonia. It certainly seems that many of the aspects of Odontogriphus morphology can illuminte the similarly squidgy Ediacarans. Anyway here are some pics for comparison:
Odontogriphus omalus from the supplementary material to (1)

Reconstruction of an unnamed dickinsoniid from (2)

The fossil on which the above reconstruction was based. Also from (2)

Following the research on Stromatoveris and Parvancorina it seems that the Ediacarans are finally finding their place on the evolutionary tree.


1) A soft-bodied mollusc with radula from the Middle Cambrian Burgess Shale p159
Jean-Bernard Caron, Amélie Scheltema, Christoffer Schander and David Rudkin
Nature 442, 159-163 (13 July 2006) doi:10.1038/nature04894

2) Anatomical Information Content in the Ediacaran Fossils and Their Possible Zoological Affinities
Integrative and Comparative Biology 2003 43(1):114-126; (free full text)
Jerzy Dzik