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

Wednesday, July 12, 2006

Sleep and weight update

I have written about a lack of sleep contributing to obesity before and the possible causes of this problem. So i was interested to see this press release from eurekalert:

Sleep deprivation doubles risks of obesity in both children and adults

Sleep deprivation could be factor in obesity

Research by Warwick Medical School at the University of Warwick has found that sleep deprivation is associated with an almost a two-fold increased risk of being obese for both children and adults.

Early results of a study by Professor Francesco Cappuccio of the University of Warwick's Warwick Medical School were presented to the International AC21 Research Festival hosted this month by the University of Warwick.

The research reviewed current evidence in over 28,000 children and 15,000 adults. For both groups Professor Cappuccio found that shorter sleep duration is associated with almost a two-fold increased risk of being obese.

The research also suggests that those who sleep less have a greater increase in body mass index and waist circumference over time and a greater chance of becoming obese over time.

Professor Cappuccio says:

"The 'epidemic' of obesity is paralleled by a 'silent epidemic' of reduced sleep duration with short sleep duration linked to increased risk of obesity both in adults and in children.These trends are detectable in adults as well as in children as young as 5 years."

Professor Cappuccio points out that short sleep duration may lead to obesity through an increase of appetite via hormonal changes caused by the sleep deprivation. Lack of sleep produces Ghrelin which, among other effects, stimulates appetite and creates less leptin which, among other effects, suppresses appetite. However he says more research is needed to understand the mechanisms by which short sleep is linked to chronic conditions of affluent societies, such as obesity, diabetes and hypertension.

Francesco Branca, the Regional Adviser for nutrition and food security in the World Health organisation (WHO) Regional Office for Europe said:

"This is an interesting piece of research putting together different lifestyle aspects with food choices. We need more research on the obese environment - the integration between medical research and socio-political research is something we should be exploring more."

There is also a Warwick Universty podcast by Professor Francesco Cappuccio on the health consequnces of a lack of sleep and how you can get more: Link

See also: Sleep and Obesity (research TV)

Warwick University's sleep research news

How many cell types does a person have?

According to recent research published in biological reviews in an adult human it is 411 with 145 of those being neurons.


"Metazoans are composed of a finite number of recognisable cell types. Similar to the relationship between species and ecosystems, knowledge of cell type diversity contributes to studies of complexity and evolution. However, as with other units of evolution, the cell type often resists definition. This review proposes guidelines for characterising cell types and discusses cell homology and the various developmental pathways by which cell types arise, including germ layers, blastemata (secondary development/neurulation), stem cells, and transdifferentiation. An updated list of cell types is presented for a familiar, albeit overlooked model taxon, adult Homo sapiens, with 411 cell types, including 145 types of neurons, recognised. Two methods for organising these cell types are explored. One is the artificial classification technique, clustering cells using commonly accepted criteria of similarity. The second approach, an empirical method modeled after cladistics, resolves the classification in terms of shared features rather than overall similarity. While the results of each scheme differ, both methods address important questions. The artificial classification provides compelling (and independent) support for the neural crest as the fourth germ layer, while the cladistic approach permits the evaluation of cell type evolution. Using the cladistic approach we observe a correlation between the developmental and evolutionary origin of a cell, suggesting that this method is useful for predicting which cell types share common (multipotential) progenitors. Whereas the current effort is restricted by the availability of phenotypic details for most cell types, the present study demonstrates that a comprehensive cladistic classification is practical, attainable, and warranted. The use of cell types and cell type comparative classification schemes has the potential to offer new and alternative models for therapeutic evaluation."

Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest
Matthew K. Vickaryous and Brian K. Hall
Biological Reviews, in press, doi: 10.1017/S1464793106007068, Published online 22 Jun 2006

Tuesday, June 27, 2006

Colour changing snake discovered

This is something I never realised existed: a colour changing snake (Via). Here is the news release from the WWF:

"Gland, Switzerland – A new snake with the ability to spontaneously change colour has been discovered in the forests of the Heart of Borneo, one of the most biologically diverse regions on Earth, possessing staggeringly high numbers of unique species across all groups of plants and animals.

This ability of the snake to change colour is known from some reptiles, such as the chameleon, but scientists have seen it very rarely with snakes and have not yet understood this phenomenon.

The snake was discovered by a German researcher who described it with the collaboration of two American scientists.

“I put the reddish-brown snake in a dark bucket. When I retrieved it a few minutes later, it was almost entirely white,” said Dr Mark Auliya, reptile expert at the Zoologisches Forschungsmuseum Alexander Koenig in Germany, and a consultant for WWF.

Dr Auliya collected two specimens of the half-metre long poisonous snake in the wetlands and swamped forests around the Kapuas river in the Betung Kerihun National Park, an area in Kalimantan (the Indonesian part of Borneo) where WWF supports conservation work. The scientists named it the Kapuas mud snake.

The genus Enhydris, to which the new snake belongs, is composed of 22 species, only two of which are widespread. All the others have a very restricted range. The scientists believe this newly discovered snake might only occur in the Kapuas River drainage system.

In the last ten years, 361 new animal and plants species have been discovered on the island of Borneo. This amounts to three new species a month in an area only a little more than twice the size of Germany.

“The discovery of the ‘chameleon” snake exposes one of nature’s best kept secrets deep in the Heart of Borneo," said Stuart Chapman, WWF’s international coordinator of the Heart of Borneo initiative.

"Its ability to change colour has kept it hidden from science until now. I guess it just picked the wrong colour that day.”

However, WWF warns that the home of the new snake is threatened. Today, only half of Borneo's forest cover remains, down from 75 per cent in the mid-1980s.

But there is also hope that this trend could be halted as the three Bornean governments – Brunei Darussalam, Indonesia and Malaysia – recently launched the Heart of Borneo initiative, which aims to preserve approximately 220,000km2 of equatorial forests and numerous wildlife species."

Here is the paper describing the snake:

J. C. Murphy, H. K. Voris & M. Auliya.
A new species of Enhydris (Serpentes: Colubridae: Homalopsinae) from the Kapuas river system, West Kalimantan, Indonesia.
The Raffles Bulletin of Zoology (vol 53, p 271) (Free PDF)

‘Chameleon' snake can turn white in minutes (New Scientist)

Tectonics and the evolution of Lupins

There has been a debate amoung scientists who study evolution as to whether evolutionary radiations occur more rapidly in island type areas than normal continental conditions.

A study in press at PNAS on the evolution of Andean Lupins suggests that it is environmental change, in this case the uplift of the andes that is a major driver of phenotypic evolution (1). The uplift of the Andes seems to have created island type conditions with many new ecological niches being formed creating opportunities for an adaptive radiation. There does not seem to have been any key evolutionary innovation in the Andean Lupins so the ecological niches created by the uplift of the Andes are the most likely cause of this rapid diversification in forms:

(Click for bigger)
"Phylogeny of Lupinus. Fifty percent majority rule Bayesian tree from analysis of the combined ITS/LEGCYCIA data sets. Posterior probabilities of major clades are shown below nodes; all nodes had posterior probabilities 0.5. This tree is congruent with the strict consensus derived from parsimony analysis. For clarity, taxon names have been omitted (see supporting information). Branch lengths are proportional to changes on the tree. A and B denote two well supported New World clades: A, eastern New World; B, western North America, Mexico, and the Andes. The map shows the distributions of these two New World clades to be largely allopatric, with limited overlap in the southern U.S. and the south-central Andes. The geographical extent of the main Andean radiation is shown in orange. Chilean accessions of Lupinus microcarpus group with their North American counterparts at the base of clade B, but the occurrence of L. microcarpus in central Chile (shown in red) is doubtfully native. Line drawings illustrate life forms encompassed by species in the Andean Lupinus radiation: a, treelet, Lupinus semperflorens; b, prostrate herb, Lupinus sp. nov; c, perennial woody shrublet, Lupinus smithianus; d, ephemeral annual herb, L. mollendoensis; e, giant stem rosette, Lupinus weberbaueri; f, woody perennial shrub, Lupinus sp. nov; g, acaulescent rosette, Lupinus nubigenus; h, perennial woody shrublet, Lupinus sp. nov; i, dwarf acaulescent rosette, Lupinus pulvinaris; j, prostrate herb, Lupinus prostratus. (Scale bars: 5 cm.)"

This study reminded me of a paper in the current issue of Antiquity (2) that suggests that human evolution could have been driven by the opening of the Great rift valley. Maybe major tectonic events have a more widespread effect on evolution than has been realised.


1) Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes
Colin Hughes and Ruth Eastwood
PNAS published June 26, 2006, 10.1073/pnas.0601928103

2) Tectonics and human evolution
Geoffrey King and Geoff Bailey.
Antiquity Volume: 80 Number: 308 Page: 265–286

Wednesday, June 21, 2006

UK beetles under threat

This is not exactly unexpected but its nice to see that it is getting some news coverage. From the BBC:

"Many species of beetles in the UK are in danger of dying out, a conservation charity has warned.

Buglife, which campaigns to protect endangered insects, says 250 of the UK's 4,000 species of beetle have not been seen since the 1970s.

The charity says it is vital for other animals that the variety of beetle-life is maintained, and "imperative" that action is taken now to protect them.

It warned that habitat decline meant many species may already be extinct.

Conservationists say beetles play a unique and vital role in the planet's ecosystems, including burying the corpses of dead animals and pollinating flowers.

But some species have not been seen for years in the UK. For example, the Sussex Diving Beetle which was common in the Lewis Levels in the 1970s but was last spotted in 2002.

Buglife director Matt Shadlow told BBC News the problems facing beetles had been indicated by research into other invertebrates, such as butterflies and moths, for which better data existed.

"The data on butterflies and moths suggests that 70% of the species that occur in the UK are currently in decline," he said.

"And in fact even with the butterflies, recent butterfly conservation data shows that in the last 10 years alone, we've lost a third of all our butterflies from the countryside.

"So other invertebrates seem to be suffering very badly. So it's not surprising that when we look at the beetles, we find that there's problems there as well."

He said it was "imperative" immediate action was taken to preserve the astonishing variety of British beetles before it was too late."

This is probably related to national insect week which started on monday, check out the website to see whats going on and if you can, do something to help our invertebrate friends.



National Insect week

The Coleopterist

Thursday, June 15, 2006

The oldest book I own

I saw this meme type thing at snail's tails and thought it was neat, so here is my oldest book: Symbolae Mycologicae by Leopold Fuckel and dates from 1869.

Its a book on fungi in german, notable because it contains the first description of several species and genera of fungi. It also has a few nice illustrations that have been hand tinted:

Oldest orb-weaving spider discovered

A drawing of the fossil spider Mesozygiella dunlopi

The discovery of the oldest true orb weaving spider has been announced in Biology letters. It was found in amber from northern spain and extends the range of the orb weavers back to the early Cretaceous. This means that the radiation of spiders occurred at the same time as that of angiosperms and the pollinating insects which form a major part of spider diets.


Oldest true orb-weaving spider (Araneae: Araneidae)
David Penney and Vicente M. Ortuño.
Biology Letters, DOI: 10.1098/rsbl.2006.0506

Early web-spinner found in amber: BBC News story

Tuesday, June 13, 2006

Fast evolution in Ciliates

The Ciliate Tetrahymena

Ciliates are a large group of unicellular eukaryotes that have a highly unusual genome architecture. They have two, a micronucleus (MIC) and a macronucleus (MAC). The MIC is where genes are stored and it is passed on during sexual reproduction but it does not produce mRNA. The MAC is not passed during sexual reproduction, it is much larger than the MIC containing several copies of each gene and it is derived from the MIC (1). Ciliates normally divide asexually and in that case both nuclei are duplicated and one copy is passed on to each daughter cell. The reason for this genome architecture seems to be the very large cell size of Ciliates making it necessary to produce large amounts of proteins from each gene; this makes it necessary to have several copies of each gene from which mRNA can be produced.

It has been hypothesized that this unusual genome causes the ciliates to evolve much faster than other organisms. A fast rate of evolution has been found in histone H4 but as this gene is related to chromosome structure this fast rate of evolution could be a cause of the strange genome rather than a consequence of it. Now the rate of protein evolution has been compared between ciliates and other organisms and within ciliates with different amounts of genome processing (2). It was indeed found that genome processing did dramatically increase the rate of protein evolution, and the more extensive the processing the faster the rate of evolution.

It is not immediately obvious just how the unusual genome architecture of ciliates causes this fast evolutionary rate. The model proposed in the paper is this:

(Click for bigger)

“Genome architecture drives protein evolution in ciliates through the impact of selection operating on processed chromosomes in a somatic nucleus that divides by amitosis. Each ciliate contains a germline micronucleus, with a canonical eukaryotic genome, and a somatic macronucleus, represented by a large polyploid nucleus. A. If a deleterious mutation occurs (shown as an X), the chromosome carrying that mutation can be lost following unequal assortment during amitosis of the macronucleus. While this mutation may eventually be completely eliminated from the macronucleus, it will be present in the micronucleus. B. During subsequent rounds of asexual division, the micronucleus will acquire additional mutations. Given sufficient time and/or population size, one or more of these mutations may be compensatory. After conjugation, individuals with compensatory mutations can increase in frequency in the population. C. These processes are exaggerated in ciliates with extensively fragmented genomes, where every allele and locus is able to assort independently.”

Its and interesting theory although a lot more data will have to be accumulated before it is validated or another explanation can be found for the rate of evolution in Ciliates.

Although ‘Developmentally Regulated Genome Rearrangements’ seem very odd, they are fairly common (3). For example Genome-wide rearrangements has been found in Nematodes, Copepods, Hagfish Foraminifera and Ciliates and Targeted rearrangements are found in places like the vertebrate immune system. It is likely that this phenomenon does have an effect on the rate of evolution and it seems that this area of study will reveal interesting results.


1) Carolyn L. Jahn and Lawrence A. Klobutcher
Annual Review of Microbiology Vol. 56: 489-520

2) Rebecca A. Zufall, Casey L. McGrath, Spencer V. Muse, and Laura A. Katz
Genome Architecture Drives Protein Evolution in Ciliates
MBE Advance Access published on June 7, 2006.

Evolution of Developmentally Regulated Genome Rearrangements in Eukaryotes

Ciliophora (Protist image database)

Thursday, June 08, 2006

Ancient Stromatolites of biological origin

Some 'egg carton' laminites from Pilbara

Some of the earliest fossils in the world come from around Australia (Pilbara Supergroup) and South Africa (Onverwacht and Nondweni groups) (1) and date to around 3.4 billion years old. These fossils consist of stromatolites, structures formed by bactera interacting with sediment. This is at least what people assumed until some researchers suggested the structures were in fact of abiotic origin. New research on the Strelley Pool Chert recently published in Nature attempts to demonstrate the biological origin of these structures (2).

Conical Pilbara stromatolites from above from Here

The research team has a Pilbara wiki and they have a good info so i will just quote from them:

"The ancient reef is cut off one end by a fault, and at the other as it disappears into what would have been deep water, not liked by the microbial communities that created the stromatolite structures, just like modern ones.

“If you start at the deep water end and trace it along the reef system, the numbers of stromatolite shapes increase and become more complex and varied, just as occurs in biological reef systems throughout the geologic record,” she says. “It is a classical biological response to the environment.”

Her other lines of evidence include the individual structures and the association of morphologies (shapes), the spatial distributions, and the way those relate to the palaeo-environment. Analysis of the rare earth element chemistry (with Balz Kamber, Laurentian University) confirms the deposition of the fine-grained sedimentary rocks known as chert and carbonate that make up the stromatolites happened in a marine environment.

“If you take a vertical section through time there is a brief change from the high temperature hydrothermal and volcanic deposition that dominated the Pilbara at the time to a shallow marine environmentt in which life flourishes virtually immediately, “ she remarks. “And then back again to another volcanic and hydrothermal episode, when the stromatolites disappear. This speaks volumes about the conditions that may have nurtured early life” From Here

Another paper recently described structures called 'endolithic microtubes' in the Strelley Pool chert (3) that they interpreted as being of microbial origin providing futher independant evidence of the biological origin of these fossils. So overall i think the case biological origin for these structures is fairly solid.

There are microfossils from the area discovered by Schopf but these are more dubious.

There are older fossils dating to nearly 3.5 billion years ago in the Pilbara Supergroup belonging to the Dresser Fromation. In the light of this research these can also probably be more confidently called biological in origin. If this is the case I think these are the oldest currently known visible traces of life on earth.


1) Fossil evidence of Archaean life
J. William Schopf
Phil. Trans. B. Volume 361, Number 1470 / June 29, 2006

2) Stromatolite reef from the Early Archaean era of Australia
Abigail C. Allwood, Malcolm R. Walter, Balz S. Kamber, Craig P. Marshall and Ian W. Burch
Nature 441, 714-718 (8 June 2006)

3) A fresh look at the fossil evidence for early Archaean cellular life
Martin Brasier, Nicola McLoughlin, Owen Green, David Wacey.
Phil. Trans. R. Soc. B. Volume 361, Number 1470 / June 29, 2006

Pilbara Wiki - excellent resource with things like images, and maps and a reef FAQ.

Leggiest animal rediscovered

Illacme plenipes - still from the supplementary video

Biologists in California have rediscovered the record breaking millipede Illacme plenipes notable for having the largest number of legs in the animal kingdom with some specimens having up to 750 legs! although the recently found ones have only a maximum of 666 legs.

The species was first discovered in 1926 but none have been found since. The current specimens comes from a tiny area only 0.8 km2 in San Benito County. Lets hope their habitat is now preserved. This also illustrates the amazing biodiversity of the California Floristic Province and will hopefully stimulate interest in conservation of this amazing area.


Biodiversity hotspots: Rediscovery of the world's leggiest animal
Paul E. Marek and Jason E. Bond
Nature 441, 707 (8 June 2006) | doi:10.1038/441707a

The supplementary information has a a video a PDF with electron micrographs and is available free to everyone: Link

Friday, June 02, 2006

TV causes sleep disturbance in children

The findings of this research are not exactly unexpected but it is always nice to have more evidence:

"Passive TV viewing related to children's sleeping difficulties

A recent Finnish randomized population-based study shows that TV-viewing, and particularly exposure to adult-targeted programs, such as current affairs programs, TV series and police series and movies, markedly increases the risk of sleeping difficulties in 5-6 year old children. Also passive exposure to TV increases sleeping difficulties.

Questionnaires concerning TV viewing, sleep disturbances, and psychiatric symptoms were administered to 321 parents of children aged 5-6 years, representing the typical urban population in three university cities in Finland.

The results of the study have been published recently in the Journal of Sleep Research.

Main results:

1. All the families that participated in the study had at least one TV set. In 21% of families, there was a TV set in the children's room. On average, the TV was switched on for 4,2 h a day. Children actively watched TV for a mean of 1,4 h a day and were passively exposed to TV 1,4 h a day.

2. Both active TV viewing and passive TV exposure were related to shorter sleep duration and sleeping difficulties, especially sleep-wake transition disorders and overall sleep disturbances.

3. There was also a clear association between the contents of actively viewed TV programs and the sleep problem scores. Watching adult targeted programs, such as current affairs programs, police series, movies, series, was related to an increased frequency of various sleeping difficulties.

4. Watching TV alone was related to sleep onset problems.

5. Watching TV at bedtime was also associated with various sleeping problems, especially sleep-wake transition disorders and daytime somnolence.

6. Particularly high passive exposure to TV (>2,1 h/day) and viewing adult-targeted TV programs were strongly related to sleep disturbances. The association remained highly significant when socio-economic status, family income, family conflicts, the father's work schedule, and the child's psychiatric symptoms were controlled for statistically. The adjusted odds ratios were 2.91 (95% CI 1.03-8.17) and 3.01 (95% CI 1.13-8.05), respectively. There was also an almost significant interaction between passive TV exposure and active viewing of adult programs (AOR 10.14, 95% CI 0.81-127.04, p=0.07). By contrast, active TV viewing time and the viewing of children's programs were not correlated with sleep problems.

Most of the previous research has concentrated on active TV viewing while passive TV exposure has only rarely been considered. Passive TV exposure can be particularly harmful to young children because it increases the risk of children coming into contact with programs intended for adults.

Quality sleep is essential for children's wellbeing and health. Therefore reducing the quantity of passive TV exposure and limiting children's opportunities to watch adult-targeted programs might help to reduce children's sleeping problems and increase average sleep duration, which could further lead to beneficial changes in children's daytime behavior. Parents should be advised to control the quantity of TV viewing, to monitor the program content viewed, and to limit children's exposure to passive TV. Watching TV at bedtime should be discouraged." (LINK)

I have mentioned before that watching television may be linked to a decline in childrens abilities. The mechanism of this could well be sleep deprivation as sleep is important for memory consolidation and other brain processes. There is also the link between sleep and obesity - if children sleep less they are more likely to get obese. It could well be that the increase in obesity in recent years is due in part to the widespread lack of sleep in children.


TV exposure associated with sleep disturbances in 5- to 6-year-old children
Journal of Sleep Research
Volume 15 Issue 2 Page 154 - June 2006, doi:10.1111/j.1365-2869.2006.00525.x

Tuesday, May 30, 2006

Trichoplax mitochondrial genome sequenced

In press at PNAS is the report of the sequence of the mitochondrial genome sequence of the very unusual metazoan Trichoplax adhaerens. Trichoplax is odd because it is an extremely simple version of a multicellular organism. It has no real organs, no axis of symmetry, a very small nuclear genome and only four distinct cell types.

This has led to the hypothesis that it is a basal metazoan. That is the first lineage to diverge from all the other metazoans. There could of course be other explanations for the apparent simplicity of Trichoplax such as it is a result of a loss of various features found in its ancestors. The mitochondrial genome sequence seems to confirm that Trichoplax is indeed a basal metazoan.

The mitochondrial genome is the largest yet discovered in metazoans at 24-kb, although this is smaller than the largest mitochondrial genome yet discovered in eukaryotes. That distinction goes to Reclinomonas americana a protozoon with a genome of 69-kb. The genome also shares features found in different branches of metazoa such as sponges and cnidarians and features that seem to be unique to all animals such as a lack of ribosomal protein genes. It seems that the Trichoplax mtDNA resembles the ancestoral condition of metazoa supporting its basal position.

Trichoplax adhaerens is a fascinating organism and with a nuclear genome on the way it seems likely to reveal more interesting discoveries.


Stephen L. Dellaporta, Anthony Xu, Sven Sagasser, Wolfgang Jakob, Maria A. Moreno, Leo W. Buss, and Bernd Schierwater.
Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum
PNAS published May 26, 2006, 10.1073/pnas.0602076103

Pharyngula::Trichoplax adhaerans.

Trichoplax: my favorite animal (PDF)

The Trichoplax story (PDF)

PDFs from Bernd Schierwater lab

Friday, May 26, 2006

Stuff Roundup 26/06

Stuff on the web/in the news that has caught my eye recently.


There was a letter sent by several leading doctors to the Times calling for the use only of medicine "based on solid evidence" and attacking bogus quackery such as homeopathy. This of course sent the quacks into a fit. It has been well covered at: Skeptico, Skepchick and rhetorically speaking.

Good news from oxford: Oxford lab injunction tightened. See also the Scientific activist's post on a Pro-test meeting.


A fabulous review of the ediacaran is in press at Earth science reviews :

The Vendian (Ediacaran) in the geological record: Enigmas in geology's prelude to the Cambrian explosion
In Press, Corrected Proof,
G.J.H. McCall.

It's 229 pages long and very comprehensive

The January-February 2006 issue of Comptes Rendus Palevol is available for free and contains loads of fascinating papers on human prehistory and evolution.

The International Journal of Biological Sciences has a nice series of papers on Amphioxus, see also the special issue (freely available) of Canadian Journal of Zoology on Protochordata.

The Quarterly Review of Biology has a free sample issue with an interesting paper on the origin of life: 'Small Molecule Interactions were Central to the Origin of Life'.


Carnivals: Skeptics' Circle, I and the Bird and Tangled Bank.

Dracorex hogwartsia a cool new dinosaur has been announced see the Hairy Museum of Natural History and another post.

No genes were lost in the making of this whale from Pharyngula,

The most freaky of all mammals: rabbits from Darren Naish.

Lovely pictures of Squid and Jellyfish from BibliOdyssey.

Monday, May 22, 2006

Bear Gulch website

Damocles serratus a fossil shark from Bear Gulch

I have just found this lovely website: Fossil fishes of Bear Gulch

"The Bear Gulch Limestone (Mississippian of Montana) is what is known as a lagerstätte, a well-bedded sequence of limestone layers containing an extremely well-preserved assemblage of fossils. This deposit has yielded one of the most diverse and well preserved fossil fish assemblages in the world. We have excavated approximately 130 species of fish from this deposit over the last 35 years. The site also contains well preserved arthropods, sponges, starfish, conulariids, worms, and other soft-bodied organisms, as well as brachiopods, bryozoans, and molluscs. The Bear Gulch fossils are so well preserved that they provide a window into the life of the Mississippian that has never been available before. This site is dedicated to bringing you and the fishes of the Mississippian together."

It has some amazing pictures, drawings and infromation about the lovely fossils that have been found at Bear Gulch. In addition to fish there are also fossil invertebrates, plants and enigmas. There is just so much content here the creators deserve alot of praise.

See also:

Whitey Hagadorn, 2002, Bear Gulch: An exceptional Upper Carboniferous plattenkalk, in Bottjer, D.J., et al., eds., Exceptional Fossil Preservation: A Unique View on the Evolution of Marine Life: Columbia University Press, New York, p. 167-183. (PDF)

Sunday, May 21, 2006

Fungal mimics

Mimicry is a fascinating and widespread phenomenon where one organism gains some benefit by resembling another organism or thing. This resemblance can take many forms including visual, chemical and molecular mimicry.

A mini review in FEMS Microbiology Letters (1) has stimulated my interest in the little known mimetic interactions of plants and fungi.

There are several ways that fungi can imitate plants and manipulate them or use them to manipulate other organisms. One particularly fascinating mechanism is the production of ‘pseudoflowers’ that is structures formed from the leaves of a plant infected by fungi that resemble flowers, they also smell like flowers and exude sweet liquid as a reward. This liquid contains fungal spores and when pollinating insects land on the pseudoflowers they pick up spores and transfer them to other flowers that the fungus can then infect. I am just amazed by this type of manipulation, it will be fascinating to learn just how this remarkable feat is achieved and how it evolved.

(A) Uninfected flowering Euphorbia cyparissias plant and (B) E. cyparissias infected by the rust fungus Uromyces pisi. (2)

Pseudoflower of an Arabis produced by the fungus puccinia monoica (3)

Fungi can also act as molecular mimics tricking the host plant into thinking that they are grains of pollen. This allows them a fantastic entry route into the plant bypassing the physical barriers found in the rest of the plant. The Stigmas of plants have evolved to capture pollen grains from the air. The normal pollen floats in the air in a similar ways to fungal spores and so end up on stigmas in a similar way. There is also some evidence that molecules on the surface of the growing fungus contain similar molecules to pollen. A similar trick is accomplished by several pathogens where surface molecules resemble those of the host.

While writing this I saw an interesting post at Thomasburg walks via the carnival of animalcules. I am not sure if they are flower mimics, they certainly look like flowers. It would be interesting to find out if they attracted pollinating insects to disperse them, or if in this case the resemblance to flowers in coincidental.


1) Mimicry in plant-parasitic fungi
Henry K. Ngugi & Harald Scherm
FEMS Microbiol Lett 257 (2006) 171–176

American Journal of Botany 87(1): 48–55. 2000.

3) Floral mimicry by a plant pathogen
B. A. Roy
Nature 362, 56 - 58 (04 March 1993) ; doi:10.1038/362056a0

Monday, May 15, 2006

Tutankhamun archive to go online

According to The Guardian the whole of the archive related to the excavation of the tomb of Tutankhamun is goinf to be made available online:

"Between 1922 and 1930, at least 5,398 objects were removed. Carter and his colleagues made meticulous index cards, notes and sometimes drawings of each find, and kept diaries and records of their progress. All of which went to Oxford, where they have been preserved since Carter's death in 1939.

From then, research progress has been slow, Dr Jaromir Malek, of the Griffith Institute in Oxford, told a Bloomsbury Academy conference in London last Saturday. "We came to the conclusion that probably 20% of the material had been properly published, and if the current rate of progress was going to continue it would probably take another 200 years," he said.

The Oxford archive, as it stands, will be entirely online within two years."

Here are links to what is currently available:

Tutankhamun: Anatomy of an Excavation is ambitious in its scope but simple in its aims: to make the complete records of Howard Carter's excavation of the tomb of Tutankhamun available on these web pages.

The Search for Tutankhamun. (Howard Carter's records of the five seasons of excavations, financed by Lord Carnarvon, in the Valley of the Kings 1915 - 1922).

The state of British butterflies

A new report called 'The state of butterflies in Britian and Ireland' by the charity Butterfly Conservation has just been resleased.

It present s a mixed picture of the state of british butterflies. Some have done quite well but many other gave continued to decline. It seems that generalists who can cope with different environments are doing quite well but specialists that rely on particular habitats have done badly. There is also evidence of range expansion of some species probably because of climate change. This is ok for species that are able to move to a new habitat, if you are a species that relies on a small patch of habitat then it's bad news.

Hopefully this survey will provide clues as to how our butterflies can be conserved and unline the importance of climate change to many species.

Some of the data from the BBC:

Painted Lady (+31%)
Red Admiral (+30%)
Marsh Fritillary (-32%)
White-letter Hairstreak(-68%)
Pearl-bordered Fritillary (-77%)
High Brown Fritillary (-82%)
Source: Butterfly Conservation, figures for 1995-2004 survey, compared to 1970-1982

Thursday, May 11, 2006

Friday, May 05, 2006

New Ediacaran type fossil

Stromatoveris (click for bigger)

In the current issue of Science (5 May 2006) There is a description of an amazing new fossil from the Chenjiang lagerstatte in China (1).

I have written about the Ediacaran (Vendian) and the strange organisms before, and although many organisms remain mysterious this fossil seems to resolve one of the most puzzling aspects of the Ediacaran – how are they related to later organisms and their modern descendants.

One of the characteristic organisms of the Ediacaran is the ‘frondose’ fossils such as Charnia (also here) and this new fossil Stromatoveris is of the frondose type.

Although Stromatoveris seems to be of Ediacaran type it is found in early Cambrian sediments. This is strange as it is usually thought that the Ediacaran biota largely went extinct at the base of the Cambrian, although fossils such as Thaumaptilon walcotti have indicated the possibility of some survivors.

There are essentially two broad schools of opinion on the relationship of the Ediacarans, that they had a unique construction unrelated to any know type of organism or that they are related fairly closely to modern phyla. The remarkable preservation of Stromatoveris allows features to be detected that suggest that it is a relative of Ctenophores. Interestingly that does not rule out the possibility that other organisms, even ones that look superficially similar, are strange ‘giant protists’ or have a similarly unfamiliar type of construction.

Proposed phylogeny of Stromatoveris (click for bigger)

This has important implications for evolution, it seems that some modern phyla had diverged before the Cambrian, as has long been suspected on the basis of molecular dates. Another recent discovery, yet again using fossils from Chengjiang, links the Ediacaran Parvancorina with the arthropods such as trilobites (2) extending the range of another phylum back in time.


1) Lower Cambrian Vendobionts from China and Early Diploblast Evolution.
D.-G. Shu, S. Conway Morris, J. Han, Y. Li, X.-L. Zhang, H. Hua, Z.-F. Zhang, J.-N. Liu, J.-F. Guo, Y. Yao, and K. Yasui.
Science 5 May 2006: 731-734.

2) A Parvancorina-like arthropod from the Cambrian of South China.
Lin, J.P., S.M. Gon III., J.G. Gehling, L.E. Babcock, Y.L. Zhao, X.L. Zhang, S-X. Hu, J.L. Yuan, M.Y. Yu, & J. Peng. 2006.
Historical Biology 18(1): 33–45.

Wednesday, May 03, 2006

The oddness of Hyaenas

In the current issue of Nature ( 27 April 06) there is an interesting article about the reason that female Spotted hyaenas (Crocuta crocuta) are exposed to very high levels of androgens such as testosterone during the later stages of pregnancy. The answer seems to be that high levels of androgens pass on high status to the offspring of high status females. It also seems to promote aggressive and dominant behavior such as mounting (1).

This seems to be related to the extremely odd reproductive behavior and anatomy of hyenas, although the precise relationship is still a mystery.

It has long been noted that female hyaenas have very unusual genitalia with the females having an enormously enlarged clitoris giving the appearance of having male genitalia. They even have pseudo testes increasing the resemblance (2).

A female hyaena with a arrow pointing to the peniform clitoris

This structure is referred to as the ‘peniform clitoris’ :

The dissected reproductive organs of a hyaena

This would appear to be a complete mystery as this imposes a variety of costs throughout life. It makes copulation extremely difficult as intromission has to occur into the enlarged clitoris (!) if mating is difficult that is nothing to giving birth:

“Toward the end of an extended period of labor, a fetal hyena fills and stretches the clitoris (outlined by white dots) of a primiparous female. The clitoral meatus (large arrow) will eventually tear and permit birth to occur. Subsequent deliveries, through the stretched and torn clitoral meatus, are much more rapid. Note nipples (small arrows).” (2)

At least thing get slightly better with further births although I shouldn’t imagine that is much consolation for the hyaena. In fact, about 60% of first births are stillborn in a captive colony due to this peculiar anatomy; in the wild it could be even higher.

There seems to be two different processes that give rise to the female morphology. The development of the peniform clitoris begins early in development before the late burst of androgens. This shows that it is not a side effect of dominance conferring androgens. It seems like this particular avenue of development has been selected for because it is beneficial in itself. Although high levels of androgens are necessary for the complete development of the peniform clitoris (3) so there is probably some sort of co-evolution.

If there are such heavy costs of this morphology then why does it exist? There are several theories, it is probably partly to do with the increased dominance, aggression and possibly other thing like increased size/muscle mass. But there could be increased dominance without the peniform clitoris so it is likely that it has a benefit in itself, this could be because there is a lot of aggression towards young female hyaenas from siblings adult females and members of other clans and the enlarged clitoris could act to fool other hyaenas into not harming the young females (4).


1) S. M. Dloniak, J. A. French and K. E. Holekamp
Rank-related maternal effects of androgens on behaviour in wild spotted hyaenas
Nature 440, 1190-1193 (27 April 2006
) doi:10.1038/nature04540

2) Cunha GR, Wang YZ Place NJ, Liu W, Baskin L, and Glickman SE. (2003). The urogenital system of the female spotted hyena ( Crocuta crocuta ): a functional histological study.
J Morph 256:205–218. (PDF)

3) Cunha GR, Place NJ, Baskin LS, Conley AJ, Weldele ML. Cunha TJ, Wang YZ, Cao M, and Glickman SE. (2005). The ontogeny of the urogenital system of the spotted hyena (Crocuta crocuta Erxleben).
Biol Reprod 73:554-564. (PDF)

4) Muller MN & RW Wrangham.
Sexual mimicry in hyenas.
Quarterly Review of Biology. 77:3-16. (PDF)

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.