Muton

3d Rock art scanning update

2006-09-24T21:24:00.000+01:00

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

2006-09-24T09:51:00.000+01:00

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.

Refs:

1) Is Phallus impudicus a mycological giant?
M. NIKSIC, I. HADZIC and M. GLISIC
Mycologist, Volume 18, Part 1 February 2004
DOI: 10.1017/S0269915X04001041

2) Dimethyl oligosulphides, major volatiles released from Sauromatum guttatum and Phallus impudicus
BORG-KARLSON A.-K; ENGLUND F. O; UNELIUS C. R.
Phytochemistry, 1994, vol. 35, no2, pp. 321-323.
http://cat.inist.fr/?aModele=afficheN&cpsidt=4067195

3) Wayne's World amazing fungi: http://waynesword.palomar.edu/ww0504.htm

Fake medicines given seal of approval

2006-09-01T18:15:00.000+01:00

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 arenÂt so great in the UK, eitherÂ (Memoirs of a Skepchick)

Water Torture (Holmes Report Blog)

Tetrahymena genome published

2006-08-29T21:24:00.000+01:00

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 (TIGR)

Electrical Walks

2006-08-24T20:42:00.000+01:00

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.

New fossil spiders

2006-07-29T15:31:00.000+01:00

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: http://homepage.mac.com/paulselden/Home/index.html

Ref:
MYGALOMORPH SPIDERS (ARANEAE: DIPLURIDAE) FROM THE LOWER CRETACEOUS CRATO LAGERSTÄTTE, ARARIPE BASIN, NORTH-EAST BRAZIL
by PAUL A. SELDEN, FABIO DA COSTA CASADO and MARISA VIANNA MESQUITA

Palaeontology Volume 49 Page 817 - July 2006
doi:10.1111/j.1475-4983.2006.00561.x

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

Moths in decline

2006-07-14T09:24:00.000+01:00

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."

Refs:

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'

Odontogriphus omalus and Kimberella

2006-07-13T20:13:00.000+01:00

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.

Ref:

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

2006-07-13T12:43:00.000+01:00

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.

Refs:

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

Sleep and weight update

2006-07-12T16:39:00.000+01:00

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?

2006-07-12T12:59:00.000+01:00

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

ABSTRACT:

"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

Colour changing snake discovered

2006-06-27T19:49:00.000+01:00

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

2006-06-27T10:40:00.000+01:00

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.

Refs:

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

UK beetles under threat

2006-06-21T09:03:00.000+01:00

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.

Links:

Buglife

National Insect week

The Coleopterist

The oldest book I own

2006-06-15T15:43:00.000+01:00

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

2006-06-15T11:59:00.000+01:00

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.

Ref:

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

Fast evolution in Ciliates

2006-06-13T13:18:00.000+01:00

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.

Refs:

1) Carolyn L. Jahn and Lawrence A. Klobutcher
GENOME REMODELING IN CILIATED PROTOZOA
Annual Review of Microbiology Vol. 56: 489-520
doi:10.1146/annurev.micro.56.012302.160916

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.
http://mbe.oxfordjournals.org/cgi/content/abstract/msl032v1

4) REBECCA A. ZUFALL, TESSA ROBINSON, AND LAURA A. KATZ
Evolution of Developmentally Regulated Genome Rearrangements in Eukaryotes
JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 304B (2005)
http://www3.interscience.wiley.com/cgi-bin/abstract/110572604/ABSTRACT

Ciliophora (Protist image database)

Ancient Stromatolites of biological origin

2006-06-08T07:41:00.000+01:00

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.

Refs:

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

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)
Link

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
Link

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

Leggiest animal rediscovered

2006-06-08T06:46:00.000+01:00

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.

Refs:

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
Link

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

TV causes sleep disturbance in children

2006-06-02T10:25:00.000+01:00

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.

Refs:

TV exposure associated with sleep disturbances in 5- to 6-year-old children
E. JUULIA PAAVONEN, MARJO PENNONEN, MIRA ROINE, SATU VALKONEN and ANJA RIITTA LAHIKAINEN
Journal of Sleep Research
Volume 15 Issue 2 Page 154 - June 2006, doi:10.1111/j.1365-2869.2006.00525.x

Trichoplax mitochondrial genome sequenced

2006-05-30T10:45:00.000+01:00

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.

Refs:

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

Stuff Roundup 26/06

2006-05-26T13:15:00.000+01:00

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

News

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.

Papers

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, http://dx.doi.org/10.1016/j.earscirev.2005.08.004
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'.

Blogs

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.

Bear Gulch website

2006-05-22T22:50:00.000+01:00

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)

Fungal mimics

2006-05-21T15:50:00.000+01:00

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.

Refs:

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

2) POLLINATOR-MEDIATED INTERACTIONS BETWEEN A PATHOGENIC FUNGUS, UROMYCES PISI (PUCCINIACEAE), AND ITS HOST PLANT, EUPHORBIA CYPARISSIAS (EUPHORBIACEAE).
MONIKA PFUNDER AND BARBARA A. ROY
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

http://evolution.uoregon.edu/Publications.htm

Tutankhamun archive to go online

2006-05-15T13:52:00.000+01:00

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

2006-05-15T13:16:00.000+01:00

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

See also The Guardian, Times and Independent

Stuff roundup

2006-05-11T14:00:00.000+01:00

Stuff on the web that has caught my eye recently.

Papers:

The current issue of the journal developmental dynamics has a nice set of evo-devo type papers on craniofacial development:

Craniofacial development in marsupial mammals: Developmental origins of evolutionary change

Comparative ontogeny and phylogeny of the upper jaw skeleton in amniotes

21st Century neontology and the comparative development of the vertebrate skull

It’s a similar issue to the free Journal of anatomy one I have mentioned before.

There is a fascinating set of papers in press at the Philosophical Transactions of the Royal Society B on the early stages of evolution of life based on a meeting "Major steps in cell evolution: palaeontological, molecular and cellular evidence of their timing and global effects" including:

Fossil evidence of Archaean life

The origin and evolution of Archaea: a state of the art

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Palaeoclimates: the first two billion years

Eukaryotic organisms in Proterozoic oceans

Darwin's dilemma: the realities of the Cambrian ‘explosion’

Blog Carnivals:

Tangled Bank & the skeptics circle

Misc:

OpenStreetMap maps Isle of Wight, Manchester next (link)

The Alphabet in Butterfly wings, Evolutionary Biology Digital Dissection Collection,

New Ediacaran type fossil

2006-05-05T12:24:00.000+01:00

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.

Refs:

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.

The oddness of Hyaenas

2006-05-03T12:27:00.000+01:00

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).

Refs:

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)

Vindolanda tablets online

2006-04-26T16:42:00.000+01:00

The famous birthday party initation from Claudia Severa to Lepidina
Link

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

2006-04-26T12:05:00.000+01:00

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)

Pygmy Elephantids

2006-04-23T11:49:00.000+01:00

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.

Refs:

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)

Pro research petition

2006-04-20T08:27:00.000+01:00

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: http://www.peoplespetition.org.uk/

See also: Pro-test

The Research Defence Society

humuhumunukunukuapuaa

2006-04-19T11:04:00.000+01:00

humuhumunukunukuapuaa

Apparently the fish know as humuhumunukunukuapuaa is going to be reinstated as the state fish of Hawaii. This wonderful name is the Hawaiian for Rhinecanthus aculeatus and Rhinecanthus rectangulus.

Plant Cellular Anatomy

2006-04-14T17:55:00.000+01:00

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

2006-04-14T13:50:00.000+01:00

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.

Refs:
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.
(LINK)

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.
(LINK)

More Sharovipteryx

2006-04-09T09:55:00.000+01:00

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.

Sauropod tracks

2006-04-07T14:20:00.000+01:00

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
http://dx.doi.org/10.1016/j.cretres.2005.10.006 (free full text as part of sample issue - lots of other interesting stuff)

DNA sequencing revolution?

2006-04-07T12:36:00.000+01:00

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

The end of light pollution?

2006-04-06T12:39:00.000+01:00

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

New fossil between fish and tetrapods

2006-04-05T20:03:00.000+01:00

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

2006-04-05T11:23:00.000+01:00

"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.

Refs:

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.
http://dx.doi.org/10.1016/j.mycol.2005.11.009 (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
http://dx.doi.org/10.1016/S0034-6667(01)00058-6

Fake eggs in China!

2006-04-04T22:33:00.000+01:00

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

http://news.xinhuanet.com/photo/2004-12/28/content_2387255.htm (news report in chinese - pics of real and fake eggs)

Sleep more - weigh less

2006-03-29T12:36:00.000+01:00

Well for children anyway:

"The less a child sleeps, the more likely he or she is to become overweight, according to researchers from Université Laval's Faculty of Medicine in an article published in the latest edition of the International Journal of Obesity. The risk of becoming overweight is 3.5 times higher in children who get less sleep than in those who sleep a lot, according to researchers Jean-Philippe Chaput, Marc Brunet, and Angelo Tremblay." [VIA]

There seems to be a direct causal link between short periods of sleep and reduced levels of leptin and higher levels of ghrelin. This seems to cause increased appetite and thus BMI so this association between a lack of sleep and obesity is probably true for everyone.

I suspect a major cause of sleep deprivation in children and adults is excessive television watching and also sadly computer use.

References:

Chaput JP, Brunet M, Tremblay A.Int J Obes (Lond). 2006 Mar 14; [Epub ahead of print]
Relationship between short sleeping hours and childhood overweight/obesity:
results from the 'Quebec en Forme' Project. [LINK]

Taheri S, Lin L, Austin D, Young T, Mignot E.
PLoS Med. 2004 Dec;1(3):e62. Epub 2004 Dec 7.
Short sleep duration is associated with reduced leptin, elevated ghrelin, and
increased body mass index. [LINK - full text]

Glaciers in retreat

2006-03-24T11:17:00.000Z

The recent retreat of the Jakobshavn Isbrae glacier in Greenland

Three Papers in the current issue of Science show the rapid changes that are occurring in world's glaciers.

Paleoclimatic Evidence for Future Ice-Sheet Instability and Rapid Sea-Level Rise
Jonathan T. Overpeck, Bette L. Otto-Bliesner, Gifford H. Miller, Daniel R. Muhs, Richard B. Alley, and Jeffrey T. Kiehl
Science 24 March 2006: 1747-1750.

Simulating Arctic Climate Warmth and Icefield Retreat in the Last Interglaciation
Bette L. Otto-Bliesner, Shawn J. Marshall, Jonathan T. Overpeck, Gifford H. Miller, Aixue Hu, and CAPE Last Interglacial Project members
Science 24 March 2006: 1751-1753.

Measurements of Time-Variable Gravity Show Mass Loss in Antarctica
Isabella Velicogna and John Wahr
Science 24 March 2006: 1754-1756.
Published online 2 March 2006 [DOI: 10.1126/science.1123785] (in Science Express Reports)

Press for these papers:
Sea rise could be 'catastrophic' (BBC)
Polar Meltdown Near: Seas Could Rise 3 Feet Per Century (Livescience)

Ediacaran website

2006-03-23T15:37:00.000Z

Vendia rachiata (?) which looks a bit like a trilobite but probably isn't

While browsing the internet for information on those strange ediacaran creatures I stumbled upon this russian website: http://vend.paleo.ru/ If you are interested in these mysterious creatures it's worth a look.

Although it is all in russian Babelfish does a fairly decent translation, here is their description of the site:

"Our laboratory is occupied by the complex of the early stages of the evolution of biosphere, which preceded the phanerozoic jump of bioraznoobraziya. Special attention in this case is paid to the vendskomu period as to the period, which completes the Proterozoic stage of the evolution of biosphere. For a long time considered as the almost silent, this section of geological chronicle is at the present time remarkable with this number of surprising findings of the remainders of undoubtedly organic nature, that it is possible to indicate that we already see the letters, which wrote the history of the evolution of the biosphere of that time, but yet we cannot understand entire text, which is collected by these letters. On this site are assembled the meaningful results of the work of our laboratory, materials about the directions of research activity, most significant publications, debatable materials."

Being russian they call this period (from the gaskiers glaciation to the cambrian, 632-542 MYA) the vendian even though the internationally accepted name is now the ediacaran.

There is lots of interesting stuff there, the best stuff is probably a nice selection of papers in english and russian that can be downloaded: http://vend.paleo.ru/pub_ru.php & http://vend.paleo.ru/pub_eng.php. Particularly good is 'Ivantsov Malakhovskaya 2003' which is in russian and has some amazing images of ediacaran fossils.

Their research is mainly conducted on the remarkable fossils found in cliffs by the white sea in russia. Other ediacaran localities are the Ediacra hills Australia, Mistaken point Canada, Charnwood in England and Namibia.

Tribrachidium heraldicum - deeply weird

sharovipteryx

2006-03-21T22:42:00.000Z

The only fossil specimen of Sharovipteryx mirabilis

Sharovipteryx mirabilis is one of the odder creatures to be found in the fossil record notable because it seems to have wings on it's hind limbs which seems to be a unique adaptation.

A new paper is in press in the Journal of Evolutionary Biology that proposes a model of how this strange beast would have flown. Their reconstruction is shown below. I have no idea if this is actually what the creature would have looked like but it seems like a fairly logical interpretation of the fossil.
Flight of Sharovipteryx mirabilis: the world’s first delta-winged
glider. G. J. DYKE, R. L. NUDDS & J. M. V. RAYNER. Journal evolutionary biology (in press) doi:10.1111/j.1420-9101.2006.01105.x

Frog spawn

2006-03-15T12:40:00.000Z

The common frog (Rana temporaria) mating and spawning season is in full swing in the garden pond. There is a fairly large amount of spawn this year. Although thats only half the battle, lets hope there isn't another really cold snap so it doesn't all die, and that it stays healthy so there is a nice big crop of froglets this year.

I have a lingering fondness for frogspawn after playing with it when i was young and I still remember being fascinated watching the tadpoles develop. I am sure that is one of the things that made me interested in biology and conservation.

Links:
Declining Amphibians Population Task Force (DAPTF)
herpetofauna
froglife

How to buy fish with a clear conscience

2006-03-13T15:26:00.000Z

There is a nice article in todays Independent called 'How to buy fish with a clear conscience'

"For years, the unpalatable details of the industry that delivers fish to supermarket shelves have been a well-kept secret, along with the scientific data that shows that some fish are being fished to near-extinction. But not any longer.

The ranks of enlightened fish consumers grow by the day, and proof that some of the supermarkets are waking up to the issue arrived when Greenpeace scaled the Asda headquarters in Leeds in January. No sooner was a banner unfurled from the roof depicting some of the dead and mutilated by-catch, than the campaigners were ushered inside for a chat about the sustainability of the supermarket's fish-buying policies.

Asda, which was rock bottom of a Greenpeace table of supermarkets ranked on their fish-buying policies several months ago, and in the bottom half of a similar Marine Conservation Society (MCS) table published earlier this month, announced immediately that it was removing skate wings, Dover sole, ling and dogfish from its stores. Since Asda's move, Sainsbury's has announced that it will no longer sell skate and huss, both endangered, while in the US, the discount giant Wal-Mart (which owns Asda) has declared that it will buy all of its fresh fish from sustainable sources within three to five years.

.....

Not all fish are so problematic. Lemon sole, red mullet, red gurnard and most salmon are generally acceptable, while Atlantic halibut, skate, swordfish and marlin are not. If a blue certification logo (a fish and a tick) is stamped on a product, it is one of the 50 products accredited by the Marine Stewardship Council, and is sustainable."

Marine conservation is a very important area that is often ignored because of the fishing lobby. This has led to awful mismanagement of fish resources, lets hope that consumer power can change things.

Some resources:

marine conservation society report mentioned in the article: http://www.mcsuk.org/press/press_release.php?cust_id=62

fish online

greenpeace sustainable fish campaign

Marine Stewardship Council

Marine Conservation Biology Institute

save the high seas

What You Can Do to Save the Deep Sea

cool origami

2006-03-06T09:13:00.000Z

There are some amazing origami design created for ther MIT origami competition (via) Two of the winners are Jason Ku and Brian Chan and several neat designs are available from their websites. The cool Katydid in the picture is by Brian Chan (link) and there are several other nice insect designs available on his website.

Awesome micrographs

2006-03-03T10:03:00.000Z

Veliger larva of the gastropod, Fusitriton oregonensis by Louise Page Posterior of juvenile kinorhynch, Pycnophyes kielensis by Andreas Schnidt-Rhaesa

Copulatory organs of the acoel, Haplocelis dichona by Matthew Hooge

All images & captions from here

These remarkable images are produced by Confocal Laser Scanning Microscopy and show what amazing detail modern technology can reveal.

The images were presented at a conference called 'The New Microscopy: Novel Characters and the Importance of Morphology in Phylogenetic Analysis'. Several papers from this conference are now avilable from the journal Integrative and Comparative Biology which seems to be open access. Lots of interesting stuff has appeared in that journal, the archives are well worth a browse.

Here are the relavent papers:

Neurophylogeny: Architecture of the nervous system and a fresh view on arthropod phyologeny

Neurogenesis in myriapods and chelicerates and its importance for understanding arthropod relationships

Postembryonic development of dorsoventral and longitudinal musculature in Pycnophyes kielensis (Kinorhyncha, Homalorhagida)

Modern insights on gastropod development: Reevaluation of the evolution of a novel body plan

Polychaete nervous systems: Ground pattern and variations--cLS microscopy and the importance of novel characteristics in phylogenetic analysis

Embryogenesis in the glass sponge Oopsacas minuta: Formation of syncytia by fusion of blastomeres

Novel methodology utilizing confocal laser scanning microscopy for systematic analysis in arthropods (Insecta)

Challenging received wisdoms: Some contributions of the new microscopy to the new animal phylogeny

Concordance of molecular and morphological data: The example of the Acoela

What a couple of dimensions can do for you: Comparative developmental studies using 4D microscopy--examples from tardigrade development

Pro-test

2006-02-26T09:42:00.000Z

After reading about the pro-test march in oxford via scientific activist I decided it was time to not just be annoyed at the awful behaviour of the 'animal rights' extremists and show support for the oxford lab and scientific research in general. So I went to oxford and waved a placard and shouted a bit. Here is a pic of me doing that stuff:

I am the one with the placard from

It was a really good march, the turnout was much larger than I expected (500-800) and dwarfed the rival demonstration (150-200). Everyone was very calm in contrast to the 'animal rights' protest which are marked by scuffles with the police. I guess it's the difference between people who have made a rational choice and fanatics who have lost all sense of perspective in pursuit of their ideology.

While in oxford I had time to check out the attractions such as the Pitt Rivers Museum, Museum of the History of Science (lovely astrolabes) and the Oxford University Museum of Natural History.

Some Links:

The Founder of Pro-test, Laurie Pycroft's livejournal: http://sqrrl101.livejournal.com/

The research defence society: http://www.rds-online.org.uk/ & Blog: http://www.rdsblog.info/

Pro-test: http://www.pro-test.org.uk/

Various blog posts about the protest: Here, here, here, here and here

Update:

The Scientific Activist has an excellent post on the demo: http://scientificactivist.blogspot.com/2006/02/oxford-scientists-bite-back-at-animal.html

Also more blog posts: Here, here, here, here and here.

Coco Pops Straws

2006-02-21T22:46:00.000Z

"Which? has today complained to the Advertising Standards Authority that the Kellogg's Coco Pops Straws TV advert is misleading and socially irresponsible by marketing a chocolate straw biscuit as a way to get children to drink more milk. "

http://www.which.net/press/releases/food/060221_kellogs_nr.html

Who would have thought that Nestle would produce deceptive adverts for unheathy food?

Nearly everything marketed as being 'healthy' is a con, you end up paying more for stuff that is worse for you than unprocessed foods.

It seems that now the companies that have spent vast amounts of money turning us into junk food addicts have now realised that they can make more money by flogging fake cures for the ailments that they have created.

More global warming

2006-02-21T13:00:00.000Z

The Arctic and global warming
Researcher describes possible disruption to marine mammals' food web

Studying Arctic phytoplankton has played prominently in Smith's research. Here, Smith (left) is shown on the Coast Guard ice breaker HEALY in 2004, recovering plankton nets.
A warmer Arctic Ocean may mean less food for the birds, fish, and baleen whales and be a significant detriment to that fragile and interconnected polar ecosystem, and that doesn't bode well for other ocean ecosystems in the future. That's the word from University of Miami Rosenstiel School's Dr. Sharon Smith who will speak on "Potentially Dramatic Changes in the Pelagic Ecosystems of the Marginal Seas of the Arctic Ocean due to Anthropogenic Warming," today at 3 p.m. HST (8 p.m. EST) in Honolulu at the American Geophysical Union's 2006 Ocean Sciences Meeting.

See also: Observations of Anthropogenic Climate Change in the Oceans and Their Implications for Society II

And more Oceanic acidity

BBC four is having a 'global warming' season, This would be brilliant if anybody actually watched BBC four, but at least it shows willing. The first programme 'Meltdown' was pretty good and presented the case that current global warming is caused by anthropogenic emissions well.

As part of this season they are running an experiment in which you can download a climate simulation that runs on home computers (windows/linux only). If you can give it a try and hopefully you will be contributing to a useful project.

http://www.bbc.co.uk/sn/hottopics/climatechange/

Arabic calligraphy

2006-02-20T17:23:00.000Z

Beautiful calligraphy by mouneer al shaarani There's more at his Gallery (via).

See also The Art of Arabic Calligraphy
Arabic calligraphy

Ugly Criminals?

2006-02-20T10:03:00.000Z

This story in the Washington post 'The Ugly Face of Crime' is being widely discussed. The original article on which this story is based is based on 'Ugly Criminals' by H. Naci Mocan and Erdal Tekin:

ABSTRACT

Using data from three waves of Add Health we find that being very attractive reduces a young adult’s (ages 18-26) propensity for criminal activity and being unattractive increases it for a number of crimes, ranging from burglary to selling drugs. A variety of tests demonstrate that this result is not because beauty is acting as a proxy for socio-economic status. Being very attractive is also positively associated adult vocabulary test scores, which suggests the possibility that beauty may have an impact on human capital formation. We demonstrate that, especially for females, holding constant current beauty, high school beauty (pre-labor market beauty) has a separate impact on crime, and that high school beauty is correlated with variables that gauge various aspects of high school experience, such as GPA, suspension or having being expelled from
school, and problems with teachers. These results suggest two handicaps faced by unattractive individuals. First, a labor market penalty provides a direct incentive for unattractive individuals toward criminal activity. Second, the level of beauty in high school has an effect on criminal propensity 7-8 years later, which seems to be due to the impact of the level of beauty in high school on human capital formation, although this second avenue seems to be effective for females only. (PDF)

It's tough being a minger.

Oceans may soon be more corrosive than when the dinosaurs died

2006-02-20T08:57:00.000Z

This could be a far bigger problem than temperature rise:

"Increased carbon dioxide emissions are rapidly making the world's oceans more acidic and, if unabated, could cause a mass extinction of marine life similar to one that occurred 65 million years ago when the dinosaurs disappeared. Ken Caldeira of the Carnegie Institution's Department of Global Ecology will present this research at the AGU/ASLO Ocean Sciences meeting in Honolulu, HI on Monday, Feb 20.

Caldeira's computer models have predicted that the oceans will become far more acidic within the next century. Now, he has compared this data with ocean chemistry evidence from the fossil record, and has found some startling similarities. The new finding offers a glimpse of what the future might hold for ocean life if society does not drastically curb carbon dioxide emissions.
"The geologic record tells us the chemical effects of ocean acidification would last tens of thousands of years," Caldeira said. "But biological recovery could take millions of years. Ocean acidification has the potential to cause extinction of many marine species."

When carbon dioxide from the burning of coal, oil, and gas dissolves in the ocean, some of it becomes carbonic acid. Over time, accumulation of this carbonic acid makes ocean water more acidic. When carbonic acid input is modest, sediments from the ocean floor can buffer the increases in acidity. But at the current rate of input--nearly 50 times the natural background from volcanoes and other sources--this buffering mechanism is overwhelmed. Previous estimates suggest that in less than 100 years, the pH of the oceans could drop by as much as half a unit from its natural value of 8.2 to about 7.7. (On the pH scale, lower numbers are more acidic and higher numbers are more basic.)

This drop in ocean pH would be especially damaging to marine animals such as corals that use calcium carbonate to make their shells. Under normal conditions the ocean is supersaturated with this mineral, making it easy for such creatures to grow. However, a more acidic ocean would more easily dissolve calcium carbonate, putting these species at particular risk.

The last time the oceans endured such a drastic change in chemistry was 65 million years ago, at about the same time the dinosaurs went extinct. Though researchers do not yet know exactly what caused this ancient acidification, it was directly related to the cataclysm that wiped out the giant beasts. The pattern of extinction in the ocean is consistent with ocean acidification--the fossil record reveals a precipitous drop in the number of species with calcium carbonate shells that live in the upper ocean--especially corals and plankton. During the same period, species with shells made from resistant silicate minerals were more likely to survive.

The world's oceans came close to an acidic catastrophe one other time about 55 million years ago, when the temperature of the Earth spiked and large amounts of methane and/or carbon dioxide flooded the atmosphere. There is no evidence, however, that this caused a mass extinction event.
"Ultimately, if we are not careful, our energy system could make the oceans corrosive to coral reefs and many other marine organisms," Caldeira cautions. "These results should help motivate the search for new energy sources, such as wind and solar, that can fuel economic growth without releasing dangerous carbon dioxide into the environment."

http://www.eurekalert.org/pub_releases/2006-02/ci-oms021706.php

Carbon Dioxide and Ocean Chemistry Change: What Does the Geologic Record Tell us About the Future (session abstract)

The Myth of Sexual Selection?

2006-02-18T12:22:00.000Z

In the latest issue of Science Joan Roughgarden has written a review that challenges current ideas about sexual selection.

"Theories about sexual selection can be traced back to Darwin in 1871. He proposed that males fertilize as many females as possible with inexpensive sperm, whereas females, with a limited supply of large eggs, select the genetically highest quality males to endow their offspring with superior capabilities. Since its proposal, problems with this narrative have continued to accumulate, and it is our view that sexual selection theory needs to be replaced. We suggest an approach that relies on the exchange of direct ecological benefits among cooperating animals without reference to genetic benefits. This approach can be expressed mathematically in a branch of game theory that pertains to bargaining and side payments."

Science 17 February 2006: Vol. 311. no. 5763, pp. 965 - 969
Reproductive Social Behavior: Cooperative Games to Replace Sexual Selection
Joan Roughgarden, Meeko Oishi, Erol Akçay
(link-science) (link- free pdf)

There is another article describing Roughgarden's theory in California wild called "The Myth of Sexual Selection" and a response by Michael T. Ghiselin: "Sexual Selection"

Interesting new blog

2006-02-17T11:19:00.000Z

Darren Naish a vertebrate paleontologist from the University of Portsmouth has a nice new blog:

"Welcome to my blog site, which over the next weeks and months will include assorted thoughts and comments on various of the issues that interest me: predominantly, what's going on in the world of tetrapod zoology, and particularly the stuff I'm researching, or involved in. Of special interest to me right now are the dinosaurs of the British Wealden (of course), the intriguing tie-ins between Wealden fossil collectors, Conan Doyle's Lost World and the Piltdown fiasco, convergence between different fossorial tetrapods, manatee evolution, and British big cats (yes, really). More to come on these matters and much more in future, honest."

excellent

His latest post is on basal whales: http://darrennaish.blogspot.com/2006/02/when-whales-walked-land-and-looked.html - interesting stuff

3D Museum

2006-02-11T09:56:00.000Z

I have found the website of the 3d museum via palaeoblog:

"Welcome to 3D Museum Website, maintained by the Vertebrate Paleobiology Lab of the University of California, Davis. This site was designed to explore the ways of communicating 3D morphological data over the Internet. The website is slowly under expansion, so please check back every three months or so to see its progress. Please send us suggestions. "

I really like this idea, it makes specimens available to a huge potential audience and they can be viewed and manipulated in ways that would be impossible with real objects. Let's hope this project is successful and continues to grow.

http://palaeoblog.blogspot.com/2006/02/3d-museum-now-on-line.html

http://3dmuseum.org/

New Herefordshire Lagerstätte fossil

2006-02-10T08:51:00.000Z

In the last few years many astonishingly well preserved fossils have been discovered in the Herefordshire Lagerstätte. The most amazing feature is that they are preserved in 3 dimensions inside nodules. Because of the way they are preserved the foosils can only be revealed by grinding thin sections of the nodules, taking pictures of the fossils and then reconstructing them in 3d in a computer.

The latest fossil to have been revealed is a platyceratid gastropod and it reveals amazing details of the soft tissue anatomy including "gonads, digestive gland, pedal muscle, radula, mouth and foot" - exceptionally unsual in fossils.

Many more fossil containing nodules have been found at this site but due to the slow process involved in extracting the information from them they have not been looked at yet. I wonder what other amazing fossils are waiting to be revealed.

Fossilized soft tissues in a Silurian platyceratid gastropod
M.D. Sutton, D.E.G. Briggs, David J. Siveter, Derek J. Siveter.
Proceedings: Biological Sciences (in press)
http://www.journals.royalsoc.ac.uk/link.asp?id=8332100l0278551q

Some Other related links:

Herefordshire Lagerstätte page: http://www.earth.ox.ac.uk/herefordshire/intro.htm

Three-dimensional preservation of a non-biomineralized arthropod in concretionsin Silurian volcaniclastic rocks from Herefordshire, England PDF

METHODOLOGIES FOR THE VISUALIZATION AND RECONSTRUCTION OF THREE-DIMENSIONAL FOSSILS FROM THE SILURIAN HEREFORDSHIRE LAGERSTÄTTE LINK

old maya excavations

2006-02-07T14:11:00.000Z

Tikal Temple I 'between 1929 and 1957'

I was browsing the Harvard Visual Information Access database and found that they have loads of old photographs from early excavations of many famous mayan sites such as tikal, copan, palenque, uxmal and chichen itza. It' s fascinating to see how different they look like today:

Tikal temple I today, pic from here

One Planet, Many People

2006-02-05T11:19:00.000Z

I have just heard about the atlas 'One Planet, Many People' via the map room and discovered that it is available to download here.

From the press release:

"Produced by the United Nations Environment Programme (UNEP), One Planet Many People: Atlas of our Changing Environment compares and contrasts spectacular satellite images of the past few decades with contemporary ones, some of which have never been seen before.

The huge growth of greenhouses in southern Spain, the rapid rise of shrimp farming in Asia and Latin America and the emergence of a giant, shadow puppet-shaped peninsula at the mouth of the Yellow River are among a string of curious and surprising changes seen from space.

They sit beside the more conventional, but no less dramatic images of rain forest deforestation in Paraguay and Brazil, rapid oil and gas development in Wyoming, United States, forest fires across sub-Saharan Africa and the retreat of glaciers and ice in polar and mountain areas."

It has some really amazing satellite imagery and scarily illustrates the rate of enviromental destruction. It is great that it can be downloaded for free, so that this information can be spread as widely as possible.

Download link: http://www.na.unep.net/OnePlanetManyPeople/AtlasDownload.php

Extinct already?

2006-02-02T15:09:00.000Z

I mentioned in my post on that the world's smallest vertebrate* that it was was threatened. It seems events have moved faster than anyone feared and it now seems that it could be already extinct. From the annotated budak

"I was supposed to study the behaviour of Paedocypris for my Research project in NUS.

JANUARY 2005 I visited North Selangor Peat Swamp (NSPSF) with Dr Tan in January 2005 to collect this fish. We visited all the sites that the fish had been previously collected. We could not catch a single fish. On top of that, of other peat swamp species, we caught fewer fish species than previous collections in NSPSF.

This may have been because of two reason, 1) The fish is seasonal, 2) North Selangor was in the process of being drained for agriculture, the disturbance may have caused the species to go extinct.

JULY 2005 I visited these same sites in July 2005. By this time the swamp was in worse condition. The streams were all nearly dry and overgrown with vegetation, we sampled here and again found no Paedocypris, and found even fewer fish species than we had in January.

OVERVIEW 50 species of fish have been collected from North Selangor Peat swamp forest (NSPSF), 20 of which can only survive in the acid water conditions of peat swamp forests, and a further 5 species restricted to NSPSF."

LINK

This is heatbreaking, it could have been extinct even before it was published.

This story illustrates the importance of World Wetlands Day which is today, the swamps of the world need your help! Via Pruned

* There is some dispute about who is the very smallest vertebrate it seems that Paedocypris may only be the smallest freshwater fish LINK

Offensive cartoons

2006-02-02T12:05:00.000Z

The row about the offensive cartoons continues. You can see them on flickr HERE.

The interesting thing is that there are regularly far more offensive and violently anti-semitic cartoons in the arab press LINK. And racist and religiously offensive lies are viewed as entertainment in the muslim world LINK. The hypocrisy is galling, and the threats of violence are an anathema to anyone who cares about freedom.

scientology

2006-01-29T11:22:00.000Z

I just caught part of a lame BBC programme called 'The Heaven & Earth Show' about scientology Which reminded me just how stoopid this lame cult is. It is incredible that people still believe this rubbish when it is absolutely clear it is complete nonsense, it illuminates an interesting aspect of religious psycology where people refuse to accept any evidence that their faith is false.

I keep getting bothered in Birmingham by scientologists offering to give 'stress test' without of course mentioning that they are scientologists - why are they afraid of being honest about who they are? This constant bothering also seems a bit desperate, lets hope it is because they are short of victims.

"Writing for a penny a word is ridiculous. If a man really wants to make a million dollars, the best way would be to start his own religion." - L. Ron Hubbard founder of scientology

'The life expectancies of books'

2006-01-27T09:45:00.000Z

At making light there is an interesting article on why extended copyright on books is a bad idea:

http://nielsenhayden.com/makinglight/archives/007181.html

'Children are less able than they used to be'

2006-01-26T10:59:00.000Z

In the 'Education Guardian' There is a report on research carried out by professor Michael Shayer of King's College London. It is claimed that research shows that:

"11- and 12-year-old children in year 7 are "now on average between two and three years behind where they were 15 years ago", in terms of cognitive and conceptual development."

And what of the cause?

" I would suggest that the most likely reasons are the lack of experiential play in primary schools, and the growth of a video-game, TV culture. Both take away the kind of hands-on play that allows kids to experience how the world works in practice and to make informed judgments about abstract concepts."

This certainly would make sense if reports that television in particular are linked to poor educational outcomes (1) and 'modest adverse effects' on cognition of TV viewing particularly by the under 3s (2) are true.

It is certainly part of the thesis of Dr Aric Sigman in his new book 'Remotely Controlled' which contains some interesting ideas.

'Children are less able than they used to be' http://education.guardian.co.uk/schools/story/0,,1693061,00.html

1) Association of television viewing during childhood with poor educationalachievement. Hancox RJ, Milne BJ, Poulton R. Arch Pediatr Adolesc Med. 2005 Jul;159(7):614-8.

2) Children's television viewing and cognitive outcomes: a longitudinal analysis ofnational data. Zimmerman FJ, Christakis DA. Arch Pediatr Adolesc Med. 2005 Jul;159(7):619-25.

The Armoured Snail

2006-01-26T10:38:00.000Z

The as yet un named “scaly foot” gastropod is undoubtedly one of the coolest organisms to be discovered in recent years (1). It’s truly remarkable feature is that the exposed parts of it’s body are covered with overlapping scales of iron sulphide that look for all the world like armour. New research about how this remarkable feature is made has just appeared in ‘Earth and Planetary Science Letters’ (2).

It was previously thought that the iron sulphide could be derived from symbiotic bacteria that are associated with the scales (3). This does not seem to be the case as the isotopic composition of the scales resembles that of the vent fluids and not bacterial metabolites. But it does seem that the control of iron sulphides in cells by this snail which was probably a necessary precursor to the ‘armour’ is related to symbiosis with the bacteria that provide the gastropod with food. These bacteria live inside the esophageal glands (3) and seem to provide the snail with all of it’s nutrition as it has an atrophied gut. The bacteria convert sulphides into compounds that the bacteria and snail can use so it is likely that the snail can regulate intracellular sulphides. It is suggested that it is this adaptation that provided the precursor to ‘snail armour’. Unsurprisingly the researchers also conclude that the function of these scales is for defense possibly against brachyuran crabs.

The snail's home at the base of a vent, showing crabs and shrimp.

There is still much to find out about this snail. For example it is not known exactly how the snail controls the iron sulphides what genes are involved in this process and how it is regulated, hopefully further research will reveal more about this incredible creature.

1) A Hot-Vent Gastropod with Iron Sulfide Dermal Sclerites. Science 7 November 2003: Vol. 302. no. 5647, p. 1007 DOI: 10.1126/science.1087696. http://www.marinegeo.uni-bremen.de/pub/pdf/PDF-Datein/2003/Waren_2003_a.pdf

2) Suzuki, Y., Kopp, R.E., Kogure, T., Suga, A., Takai, K., Tsuchida, S., Ozaki, N., Endo, K., Hashimoto, J., Kato, Y., Mizota, C., Hirata, T., Chiba, H., Nealson, K.H., Horikoshi, K., & Kirschvink, J.L.
Sclerite formation in the hydrothermal-vent "scaly-foot" gastropod—possible control of iron sulfide biomineralization by the animal. Earth and Planetary Science Letters 242, 39-50. http://dx.doi.org/10.1016/j.epsl.2005.11.029
Free Full text: PDF

3) Novel Forms of Structural Integration between Microbes and a Hydrothermal Vent Gastropod from the Indian Ocean. Shana K. Goffredi, Anders Warén, Victoria J. Orphan, Cindy L. Van Dover, and Robert C. Vrijenhoek. Applied and Environmental Microbiology, May 2004, p. 3082-3090, Vol. 70, No. 5. http://aem.asm.org/cgi/content/full/70/5/3082

The smallest vertebrate

2006-01-25T14:51:00.000Z

Some mature members of this species are only 7.9 mm long, aww. But it is depressingly inevitable that their habitat in Southeast asia is threatened so they might not be around for much longer.

Paedocypris, a new genus of Southeast Asian cyprinid fish with a remarkable sexual dimorphism, comprises the world’s smallest vertebrate. Proceedings: Biological Sciences. In press. http://www.journals.royalsoc.ac.uk/link.asp?id=y0g7834174u82404 (featured article available free for a limited period)

In praise of Richard Dawkins

2006-01-11T14:45:00.000Z

In praise of Richard Dawkins by Johann Hari

Quite right too, he is a national treasure.

Balblair rock art update

2006-01-06T13:14:00.000Z

I have mentioned the rock art at Balblair previously, so its nice to see there is an article on the site in Past the newsletter of the prehistoric society which includes the nice drawings of the art (see above)

http://www.ucl.ac.uk/prehistoric/past/past51.html Which also includes a nice article on loughcrew megalithic cemetary.

Earliest Maya Writing Found

2006-01-06T11:32:00.000Z

The story at national geographic: HERE

Link to the paper in science magazine HERE

Old Herbals

2005-12-21T12:33:00.000Z

Old Herbals are just fantastic, they contain so much interesting historical and medical information about plants. I particularly like 'The Herball' by John Gerarde. It has now been scanned and made available at the amazing Kurt Stüber's Online Library:

http://caliban.mpiz-koeln.mpg.de/~stueber/gerarde/index.html

A new herbal, or historie of plants (1619) by Henry Lyte is also available:

http://caliban.mpiz-koeln.mpg.de/~stueber/lyte/index.html

It’s well worth browsing the online library which contains a huge variety of mostly science related books on everything from botany to geology and mycology. Particularly recommended is "Die Radiolarien Tafeln" and "Kunstformen der Natur" by Ernst Haeckel.

Tawaraya Sotatsu

2005-12-11T11:37:00.000Z

Tawaraya Sotatsu (17th century died 1643) is in my opinion one of the great artists of the world and above is a small section of a folding screen produced by him. The image comes from the Tokyo national museum which is a shining example of providing worldwide access via the interent to high quality pictures of it's collection. Compared to the pathetic efforts of british museums it is amazing.

If you want to download a larger version of the above picture of get your hands on other pictures of the screen go to: http://www.tnm.go.jp/jp/gallery/material/film/index.html
and in the lowest section of the search form (フィルム番号 in japanese) there are two boxes with C in from of them. In the left hand box type: 0028941 and then press the search button (containing red text). That should take you to a results page and clicking the top link will take you to the above image.

If you want to search for the artist return to the search page and copy and paste this: 俵屋宗達
into the third box from the top (labelled 作者). The best images of the screen start at C28931.

needless to say Sotatsu is not the only artist in the collection try searching for:

ogata korin: 尾形光琳
hasegawa: 長谷
koetsu: 光悦
liang: 梁
Tosa mitsunobu: 土佐光信
kuniyoshi: 国芳
Suzuki Kiitsu: 鈴木其一

Some Sotatsu links:
http://www.clevelandart.org/Explore/artist.asp?artistLetter=S&recNo=218
http://www.metmuseum.org/toah/ho/09/eaj/ho_1975.268.59.htm
http://www.japanese-arts.net/painting/schools_rinpa_sotatsu.htm

Mayan codices

2005-12-08T20:23:00.000Z

An image from the Kingsborough edition of the Dresden codex that seems to represent a god formed from a mixture of various deities

I have been interested in the mayan civilisation for a long time so I was very happy to discover that FAMSI has made copies of all the mayan codices available to download:

The Dresden Codex
The Grolier Codex
The Madrid Codex
The Paris Codex

They are available to view online of download as PDFs which are up to 90 megs!

The magnitude of the destruction of mayan culture that followed the spanish invasion can be appreciated by the fact that these are the only four mayan codices in existance (although one must always hope that some more have been miraculously preserved)

There are also Aztec and Mixtec codices available (mostly just as images online) see complete list: http://www.famsi.org/research/graz/

Interesting stuff in the Journal of Anatomy

2005-12-04T10:02:00.000Z

The current issue of the Journal of Anatomy (November 2005) has a whole load of interesting papers. And best of all it is a free sample issue so everyone has access to the articles. My picks are:

Evolution of cranial development and the role of neural crest: insights from amphibians
Developmental studies of the lamprey and hierarchical evolutionary steps towards the acquisition of the jaw
Reassessing the Dlx code: the genetic regulation of branchial arch skeletal pattern and development
mechanisms facilitating the evolution of bills and quills
Deer antlers: a zoological curiosity or the key to understanding organ regeneration in mammals?

http://www.blackwell-synergy.com/toc/joa/207/5

"Schemae of gnathostome chondrocrania demonstrating the conservation of an ordered series of splanchnocranial elements in the gnathostome bauplan. Maxillary arch derivatives are depicted in yellow,mandibular arch in lavender and caudal arches in salmon and/or white. The neurocranial chondrocranium is in light blue. " from 'Reassessing the Dlx code', for full label see the original article.

Carbon dioxide level highest in 650,000 years

2005-11-27T12:26:00.000Z

Refs: Spahni, R., J. Chappellaz, T.F. Stocker, L. Loulergue, G. Hausammann, K. Kawamura, J. Flückiger, J. Schwander, D. Raynaud, V. Masson-Delmotte, J. Jouzel, Atmospheric methane and nitrous oxide of the late Pleistocene from Antarctic ice cores, 310, Science, 1317-1321, 2005.
http://spot.colorado.edu/~flueckig/publications.html

Siegenthaler, U. T.F. Stocker, E. Monnin, D. Lüthi, J. Schwander, B. Stauffer, D. Raynaud, J.-M. Barnola, H. Fischer, V. Masson-Delmotte, J. Jouzel, 2005, Stable carbon cycle-climate relationship during the late Pleistocene. Science 310, 1313-1317.
http://www.climate.unibe.ch/~stocker/publications.html

MRSA And Bad Reporting

2005-11-05T15:01:00.000Z

The latest saga of the dodgy MRSA lab is available from bad science:

Microbiologists raising doubts? It must be a cover-up

This story really does illustrate how dishonest tabloid reporting is here in the UK (guilty papers: Sun, Mirror, Mail, Evening Standard and more) Reporters seem to think it is OK to essentially fabricate evidence of MRSA contamination and then sling allegations of a 'cover-up' around when their dishonesty is exposed.

Other posts on this story:
After feeding the scare he’ll sell you the solution
The man behind the Mop of Death
Lab that finds bugs where others do not

New Brain Atlas

2005-11-05T13:49:00.000Z

I have just found this site via neurodudes and it looks pretty neat:

"BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on scanned images of serial sections of both primate and non-primate brains and that is fully integrated with a high-speed database server for querying and retrieving data about brain structure and function over the internet"

http://brainmaps.org/index.php

It is still in development so it should get even better in the future!

If you like brains, see also: The Brain Museum

New Dmanisi paper

2005-11-05T09:16:00.000Z

Dmanisi Skull D2282

Dmanisi in Georgia is a very important site in the understanding of human evolution so it is nice to see that a new paper on these finds is soon to be published in the journal of human evolution. The bones in this site are very well preserved so reveal alot of information about our ancestors. Dmanisi hominins are probably some of the earliest human ancestors to venture out of Africa - possibly due to greater intelligence enabling exploitation of new environments.

To get to Georgia the Dmanisi hominins must have travelled through Turkey - i wonder if there are more fossils of this age still to be found in this part of the world?

Anatomical descriptions, comparative studies and evolutionarysignificance of the hominin skulls from Dmanisi, Republic of Georgia

Philip Rightmire, David Lordkipanidze, Abesalom Vekua

Journal of human evolution - in press

Abstract: Evidence for ancient hominin occupation in Eurasia comes from Dmanisi in the Georgian Caucasus. Stratigraphic and sedimentological arguments,geochemical observations, paleomagnetic sampling and radiometric dates all point to the conclusion that bones and artifacts were depositedat this site during a brief interval following the close of the Olduvai Subchron (1.77 million years ago). In this report we presentfurther descriptive and comparative studies of the D2280 braincase, the D2282 partial cranium, now linked with the D211 mandible, and theskull D2700/D2735. The crania have capacities ranging from 600 cm3 to 775 cm3. Supraorbital tori and other vault superstructures are onlymoderately developed. The braincase is expanded laterally in the mastoid region, but the occiput is rounded. The pattern of sagittal keelingis distinctive. D2700 displays a prominent midfacial profile and has a very short nasoalveolar clivus. Also, the M3 crowns are reduced insize. Although there is variation probably related to growth status and sex dimorphism, it is appropriate to group the Dmanisi hominins together.With the possible exception of the large D2600 mandible, the individuals are sampled from one paleodeme. This population resembles Homohabilis in brain volume and some aspects of craniofacial morphology, but many of these features can be interpreted as symplesiomorphies. Otherdiscrete characters and measurements suggest that the Dmanisi skulls are best placed with H. erectus. There are numerous similarities to individualsfrom the Turkana Basin in Kenya, but a few features link Dmanisi to Sangiran in Java. Some traits expressed in the Dmanisi assemblageappear to be unique. Reconstructing the evolutionary relationships of these ancient populations of Africa and Eurasia is difficult, as the record isquite patchy, and determination of character polarities is not straightforward. Nevertheless, the evidence from anatomical analysis and measurementssupports the hypothesis that Dmanisi is close to the stem from which H. erectus evolved.

Some nice pictures of the excavation in progress and people involved: http://www.fas.harvard.edu/~skeleton/pontzerDmanisi.htm

3D scanning of prehistoric art

2005-10-31T22:01:00.000Z

Archaeoptics has just relased the news that they have finished scanning several rock art panels: Ketley Crag, Chatton Park 1, Huntersheugh Howgill and Cotherstone. This is good news as laser scanning is the most accurate and non destructive way of recording rock art and so will provide an excellent record of these carvings many of which are threatened in many different ways.

Link

Beckensall Archive of Northumberland Rock Art

I have also come across a nice article on the scanning of the art at Long Meg: http://www.ucl.ac.uk/prehistoric/past/past50.html#LASERSCANNING

See also: Dr. Margarita Díaz-Andreu

Brush up on your Yucatec

2005-10-30T14:29:00.000Z

I was interested to learn that Mel Gibson's new film Apocalypto will be performed in the maya language Yucatec. This has to be a first but it is a good idea as Mayan history contains some brilliant stories, impressive spectacle and loads of violence. In case you wanted to learn more about this language here are some resources:

A Brief Introduction to Yucatec Maya

Combined Dictionary–Concordance of the Yucatecan Mayan Language

an online dictionary of all Mayan languages

Story about the film

Eastern Zhou grave discovered

2005-10-30T13:56:00.000Z

The eastern zhou (770-256 BC) has produced some absolutely amazing relics so it’s nice to learn that a new tomb from that era has been discovered near Luoyang and properly excavated rather than being looted.

Link

Saving China's antiquities

New Rock Art

2005-10-24T17:28:00.000+01:00

I do love megalithtic art so i was very excited to hear about the discovery of a new decorated tomb in Scotland. The find was at Balblair Quarry, Beauly near Inverness an area that does not contain any similar art. It looks like the sort of thing that is found in Ireland and areas influenced by Ireland so the discovery on the east coast is an enigma. More information on the excavation and further pictures can be found here.

Palanth up again

2005-10-22T08:35:00.000+01:00

The palanth forum where various aspects of human evolution are discussed is back up again after being down for some time due to technical problems:

http://forum.palanth.com/index.php

Wren's Nest

2005-10-16T08:42:00.000+01:00

I live near the lovely Wren's Nest national nature reserve so was very happy to learn (via discuss fossils) that a website with pictures of fossils collected there has been created by Geoff Broughton here:

Link

It's well worth a look.

If you want to see the fossils in real life you can visit the Dudley Museum & Art Gallery, or the Lapworth Museum, or of course you could visit Wren's Nest itself. The picture is of the trilobite Calymene blumenbachii from Wren's Nest in the Dudley museum.

I have a set of photos taken at the Dudley museum on flickr here.

Morphbank

2005-10-11T19:05:00.000+01:00

Above is an image from Morphbank a a cool new wesite I have just heard about via Eurekalert. It will apparently be an 'international Web database that contains thousands of high-resolution photographs and other images of plant and animal specimens.' The images here are all very high quality and it is possible to download vey high resolution versions which is nice, especially as there seem to be lots of nice SEMs, and i do like a nice SEM. The taxonomic coverage is limited at the moment (mainly to wasps) but it could be an amazing resource in the future.

The picture is the wasp Aylax papaveris and morphbank can be found at http://www.morphbank.com. Press release: http://www.eurekalert.org/pub_releases/2005-10/fsu-tso101105.php

Flower Development

2005-10-01T10:31:00.000+01:00

A nice Review of flower development has just been published in Nature Reviews Genetics:

Krizek, B.A. and Fletcher, J.C. (2005) Molecular mechanism of flower development: An armchair guide. Nat. Rev. Genet. 6, 688-698.

Abstract
An afternoon stroll through an English garden reveals the breathtaking beauty and enormous diversity of flowering plants. The extreme variation of flower morphologies, combined with the relative simplicity of floral structures and the wealth of floral mutants available, has made the flower an excellent model for studying developmental cell-fate specification, morphogenesis and tissue patterning. Recent molecular genetic studies have begun to reveal the transcriptional regulatory cascades that control early patterning events during flower formation, the dynamics of the gene-regulatory interactions, and the complex combinatorial mechanisms that create a distinct final floral architecture and form.

It is available to download from the Krizek lab homepage: http://www.biol.sc.edu/~krizek/0905NRG.pdf

Worms!

2005-09-29T19:55:00.000+01:00

Above is a picture of the parasitic tapeworm Taenia crassiceps I thought i would post it becuase it is a neat picture. This parasite does look horrifying but there is some evidence to suggest that these and other parasites can be beneficial, manipulating the host immune response and preventing diseases such as asthma. Although a reduction in worm infection is probably not the only reason for the recent dramatic rise in asthma and other inflammatory diseases.

Microscopy and the helminth parasite http://dx.doi.org/10.1016/j.micron.2003.12.001 (source of image)

Parasite role reversal: worms on trial http://dx.doi.org/10.1016/j.pt.2005.02.002

Wheeze, allergic sensitization and geohelminth infection in Butajira, Ethiopia. doi:10.1111/j.1365-2222.2005.02181.x - evidence contra to the beneficial effect of worms?

The social bond between dogs and people

2005-09-27T20:16:00.000+01:00

An interesting article on the history of the human relationship with dogs is soon going to be published in the Journal of Archaeological Science. Based on the earliest deliberate burials of humans and dogs it is estimated that this relationship was established by 14,000 years ago, although molecular techniques put this date much earlier. Humans certainly seem to have a strong bond with dogs and dogs have been shown to understand human cues such as gaze direction extremely well. This ability is better than that of the great apes or human reared wolves.

Even though this bond is strong it seems that this ability is quite easy to breed. A Russian experiment with silver foxes has managed to domesticate them in around 30 generations merely by selecting those that showed the least fear of humans. This has lead to a number of other interesting changes including an increase in: ‘floppy ears’ ‘curly tails’ a white star on the forehead and short rolled tails. These traits are also common in domesticated dogs. This shows how easy it is to domesticate an animal, although I wonder what would happen in a non canid?

It is also interesting to speculate why dogs were domesticated in the first place. I am inclined to think it was something like dogs being useful to track or herd animals. But the stability of this relationship for 14,000 years is probably in large part due to the close relationship human and dogs have developed, based on the ability of our two species to communicate in a unique way.

Burying key evidence: the social bond between dogs and people
Darcy F.
Morey. Journal of Archaeological Science. http://dx.doi.org/10.1016/j.jas.2005.07.009

Abstract
People have been burying or otherwise ritually
disposing of dead dogs for a long time. They sometimes treat other animals in
such a fashion, but not nearly as often as dogs. This presentation documents the consistent and worldwide distribution of this practice over about the past 12,000e14,000 years. Such practices directly reflect the domestic relationship between people and dogs, and speak rather directly to the timing of canid domestication. In doing so, they contradict recent genetics-based inferences, thus calling into question the legitimacy of focusing mostly on genetic factors
as opposed to other factors. This discussion seeks to work towards a sound framework for analyzing and thus understanding the social compatibility between people and dogs. That compatibility is directly signified by the burial of dogs, with people often responding to the deaths of individual dogs much as they usually respond to the death of a family member. Moreover, that special social relationship continues, as illustrated clearly by the establishment, maintenance, and ongoing use of several modern dog cemeteries, in different countries of the world.

Early Canid Domestication: The Farm-Fox Experiment
http://www.floridalupine.org/publications/PDF/trut-fox-study.pdf

Dogs respond appropriately to cues of humans' attentional focus
http://hal.psych.uw.edu.pl/2004zalaczniki/Viranyi%20i%20in%202004.pdf

Transitional Dinosaur - Bird Eggs

2005-09-24T20:59:00.000+01:00

Evolutionary trends in eggs and egg-laying from basal archosaurs to modern birds

An interesting new article is available from Naturwissenschaften reporting the discovery of eggs with dinosaur-like and bird-like characteristics. This is of course exactly what you would expect to find if birds had evolved from dinosaurs.

Minute theropod eggs and embryo from the Lower Cretaceous of Thailand and the dinosaur-bird transition

Eric Buffetaut, Gerald Grellet-Tinner, Varavudh Suteethorn, Gilles Cuny, Haiyan Tong, Adrijan Košir, Lionel Cavin, Suwanna Chitsing, Peter J. Griffiths, Jérôme Tabouelle1 and Jean Le Loeuff.

Abstract

We report on very small fossil eggs from the Lower Cretaceous of Thailand, one of them containing a theropod embryo, which display a remarkable mosaic of characters. While the surficial ornamentation is typical of non-avian saurischian dinosaurs, the three-layered prismatic structure of the eggshell is currently known only in extant and fossil eggs associated with birds. These eggs, about the size of a goldfinch's, mirror at the reproductive level the retention of small body size that was paramount in the transition from non-avian theropods to birds. The egg-layer may have been a small feathered theropod similar to those recently found in China.

Link - journal website

Free full text: PDF