I recently signed the Sense about Science petition in favour of their GM wheat trials. I have just received the following email which suggests that the Take the Flour Back pressure group are afraid to discuss the issues around this GM work in a public forum.  I can only conclude that they realise their opinions of this work are without merit compared with the efforts that the Rothamsted scientists have made in engaging with the public and explaining the nature of their work.The research is legal, and has passed all regulatory hurdles. The actions of Take the Flour Back are to be deplored. I urge all to read the information at the website and sign the petition.

Dear Petition SignatoryYou supported the appeal by Rothamsted scientists against plans by a group to take direct action against their research into whether GM wheat can warn off aphids.The Take the Flour Back group is pursuing this action but had agreed with the researchers’ proposal to debate their concerns before 27th May.  The researchers organised a neutral venue and chair for a debate. Unfortunately Take the Flour Back has announced they will not take part. There is a timeline of the exchange between Professor John Pickett and Take the Flour Back at http://www.rothamsted.ac.uk/Content.php?Section=AphidWheat&Page=ProtestThere’s lots of other discussion going on. Professor Pickett will be on Newsnight on BBC2 at 10.30 tonight. Many of you left comments on the petition asking about aspects of the research and we have received many questions and points by email and twitter. The scientists at Rothamsted, and colleagues at institutions doing related work, have been responding to many of them; some of this is now up on http://www.senseaboutscience.org/pages/rothamsted-appeal.htmlPlease send the message far and wide: forward the scientists' appeal to your friends and colleagues, share the petition on Facebook and use Twitter hashtag #dontdestroyresearch.http://www.senseaboutscience.org/petition.phpBest regardsSíle Lane

Way back in 2008 I wrote a brief blog article about the sequencing of the genome of a rather poorly unusual organism, Trichoplax adhaerens (What the heck is a Placozoan, anyway?).  The interest there was that the genome had a variety of genes associated with organisms with a more 'complex' structure (Trichoplax looks rather like a flattened blob of cells), while no-one really knew much about the biology of the animal.A paper describing sexual reproduction in Trichoplax has just been published in PLoS One (Eitel M, Guidi L, Hadrys H, Balsamo M, Schierwater B, 2011 New Insights into Placozoan Sexual Reproduction and Development. PLoS ONE 6(5): e19639. doi:10.1371/journal.pone.0019639).  Here's an excerpt from the abstract:

[...] Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. [...] Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction.

All rather interesting - the authors note that the genome sequence was in the hands of scientists before the Trichoplax life cycle was in any way understood.  I imagine that this sort of situation will occur more often, as projects that are randomly trawling the environment for novel DNA sequences have been carried out (Venter et al (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea.  Science 304; 66-74).

According to a report in the Daily Telegraph (Last refuges of England’s rarest species revealed), Natural England has released a list of the most sensitive SSSIs, often the refuge of some of the most endangered species in the UK.It's often seemed to me (on the basis of nothing more than reports in the national media) that SSSI status offers little in the way of protection.  Indeed, in my (increasingly frequent) moments of black humour, I often suggest that SSSI status seems to indicate the next place to be tarmacced over in some property development.Anyway, it turns out there are over 4000 SSSIs, including the habitats of the startlingly lovely ladybird spider (illustrated in the Telegraph article), and the alarmingly named Queen's executioner beetle.  I looked up the Queen's executioner beetle in Wikipedia, and discovered that it's only had that name since July 2010, when a newspaper competition was run to find a common name for it.

Here in the UK, there are few haematophagous arthropods which trouble me. While mosquitoes provide a minor irritation, the Scottish midge Culicoides impunctatus is massively annoying, principally because of the sheer number that typically assail one. For me the bite is more irritating as it occurs rather than an itching after-effect. Generally I come into contact with the Scottish midge while on cycling holiday, and swarms of the blighters can make even the most lovely campsite intolerable.  However the beast that irritates me more than any other is Neotrombicula autumnalis, commonly known as the harvest mite or berry bug. The common names reflect both the season in which N. autumnalis larvae become active and the activities which bring people into contact with them. This blog article was inspired by a pair of bites I picked up this week.[caption id="" align="alignleft" width="220" caption="Life cycle of trombiculid mites"][/caption]Most people who suffer from N. autumnalis first become aware of quite severed itching and raised reddened lumps that are typically found around clothing constrictions, typically underwear elastic. But by this time the little devils are usually long gone, leaving several days of irritation behind them. So what are harvest mites?The biology of trombiculid mitesHarvest mites are small arthropods, with a life cycle as shown in the figure (from Wikipedia). It's a typical mite life cycle: the offending stage is the 6 legged larval stage, of which more later: one phase of the nymph stage and the adults are active predators on other small arthropods.This life cycle diagram is a slight simplification.  The nymph stage is actually composed of three stages, the protonymph (an inactive stage entered after the larva has finished feeding and left its host), the deutonymph (the active nymph stage during which the animal feeds on other, presumably smaller, arthropods) and the tritonymph (a second inactive stage after which the adult emerges).[caption id="attachment_998" align="alignleft" width="150" caption="Larval trombiculid mite"][/caption]For this purpose, it's the larval stage that is of interest: this is the only stage in which the animal feeds on a vertebrate host (see image to left). These beasts lurk on the tips of grass and other leaves awaiting a passing animal.  When the animal brushes the leaf, the larval mite climbs aboard and crawls about, seeking a suitable attachment point.  For some animals this will be areas devoid of hair or thin skin, such as around the eyes or in the ears.  In the case of humans, this is frequently at points of clothing constriction - usually the last place you want to develop an itch!Larval trombiculid mites don't actually bite, or drink blood (so my depiction of them as haematophagous is rather stretching the point): rather they pierce the skin, injecting digestive juices and sucking up the resulting fluids.  This goes on for a few days after which the mite drops off the host and falls to the substrate.  This process causes a tube of hardened skin called the stylostome to form, and it's through this that the mite continues to feed.Apparently it's only after the mite has departed that the bite becomes noticeable, by which time the culprit is long gone.  Fortunately in temperate areas such as the UK, trombiculid mites only have one annual generation, with larvae being active in summer and early autumn (hence the association with berry picking, crop harvests and, in my case, mushroom collecting).  In tropical areas, trombiculids breed rather more frequently, with the life cycle being completed in around 40 days.Trombiculid mites and diseaseHere in the UK, harvest mites don't transmit disease, but this isn't the case elsewhere.  In south east Asia, trombiculid mites are knwon to transmit scrub typhus (also known as Tsutsugamushi), caused by the bacterium Rickettsia tsutsugamushi (aka R. orientalis) - rather than being a typhus, it's actually a Rickettsiosis.Treatment of harvest mite bitesSevere attacks may lead to dermatitis as the rashes and pustules merge.  I'm not personally aware of any particularly effective treatment for the "berry bug itch".  The Pied Piper pest control website has a section on harvest mites that recommends the following - both seem to be very sensible advice. If you've visited a site known for harvest mite infestation, wash your clothes in hot soapy water, and have a good hot shower.  The larval mites will be wandering around your body and clothes, the hot wash should kill them.  Unfortunately the realisation that one may have been in infested terrain may only surface once the mites have gone and you have the itch... Scratching can cause secondary infections: temporary relief may be provided by ointments of benzocaine, hydrocortisone, calamine lotion, or other things that may be recommended.  For what it's worth, I've tried calamine lotion, it works for a very short time!The pet health website PetWellBeing.com recommends (for dogs) the topical application of steroids to alleviate the severe itching.  Ultimately, my opinion is that the best treatment is probably to ensure you don't scratch the lesion!Further readingWikipedia entry TrombiculidaeLane & Crosskey "Medical Insects and Arachnids" Pub 1993 Chapman & Hall.Wikipedia entry TsutsugamushiNote: this article should not be considered medical advice

There's been some discussion in the columns of Nature recently concerning the possibility of eradication of mosquitoes. In an article entitled A World Without Mosquitoes, Janet Fang (1) presents a variety of opinions whether large-scale mosquito eradication is practical and if so whether such a course of action is desirable. In the latest issue of Nature, a collection of four letters revisit the controversy.So, there are two issues here: Can we?, and should we?[caption id="attachment_1044" align="alignleft" width="300" caption="Anopheles gambiae feeding"][/caption]Some years ago, I had a brief foray in to the world of the Anopheles gambiae species complex, an experience which was quite novel for me as my experiences had been with a very different and more docile fly, Drosophila melanogaster.  And for several years I maintained a colony of A. gambiae in my laboratory, which while not in itself particularly difficult was certainly quite arduous and one strain required considerably more commitment and care than keeping several hundred Drosophila strains. At that time, there was quite a deal of excitement about the prospects of driving transgenes through wild populations, using as a model the spread of P-elements through wild populations of D. melanogaster during the 20th century.  There have always been concerns about the extent to which the entities known as 'species' really are homogeneous populations with consistent gene flow through them across their range: certainly within the A. gambiae species complex, there appear to be 'incipient species' which represent fairly hefty gene flow barriers within the individual sibling species of the complex.One caveat would be that even if one could eliminate an entire species, or a species complex, what would fill the vacant niche?  A. gambiae may be the most significant malaria vector in sub-Saharan Africa, but there are others, that I guess could move in an colonise a vacant niche.  An argument for species control by transgenic means might be for eliminating a species that's newly colonised areas in which they haven't formerly been present: a good case might be if A. gambiae were to be introduced into South America.  More subtle interventions might be to introduce transgenes that impact on malaria parasite propagation within the mosquito: the downside would probably be that given the huge scale of the parasite population out there, somewhere there is likely to be parasites that can evade the introduced transgene.Sterile male release can be effective in controlling insect pests, but is really most effective where the female generally mates only once.  Drawbacks can include fitness of the males, either from irradiation used to sterilise them or because the laboratory-bred strains are uncompetitive in the wild.  Sophisticated technologies exist by which terile males can be made, so this may not be so major a hurdle in the future.Other, more traditional, methods of insect control are really very blunt instruments such as insecticide usage.  Obvious drawbacks would be collateral damage to other insect species, with the potential for massive ecological damage.  There are also health implications.  In the past, mosquito control by application of DDT was quite effective in Sri Lanka, then Ceylon, until over-enthusiatic and inappropriate use of DDT caused the appearance of DDT-resistant mosquitoes.  In the intervening years, malaria incidence had dropped, with the consequence that the resurgence of the disease as mosquito populations recovered was particularly severe (2).  I would be surprised if global eradication by insecticide would ever be approved.  And I cannot see a means by which wholesale eradication of many different mosquito species could be undertaken.  Fang's article provides a concise overview of the eradication/control techniques that have been tried in the past, and some that may be options in the future.In the context of should we eradicate mosquitoes, I'm really less well informed about the ecological implications of such a course.  Much of the online discussion seems to revolve around the ecological consequences of eliminating all mosquitoes, across all ecosystems, even in sub-Arctic tundra regions.  It would not be surprising to me if the ecological effects would be severe, but it also occurs to me that those consequences might well be unrecoverable. At the end of the article, Fang concludes that in her penultimate paragraph that:

Given the huge humanitarian and economic consequences of mosquito-spread disease, few scientists would suggest that the costs of an increased human population would outweigh the benefits of a healthier one. And the ‘collateral damage’ felt elsewhere in ecosystems doesn’t buy much sympathy either. The romantic notion of every creature having a vital place in nature may not be enough to plead the mosquito’s case. It is the limitations of mosquito-killing methods, not the limitations of intent, that make a world without mosquitoes unlikely.

The conclusions seems to be that (a) we couldn't do it, but that (b) if we could, we should, and it wouldn't make much difference ecologically.  Well, actually, I'd rather not try the ecological experiment![caption id="attachment_1045" align="alignnone" width="500" caption="Sabethes sp. mosquito"][/caption][caption id="" align="alignleft" width="269" caption="Sabethes cyaneus"][/caption]And anyway, would the world really be better without the beauty pictured above, a species in the genus Sabethes?  Sabethes species are often regarded as the "butterflies" of the mosquito world, frequently bearing brightly coloured or iridescent paddles on their legs.Here's another image (left), this time of a couple of Sabethes cyaneus, from the BBC website (click on the image for the full-size version).Finally, I've scanned in a plate (below) from F. V. Theobald's Monograph of the Culicidae or Mosquitoes, published in 1901 by the British Musem (Natural History) - The Plates volume.  These are (from left to right) Megarhinus inornatus (male), M. inornatus (female), M. separatus and M. immisericors.[caption id="attachment_1048" align="alignnone" width="708" caption="Megarhinus species (click for full size image)"][/caption]1.  Janet Fang (2010) Ecology: A world without mosquitoes Nature 466; 432-434 . doi:10.1038/466432a2.  Gordon Harrison (1978)  Mosquitoes, Malaria and Man, Chapter 26 Pub John Murray (record at Amazon.com)via ScribeFire

Looks as though the practise of patenting genes may be at an end (at least in the USA) Judge Invalidates Human Gene Patent - NYTimes.com.  It's always seemed odd to me that patents of natural objects suc as genes were allowed in the first place - this case concerns patents held by Myriad Genetics on the use of BRCA1 and BRCA2.

A federal judge on Monday struck down patents on two genes linked to breast and ovarian cancer. The decision, if upheld, could throw into doubt the patents covering thousands of human genes and reshape the law of intellectual property.

The case was brought jointly by the American Civil Liberties Union and the Public Patent Foundation.  This case has been interesting - my memory of events is that Myriad knew where the genes were, but that it was the public human genome sequencing projects which provided the raw data that enabled Myriad to determine the gene sequences.The implication of this ruling, if it's upheld, may be interesting.  I suppose smaller biotech companies with principal IP assets in the form of gene patents might find themselves in trouble.  The NYT article continues:

Judge Sweet, however, ruled that the patents were “improperly granted” because they involved a “law of nature.” He said that many critics of gene patents considered the idea that isolating a gene made it patentable “a ‘lawyer’s trick’ that circumvents the prohibition on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result.”The case could have far-reaching implications. About 20 percent of human genes have been patented, and multibillion-dollar industries have been built atop the intellectual property rights that the patents grant.

I notice from a quick Google search that John Sulston released a statement back in 2009 supporting the ACLU case (BRCA - Statement of Support: Sir John Sulston):

I applaud the efforts of the ACLU and the Public Patent Foundation in challenging the patenting of human genes, and in particular the patents on BRCA1 and BRCA2. A patent on a gene specifically bestows the right to prevent others from using that gene. Rather than fostering innovation – one of the primary goals of the patent system – gene patents can have a chilling impact on research, obstruct the development of new genetic tests, and interfere with medical care.Genes are naturally occurring things, not inventions, and the heritage of humanity. Like a mountain or a river, the human genome is a natural phenomenon that existed, if not before us, then at least before we became aware of it.

Sulston's statement also illustrates the chilling effect of gene patents on research and development, specifically citing the chain of events which led to Myriad's patent application. Of course there are differing views on this: the NYT report quotes various individuals from the patent/legal/business side of the affair who clearly believe that medical research progress will be dented if individuals or companies are prevented from profiting financially from gene discovery (rather than inventing some application based upon gene discovery).This decision is to be welcomed, although the NYT reports that the decision is likely to be appealed.

Three months after returning from Belize, Vanessa of NatureBreak.org felt and heard the activity of a botfly larva in her scalp (I can recall reading an article in BBC Nature magazine about a cameraman who suffered this - he reckoned it was scritching against his skull!).

Botfly larvae are bulb-shaped, the the posterior spiracles poking out through a small hole in the skin - the main body of the larva is covered in backward pointing spines which serve to prevent the larva from being removed.

One of the issues that face those of us with research interests in the biology of ageing is the selection of a model system - and how well that model reflects the biology of ageing in humans.  The two main invertebrate models (the fruit fly Drosophila and the nematode worm C. elegans) have major advantages in their powerful genetics and short lifespan, but of course do differ from vertebrates in significant aspects of their biology.  The difficulty in studying primates lies in no small part in the length of lifepan - in the case of Rhesus macaques studied here, average lifespan is 27 years, so conducting a complete experiment in this system is likely to be a career-long endeavour.

One of the much investigated interventions known to extend lifespan is caloric restriction - this has been shown to be effective in several systems.  This paper reports the results (20 years in) of a research project started in 1989 to investigate the impact of caloric restriction on the

 This cute little fish is Macropinna microstoma. The green objects under the transparent carapace are its eyes: the dark blobs above its mouth are olfactory organs.

 [video:http://www.youtube.com/watch?v=RM9o4VnfHJU 480x295]

After a bit of teasing in the blogosphere that the draft sequence of the Neanderthal genome would be released in time for Charles Darwin's birthday this week, I was eagerly looking for a paper.  Instead what I find are three news articles in Science, one describing some of the outcomes of the work, and two setting it in context. Some quotes:

Initial comparisons with our own 3 billion bases indicate that a mere 1000 to 2000 amino acid differences, as well as a yet-unknown number of non-coding changes, do that job. For comparison, about 50,000 amino acid differences separate us and chimpanzees. 

A bit of a rumpus about UK science funding policy erupted this week, following publication of a letter to the Times Higher about the move to increase the emphasis towards funding science with a more immediate benefit to the UK economy. This manifests itself as a two page document (the Impact Summary) that now forms part of every Research Council grant application (in addition, I think, to the short "Beneficiaries" section that already exists.

This policy seems to be favoured by the Science Minister, Paul Drayson.  Lord Drayson is a politician with a commercial science/engineering background, but who has never been elected to public office.  he was ennobled, and reaches Minister status via a seat in the House of Lords.  Interestingly, as befits a proponent of grant applicants predicting and outlining future benefits of their yet to be performed research (not just economic but social as well), he appears to claim sixth sense "I saw it coming, says minister of sixth sense Lord Drayson".

The journal Current Biology invited a number of prominent biologists from a number of disciplines to re-read Darwin's On the Origin of Species, and to write commentaries - they can be found at (Re)Reading The Origin.

Charles Darwin's 1859 book On the Origin of Species is much referenced, especially in this double anniversary year. But, does anyone still read it? And, if so, what is the book itself like as a text? We have asked biologists from a range of fields evolutionary biologists, but also geneticists, ecologists, paleontologists and molecular biologists to re-read (or read) The Origin for Current Biology. Below are the responses, contributed by: Andrew Berry, Matthew Cobb, Simon Conway Morris, Jerry Coyne, Hopi Hoekstra, Peter Lawrence, Robert May, Christiane Nüsslein-Volhard, Mark Ptashne, Matt Ridley and Marlene Zuk.

There's been a bit of a rumpus echoing through the blogosphere following a series of pop sci articles about Darwin and his legacy (see for example this review of recent stories).  Generally, and presumably to attract readers, many make some kind of provocative claim in the title, such as "Was Darwin wrong?" or similar.

In contrast, the February 2009 edition of National Geographic features a rather excellent article by Matt Ridley: Darwin's Legacy. In a refreshing change from the tabloid-style hatchet jobs often seen in the press, this is a measured view of how modern biology has built on Darwin's foundations, and quite responsibly points out that Darwin, for all his breadth of knowledge never knew the physical basis for inheritance.

The latest in the ongoing saga of our fly shipment from the USA is that our packet of flies finally made it to the lab.  They've been in transit for exactly three weeks*, and of course kept in in known conditions.  I'm very grateful to various people at Animal Health, who were able to make an exception to the regulations.

Nonetheless, I think the application of tight control of over the international transport of live insects such as these is a bit over the top - the legislation that I've looked through seems principally aimed at commercially important farm stock and other animals important to the human food chain.   I understand there's a general unhappiness in the UK Drosophila research community, especially since the international postal union recently relaxed its regulations regarding the transport of live Drosophila through regular mail.  I'm not particularly optimistic that we can make a change to the enforcement of the new regulations, but it's most definitely worth a try.

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

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

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

The article, Extinct ibex is resurrected by cloning,saysthat

Quite a few of the bloggers at ScienceBlogs have been writing about an exciting new fossil find: a newly discovered fossil ancestor of whales.  The exciting thing here is that the fossil contains the remains of foetal whales.  Here's the University of Michigan podcast.

The fossil confirms that Maiacetus inuus was amphibious, or at least gave birth on land, as the foetus is oriented to emerge head-first (clearly not adaptive for aquatic birth, and something not seen in present-day cetaceans).

A paper in the current issue of Nature [Love et al (2009) Nature 457; 718-722] suggests that multicellular life existed about 100 million years before the explosion of bilaterian animals in the Cambrian. The evidence comes from analysis of rocks from the Arabian peninsula, in which geologically preserved derivatives of characteristic chemicals have been detected. Now, this paper interested me because of its message concerning the dating of the origins of multicellular life; I am not a geologist or a chemist, so many of the details escape me.

Identification of the presence of soft bodied animal in the fossil record is always difficult: it's generally the hard parts of the animal that are preserved by fossilisation (there are exceptions). The Cambrian explosion (see timeline diagram- click on it to link to the interactive Wikipedia diagram) resulted in a wide variety of animal forms: what's less clear is from where this abundance of diverse forms arose. This paper takes chemical approach to establishing the presence of animal remains in rock samples.

The Wordpress blog I described the other day has been fully launched - Wonderful Life - and is hosted here rather than at Wordpress.com.  I wanted to be able to do some css tweaking, and that proved a bit easier I installed it in my own domain.  I'm rather pleased with the clean and uncluttered layout of the template I chose.

I've entitled the blog Wonderful Life because it's the sense of wonder and excitement I gain from observing and explaining the world around me that motivates me as a biologist.  It's a forum for me to sound off on atheism and related matters.  Of course, it remains to be seen whether I keep it (the blog, I mean, not my biology!) rolling after the initial excitement.  And of course this blog will still be needing attention, as does the Team Grumpy blog (though that's more of a joint effort). 

There's been a profusion of articles in the popular press as he big Darwin anniversary swings into top gear.  Many of these make over-stated cases that Darwin's theory of evolution by natural selection has been "shaken up", or "over-thrown" (see for example this blog post).

There's another at the Daily Telegraph today: Charles Darwin's tree of life is 'wrong and misleading', claim scientists. Setting aside the obvious point that Darwin couldn't have got all the details right given the scientific knowledge of the time, the article seems to restate the popular myth of the big icon of evolution - the diagram of evolutionary relationship as an oak tree: