It looks like Drosophila melanogaster, the subject of a recent Sunday Spinelessness post, is about to be lost the world. The species itself isn't under threat of extinction, you can still have them delivered to your door, it's the name that looks set to go the way of the Brontosaurus.

One of the goals of taxonomy is to give scientists a precise set of terms that refer to a mutually understood group of organisms. The name D. melanogaster is a case in point, geneticists frequently refer to that species as "the fruit fly" but the common name "fruit fly" could equally be applied to the whole genus Drosophila (more than 1400 species), the family Drosophilidae (containing another 50 or so genera) or the related family Tephritidae. Believe it or not, the lack of precision conveyed by the term fruit fly became part of the USA's 2008 presidential election. Sarah Palin made some snide and ignorant remarks about "fruit fly research" in one of her speeches which were interpreted by scientific types all over the world as a swipe at basic research. People wrote pieces on the importance of D. melanogaster research in understanding human disease and media picked up the story. But Palin wasn't talking about Drosophila, she was referring to a project on an economically important Tephritid. She was still being ignorant and playing the "aren't those scientists stupid" card, be she was doing it about a project that stood to help a multi-million dollar industry that employs thousands of people.

When we say D. melanogaster instead of fruit fly we all know what we're talking about, and in modern biology a species name can be a key to huge amounts of information. But there's a problem with Drosophila. The genus as it is currently prescribed is a mess, species currently included in the genus come out in disparate groups in phylogenetic analyses like the one one the left. The solution is obvious, break up the big malformed genus into a set of smaller ones, giving all but one a new name. Such a process is pretty common in taxonomy, and the code used to my animal taxonomists explains how to go about doing it. Each genus has a "type species" which acts as the name bearer and when a genus is split, it's the group with the type species that keeps the original name. In molecular biology D. melanogaster is very much the name bearing Drosophila (it's frequently referred to just by that name or even as "the fly") but the same isn't true in taxonomy. The type species is D. funebris and no matter how Drosophila is broken up D. funebris and D. melanogaster are going to end up in different genera so melanogaster will lose its forename. But D. melongaster isn't just any fly - changing that name would render thousands of textbooks, papers and databases out of date.

Kim van der Linde saw the coming of the Drospho-pocalypse, and applied to the International Committee of Zoological Nomenclature (ICZN) to have D. melanogaster installed as the type species, preventing any changes to the taxonomy of the group from changing the species name. A couple of weeks ago the ICZN made their decision: the application was turned down and D. melanogaster will almost certainly have it's name changed. You can read the decision online - the committee make arguments for their decision with varying degrees of credibility. Perhaps the weakest justification revolves around this mosquito (I couldn't have two Sunday Spinelessness posts in a row without one photo from me!):

This photo was taken on Mitiaro in the Cook Islands, and at the time I took I knew for sure that those white striped legs marked it out as Aedes aegypti. If that species of mosquito had bitten me on any other island in the Cooks I wouldn't have calmly framed a photo, it's a vector for dengue fever which is, by all accounts, a horrible disease to have (Mitiaro's population of 200 people isn't enough to sustain Dengue, and since the main features of the island are two huge brackish lakes fill of mosquito larvae you soon give up on swatting bugs and spraying DEET). But the point of me showing you this photo now is to tell you that mosquito is no longer Aedes aegypti. Some ICZN committee members cited the fact this species has recently been renamed to Stegomyia aegypti as evidence that renaming a widely studied organism isn't the end of the world, which rather ignores that fact medical workers, ecologists, parasitologists and geneticists have ignored the reassignment entirely and some prominent journals have even issued editorials encouraging researchers to use the "old" name.

Surely in Aedes aegypti we have a model of what will happen when D. melnoagster gets its genus reassignment - taxonomists will refer to it by the new name and the rest of the world will cray on as if nothing had happened. By refusing to make a small change to the existing taxonomy of the group the ICZN runs the risk of driving a gap between the taxonomic community and other scientists. The only good thing to come from the whole ordeal is that "D. melanogaster" will almost certainly become Sophophora melanogaster which tranlates as "dark bodied bearer of knowledge", a fitting name for such an important fly.

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Plenty of other bloggers have been talking about this story, some with quite different takes than mine. You should check out Kim van der Linde who made the the application to the ICZN and has been blogging the aftermarth as well as Micheal at Arthropoda, Chris at Catalogue of Organisms and Dave at Seed.

Labels: Cook Islands, diptera, drosophila, environment and ecology, Field Trip, photos, sci-blogs, sunday spinelessness, taxonomy

Urrrgh, I screwed up the maths here. Garth George is really, really wrong. But sadly he's not the wrongest person ever. A post showing the error of my own ways can be found here and the last graph now includes my own error.

Garth George has this climate science stuff sorted out, it's a scam you see. And even if it weren't, New Zealand's emissions make such a tiny proportion of the worlds carbon dioxide we should just do nothing. You want evidence or New Zealand's tiny carbon footprint? Well, George doesn't need evidence because he has his suspicions:

I suspect that the eruption of Mt Eyjafjallajokull in Iceland shot more gases into the atmosphere in five minutes than New Zealand would in five years.

But, as Gareth Renowden points out at Hot Topic, George's suspicions don't match the data. In order to work out how much carbon dioxide Mt Unpronounceable (Paul Litterick's joke, not mine) was shooting into the atmosphere the Guardian took the surprising step of asking some scientists. The upper bound of their estimates is 300 000 tonnes of carbon dioxide per day (or about 1040 tonnes in 5 minutes). Impressive, but not much when compared with the 377 million tonnes New Zealanders managed between 2004 and 2008.

Amazingly, Garth George's estimate is out by a factor of 2.75 million 375 000 [damn!]. That's equivalent to estimating the driving distance between Dunedin and Auckland as being 3.7 metres. I couldn't let a week that combined such breathtaking stupidity with this nice infographic go without memorialising George's folly:

And, because it's pretty hard to see those few red pixels, a close up:

I've just spent a lunch break trying think of any one who has ever made a larger error of estimation. I couldn't come up with one, but here, to provide some context, is George's error against some of history's more famous mis-measurements (if you have some more to add I'd be happy to hear them, especially if you can beat George's effort):

Labels: climate change, environment and ecology, media, pretty data, sci-blogs

Over at sciblogs Peter Griffin has a post about apparently contradictory evidence on the role of multi-vitamins in breast cancer. We probably shouldn't be too surprised that different studies can look at the same question and get a different answer - biases, methodological errors and sheer dumb luck can affect the results of individual studies. For that reason we should try to draw conclusions on a body of literature, not a single paper. The Guardian's article probably does the best job of summing up how the new paper should update our picture of breast cancer risk:

If you are a woman and regularly take a multivitamin, you may be concerned by these findings. However, we don't yet know whether multivitamins actually increase the risk of breast cancer. We need more studies.

However, we also don't know whether these supplements have benefits for most healthy people. If you eat a well-balanced diet, you might reconsider whether you need to take a multivitamin.

Let's compare that with The Herald

Women who regularly take multi-vitamin pills face a much higher risk of breast cancer, a study has found.

The Swedish study, which looked at more than 35,000 women aged between 49 and 83 during a 10-year period, found that women who take daily multi-vitamin pills are nearly 20 per cent more likely to develop breast cancer.

How can the Guardian be so calm when the Herald is clearly terrified? Part of the reason is the Herald's article, like most stories on heath studies, is parroting a potentially misleading statistic called the relative risk. That's the difference in the risk of getting some disease for a group exposed to some factor (in this case multi-vitamins) and those that aren't exposed. The relative risk can be a useful summary of a study's results, because it tells us how big an effect the risk factor being study has on the disease in question, but it doesn't tell the whole story.

Take the recent story about pancreatic cancer and soft drinks. That study found people who regularly drink soft drinks face an 87% greater risk of developing pancreatic cancer, which sounds like really bad news until you realise your lifetime risk of pancreatic cancer is about 0.2%. If the papers had to run a story saying the absolute risk of pancreatic cancer moved from 0.2% to 0.37% when you drank a couple of cokes a week the headlines would have been a little more subdued than they were.

The other problem is papers usually focus exclusively on the point estimate of the relative risk ("nearly 20% more likely", "87% higher risk"...) and ignore the uncertainties associated with those estimates. Carl Sagan got a little religious about error bars in The Demon Haunted World where he described them as "pervasive, visible self-assessments of the reliability of our knowledge" and wished all political statements included them. In fact, error bars don't represent the full extend of our uncertainty, only how far our estimate of the risk might be from the mark if the study has avoided selection biases and applied its methods correctly. Still, wouldn't it be nice if newspaper stories on new medical studies had a little graphic like this to but the results in context:

Labels: health, pretty data, sci-blogs, statistics

Stuff.co.nz has a very cool video that was shot from an underwater video camera as it was grabbed by a lurking octopus:

It's amazing to see the octopus's suckered arm shoot out from a reef and grab at the diver, and to see the octopus enjoying a ride on the blunt side of the diver's spear a little later. But for me, as someone who spends his days studying landsnails, it really set me to thinking about the remarkable diversity of form in the phylum Mollusca.

This series has focused on the other great animal phylum, the Arthropoda, and with good reason. Most animals are arthropods. But that group has achieved its dominance by finding a good basic body plan, an exoskeleton and set of jointed limbs, and making a million variations on the theme. By comparison, evolution has molded the soft mollusc body into thousands of forms. Cephalopods like the Octopus maorum featured above are perhaps the most amazing result. They are intelligent, free swimming predators with three hearts and amazing powers of disguise. Which is why I still find it amazing that cephalopods likely evolved from snail-like ancestors.

I really shouldn't be so surprised. There are plenty of snails around today that cast off that group's reputation for a sedentary lifestyle to swim the seas as predators. One example that might be familiar to readers is the violet snail, Janthina sp., whose pretty purple shells are occasionally washed up on New Zealand beaches. The violet snail can't actively swim as an adult, instead it builds a raft of air bubbles trapped in chitin and floats on the surface where it eats swimming jellyfish.

Violet snails shell from Flickr user quadprop and washed up animal with raft from wikipedian Rez242

The violet snails are pretty cool, but they aren't a massive divergence from the gastropod body plan. The snails that used to be known as pteropods are much more radically adapted to swimming. These snails are now recognised as two distinct groups, the "sea butterflies" (Thecosomata) which have retained their shells and the "sea angels" (Gymnosomata) which have lost them. As you might have guessed form their names, both of these groups have developed "wings" (derived from the foot muscle) they use to flap their way through the water column.

Sea angel from USGS and sea butterfly from NOAA

There is one group of swimming snails that are even more stunning than the sea angels and the sea butterflies. The nudibranchs (commonly referred to as "sea slugs") are pretty weird bunch of gastropods to start with. They come in a bewildering range of colours and some of them are even solar powered and there are a couple of species that have become adapted to swimming, or at least floating, on the ocean surface. Two species from the family Glaucidae, Glaucus atlanticus and Glaucilla marginata have developed swim bladders and long limb like protuberances that make the look, to me at least, a little like fish:

Glaucus atlanticus licensed CC 2.0 by flickr user tarotastic

Labels: cephalopods, environment and ecology, molluscs, octopus, photos, sci-blogs, snails, sunday spinelessness

We are starting to get that feeling in Dunedin, the days are getting shorter and cooler, and we can't enjoy a sunny weekend without wondering how long it will be until we see another one. So, to cheer me up, let's use this post to celebrate a group of very summery insects, the hover-flies (family Syrphidae) .

Hover-flies rank alongside bees, both honey and bumble, as the most frequent visitors to garden flowers during summer. Thankfully for me, hover-flies don't limit themselves to well tended gardens, they are just as likely to brighten up weed infested patches:

Plenty of other flies can hover, but hover-flies make an art of it. You'll often see them suspended above a flower, their wings beating to fast to see and their heads completely motionless. As this stunning photo from wikipedia user Fir002 (whose other photos can seen here) shows, hover-flies can do all sorts of things in mid air:

Labels: diptera, environment and ecology, hover-fly, photos, sci-blogs, sunday spinelessness, Syrphidae

I think invertebrates are important. The 95% of animal species that don’t have a backbone are not simply the base of the animal kingdom’s pyramid, they are the little creatures that run the world. A third of the planet’s food production relies on honey bees, collembola and corpse-feeding insects turn dead tissue into living tissue and coral reefs can turn the nutrient-poor tropical seas into submarine rainforests. There are even a couple of invertebrate animals that have won the Nobel Prize.

Drosophila melanogaster has probably taught us more about genetics than any other animal on earth. In the wild D. melanogaster larvae develop on rotting fruit so, just like the flesh-flies that were featured here a couple of weeks ago, they are faced with the problem of having to complete their entire developmental program in the short period of time the fruit they are born in is a viable food source. Thanks to these environmental constraints, D. melanogaster has a very short life cycle. Under optimal conditions they can go from egg to adult in a week. This remarkable developmental haste means drosophilists can run genetic experiments that cover many generations in a few months, and they can run many replicates of these experiments because each of them takes up about this much space:

Drosophila has been kept in laboratories since the the turn of the 20th Century but T.H. Morgan was the first person to put Drosophila at the forefront of genetic research. Morgan was an embryologist by training and, like a lot of embryologists then and now, he became interested in a school of evolutionary thought called mutationism. As the name suggests, the mutationists argued that one-off mutations were the creative engine of evolution, relegating natural selection to weeding out maladaptive mutants. In order to test the creative power of mutation Morgan grew up generation after generation of Drosophila and bombarded them with anything he thought might mutate them; radium, salts, sugars, acids, bases and even centrifugal force. Two years of this mutational bombardment got Morgan nowhere, he could induce changes in his flies but none that would be stably passed on. In 1910 he found a single white eyed male.

There is a story, which I can't find repeated by reliable sources, that holds that Morgan took the first white eyed male home with him in jar and slept with the jar next to his bed that night. I don't know if that story is true but that one fly does have a treasured place in the history of genetics. By crossing it to normal eyed (what geneticists call "wild type") females he was able to show that the genetic factor that made the fly's eyes white was part of the sex determining chromosome. For the first time a gene had been shown to be reside on a chromosome. A few years later he showed that multiple genes are arranged in linear fashion along chromosomes by demonstrating crossing over between the white eye gene and another called rudimentary. At Otago second year geneticists repeat Morgan's experiments, so this picture, sorting flies under a binocular microscope, will be familiar to anyone whose been through the program. (it will probably also bring back memories of escaped flies and a whiff of the (dilute) ether used to knock the files out...)

Morgan was awarded the Nobel Prize in 1933, in 1948 Drosophila research got another Nobel, this time to Hermam Muller for showing X-ray radiation could induce mutations. Geneticists have continued to use Drosophila as a model organism, perhaps most usefully in untangling the genetic interactions that underly the development process. In 1980 Christiane Nüsslein-Volhard and Eric Wieschaus presented the results of a mutational screen; that is, they mutated Drosophila stocks at random and recorded the developmental phenotypes that resulted. Nüsslein-Volhard and Wieschaus identified 15 genes involved with the very early stages of development. In quick time Drosophilists mapped that those genes to chromosomes and worked out how their products combined to pattern a developing embryo. Nüsslein-Volhard and Wieschaus' work laid the ground work for one of the most staggering findings of modern biology, almost all the genes that help shape the Drosophila embryo have counterparts in the human genome that play similar roles in our development. An insect can be a useful model for human development and disease genetics. Nüsslein-Volhard and Wieschaus were awarded the Nobel Prize in 1995, the third Nobel for work on Drosophila.

A big thanks to Sarah Morgan, one of Otago's fly pushers, for the photos that illustrate this post. Sarah's off to the US of A this week to show off her research at The Big Drosophila Meeting in Washington DC so she will probably have some less historical Drosophila science to talk about in the next little while...

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Nüsslein-Volhard C, & Wieschaus E. (1980) Mutations affecting segment number and polarity in Drosophila. Nature, 287(5785), 795-801. PMID: 6776413

Rubin GM, & Lewis EB. (2000) A brief history of Drosophila's contributions to genome research. Science, 287(5461), 2216-8. PMID: 10731135

Labels: diptera, drosophila, environment and ecology, genetics, might interest someone, photos, sci-blogs, sunday spinelessness