Friday, March 9, 2012

A giant insect saved from extinction

A giant insect saved from extinction:
I’m quite familiar with Lord Howe Island, for I’ve published on its bird fauna (garnered from the literature; I haven’t been lucky enough to visit there), and wrote a “news and views” on its flora for Current Biology, a piece that I described on this website (see the link for the geography and location of the island).  It turns out that Lord Howe was once home to a bizarre variety of stick insect, the species Dryococelis australis, the heaviest flightless insect in the world.  Here it is:

The Lord Howe stick insect. Photo by Rod Morris/www.rodmorris.co.nz
This beast, called “the Lord Howe stick insect,” can be nearly six inches long and weigh up to 25 grams—about 0.9 ounces. It’s in the order Phasmatodea (“phasmids”), which includes stick insects, walking sticks, and all manner of bizarre species (see the Wikipedia page for some cool phasmid photos).

Photo by Matthew Bulbert/The Australian Museum
At any rate, Robert Krulwich reported yesterday at KrulwichWonders, his website at National Public Radio, about the near-extinction and rehabilitation of this insect. It was once common on the isolated Lord Howe island, but was completely wiped out within two years when a British ship ran aground in 1918 and accidentally released rats, who made a handy meal of these large, tasty, and defenseless insects (their other name is “tree lobsters”).
For 83 years the species was thought to be extinct, until in 2001 some hardy climbers scaled a nearby spire of rock, the famous “Ball’s pyramid,” a spire of naked rock about 12 miles SE of Lord Howe. It, like Lord Howe itself, is of volcanic origin:

Credit: Stephanie d'Otreppe / NPR
The climbers spotted insect droppings and went back at night, finding at least one living insect.  The obvious thing to do was breed them in captivity.



At any rate, go read Krulwich’s description of how a few breeding pairs of insects (the species was down to an estimated 30 individuals) were taken to Australia for breeding, and how they’re now ready for re-release on Lord Howe. First, though, the rats have to be extirpated. And. . . the residents of the island have to want the insects back; curiously, a few are balking.
Be sure to see the awesome Vimeo video (also on Krulwisch’s page) of one of these insects hatching. Don’t miss this one! It’s from the Melbourne Zoo, where the phasmids are being reared, and it’s the first video of this species actually hatching (the eggs incubate for six months).
h/t: Rev. El Mundo

Tuesday, March 6, 2012

What Evolutionary Biologists Do

What Evolutionary Biologists Do:
This meme has been going around. Recently someone did What Scientists Do, so…it’s time for evolutionary biology. Obviously YMMV if you’re not an evohacker, but even you field biologists end up coming to us in the end anyway when you have to turn your pet hypothesis into a statistically testable model. (Insert maniacal laughter.)
HT: What I do generator

Thursday, March 1, 2012

Should a doctor fire an anti-vax patient?

Should a doctor fire an anti-vax patient?:



The anti-vaccination movement continues to grow, despite the retraction and thorough discrediting of the 1998 scientific study that spurred much of its growth. The stubborn persistence of anti-vaxxers shows how difficult it is to dispel misinformation once that information is out there, even after dozens of new studies and millions of dollars in research that demonstrate that vaccines are safe.



One of the most dangerous trends is the growing number of parents who refuse to vaccinate their kids, or who choose "alternative" vaccine schedules, such as the one promoted aggressively by Robert Sears (who goes by "Dr. Bob"). Sears appears to have simply invented this alternative schedule without bothering to conduct any scientific studies, in part to promote sales of his 2007 book, The Vaccine Book: Making the Right Decision for Your Child. Vaccine expert Dr. Paul Offit explained, in a 2009 article in the journal Pediatrics, why Dr. Sears' schedule was a very poor choice for children and for the public health. After thoroughly dismantling Sears' anti-science positions, Offit concludes, "Sears has a poor grasp of the scientific method." That's an understatement.


Other doctors, perhaps jealous of all the attention that Sears has gained through his anti-vaccine writings and television appearances, have created their own alternative vaccine schedules. One of them, Donald Miller, even goes so far as to say that vaccines cause childhood cancer, despite the complete lack of evidence for this wild claim. Somehow Sears, Miller, and others like them have managed to convince many parents that their children don't need vaccines.



In response to parents who don't want to vaccinate, many of whom show up with Dr. Bob's schedule in hand, pediatricians have struggled to find an effective response. Parents can be utterly convinced by the misinformation they find on the Internet, which is all too easy to find. (For example, Googling "vaccine" brings up the National Vaccine Information Center, a hotbed of anti-vaccine propaganda and pseudoscience, on the first page of hits.) By the time parents arrive with their babies for the first vaccine, convincing them to change their minds can be nearly impossible.



Perhaps in frustration, doctors have started to "fire" their patients if they refuse to vaccinate. As reported by Shirley Wang in The Wall St. Journal last week, 20-30% of doctors in two different surveys, in Connecticut and the Midwest, reported having to kick patients out of their practices because of vaccine refusal. These numbers have roughly doubled over the past ten years, according to the American Academy of Pediatrics.


Is firing a patient the right thing to do? It's a difficult question. On the one hand, doctors should do everything they can to make sure kids are vaccinated. If a doctor kicks a parent out, that parent may find another doctor who doesn't insist on vaccinating children, which ultimately harms the children. Doctors have to spend more time educating parents about the tremendous benefit of vaccines, about the very strong evidence (based on tens of millions of doses) for vaccine safety, and about the frightening consequences of infection with meningitis, hepatitis, measles, polio, and other vaccine-preventable diseases.

On the other hand, unvaccinated children bring diseases into the pediatrician's office, where they can spread them to other children. Some of these other children are too young to be vaccinated, and childhood infections can be extremely dangerous, even fatal, in the very young. From this perspective, "firing" a patient might be the only responsible action, after first trying to convince the parents to vaccinate. I know that I wouldn't want to bring my child to a doctor's office where unvaccinated children were in the same room.



I understand how nervous a parent can be about vaccinations. I will never forget the day my older daughter got her first vaccine: the needle looked huge compared to her tiny leg, and she screamed when the doctor gave her the shot. But she was fine a few minutes later, and she'll be protected against a dangerous infection for her entire life. Vaccines have been so successful at eliminating childhood infections that parents no longer see these infections as a threat. Ironically, the very success of vaccines has allowed the anti-vaccine movement to sway so many people.



Doctors may have to keep firing the parents of their young patients, but I hope they'll first make every effort to educate them. They need to explain that vaccines do not cause autism, nor do the ingredients in vaccines, and that scientific studies involving hundreds of thousands of patients support these conclusions. They should also explain that many of the anti-vaccination claims on the Internet started when Andrew Wakefield published one small study of 12 patients, now retracted, claiming a link between the MMR vaccine and autism. Investigations later revealed that he was paid by lawyers to recruit patients for a lawsuit against vaccine makers, that he didn't reveal these payments to his co-authors or the patients, and that he manipulated the data. Since then, the anti-vaccine movement has exploded and we've experienced multiple outbreaks of measles, mumps, and other illnesses linked directly to unvaccinated children.



Doctors interviewed by the Wall St. Journal reported that they had convinced at least some parents to follow the recommended vaccine schedule. Perhaps that's the best we can hope for. If we're going to avoid a return to the era when children routinely died from infections, we must keep trying.

Friday, February 17, 2012

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report:
by Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake, on behalf of the Gene Ontology Consortium
A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the “ortholog conjecture” (or, more properly, the “ortholog functional conservation hypothesis”). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis.

Friday, February 10, 2012

02/08/12 PHD comic: 'Naming Themes'

02/08/12 PHD comic: 'Naming Themes':


Piled Higher
& Deeper
by Jorge
Cham


www.phdcomics.com

Click on the title below to read the comic

title:
"Naming Themes" - originally published
2/8/2012
For the latest news in PHD Comics, CLICK HERE!



Monday, January 30, 2012

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus [RESEARCH]

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus [RESEARCH]:
Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.