biology
evolgen | March 7, 2008Identifying and cataloging biological diversity is challenging. One way to do go about IDing all the life forms is to sequence a known region of the genome in all those species. This is known as DNA barcoding. An article in PNAS reports on the DNA sequence of a gene found useful for DNA barcoding in plants. In a review of the paper, the following table is presented:
DNA Barcoding
Genomics
Number of species
All (or most)
One (or few)
Number of gene regions
One (or few)
All (or most)
The gist: DNA barcoding results in the sequencing of a single gene in a bunch of species, while genome…
bioephemera | March 6, 2008Zooillogix posted this video of an elephant that paints "realistic paintings of other elephants:"
It's a fluff piece, granted, but it gestures towards credibility by bringing in an "art expert" (and, I'm guessing, cutting 98% of her comments). The genial narrator, anticipating our astonishment that an elephant could learn to paint portraits, reassures us that it is indeed possible, and that "what makes it possible is the trunk." Uh, no. The trunk is what makes it possible for the elephant to grasp a human-style brush and execute fine motor movements. The brain is what makes any artist an…
revere | March 5, 2008Every once in a while we run across introductory presentations of basic bird flu-ology we think are particularly good. This is one. If you follow this area you won't learn anything new, but I think you'll be impressed by how concise and well chosen this material is. I have a few quibbles with the material but on the whole it is accurate and informative. If you are new to the subject of flu science, this is a very quick and efficient starter kit. You can find more detailed explanations in a number of our posts (here, here, here, here, here):
revere | March 3, 2008Scienceblogs has a German cousin, Scienceblogs.de where I found this absolutely hilarious YouTube music video, "Scientists for a better PCR." Yes, it's an advert for a PCR device called a thermocycler but it's incredibly funny -- if you have that kind of sense of humor.
PCR is a technique called polymerase chain reaction. It can take pre-specified tiny bits of DNA or RNA and grow them up into huge amounts. That's how they can do forensic DNA identification from the small amounts in spit or semen stains. They pre-specify parts of DNA that are unique to an individual and amplify it up by PCR.…
tqa | March 3, 2008
In Friday's picture quiz, I posted a picture that I took that contained two Hawaiian Monk seals (Monachus schauinslandi), and asked you to take a guess at what percent of the total population of the species appears in the picture. As David noted, if you're asking that sort of question, the answer isn't likely to be good. It certainly isn't good in this case.
The Hawaiian Monk Seal has been on the Endangered Species List since 1976. A five-year assessment of the seal's current situation was concluded in August, and examined whether or not the species has met the three biological factors…
aardvarchaeology | March 3, 2008I read Donald Prothero's Evolution for the palaeontology and general evolutionary zoology, and I was not disappointed. The book is up-to-date, well-argued, well-illustrated and aimed at the educated lay reader. Stylistically, it's not bad, though poorly copy-edited, and I did find the author's use of exclamation marks and italics a little overdone. Nevertheless: this is good solid pop-sci, very enjoyable.
But it's not just a book about evolutionary zoology. It's also a salvo in a war that's being fought on that far-off continent, Northern America. In this respect it reminded me of another…
revere | February 29, 2008Flying like a bat out of hell is supposed to mean sudden, fast and wild.But how do bats fly? It turns out they have some unique tricks:
Bats have a clever aerodynamic trick to make flying easier, researchers have found: the sharp edge at the front of their wings cuts through the air in such a way as to create a vortex on top of the wing, producing up to 40% of the lift needed to stay aloft.
"It explains how these animals are able to fly at very slow speed," says Anders Hedenström from Lund University in Sweden, who led the research -- published in Science 1 -- that showed the effect with a…
tqa | February 29, 2008
I took the picture below at Ka'ena Point, Oahu in January of 2006. In this picture, there are two Hawaiian Monk Seals. (They can be hard to spot, so I've marked the two animals in a second version of the picture below the fold.) Here's the quiz question that goes with this image: without recourse to Google, estimate the percentage of the total population of the species that can be seen in this one picture.
(Click on the pictures to view larger versions.)
terrasig | February 29, 2008Bisphenol A (BPA) is currently one of the major lightning rods for controversy in consumer products and public health research. The compound is used in the manufacture of plastic bottles, polycarbonate (PC) in particular, as well as in the lining of many food and beverage cans. The compound has been recognized since the 1930s as having estrogenic activity but it appears to have developmental, carcinogenic, and neurotoxic effects at concentrations well below those at which it binds to the two forms of estrogen receptor.
Confused?
US governmental advisory committees can't even agree on BPA…
evolgen | February 28, 2008Poorly done and over clicked?
Rod Page has a post worth reading in which he's "deliberately critical" of the Encyclopedia of Life (EOL). You should be able to visit the EOL at that link. Only you can't, as of two days following the release. You see, they weren't able to handle the 11.5 million hits they received within the first few hours of going live. We're only left to wonder whether this thing will ever get off the ground.
tqa | February 28, 2008
On Tuesday, I posted a "can you identify this animal" quiz. I put a picture of an animal up, along with some information about it. The photograph was taken with the animal in captivity, at a location that was relatively near where the animal lived in the wild. The picture was not taken in Australia, and the DNA sequence that was superimposed over the image came from the animal in the picture.
Shawna was the first person to correctly identify both the species of the animal and the location where the picture was taken. The animal is a Brush-Tailed Rock Wallaby (Petrogale penicillata), and…
tqa | February 26, 2008
Here's a picture of an animal that I took (and played around with) a few years ago. The DNA sequence that's superimposed over the picture came from that individual, so you can probably use it to figure out what species you're looking at (if you're so inclined). You can click on the image for a higher resolution version. The animal in question was (obviously) in captivity when the picture was taken, but it has since been re-released into the wild. It was held within 10 miles of the place it was captured, and the picture was not taken in Australia. Can anyone guess where the picture was taken…
oracknows | February 26, 2008
...and this time it's a home invasion.
Abel Pharmboy at Terra Sig pointed me to this incident, which has all the markings of still more animal rights terrorism. This time, the attack occurred at the University of California Santa Cruz and involved a home invasion by masked intruders:
SANTA CRUZ - A UC Santa Cruz faculty member whose biomedical research using animals sheds light on the causes of breast cancer and neurological diseases was the target of an attack Sunday afternoon, reportedly by animal rights activists.
UCSC Chancellor George Blumenthal confirmed late Monday that an off-…
evolgen | February 26, 2008Jonathan Eisen is the new Academic Editor in Chief at PLoS Biology, and he's kicking it off with this editorial. In his editorial, Jonathan describes how he became an Open Access publishing advocate. The header of his article features a short biography with an interesting item:
Jonathan A. Eisen is Academic Editor-in-Chief at PLoS Biology. He is also at the University of California Davis Genome Center, with joint appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of…
moleculeoftheday | February 25, 2008Longtime readers will know I like big dye molecules.
Once you get to the size of a phthalocyanine - a little over 1 nm across in any dimension (one of those bonds is about 0.15nm) - weird stuff happens. This explains, in part, G-quadruplexes and liquid crystals,
A friend of mine that made phthalocyanines saw something neat once - you can see them making swirly patterns if you leave a vial containing a solution of them on the bench for awhile, shake it up, it goes away, and it comes back later.
Once you make a molecule about this big (even a little smaller), things get a little weird.
Please…
evolgen | February 24, 2008I have an intuition, backed up by absolutely no evidence, that my particular area of interest (evolutionary genetics) has more faculty blogging about stuff related to their research than other fields. This is most likely the result of my interest in those blogs, and, hence, my increased awareness of them compared to blogs of faculty in other research areas. From a quick scan of my blogroll and the feeds I subscribe to, here's a list of research faculty who blog about evolutionary genetics:
TR Gregory
Rod Page
John Hawks
John Logsdon
Jonathan Eisen
Larry Moran
That's not a lot of blogs, but…
moleculeoftheday | February 22, 2008All of life links up biomolecules effortlessly, from the august readers of this blog, to the humble bacteria that colonize the half-eaten food on their desks. It makes it frustrating for scientists who are trying to synthesize them. We have methods, but they're inefficient. (It gets even worse for DNA.).
It gets even worse when you try and work on a biomolecule you already have in water. Most of our chemical tricks rely on us avoiding water like the plague - a lot of what we use will react with it. It doesn't help matters that a biological reaction might have 10 million times more water…
grrlscientist | February 22, 2008tags: Charles Darwin, crabs, crustaceans, University of Oxford, Oxford Museum of Natural History, online database
Fiddler crabs are easily recognised by their distinctive asymmetric claws. This specimen was captured in May 1835 when the Beagle arrived in Mauritius.
Image: Oxford University Museum of Natural History [larger view].
The University of Oxford Museum of Natural History has electronically catalogued Charles Darwin's crabs that had been collected by the famous naturalist while he was making his voyage around the world on the HMS Beagle from 1831 to 1836.
These crustaceans were…
revere | February 21, 2008A notice from ProMed yesterday alerted many of us to a new published report [subscription firewall] about H5N1 influenza detection in an arthropod species in the vicinity of an infected poultry farm. The arthropods were mosquitoes (Culex tritaeniorhynchus) in Thailand. Two years ago a similar report implicated blowflies (Calliphora nigribarbis and Aldrichina grahami) near some infected farms in Kyoto, Japan. Both papers suggested using arthropods near infected farms as surveillance tools. But both, especially the Japanese paper, raised the open question whether arthropods might play a part in…
revere | February 20, 2008A paper published on Monday in the Proceedings of the National Academy of Sciences (PNAS) extends the work of a group of glycobiologists at MIT on unravelling why some flu virus likes bird cells and others like human cells. Glycobiology is the science that investigates the sugar studded proteins on the outside of cells. Like a suit of clothes, a cell's glycoprotein cover plays important functions in protecting the cell, identifying it and as a signal to interact with things outside of itself, such as hormones or immune cells. But other organisms have learned to use the same signals and can…