Molecular Biology
pharyngula | May 20, 2010We're hearing the first stirrings of a big story: Craig Venter may have created the first organism with an artificially synthesized genome. Conceptually, building a strand of DNA and inserting it into a cell stripped of its genome is completely unsurprising — of course it will work, a cell is just chemistry — but it is a huge technical accomplishment.
Carl Zimmer has more background. I want to see the paper.
pharyngula | May 19, 2010
The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn't junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is…
pharyngula | May 14, 2010
Only ours are methodologically valid. It's a common creationist tactic to fling around big numbers to 'disprove' evolution: for instance, I've had this mysterious Borel's Law (that anything with odds worse than 1 in 1050 can never happen) thrown in my face many times, followed by the declaration that the odds of the simplest organism forming by chance are 1 in 10340,000,000. It's complete nonsense, of course — their calculations all ignore the reality of the actual events, assuming that everything must form spontaneously and all at once, which is exactly the opposite of how probability plays…
grrlscientist | April 22, 2010tags: Glowing Life in an Underwater World, marine biology, bioluminescence, luciferase, luciferin, green fluorescent protein, eye-in-the-sea cam, ethology, evolution, Edith Widder, TEDTalks, streaming video
Some 80 to 90 percent of undersea creatures make light -- and we know very little about how or why. Bioluminescence expert Edith Widder explores this glowing, sparkling, luminous world, sharing glorious images and insight into the unseen depths (and brights) of the ocean.
TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's…
grrlscientist | April 19, 2010tags: evolutionary biology, evolutionary biogeography, molecular biology, medicine, ectoparasite, orificial hirudiniasis, mucosal leech infestation, hirudinoids, leech, Tyrannobdella rex, public health, zoology, PLoS ONE, anatomy, phylogenetic analysis, taxonomy, researchblogging.org,peer-reviewed research, journal club
Figure 1. Mucosally invasive hirudinoid leeches. Known from a wide variety of anatomical sites including eyes (A) as in this case involving Dinobdella ferox (B), mucosal leech species, as in a case involving Myxobdella annandalei (C), more frequently feed from the…
grrlscientist | April 8, 2010tags: evolutionary biology, behavioral ecology, molecular ecology, personality, novelty seeking, exploratory behavior, dopamine receptor, dopamine receptor D4 gene, DRD4 gene polymorphism, ornithology, birds, Great Tit, Parus major, researchblogging.org,peer-reviewed research, peer-reviewed paper
Bold or cautious? Individuals with a particular gene variant are very curious --
but only in some populations.
Image: Henk Dikkers.
Research suggests that personality variations are heritable in humans and other animal species, and there are many hypotheses as to why differences in personality…
grrlscientist | March 29, 2010tags: evolution, evolutionary biology, behavioral ecology, animal behavior, molecular ecology, parental care, mating systems, monogamy, sexual selection, frogs, poison dart frogs, Dendrobatidae, Ranitomeya, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club
Peruvian mimic poison frog, Ranitomeya imitator.
Image: Jason Brown [larger view]
To know the breeding system is to know the genetic architecture of a species.
To know the evolution of a breeding system is to know how evolution works ..
~ Lewis & Crowe, Evolution (1955)
Genetic tests have revealed the…
neurophilosophy | March 17, 2010SNAKES have a unique sensory system for detecting infrared radiation, with which they can visualize temperature changes within their immediate environment. Using this special sense, they can image the body heat radiating from warm-blooded animals nearby. This enables them to track their prey quickly and with great accuracy, even in the dark, and to target the most vulnerable parts of the prey's body when they strike. It also warns them of the presence of predators, and may be used to find appropriate locations for building dens.
Infrared detection is known to be mediated by a specialized…
pharyngula | March 16, 2010
First, you start with a lizard.
Really, I'm not joking. Snakes didn't just appear out of nowhere, nor was there simply some massive cosmic zot of a mutation in some primordial legged ancestor that turned their progeny into slithery limbless serpents. One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.…
edyong | March 14, 2010Take a whiff of mustard or wasabi and you'll be hit with a familiar burning sensation. That's the result of chemicals in these pungent foods hitting a protein called TRPA1, a molecular alarm that warns us about irritating substances. The same protein does a similar job in other animals, but rattlesnakes and vipers have put their version of TRPA1 to a more impressive and murderous purpose. They use it to sense the body heat of their prey.
Pit vipers are famed for their ability to detect the infrared radiation given off by warm-blooded prey, and none more so than the western diamondback…
grrlscientist | March 12, 2010tags: evolution, evolutionary biology, gynandromorph, bilateral gynandromorph bird, half-sider, mixed-sex chimaera, sex determination, molecular biology, genetics, developmental biology, endocrinology, birds, chicken, Gallus gallus, ornithology, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club
Half-sider.
Almost exactly one year ago, hundreds of American birders
were thrilled by sightings and photographs of this remarkable
Northern Cardinal, or Redbird, Cardinalis cardinalis,
photographed in Warrenton, VA.
Image: DW Maiden, 2 March 2009.
I'll never forget…
grrlscientist | March 10, 2010tags: evolution, evolutionary biology, ancient DNA, aDNA, molecular biology, molecular ecology, archaeology, paleontology, fossil eggshell, extinct birds, giant moa, Dinornis robustus, elephant birds, Aepyornis maximus, Mullerornis, Thunderbirds, Genyornis, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club
Elephant bird, Aepyornis maximus, egg
compared to a human hand with a hummingbird egg balanced on a fingertip.
To conduct my avian research, I've isolated and sequenced DNA from a variety of specimens, such as blood, muscle, skin and a variety of internal…
grrlscientist | March 2, 2010tags: handheld thermal cycler, LavaAmp, PCR, Polymerase Chain Reaction, DNA, molecular biology, Unreasonable Insitute, DIY, technology, Guido Núñez-Mujica, streaming video
Millions of people in the Global South suffer from neglected diseases, many of which could be treated, even cured, if they were detected early enough. But reliable, low cost diagnosis hasn't been available, as drug companies have no incentive to invest in the diseases of the poor. New pandemics can go undetected until they have spread out of control, like HIV, and treatable ailments can cripple impoverished communities…
cagapakis | February 18, 2010Almost every living thing shares an identical genetic code, with three nucleic acids in an RNA sequence coding for a single amino acid in the translated protein sequence. While there are 64 three-letter RNA sequences, there are only 20 amino acids and degeneracy in the code allows some amino acids to be coded by multiple codons. Chemists and synthetic biologists in the past few years have been working to expand this genetic code, with unnatural nucleotides that can be incorporated into DNA and RNA sequences and unnatural amino acids that can expand the chemical functionality of proteins.…
edyong | February 16, 2010All of our cells are staffed by armies of executioners. They are usually restrained but when unleashed, they can set off a fatal chain reaction that kills the cell. This suicide squad does away with billions of cells every day. It helps to balance the production of new cells with the loss of old ones, to sculpt growing tissues and to destroy potential cancer cells.
But a new study suggests that the executioners aren't always lethal. In fact, they're essential for life. Through the unorthodox method of damaging our DNA, they can actually activate important genes. This technique for switching…
grrlscientist | February 8, 2010tags: evolutionary biology, molecular biology, Thoroughbred race horses, horses, aerobic capacity, muscle development, myostatin, MSTN, myostatin-suppressing C variant, myostatin-suppressing T variant, Horse Genome Project, Equinome, researchblogging.org, peer-reviewed research, peer-reviewed paper
Emerging from the mist is Rachel Alexandra, a champion American Thoroughbred who excels at winning both long and short distance races.
Image: Rob Carr, 2009, Associated Press [larger view]
If you've worked at or been around a racetrack very much, as I have, you'll quickly realize that everyone…
grrlscientist | January 26, 2010tags: evolutionary biology, behavioral ecology, biochemistry, biophysics, magnetoreception, photoreceptor, cryptochromes, geomagnetic fields, butterflies, Monarch Butterfly, Danaus plexippus, birds, migration, signal transduction, researchblogging.org,peer-reviewed research, peer-reviewed paper
Every autumn, millions of monarch butterflies, Danaus plexippus, each weighing less than one gram (one US penny weighs 2.5 grams), migrate nearly 4000 kilometers (3000 miles) between their summer breeding grounds in the United States and their wintering areas either in southern California or in the…
grrlscientist | January 21, 2010tags: synthetic biology, molecular biology, genetics,Bacteria make Mexican Waves, A synchronized quorum of genetic clocks, bacteria, fluorescence,biological clock, NPG, peer-reviewed research, NATURE, 10.1038/nature08753, streaming video
By synchronizing our clocks, we can coordinate our activities with people around the world. Now, scientists have genetically engineered bacteria to synchronize their molecular timekeepers, creating the stunning fluorescent waves that you see in this video (this video shows new research published today in NATURE).
Read the original research here: http://dx.…
grrlscientist | January 7, 2010tags: evolutionary biology, immunology, immune response, antibodies, parasite, avian pox virus, Poxvirus avium, nest fly, Philornis downsi, birds, ornithology, Darwin's Finches, Medium Ground Finch, Geospiza fortis, Ecuador, Galapagos Islands, researchblogging.org,peer-reviewed research, peer-reviewed paper
A male Medium Ground Finch, Geospiza fortis, sits on a tree branch in Ecuador's Galapagos Islands.
Image: Jen Koop.
People often view the Hawaiian islands as a tropical paradise, the ideal vacation site, but you wouldn't agree with this assessment if you happen to be a bird. According…
grrlscientist | January 4, 2010tags: researchblogging.org, new species, insects, American cockroach, Periplaneta americana, DNA barcoding, Brenda Tan, Matt Cost, Mark Stoeckle, Rockefeller University, American Museum of Natural History, AMNH
Mystery cockroach found in NYC apartment.
Image: Brenda Tan and Matt Cost.
Moving overseas has been a challenge, but worst of all for me has been the fact that my writing has suffered. I still read scientific papers and science news stories, but have been unable to find the time necessary to write these stories for you. Hopefully, my life is returning to some semblance of…