Evolution

This month's cover of The Scientist has a mistake that makes me cringe. Can you spot what's wrong?
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And they call themselves "The Scientist" humph!Read more
An NSF post on Twitter this morning described an interesting study from the University of Pennsylanvia and Cornell University, that found that some people who call themselves "African Americans" may only be 1% West African, according to their DNA. The University of Pennsylvania press release contains other interesting findings as well. 365 individuals were studied and 300,000 genetic markers were examined. Some of the findings were:
  • If you're African American, the genes most likely to have an African origin are those on your
  • ... Read more
Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, ... Read more
Two interesting events are happening, Monday night, Oct. 27th. At the UW: Josh Rosenau from the National Center for Science Education will be speaking at 6 pm about Creationist attacks on science education. (Josh is also a Science Blogger). In Ravenna, at Third Place Pub: Ted White from the Seattle Biomedical Research Institute will be talking at 7 pm about infectious disease. If you're interested hearing Josh, contact ... Read more
The Galápagos islands rank high on my list of places that I really, really, really want to visit. But for many reasons, it's always looked like a trip to the Galápagos would be at least a decade or two away. Now, I'll be able to go in January and so will all of you. Thanks to the University of Cincinnati, we'll be able to follow in Darwin's historic steps, and experience some of his amazing journey. The only difference is we'll do this trip as avatars in Second Life. The University is stocking this ... Read more
One of the holy grails of modern medicine is the development of a vaccine against HIV, the virus that causes AIDs. An obstacle to attaining this goal has been the difficulty in stimulating the immune system to make it produce the right kinds of antibodies. A recent finding in Science describes a gene that controls production of these antibodies and may provide insights to the development of an effective vaccine. (1). Antibodies are special kinds of proteins that bind to things, often very tightly. If they bind to the right molecules, they can prevent viruses from infecting ... Read more
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes. Now, in one of our last projects we are determining where ... Read more
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find in the sequences of 16S ribosomal RNA are related antibiotic resistance. This is related to our ... Read more
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
  1. Build a data set
  2. Align the sequences
  3. Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we' ... Read more
If you look below the fold, you can see two molecules locked in a tight embrace. These molecules or their closely related cousins can be found in any cell because their ability to evolve is slowed by their need to interact with each other in the right way. In an earlier post, I asked: Who are they?
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One partner is a small bit of ... Read more

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