I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics ...
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 ...
Sometimes when you go digging through the databases, you find unexpected things. When I was researching the previous posts on insulin structure and insulin evolution, I found something curious indeed. Human insulin, colored by rainbow. Image from the Molecule World iPad app by Digital World Biology. I wanted to find ...
One of the places that I've always wanted to visit in Portland, OR, is Powell's City of Books. Powell's is the kind of bookstore that people in Seattle discuss in the same reverent tones that they use when they're describing Cody's in Berkeley or City Light in San Francisco. It's ...
Yes, yes, I know Darwin Day was Februrary 12th. Nevertheless, the Alliance for Science is sponsoring an essay contest in Darwin's honor and, if you're a high school student you can still celebrate by writing an essay. And if you're a high school teacher, and your student wins, you win ...
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, Panic in Level 4: Cannibals, Killer Viruses, and Other Journeys to the Edge of Science but I ...
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we ...
Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences ...
As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration. Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue our analysis ...
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance ...
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck ...
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things. In this installment, we found that humans have practically an entire mitochondrial genome stuck ...
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more ...
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment. At first it appears ...
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 ...
This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid. If I gave you the amino acid sequence of this protein, or the nucleotide sequence of this nucleic acid, what is the probability of finding a similar sequence in a different ...
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is ...
Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®) Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds. One protein structure is from a strain ...
You can get a jump on the Darwin Day festivities. Once again the Alliance for Science is sponsoring an essay contest for Darwin Day. If you download their suggestions for good essay writing, you can get your essay done over winter break and have a good crack at winning on ...
In my last post, I wrote about insulin and interesting features of the insulin structure. Some of the things I learned were really surprising. For example, I was surprised to learn how similar pig and human insulin are. I hadn't considered this before, but this made me ...
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 ...
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 ...
Not content with his recent exploits in human experimentation and cavorting with Plosites in San Francisco, Professor Steve Steve jetted across the country once again, last week, hitting both both Blacksburg, VA and Seattle, WA, and creating pandemonium wherever he went. And raising the question - how does he get ...
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 ...
Thanks to Steven Colbert you can hear about DNA directly from Dr. Spencer Wells from the National Genographic Project. I read about this video in the GenomeWeb Daily Scan and had to check it out. Who would have thought scientists could be so funny? Watch it quick! There was a ...
Evolution! Wow! A jolt of electricity went down my spine. I feel like Harry Potter saying " Voldemort." Apparently, in biomedical journals, drug resistance and other phenomena can " emerge," " arise," or " spread." It can " appear", " develop", " become common", or " be acquired." As long ...
tags: A few months ago, I wrote about a contest, sponsored by the Alliance for Science, in celebration of Darwin Day. High school students were asked to write an essay on the topic: " Why would you want your doctor to have studied evolution?" The winners have been announced and ...
Have you ever wondered if creationism was intelligently designed? Most of my colleagues tend to dismiss creationism as generally nutty and not worth bothering about. But, every now and then, we did get the odd situation with a few students who disagree or state legislatures that get a little confused ...
Five Bulgarian nurses and a Palestinian doctor ( dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children ...
By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes. tags: Because of these changes ...
An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment. I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your ...
If we asked any biologist to pick the five most important techniques in biology, that list would certainly include PCR. PCR stands for Polymerase Chain Reaction. It's used everywhere. We use it to amplify DNA for cloning, we use it for diagnostic tests, for DNA sequencing, for identifying pathogens, for ...
The first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound-inducible genes ...
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as ...
Let the experiment begin. We're experimenting with HIV in this series. And yes, you can try this at home! If you want to see where we've been and get an idea where we're going, here are the links. Part I. Meet HIV and learn how we're going to use it ...
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the ...
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out. All of the sequences in the image below (except for ...
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 ...
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper ...
Razib inspired me to share some of the story behind why white people are considered derivatives. No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1). These zebra fish had an unusual golden color that turned out ...
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 ...
