One time, I suggested in a list-serve that science teachers make more use of primary scientific literature. Naturally, I learned all the reasons why teachers don't do this-lack of access being one of the biggies- but I also learned something surprising. One teacher wrote that she re-writes a lot of ...
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 teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced. I like this story. One of my ...
iGEM is all about synthetic biology, kids. It's the annual International Genetically Engineered Machine competition. Each team in the IGEM competition has to make something using a kit of biological parts from the Registry of Standard Biological Parts. Teams of students use these parts to design, build, and operate biological ...
Last summer, I had the good fortune to attend a conference in Washington D.C. on Vision and Change in Undergraduate Biology education. There were lots of inspiring speeches, cool videos, and talks about building more student-centered classrooms and strategies for change. Surprisingly, many of the attendees seemed unaware that there ...
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 ...
Why should students blog about science? Don't they have enough to do already? Last Thursday night I participated in a panel discussion about science blogging (see the video) at ScienceOnline Seattle ( #scioSEA)(video) and mentioned that we have two students blogging for us at Bio-Link. A question I saw afterward ...
The Backstory: As it stands today,when one of the National Institutes of Health (NIH) provides the funding for a scientific research project, and those results are published, they must be made freely available to public, within a set period of time. The reasoning behind this requirement is that taxpayers funded ...
This summer, I had the good fortune to attend three (or was it four?) conferences on science education. One of the most inspirational conferences was one on Vision and Change in Biology Education. This conference was co-sponsored by the National Science Foundation and the AAAS. It was a call to ...
I've been reading quite a bit lately about Universities setting up virtual classrooms in Second Life, so when Bertalan Meskó from ScienceRoll invited me to come give a poster, I decided it was time to take the plunge. Besides, I'm going to be teaching an on-line bioinformatics course this spring ...
Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both ...
Are you curious about Second Life? Next week you can satisfy your curiosity and learn about the personal genomics frontier at the same time. Bertalan Meskó announced that Erin Davis (science writer) and Joyce Tung (human geneticist) from 23andMe will be giving a presentation next week in Second Life on ...
This morning I had a banana genome, an orange genome, two chicken genomes ( haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit ...
start all over again. MDRNA Inc., a Puget Sound area company formerly known as Nastech, announced on Monday that they'd be laying off 23 people including their president and chief business officer. This might not sound like a lot, but according to Joseph Tartakoff, from the Seattle PI, this brings ...
A long time ago, I saw a Star Trek episode where the crew encountered aliens who lived at a different frequency. I may have this backwards, but I think the aliens moved so quickly that no one knew they were there. And until problems struck, our heroes were happily oblivious ...
Many regions in the United States, and the world for that matter, are seeking to entice biotech companies to relocate. As Lorraine Ruff and David Gabrilska describe in their Genetic Engineering News Article, " Metrics for Economic Development," the exhibitors at meetings like BIO work hard to: ".. entice founders ...
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 ...
I read about this in Science and immediately had to check it out. Instant gratification on the internet is such a wonderful thing! The Ed Kravitz lab has made movies of fights and even put them on the web for your viewing pleasure. You can see the following fly fights ...
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 wonder about the ...
Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C. All of three reads were obtained by sequencing PCR ...
Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data ...
I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement. Today, the school sent all the faculty emails telling us to stay home if we're ...
Before mammals, before dinosaurs, before bacteria, or plants, there was something else; a protocell containing RNA. The Exploring Origins Project has excellent animations of protocells, a timeline of life's evolution, and best of all- fantastic animations of the RNA world. You can see how RNA folds, ribozymes (RNA that catalyzes ...
Over the summer, a few ScienceBloggers were pondering the question of why students disappear from science courses, never to return. James Hrynshyn wrote that we're teaching youngsters the wrong thing. Zuska boldy pointed out the things that many of us think but don't say out loud. Chad Orzel noted that ...
Although, I didn't believe it when I first saw it. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my eyes. Yet here is parallel DNA, with both strands oriented in the same direction, right here on your monitor. And ...
Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure. Yet here is, on the screen, parallel DNA ...
If you haven't seen these, check out Jake Young's collection of videos showing T cells getting infected by HIV. The best one is at the bottom of the post.
We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because ( quoting Jerry Garcia): Power is a scary thing ...
Science labs are not for all people. I've always enjoyed teaching lab courses, so some of you might find it strange that I agree with some of the comments from Steve Gimbel and fellow Sb'ers on the questionable benefits of laboratory courses in introductory physics. But you see, I wasn't ...
I wrote earlier about videos of lab protocols and the benefit these could bring to people who are trying to learn new techniques or perhaps troubleshoot their own. Unfortunately, I suspect that the people who would benefit the most from movies of others doing lab procedures correctly are those who ...
The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college ...
The 2009 Summer Research Experience for Undergraduates in Environmental Microbiology at UNLV is now accepting applications. This NSF supported program provides undergraduates with an opportunity to perform independent research under the guidance of a faculty mentor. Students will collaborate with faculty mentors in developing and carrying out hypothesis-based projects on ...
I've just returned from two conferences that focused on educating students for careers in science and technology and what do I find here at the home fort? There's Chad writing a very nice series on science careers! I was a little puzzled by PNAS acryonym in his titles since to ...
Tired of waiting for congress and you don't want to move to California or out of the US? Attila Csordas shows us in a few photographs how to isolate placental stem cells at home. His series brings back memories. My very first paid technician job in college involved visiting the ...
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt? This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman ...
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 ...
One of the newfangled ideas that's popped up in education in the past few years has been notion that more interactive methods of teaching will lead to better results. There's an appealing logic to this notion. Figure 1. A traditional lecture may not be the ideal way to transfer information ...
DNA sequence traces are often used in cases where: We want to identify the source of the nucleic acid. We want to detect drug-resistant variants of human immune deficiency virus. We want to know which base is located at which position, especially where we might be able to diagnose a ...
tags: Keith Robison from Omics! Omics! and that fellow Evolgen, with a curious fixation on manatees, have been reminiscing about their college math requirements and speculating on which math courses biologists should take. They've raised some interesting questions that, I think, make a good meme. If you answer the questions ...
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 ...
I found it in the MeSH database. Really! Looking for a quick answer? Don't ask a scientist It doesn't take long to realize that scientists can spend countless hours debating the meaning of words. Our very own ScienceBlogs is a great example, just look at the many ways we can ...
The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad." All they see are the base calls ...
For the record: Chlamydia is NOT a virus. I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun. But I was perusing the archives and I found this: I could ignore this if it came from a different source, but MicrobeWorld is ...
How does biomedical research impact you? Have you (or has someone in your family) benefited from vaccinations, pharmaceutical drugs, medical devices, surgery, or transplants? How does biomedical research affect the health of your dog, cat, or other pet? How might biomedical research touch your life in the future? Do you ...
Calling all scientists and science-fans: you can help with science education by letting students know you're interested. How? Go and comment on classroom blogs and wikis. I've been gradually collecting some blogs from different classes and I've even had some brave volunteers offer theirs for review. So here goes: www.missbakersbiologyclass.com/blog ...
What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic ...
There's nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job. For the month of January, I'm teaching a night class in bioinformatics at a local community ...
You've probably heard about enterprising researchers attaching cameras to dolphins, dogs, and other animals, in order to learn how things look from the critter-point of view. Now, some enterprising lab rats have added a new twist to this technique. It's lab cam! From Attila Csordas , we have a report ...
Liveblogging from the Hi-Tec conference I'm currently at the Hi-Tec conference in Scottsdale, Arizona. (If you follow me on Twitter - www.twitter.com/@digitalbio - you may have seen me complaining about the temperature). It's an interesting conference, so I'm going to share some of the things that I'm learning. Dr. Travis ...
