Quoth Dr. Stemwedel, from Adventures in Science and Ethics. In the case of Universities and four-yr colleges, I completely agree. If you're looking for job training, go to a community college. This post is in response to one of the comments from the other day. This commenter expressed frustration at ...
"Yo, you regulate it's genes" The English makes me cringe, but I love the idea. Tom McFadden, an associate instructor at Stanford, has made a series of Biology rap videos and posted them on YouTube. Yo, check it out.
"It's all about saving Aunt Millie" – Bob Swanson Co-Founder of Genentech. Jim DeKloe wrote this post as a guest author a few years ago. Jim is one of the most inspirational educators I know and he's the sort of person that reminds you why educating students about biotechnology careers ...
Blogging from Bio-Link, part III[[{"type":"media","view_mode":"media_large","fid":"2636","attributes":{"class":"media-image","typeof":"foaf:Image","style":"","alt":"i-6acc85780a72ebc76de64b3369707f04-clock.jpg"}}]] High school teachers have different techniques for selling their students on the benefits of science and math. When some high school instructors step in front of a class, the quiet demeanor gets put away and another persona steps out - the USED-CAR SALESMAN SCIENCE EVANGELIST ...
There aren't many reports of 14 year-olds making scientific contributions. Even in the field of astronomy, Caroline Moore, the youngest person to discover a supernova, is a bit unusual. This supernova comes from Astronomy Picture of the day. Photo credits: High-Z Supernova Search Team, HST, NASAHT: National Science Foundation The ...
It must be spring. Summer course announcements are popping up everywhere and this site is no exception. Last Friday, I posted an announcement about our summer bioinformatics course in Alaska, June 27-29th. This week, I have a couple more conferences to announce. Naturally, I'll be at both of them, leading ...
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 ...
What do you call a biologist who uses bioinformatics tools to do research, but doesn't program? You don't know? Neither does anyone else. The names we use People who practice biology are known by many names, so many, that the number of names almost reflects the diversity of biology itself ...
No one in a life science-related industry or research lab, in Western Washington, is safe at this time of year. Surely, you're joking! No, seriously, there are teachers and science enthusiasts everywhere looking to sign you up! And don't call me "Shirley." Sign me up? That's right, it's time to ...
Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon. In the meantime, here's your puzzle: What's unusual about this pair of bases? tags ...
One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that ...
Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things. In this last part, I discuss a ...
Antibiotics are molecules of biological warfare. Produced by bacteria and some fungi, in response to extracellular signals, antibiotics represent a diverse group of compounds that inhibit bacterial growth at different points and different stages of the life cycle. We will get around to antibiotic resistance, but in these few words ...
yep, I've become a videoblogger, at least sometimes. See the first video below. Be kind in the comments, this is a new thing for me. This video introduces the different blast programs, discusses word size, and how blastn works, the blastn score and the E value. The treatment is light ...
I learned via e-mail yesterday that the biotechnology program, that I taught with for ten years during the 90's, is ending due to low enrollments. I also learned yesterday, via the Seattle Times, that a resurrected version of ICOS called CMC Icos Biologics is planning a $35M expansion of their ...
It was a wet and rainy day yesterday, and we have a dissecting microscope, so I decided to see if I could find some tardigrades. Tardigrade photo by nebarnix Reposted from Nov. 2006 I went outside and scraped a bit of moss and some lichens off of our deck. Then ...
Amateur astronomers unite! The pros want your help! image from Astronomy Picture of the Day, Credit: NASA, ESA, A. Aloisi (STScI / ESA), Hubble Heritage (STScI / AURA) - ESA/Hubble Collaboration I learned about this from the Washington Science Teachers Assocation. Galaxy Zoo and the Sloan Digital Sky Survey are ...
A few years ago, I heard an interesting thing from another mother when I picked my oldest daughter up from daycare. The other mother was suffering from a head cold and confessed to me her fear that she had become "antibiotic resistant." I found this statement pretty funny at the ...
This morning I attended the Fifth Annual WBBA Governor's Life Sciences Summit. The breakfast was great; the talks were okay. I do enjoy the stories about people who's lives were saved because of biotechnology and I agree that the focus of the summit, research and discovery are important, but I ...
Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching. Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux ...
Science education faculty don't get no respect At least that's a strong conclusion from a paper in the December 19th issue of Science (1). According to the article almost 40% of the 59 science education specialists, surveyed in the California University system, were "seriously considering leaving" their current jobs and ...
It seems kind of funny to be thinking of anti-freeze at the moment, with heat waves blanketing the U.S., but all this hot weather makes me miss winter. And so I decided it was time to re-post this from the original DigitalBio. Winter is coming soon, my bike ride to ...
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for ...
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics ...
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the ...
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live ...
This is a video that a friend made that shows, very clearly, how to pour an agarose gel, load the samples and run it. I especially like the way he used a bit of time lapse photography to show the dyes separating as the gel ran.
Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes ...
"How much do I love you? I'll tell you no lie. How deep is the ocean? How high is the sky?" - Irving Berlin The other installments are here: Part I: Introduction Part II: Sequencing strategies Part III: Reads and chromats Part V: checking out the library We all know ...
About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught. I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question: How do you sequence a genome? Before we ...
Shotgun sequencing. Sounds like fun. Speculations on the origin of the phrase I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage ...
tags: PZ's morning post about a bear killing a moose in someone's yard ( they do live in Alaska, after all), reminded me that it's time to make an announcement about our upcoming course. No, no, no! We're not going to kill any moose on the premises. We're going to ...
The Wired Campus has an interesting article on nursing students at Tacoma Community College. In John Miller's class, the students practice interviewing patients in Second Life. This sort of activity, of course, is one that could be carried out in a classroom, but I can see the advantages of having ...
I don't usually publish press releases, but I'm making an exception for this one, since your's truly is one of the Co-PI's. If you're a teacher within commuting distance of Seattle, the schedule and sign up information is here. NSF AWARDS $1.3 MILLION TO NWABR FOR BIOINFORMATICS EDUCATION Innovative Technology ...
The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics ...
Registration has opened a bit late this year, but it's always tricky when large programs change hands. The Chautauqua Short Course program for College Teachers is no different. In fact, as far as I know, we may still be waiting for the National Science Foundation to make a final decision ...
Biology as a second-language: the immersion method Language teachers say the best way to learn a language is by total immersion and even better, spending time in the country where it's spoken conversing with native speakers. See it, hear it, speak it, use it! Put yourself in a position where ...
`When I make a word do a lot of work like that,' said Humpty Dumpty, `I always pay it extra.' -Through the Looking Glass by Lewis Carroll In biology, we often ask our words do a lot of work. In what other field would we write direction like this "Transfer ...
Vizzini: He didn't fall? Inconceivable! Inigio: You keep using that word. I do not think it means what you think it means. - William Goldman, The Princess Bride Excuse me while I temporarily interrupt the genome sequencing series to define a word. Artifacts in the classroom It's disorienting. You learn ...
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 ...
Students, teachers and scientists converge tommorrow morning from all around the Puget Sound region and elsewhere in Washington to share their experiences and talk about science. The students will present posters, science-themed music, art, drama, and many different types of projects that involved first-hand research and investigation. Scientists from the ...
One of the commenters on a previous post, pointed out that proteases have pretty diverse structures, even though they also share a common function. What else could I do? I had to take a look. I found structures for chymotrypsin (from a cow) and subtilisin (from a soil bacteria, Bacillus ...
Like everything else, if we want to know what's going on, we have to ask. So, it's time once again for the 2011-2012 National Biotechnology/Life Sciences Program Survey. Yes, indeed. Federal and state agencies will use the results to determine how best to support programs like yours. This study will ...
Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class? If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st. ( Yes, it's the same Virgina Tech, and ...
No more delays! BLAST away! Time to blast. Let's see what it means for sequences to be similar. First, we'll plan our experiment. When I think about digital biology experiments, I organize the steps in the following way: A. Defining the question B. Making the data sets C. Analyzing the ...
No biology course is complete these days without learning how to do a BLAST search. Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key. Development of the tutorial and the activity were ...
[[{"type":"media","view_mode":"media_large","fid":"2632","attributes":{"class":"media-image","typeof":"foaf:Image","style":"","alt":"i-d336adebb31e5453376e5d20cec6c970-ck_yarrow.jpg"}}]] Blogging from Bio-Link, part I I am currently in Berkeley attending the 2006 Bio-Link summer fellows' workshop. It's hard to believe that it's been eight years since the first workshop was held. We're still meeting here in the same lovely Clark Kerr Center and I'm still, as every year ...
" Did you know," my friend whispered, " that the Humane Society funds terrorists?" I was stunned. What? That's crazy! I've adopted pets from there. No way! How could those be the same people?? My friend and I were suffering from "brand confusion." In business, this happens when different companies ...
If you're in Seattle, Dr. Bruce Alberts will be talking tomorrow night (Jan 5th) at the Seattle Aquarium on science education and the role that scientists play. There are also some really interesting talks at a day-long workshop, Wednesday (Jan 6th) at the UW South Campus Center. The details and ...
Last week I found a bug in the new NCBI BLAST interface. Of course, I reported it to the NCBI help desk so it will probably get fixed sometime soon. But it occurred to me, especially after seeing people joke about whether computer science is really a science or not ...
