My husband brought this fantastic book home from the ASHG* that I think many of you will find interesting. The book is: Making the Right Moves A Practical Guide to Scientific Management for Postdocs and New Faculty, published in 2006 by the Burroughs Wellcome Fund and the Howard Hughes Medical ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
It's hard to teach bioinformatics when schools work so hard to keep us from using computers. Anecdotes from the past Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT ...
When in doubt, turn to the internet. In a couple of weeks, I'm going to start teaching my first on-line course. So far, I've been preparing by: learning how to use Blackboard getting a subscription to iFinch so we can do bioinformatics in style, and share data and other files ...
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit ...
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 ...
One time I was watching a football game on TV and they had a short quiz, called "You make the call" or something like that, and you had to watch a play and pretend to be a referee. A short video clip showed football players falling over each other. Then ...
This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes ...
Wow! One of my commenters, Ms. Baker, suggested an entirely new way that scientists can help with science education. The only requirement is that a science class have their own blog. So, if your science class has a blog, let me know, so I can share the URL and maybe ...
How can you extend a blood typing activity with an active learning approach? The blood typing lab, part I. What went wrong? and why? Blood typing part II. Can this laboratory be saved? The learning objective: To understand the inheritance of blood type. In this activity students: 1. Identify which ...
I had some strange notions when I made the jump from working at the lab bench to teaching at the white board. I thought good teaching meant interesting lectures. And I was completely unaware that people actually conducted research in science education. If I had been asked about education research ...
I've been writing quite a bit this week about my search for a cross platform spread sheet program that would support pivot tables and make pie graphs correctly. This all started because of a bug that my students encountered in Microsoft Excel, on Windows. I'm not personally motivated to look ...
When I was a post-doc, I spent a few months seriously thinking about changing careers and teaching high school. I might have followed through on that plan, too, but I didn't know how to pay for it. Today, if you have a background in science, technology, math, or engineering, you ...
If you have a little time, the Dolan DNA Learning Center at Cold Spring Harbor will be presenting some really interesting workshops on neuroscience and genetics. The dates are: Nov. 5, 2009: Inside Cancer - workshop on teaching cancer; Raritan Valley Community College, Somerville, NJ Nov. 6, 2009: Genes To ...
The first lab mouse I touched had soft white fur and a light pink tail. It looked cute enough to snuggle and take home as a pet and I was smitten. I slipped my hand into the cage, thinking the mouse would respond like my pet gerbils or my brother's ...
HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun. I learned about HealthMap awhile ago from Mike the Mad Biologist, but I ...
If like me, you were a little disoriented and confused when you visited Second Life and traveled through orientation island, then you may like this. The Wired Campus (from The Chronicle for Higher Education) led me to an interesting post from the New Media Consortium and a new place to ...
Why should professional scientists have all the fun? Researchers have been engineering glowing cats, and selling glowing fish at pet stores. High school kids can do genetic engineering too, if they have the right equipment. And you can help them get the equipment by contributing to our DonorsChoose fund drive ...
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 ...
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 ...
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 ...
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 ...
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 ...
Do course evaluations have to be a popularity contest? Or can they be useful tools for improving a class? tags: A few days ago, evolgen lamented that his students weren't giving him useful information on their end-of-course evaluations. I'm not surprised. When I first started teaching, I was a given ...
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 ...
We've been fans of the Molecule of the Month series by David Goodsell, for many years. Not only is Dr. Goodsell a talented artist but he writes very clear descriptions of the ways molecules like proteins, RNA, and DNA work together and function inside a cell. To learn about proteins ...
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 ...
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 ...
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 ...
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 ...
A friend of mine; serial entrepreneur, and former president of Genetic Systems; Joe Ashley, told me once that starting a business is an unnatural act. Now that I've done it, I agree. Even with my multiple back-up plans, possible grants, and part-time activities, my stomach still hurts and my mind ...
I love using molecular structures as teaching tools. They're beautiful, they're easy to obtain, and working with them is fun. But working with molecular structures as an educators can present some challenges. The biggest problem is that many of the articles describing the structures are not accessible, particularly those published ...
I received a mysterious file last week, via e-mail from one of my students. According the e-mail, the file contained the answers to an assignment. I downloaded the file and double-clicked it. Nada. I did notice that the file had an unusual extension. Most Word documents have ".doc" at the ...
A few weeks ago I attended a education conference at Pacific Science Center entitled, " A Conversation that Can Change the World." It was interesting. Everyone was pretty enthusiastic at the meeting and there was a lot of positive energy. We got to see Theresa Britschgi from Seattle Biomedical Research ...
I heard some intriguing presentations this week about education in Second Life, but I happen know that there is an open-source, free (?) alternative called "Croquet." Do any of you have experience with Croquet vs. Second Life? I'd love to hear about it in the comments. I attended two talks ...
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared ...
