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Discovering Biology in a Digital World

My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.

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Sandra Porter I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).

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    Workforce shortages in biotechnology, part I. Why is this a problem?

    Workforce shortages are a growing problem in the biotech industry. Communities are concerned that a lack of trained workers will either keep companies away or cause companies to move. If companies do have to move, it's likely those jobs might be lost forever, never to return. According to Robert Reich, former U.S. secretary of labor, now a professor at UC-Berkeley,...

    Would your class like to clone and sequence plant genes?

    Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example. Plus, since GAPDH is a highly conserved, it's a great...

    Comparing mutant and wild type structures

    How to compare mutant and normal protein structures.

    The Personal Genome discussion

    Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington. We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases shortened and paraphrased....

    The wonders of webinars

    One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my headphones,...

    Mapping polymorphisms in 16S ribosomal RNA

    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...

    Meet the ribosomes

    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...

    How much do you know about Genetic Genealogy?

    You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz....

    Open Access and using molecular structures in education

    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 by the ACS (American Chemical Society). I'm hoping that the...

    I eat genomes for breakfast

    And so do you.

    Google Docs has pivot tables!

    Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...

    What do computer scientists do anway? Inquiring minds want to know.

    Our new Scibling, Jane, is a real life computer scientist. If you've ever wondered what computer scientists really do during the day, Jane will set you straight (I guess they're not playing Nintendo. Darn! Another illusion shattered, just like that.)...

    A beginner's guide to making a phylogenetic tree

    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 experiment with the multiple copies of 16S ribosomal RNA (rRNA)...

    How to use Cn3D

    A video tutorial on molecular structures.

    Hey instructors, do you know what kinds of operating systems your students use?

    It's not Linux.

    Starting a new biotech program? Teaching a biotech course?

    Bio-Link is accepting applications for this year's National Summer Fellows forum, June 2-6th, in Berkeley, CA. You can get an application at www.bio-link.org I'll be there, doing some kind of bioinformatics workshop. I'll probably be talking about either metagenomics or comparing protein structures and drug resistance, but if you have topic requests, feel free to submit them in the comments....

    DNA sequencing errors hit home

    One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....

    Exploring Open Office: part II, can we have our pie and eat it too?

    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 for something new, since Office 2004 on Mac OS 10.5...

    Exploring OpenOffice: what did we learn?, part I

    I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...

    The OpenOffice challenge: can you do what needs to be done?

    Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...

    Linux is amusing, but this is why I teach with Excel

    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. More than one person told me that I should have...

    An unexpected challenge with teaching on-line

    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, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...

    Bacterial metagenomics on the JHU campus: analyzing the data, part IV

    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 in each biome. Then, we'll make pie graphs so that...

    Bacterial metagenomics on the JHU campus: analyzing the data, part III

    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 different numbers of each genus....

    Bacterial metagenomics on the JHU campus: analyzing the data, part II

    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 is concerned with fixing data entry errors and spelling mistakes....

    Bacterial metagenomics on the JHU campus: analyzing the data, part I

    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 sequencing, and use blastn to identify what they found. Every...

    Obsolete lab skills are what we teach best

    When will science lab courses start teaching more of what we do now, and less of what we did twenty years ago?

    Feeling ethically challenged?

    Confused about terms like "autonomy" and "beneficance" and their relationship to biomedical research? The Northwest Association for Biomedical Research (NWABR) is offering a short course at the University of Washington, Feb. 29th and March 1st, on Ethics in Science. Registration details and a description are below....

    What could be better than undergraduate research in Las Vegas?

    Getting paid to do it?

    A quick introduction to BLAST

    A quick video introduction to BLAST.

    Ruminating on the digital divide

    A few weeks ago I attended a education conference at Pacific Science Center entitled, "A Conversation that Can Change the World."...

    Where do you go to learn SQL? I go to the zoo

    A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind...

    Science educators mourn Ron Mardigian

    We often see memorials written about famous scientists, but we rarely see them about the people who work in the background to help people learn the science in the first place. Ron was one of those people whose work inspired teachers and helped spark excitement in science students throughout the world. I just learned last week that Ron passed away...

    Desperately seeking suggestions: what works best with on-line teaching?

    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 getting a microphone and some software for making video podcasts...

    If you have free time over winter break...

    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 those cash prizes! The Alliance for Science is pleased to...

    Digital Biology Friday: Free to evolve? - the answer

    Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers....

    Digital Biology Friday: Free to evolve?

    This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid....

    Science Cliches: what are your favorites?

    The perpetual science student's contribution to modern language.

    Did she or didn't she? Genetic testing and virgin birth

    If we suspected a virgin birth, how could we prove it?

    Interpreting DNA sequencing data: answers to the quiz

    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 products, generated with the same set of primers. The quality...

    Interpreting DNA sequencing data: what can you get from quality scores?

    Kind of like reading tea leaves, but more meaningful.

    Digital Biology Friday: Animal Mitochondria and Evolution, part II

    You too, can compare chimp and human DNA.

    Match the trace with the sample

    Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.

    High school students uncover their past through their DNA

    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 isolated from the cheek cells, and genetic markers are used...

    Before practicing on real patients, you can practice in Second Life

    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 student interview other "people" who are for the most part,...

    Public high-school students from San Francisco place take honors in the International Genetically Engineered Machine Competition

    Congratulations to George Cachianes (who I've written about before), his amazing students from Abraham Lincoln High School, and collaborators at UCSF! These students, from a public high school no less, placed in the top 6 finalists, along with only one other US team. The other top teams were: Peking University (China), University of Science and Technology (China), University of Paris...

    Collaborating on a data analysis project: students do the math with the Google Docs spreadsheet program

    For many years, I had my biotech students do projects where each group of students would analyze their own data, in addition to all of the data gathered by the class. I would draw a table on the white board and each group would enter their data. At the end of the class, all the groups would copy all the...

    Evidence-based teaching, open access, and the digital divide

    Open access to educational research would benefit us all.

    Digital Biology Friday: Animal Mitochondria and Evolution Revisited

    An evolution activity for the classroom.

    The Halloween aftermath: graphing the candy, part I

    Fun ideas for your Halloween loot

    Win fabulous prizes! (by helping schools)

    I missed my chance to get my own DonorsChoose challenge together, but that doesn't mean that you have to miss your chance to contribute and, of course:   WIN FABULOUS PRIZES!!!!   WIN FABULOUS PRIZES!!!! WIN FABULOUS PRIZES!!!! It's easy.  Just head on over to one of these pages On Being a Scientist and a Woman   (Her teachers still...

    Digging up the dirt on campus bacteria: how do we know if we have good data?

    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 that's killing the honeybees. We're also trying to find out...

    Metagenomics, biomes, and dirt: separating good data from bad

    Sequencing the dirt: see how it's done

    Playing in the dirt: metagenomics on the JHU campus

    We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles....

    Making discoveries in the open: doing digital biology with the class

    Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...

    Computers vs. the science class: IT 1, Instructor 0

    It's hard to teach bioinformatics when schools work so hard to keep us from using computers....

    Fall bioinformatics class: welcome students!

    Welcome Bio256 students! This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a...

    ScienceBloggers in Second Life

    Our adventures with presenting posters in Second Life.

    How to attend a poster session in Second Life

    Bora and I are giving posters in Second Life. Here's how you can attend.

    MicrobeWorld: what have you done?

    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:...

    Biology as a second language, Nature podcasts, and why fireflies glow in the dark

    Why I love Nature podcasts

    How does a single nucleotide change make influenza virus resistant to a drug?

    Fun with molecular models!

    Biology bookstore helpers: Portland needs you!

    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 not just a bookstore. It's a destination. I guess that's...

    Overwhelmed by information?

    Bertalan Meskó shares his strategies for keeping up and gives instructions so you can do the same. He shows how you can save your favorite PubMed searches and have NCBI send you e-mails about new papers. He describes some third party PubMed tools that make pretty graphs. Last, he discusses RSS readers, Connotea, and BioWizard. It's all very helpful and...

    Digital Biology Friday: What sequences do you believe?

    During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...

    Genetic Variation I: What is a SNP?

    If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...

    What happens to graduates of high school biotech programs?

    Some of them work for Bayer.

    Got DNA sequencing problems? Who ya gonna call?

    Why the ABRF of course! I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university...

    Digital Biology Friday: A helpful hint

    I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....

    Godzilla, tuberculosis, and XDR-TB

    What's the connection?(image from Newton TAB blog) I have to admit, I don't know. But, I do know where you can find out. Dr. Gerard Cangelosi, from the Seattle Biomedical Research Institute, will be speaking about tuberculosis, godzilla, and XDR-TB, Monday night, 7 pm at the Pub at Ravenna Third Place as part of Science on Tap. tags: tuberculosis, informal...

    Grants for kids to study beetles

    Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too. They're providing grants for kids, in grades 7-12 to work on beetle biology. Applications are due by November 15, 2007....

    Do biologists need to learn programming?

    I get asked this question often enough and now that's it's come up again, it seems that I might as well answer it once and for all and get it over with....

    Digital Biology Friday: You make the call!

    Developing "biological intuition" through case studies

    A visit to the galaxy zoo

    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 looking for your help in sorting out different galaxies. It's...

    Digital Biology Friday: More puzzling structures

    I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it. So, here's one for you to chew on over the weekend. This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I...

    Professor Steve Steve bears all at Virginia Tech

    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 back and forth across the coast so quickly? Will you...

    Bug hunting is a BLAST

    Software testing and the scientific method.

    Careers in biotechnology, part II bioinformatics

    Where does bioinformatics fit in the biotech food chain?

    Teaching with the new BLAST

    Some things I like, some were surprises.

    Professor Steve Steve caught experimenting with human subjects!

    It's okay, they're science teachers.

    It's still a DNA puzzle, but this is the answer

    This DNA is nonpareil.

    Updates to the BLAST for beginners tutorial

    BLAST has gotten harder.

    Careers in biotechnology, part I.

    What do people in biotechnology do on the job? What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone who's considering biotechnology for a potential career. My favorite part of...

    A DNA puzzle

    It's a pair of bases, but something's not quite right.

    "A college education is not job training"

    Answers to a commenter who bemoans bioinformatics education.

    To bioinformatics students everywhere: advice from the pros

    Know your biology! I get asked often about the type of bioinformatics training that students should get and whether it should be a special course or not. And I answer that I think teaching bioinformatics in the absence of biology is like teaching Microsoft Word in the absence of writing. There isn't much point. tags: bioinformatics, education So I was...

    Digital Biology Friday: hot plants and viruses, the finale

    Could a protein from a virus help plants handle global warming?

    Using Bioinformatics to Study Evolution: reading assignments

    Assigned readings on BLAST and phylogenetics.

    Digital Biology Friday: hot plants and viruses V

    Through the Related Structures tab and what I found there.

    Finding scientific papers for free, one more experiment

    One last experiment with PubMed (for now).

    Math for Biologists: which courses add up?

    Which math courses are best for biologists?

    Finding scientific papers for free, part III: my new favorite method

    Instructions for using my new favorite method.

    Finding scientific papers for free, part II: comparing methods

    We do an informatics experiment with PubMed to compare different search techniques.

    The Alliance for Science wins big

    Why do high schoolers think doctors should understand evolution?

    Wanted: high school students to play a lunar geology computer game

    Learn astronomy by playing the game

    Finding scientific papers for free, part I

    The trials of an English physician.

    Digital Biology Friday: hot plants and viruses, part IV

    How does grass grow in the hot, inhospitable soils of Yellowstone National Park?

    Biotechnology Education in Viriginia

    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 that's why I waited to post this announcement). There's something for...

    Bears, moose, and bioinformatics are all happening in Alaska

    tags: moose, bioinformatics class, willows, plant genes 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 learn about the moose and...

    Learning styles and science labs

    Science labs are not for all people.

    Ethics in the Science Classroom

    Learn how to integrate ethics into your science classroom.

    2007 Bio-Link Summer Fellows Workshop

    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 hands-on workshops for college and high school teachers in using...

    Bioinformatics in Alaska: Of course it's a course, of course, of course

    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 on funding. Still, summer is rapidly approaching and I know...

    What made me sick?

    How do microbiologists determine which microbe caused a disease? As Tara has eloquently described (I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame?...

    Celebrate Darwin Day by writing an essay!

    Win cash or other prizes!

    MeSH part I. Where can you find the meaning of "life"?

    The best place for biology words.

    Sequencing a Genome, part VII: Want to win $10 million dollars?

    How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning team would also win in the IP (intellectual property) game...

    Biology as a second language, part II. How many ways can we use a word in one sentence?

    `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 10 lambda of lambda phage DNA into a cuvette and...

    Biology as a second language: what is a vector?

    Defining a biology term for scientists in other disciplines.

    Sequencing a Genome, part VI: Chimeras are not just funny-looking animals

    Chimeras invade the sequencing lab!

    Sequencing a Genome, part V: checking out the library

    Send in the clones, but only the random ones.

    Basics: How do you sequence a genome? Part IV. How many reads does it take?

    "How deep is the ocean? How high is the sky?"

    Do Science in Las Vegas: Undergraduate Research Opportunities in Environmental Microbiology

    Hot springs, salty lakes, arid soil and good science.

    Basics: How do you sequence a genome? part III, reads and chromats

    In which we define reads, chromatograms, and shotgun sequencing.

    Basics: How do you sequence a genome, part II

    Some background on the strategies: mapping vs. shotgun