One of most wonderful things about the Internet has been the emergence of research projects that involve the general public. Universities like Cornell, Kansas University, and the University of Minnesota, to name a few, have established web sites and on-line databases that encourage both students and amateur biologists to participate ...
Students in the United States take many convoluted and unnecessarily complicated paths when it comes to finding careers in biotechnology. If Universities and community colleges worked together, an alternative path could benefit all parties; students, schools, industry, and the community. The image below illustrates the current paths and the approximate ...
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 ...
I had an enlightening experience recently, after I wrote some bioinformatics activities, under contract, for a community college. At the end of the project, the person at the college asked me if the activities were anything like the things that a " bioinformatics technician" would do on the job. tags ...
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 ...
Next Saturday afternoon, at ScienceOnline2010, the science goddess, the chemspider, and I will be presenting a workshop on getting students involved in citizen science. In preparation, I'm compiling a set of links to projects that involve students in citizen science. If you know of any good citizen science efforts, please ...
Do citizen science efforts ever go beyond "feel good" contributions? Do the data get published in peer-reviewed journals? In an earlier post, I started a list of citizen science projects that allow students to make a contribution. Many commentors are graciously adding to that list and I thank you all ...
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 ...
I was in in Washington D.C. this last week attending the National Science Foundation's Advanced Technology Education conference. During the conference, I attended one workshop and one talk on Second Life. Both of the presentations were focused on Teen Second Life, which was interesting, but neither presentation did a very ...
Over the years, I've seen many biotechnology education programs at community colleges embrace outreach to high schools as part of their mission. This kind of enthusiasm for outreach seems unique to biotech. No other kind of science or engineering program seems to do this sort of thing, at least not ...
If all the information you had about scientific careers came from newspapers or TV, it would be easy to think that everyone who works in life sciences / biotechnology is either a Ph.D. scientist, post-doc, or graduate student. In reality, the life sciences are more like an iceberg. The public ...
Getting kids involved in science, outside of the classroom. A conversation with a friend last night reminded me of some posts I wrote earlier about helping scientists connect to programs for helping students. My friend, as a parent, approached this idea, of connecting scientists with students, from a different angle ...
Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein? If the structures of the mutant and wild type (normal) ...
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 ...
The Ask a Science Blogger question of the week asks if organic foods are really worth the hype. I'm afraid my answer can't fit into one blog post. Let me start by telling you about my garden. This year my garden has been a home to local wildlife, but during ...
Many of you may remember a time when music-stealing was rampant on the internet. Apple changed this situation by establishing a new kind of marketplace. Now people pay for music and download it from iTunes. What if there were a third party group, with an iTunes-like model, where scientific publishers ...
Blaine Bettinger has an absolutely wonderful post where he compares his results for type 2 diabetes from 23andMe and DeCODEme. I really liked his post and I appreciated the way he showed the data from the two companies and elaborated on their interpretation of his genotype and his risk. Interestingly ...
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 ...
'Tis the holiday season and, according to ancient lore, the time when miraculous events are most likely to take place. One of those well-known and miraculous events of ancient days was the birth of a son to a young girl, who, although she was married ( Okay, I'm not sure ...
This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. UPDATE: I'm not so certain anymore that the strains are the same. I'm doing ...
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 ...
"What's in a name? that which we call a rose By any other name would smell as sweet" - Juliet, from Romeo and Juliet by William Shakespeare I realized from the comments on my previous post and from Mike's post that more explanations were in order. It seems we have ...
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 ...
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 ...
Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at ...
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 ...
tags: How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues. Read part I, part II, part III, and part IV to see how we got here. And read onward to see where will we go. In our last episode, I discovered a new ...
tags: Quick synopsis: A type of grass grows in Yellowstone National Park in hot (65° C), unfriendly soil. How the plant manages this feat is a mystery. What we do know, is that the grass can only tolerate high temperatures if it's been infected by a fungus, and the fungus ...
How does grass grow in the extremely hot soils of Yellowstone National Park? Could a protein from a virus help plants handle global warming? Okay, that second sentence is wild speculation, but we will try to find the answer to our mystery by aligning our protein sequence to a sequence ...
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 ...
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 ...
Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure. First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D. 1K9L If you want to do this at home and you haven't ...
In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed. Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step ...
Why do I love Cn3D? Let me count the ways. What does Cn3D do? ( Hint: say "Cn3D" out loud). Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly ( to some) ...
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 ...
Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge ...
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 ...
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 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 ...
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. DAG made me clarify my question by asking what I meant by ...
Let's play anomaly! Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of ...
Yikes, I've spilled some DHMO on my hands! What do I do now? Do you know the truth about DHMO? Look at this web site and tell me if you still want to go swimming.
My oldest daughter's favorite sweatshirt is one from the Seattle Children's Theatre Drama School, with the motto, " What's your motivation?" I was reminded of motivation the other day, as I talked about projects with the DIY biology group. It's pretty clear that you can't pick a project without knowing ...
This afternoon, I attended the first meeting of a DIY biology group in Seattle, after a kind invitation from one of the founders. DIY, for those of you new to the acronym, stands for "Do It Yourself." But, you say, there are lots of people who do biology on their ...
The American Society for Human Genetics is sponsoring the second annual DNA Day Essay contest. If you are a high school teacher here's your chance to combine an interesting assignment along with a contest. This year's essay questions are: If you could be a human genetics researcher, what would you ...
What happens when high school students clone and sequence genomic DNA? Background DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will ...
