sporte | August 4, 2008What 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 have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of…
sporte | August 4, 2008Pfizer has pledged to donate up to $10,000 to the cause of science education, through Donorschoose.org, but only if enough of you, dear readers go to Big Think: Think Science Now and vote for your favorite video.
If you're not familiar with Pfizer, they're a pretty well-known drug company. You probably read about one of their products every time you delete messages from your e-mail in-box.
You don't even have to watch the videos, just vote.
I strongly recommend watching the videos, though. They are all profiles of scientists who work at Pfizer or other research organizations. It's…
sporte | June 24, 2008or is it just an idea that's ahead of the curve?
Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here.
Now, an oversight like this is a little understandable. The titles of the entries do include the name of the wrong gene (DRD2 - the dopamine D2 receptor). And it was only four years ago that people figured out that the marker in the title of the articles mapped somewhere else.
If computers were responsible for the annotation, well, this would be understandable.…
sporte | June 23, 2008It was a -1 tide on Sunday and great entertainment for people and birds.
We got there about lunch time.
We found two moonsnails.
Lots of moonsnail egg cases.
Some moonsnail food.
Anenomes everywhere.
And at the end, we had quit being crabby.
And everything was clam.
sporte | June 21, 2008Arrgh. Fremont is just crawling with Pastafarians.
Photos below the fold.
More Solstice parade pictures.
sporte | June 21, 2008Are 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 personalized genetics.
As travel costs rise and traveling becomes harder, I think we'll see many more things happening in alternative places like Second Life. Virtual environments like this can make on-line communication entertaining in ways that conference calls and webinars can't. I may…
sporte | June 20, 2008
"Let this sleepin' dog lie, son. Dog-gone it, I'm dog tired. I'm tired of leading the dog's life and fightin' likes cats and dogs against cats and dogs, a young pup's doggin' my trail tryin' to become top dog. I'm going to the dogs in a dog eat dog world, son. I... I'm so far over the hill... I'm on the bottom of the other side. "
- Wylie Burp from Fievel Goes West
I don't know why I find these stories about cloning puppies so interesting, but...
Someone sent me a press release on a dog fight between cloning companies.
It turns out that there's a third company, from South Korea, that's…
sporte | June 20, 2008It's pretty common these days to pick up an issue of Science or Nature and see people ranting about GenBank (1). Many of the rants are triggered, at least in part, by a wide-spread misunderstanding of what GenBank is and how it works. Perhaps this can be solved through education, but I don't think that's likely. People from the NCBI can explain over and over again that some of the sequence databases in GenBank are meant to be an archival resource (2), and define the term "archive," but that's not going to help.
Confusion about database content and oversight is widespread in this…
sporte | June 19, 2008Right or wrong, the word "dopamine" always conjures up images in my head of rats pushing levers over and over again, working desperately hard to send shots of dopamine into their tiny little rodent brains.
Dopamine, like many other neurotransmitters (chemicals that send signals in the brain), works by binding to proteins on the surface of brain cells and sending a signal to the cell. There are five different subtypes of receptors for dopamine (D1-D5) with somewhat different activities (1) and drugs that bind to these receptors are known to have potent effects on brain activity and behavior (…
sporte | June 18, 2008In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning.
One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI.
The article that I wrote about definitely made a mistake and I don't understand why it wasn't caught by the reviewers. I found it pretty quickly by searching OMIM and I was only trying to find information about dopamine, not verify results.…
sporte | June 17, 2008In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all know people who aren't deterred by the idea of punishment. We all know people who never seem to learn.
Could there be a physical reason, hidden in their genes?
In December 2007, Science published a study by Klein et. al. (1) where they asked if a specific genotype at a location called "DRD2-TAQ-IA"…
sporte | June 16, 2008Pet cloning is back!
Pets are funny things. Some owners find their pets to be closer than some human friends, other owners never really bond with their pets at all.
BioArts, a California biotech company, founded by ex-CEO of the now defunct Genetic Savings & Clone, is counting on the strength of those human-dog emotional bonds .
I've had several pets during the course of my life; dogs, cats, fish, scorpions, spiders, frogs, turtles, gerbils, and a hermit crab. Some pets were really easy to train and live with and some - well, let's just say some were more challenging. So, I…
sporte | June 14, 2008A few months ago, I made a new page for a more complete blogroll. Now, that my class is over and I have a break from traveling around leading workshops, I'm ready to add some links.
Other bloggers; Bora, Mike the Mad, PZ, Janet, DM, and Abel; use a nice technique called "blogroll amnesty" where they offer other writers a chance to be on their blogroll. I like that.
So, to paraphrase Mike:
If you link to me and you're not a creep, let me know and I'll return the favor (instructions below). For those you who've written to me and asked me to add you to the list, here's your chance.
Add a…
sporte | June 12, 2008Students 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 time that each one takes.
I was at two meetings recently, one in Arizona and the Bio-Link workshop in Berkeley, where we spent time discussing the paths to careers in the biotech industry. You might think, if you consider the number of years…
sporte | June 11, 2008Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog.
It also looks like he's looking for post-docs (see the side bar on the right of this page.)
sporte | June 9, 2008What are you learning in school?
xkcd has the inside track on the really important stuff.
sporte | June 4, 2008Have you ever wondered what kinds of viruses can be found in human waste?
Mya Breitbart and team have been sequencing nucleic acids from fecal samples in order to find out. You might expect that we'd find viruses that infect humans or viruses that infect the bacteria in our gut.
I wouldn't have expected to learn the result that they found.
A large number, 60% of the viral DNA sequences were from unknown viruses. That's not a surprise. The surprise came when they looked at the RNA viruses.
Instead, the viral sequences most often came from a plant pathogen called the pepper mild mottle…
sporte | June 4, 2008I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials.
Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly.
They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done. There's no sound, but the animations are…
sporte | June 3, 2008A little over ten years ago, Dr. Elaine Johnson obtained funding from the National Science Foundation to start Bio-Link, an Advanced Technology Education center, focused on biotechnology. Since that time, Dr. Johnson has become a national leader in biotech education, enlisting the country's top educators and industry captains to ensure that community college students receive a quality education and the best preparation possible for entering the workforce.
In this radio interview from Tech Nation, Dr. Johnson talks with Dr. Moira Gunn about the easiest way to a biotech career.
A Career in…
sporte | June 1, 2008In part I, I wrote about my first semester of teaching on-line and talked about our challenges with technology. Blackboard had a database corruption event during finals week and I had all kinds of struggles with the Windows version of Microsoft Excel. Mike wrote and asked if I thought students should be working more with non-Microsoft software and what I thought the challenges would be in doing so.
I can answer with a totally unqualified "it depends."
First, I think knowing how to use a spread-sheet program is an advantage in many different kinds of fields and even in real-life, outside of…