sporte | June 1, 2008This month's edition of Medicine 2.0 focuses on connections. You'll learn how new technologies are empowering patients by connecting them with their own health records, connecting patients and paramedics with doctors, and connecting doctors with each other.
Nothing connects like Web 2.0.
Let's hit the Midway!
Many submissions to this carnival certainly captured the carnival spirit. I had just become resigned to the notion of scouring the internet myself, looking for posts that would fit today's collection, when a couple of days ago, I was inundated with email submissions.
Great! I thought,…
sporte | May 30, 2008For aspiring technicians, who live in the right parts of the country, biotech jobs are out there and waiting. But what if you don't want to be a technician? Or what if you're in graduate school, in a post-doc, or have a Ph.D. and simply want to do something else?
Where do you begin?
How do you know what sorts of positions are going to be a good match for your skills and talents? Is the outlook really as bleak as it may seem?
First, the prelude. Most of what I'm going to write will apply to many more people than the small population with Ph.D.s. This little bit of advice is an…
sporte | May 29, 2008I got my copy of "A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As soon I skimmed through it and read some of the questions and answers, I knew this would be the kind of quick reference that I would like to have sitting above my desk.
Scherer has compiled a wonderful text that not only answers many of the kinds of questions that I can think to ask about the human genome, but the kinds of…
sporte | May 29, 2008RFLP is an acronym that stands for "Restriction Fragment Length Polymorphism." That's quite a mouthful and once you've said this phrase a few times, you realize why we use the initials instead.
I know a Restriction Fragment Length Polymorphism sounds like something that must be impossibly complicated to understand, but if we take the name apart, it's really not so bad.
Let's start with most familiar one of the four words and work from there. My guess is that for many of you, that word is "length." When we talk about length in this context, we are talking about the length of a piece of…
sporte | May 29, 2008"Why won't biotech companies hire people with Ph.D.s to be technicians?"
"I already have a Ph.D., how do I find a job?"
These were some of the questions that commenters left after my earlier posts (here, here and here) on biotechnology workforce shortages.
Unfortunately, for these students and post-docs, the shortfall of employees in the biotech industry is largely a shortfall of technicians. It is a sad thing that promoting science careers can have the unintended consequence of creating a surplus of unhappy post-docs and even more unhappy graduate students. Perversely, many of the…
sporte | May 28, 2008After leading the Human Genome Project and the National Human Genome Research Institute at the NIH for many years, Francis Collins is retiring.
No matter what you think of Francis Collins, he's been successful in getting the genome project done and he's done some amazing things during the 15 years that he's headed NHGRI.
My friend, Dr. Joan Messer, told me many times about the hours he spent talking with students at one of the AAAS meetings. I will always remember him from the NWABR fund-raising dinner where he pulled out his guitar and had the entire audience singing about DNA.
sporte | May 28, 2008On-line courses were a still a new phenomenon when I was teaching full-time. Our school was pretty gung-ho about on-line education but many instructors were skeptical, some were still lamenting having to learn how to use a computer and losing the services that used to be provided by departmental secretaries. Other instructors simply distrusted the entire idea, seeing distance learning as the equivalent of an educational scam, a kind of "get rich quick scheme" that would allow the school to collect more tuition dollars without paying instructors.
I never did teach an on-line course during…
sporte | May 28, 2008Where have all the flowers gone?
Long time passing
Where do all the flowers gone?
Long time ago
Where do all the flowers gone?
Young girls picked them everyone,
When will they ever learn? When will they ever learn?
-Pete Seeger
Where do graduate students and post-docs go when they decide it's time to leave the pipeline? And, if they're thinking about going, how do they find a path into something new?
These questions are especially timely given all the current NIH funding issues. It's odd, too, that we probably have the data, that is, I think we can count the number of people who've gotten…
sporte | May 27, 2008In part I, I wrote about the shortage of technicians in the biotechnology industry and the general awareness that this problem is getting worse. This part will address the challenge of getting more students into programs that will prepare them for jobs in the biotech field. I've also been asked to write a bit more about finding jobs in companies, that post will be a bit later. Before proceeding, there are two points that need a bit of discussion. The first point is the whether there's a shortage at all and the second applies to the kind of shortage.
It's hard to see the forest when you're…
sporte | May 27, 2008Students, 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 local biotech companies and research institutions talk with the students and judge the projects.
The public viewing time is tomorrow, May 28th, between 9 am-12 noon at the Meydenbauer Center. More information can be found here.
This…
sporte | May 22, 2008On June 1st, I'll be hosting the next edition of Medicine 2.0, a carnival devoted to exploring the impacts of web 2.0 technologies on medicine and medical practice.
All topics that consider the impacts of web 2.0 on medicine and healthcare are fair game.
Are you talking with doctors about sexually transmitted diseases in Second Life?
Have you had your genome sequenced? Do your doctors send you e-mail?
Are you using web technologies to measure your food consumption and calorie burning?
If you have an article that you think fits the description, feel free to submit it to me, either via e-…
sporte | May 9, 2008Workforce 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, biotech companies that can't hire in the U.S. will recruit foreign workers or open research centers overseas (Luke Timmerman, Seattle PI).
The reason for concern is that biotech jobs, in general, are pretty good. They pay well…
sporte | May 8, 2008Dave 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 model for looking at evolution.
You can get more information and register here.
The cool thing about plants is that there's lots of material to work with.
sporte | May 8, 2008Community colleges are such extraordinary places that even California's governor, Arnold Schwarzenegger credits his time at Santa Monica community college as one of the secrets to his success.
From the SF Chronicle:
"People always ask me 'What is the secret of your success?' " he said Tuesday. "I always say, 'Come to America. Go to community college. And marry a Kennedy. It's all very simple.' "
HT to Jim DeKloe.
sporte | May 1, 2008Good news! Good news!
Last week the Senate passed the Genetic Nondiscrimination Act (GINA). This week it was passed by the House. It only needs one signature and GINA will become law.
For years, those of us who teach genetics have had to caution students about genetic testing. The biggest reason was the fear that having a genetic test would cause them to lose their health insurance.
There were just too many stories about people who had been denied insurance because they took a genetic test and discovered a predisposition to something like Huntington's disease or breast cancer.
But…
sporte | May 1, 2008Yesterday morning I was sitting at conference table, downing coffee to keep my eyes open, when I heard someone say that it's springtime now and the snakes are waking up. Well, those kinds of statements at the breakfast table do have a way of getting my attention.
I turned sideways and realized the words were coming from a high school science teacher, that I know, from Arizona.
"Snakes hibernate?"
"Sure," she said, "and people who move here in the winter time are pretty surprised when a snake wakes up and crawls out from under their porch."
A few other questions and everyone at the table…
sporte | May 1, 2008APRIL was so much fun, that I thought I should find a molecule for May. I searched both the Gene database, the structure database, everywhere, without any luck.
Finally, I decided to change the search and use the date instead of the name of the month. And here we have it, straight from PubChem. A molecule for May. 05012008 is the compound substance ID.
5/1/2008 Update:
This structure turned out to be a bit surprising. Not does it look highly reactive, it also seems to disappear in the PubChem database. Sometimes I can find it by using the SID, sometimes I can't. I hate that.
For those of…
sporte | April 27, 2008A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well.
The April 25th version of Nature News reports (1) that two viruses, HPV (Human papilloma virus) and measles virus, have been found in lung tumors.
From Nature News:
Samuel Ariad of the Soroka Medical Center in Beer Sheva, Israel, and his colleagues began by analyzing tumours taken from 65 lung…
sporte | April 26, 2008Over 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) proteins have been solved, NCBI has a program called VAST that can be used to align those structures. I have an example here where you can see how a single amino acid change makes influenza resistant to Tamiflu®.
This 4 minute movie below shows how we can obtain those aligned structures from VAST and view them with Cn3D.…
sporte | April 24, 2008Bill 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 room in Kane Hall at the UW was already warm when we arrived last night (yes, I do go to evening seminars). A student handed us cards and cute little pencils for writing our questions and we sat down. We fought the impulse to write "What's the air speed velocity of a coconut-…