What do you call a biologist who uses bioinformatics tools to do research, but doesn't program? You don't know? Neither does anyone else. The names we use People who practice biology are known by many names, so many, that the number of names almost reflects the diversity of biology itself ...
One of the many interesting sessions I attended at ScienceOnline 2010 (#scio10) covered the questions of trust and critical thinking. Sitting in the audience, I couldn't help but think of a mash-up (like on Glee!) between this session the one on Fact checking. Granted, I know I'm a nitpicky scientist ...
It'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 ...
A 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 ...
If you're in Seattle, Dr. Bruce Alberts will be talking tomorrow night (Jan 5th) at the Seattle Aquarium on science education and the role that scientists play. There are also some really interesting talks at a day-long workshop, Wednesday (Jan 6th) at the UW South Campus Center. The details and ...
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 ...
Is there a place for citizen scientists in the world of digital biology? Many of the citizen science projects that I've been reading about have a common structure. There's a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting ...
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 ...
One of the greatest shocks when I started working in industry was the realization that the peer-reviewed paper, the most valuable form of currency in the academic world, was valued so little. In academics, there is a well-established reward system for getting your work published in peer-reviewed journals. Whether or ...
"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 ...
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 ...
ScienceOnline 2010 was one of the most amazing meetings I've attended in a long time and it's going to take some time to process it all, but in the mean time, it seems other bloggers ( phylogenomics, CogSci, and Ed) have started one of those meme things and so, here ...
Reposted from the original Digitalbio. About a decade ago, I took a fascinating summer course at the UW on bioethics. We read about the Nuremburg trials and the Geneva conventions. We learned about horizon problems and eugenics. And we discussed lots of challenging scenarios with genetic testing, autonomy, family relationships ...
Ozzie's will never be the same. The sun shone so brightly yesterday afternoon that it left us with no choice. We had to go outdoors. Luckily, Ozzie's has a wonderful upper deck in full view of the daylight and well-equipped with chairs. Photo footage below. The scene of the crime ...
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 ...
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 ...
Usually, I wait until the end of December to take care of holiday-related shopping and shipping. This year, I've resolved to do better. This year, I'm hoping to ship holiday gifts before Christmas. Fortunately, my SciBlings have come up with lots of great holiday recommendations to help you share science ...
Brian Switek, from Laelaps, could probably tell you. And, if you vote for him in the 3rd Annual College Blogger Scholarship competition, he just might. He'll tell you why should you vote for him, too, and I agree. And below the fold, is an inspirational cartoon. From xkcd.
This summer, I had the good fortune to attend three (or was it four?) conferences on science education. One of the most inspirational conferences was one on Vision and Change in Biology Education. This conference was co-sponsored by the National Science Foundation and the AAAS. It was a call to ...
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 ...
Are 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 ...
[[{"type":"media","view_mode":"media_large","fid":"2643","attributes":{"class":"media-image","typeof":"foaf:Image","style":"","alt":"i-d79be3a9aad20b816d5f917998d157dc-bay.jpg"}}]]Some of us walk by the bus stop and nervously glance at the scruffy-looking man carrying the ragged sign. I try not to breathe through my nose while I read the sign, carefully pretending all the while that I'm not really interested. Ah, it says "Repent! The world will end ...
I recently completed a long trip out-of-town, giving a presentation at a Bio-Link conference in Berkeley, and teaching a couple of bioinformatics classes at the University of Texas, through the National Science Foundation's Chautauqua program. The Human Subjects Protection Course Before I left town, I had to take a class ...
or 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 ...
One of my favorite books, "The Phantom Tollbooth," by Norton Juster, has a wonderful description of the penalties for making decisions without carefully evaluating the facts. Whenever the characters in the book arrive at a decision too quickly, they end up, literally, "jumping to Conclusions," an island far off the ...
Theo chocolate is situated in a neighborhood called Fremont, in the city of Seattle, in the former Redhook brewery. I used to consult for Redhook in my microbiology days, when I had access to a -80°C freezer and a proper microscope, so the building has a comfortable feel and some ...
On 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 ...
This 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 ...
Have you ever wanted to volunteer your talents and help with fun projects like these: * Refurbish computers for schools * Teach students how to use popular software or online services * Build a database for a nonprofit * Help out in your school's computer lab * Become an online ...
I touched a nerve in another post by mentioning molecular biology kits. Let's face it. Cloning kits, sequencing kits, and their relatives are the laboratory equivalent of frozen cookie dough. With frozen cookie dough, anyone can bake hot, steamy, chocolate chip cookies that taste great. You don't have to read ...
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 ...
Where 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 ...
Okay, I'll grant that visiting Second Life can seem a bit uncomfortable, especially at first, but it does open some new doors and present an alternative to travel. In flu season, virtual visits could be the next best thing to being there. ( Yikes, that sounds like an ad. No ...
Every now and then, people hire me to travel places and give workshops for college instructors and teachers on using bioinformatics. In a couple of weeks, I'll go to Long Branch, NJ. This week, I went to Corpus Christi, Texas and gave two workshops at Del Mar College; one on ...
Bora had an enjoyable post yesterday on obsolete lab skills. I can empathize because I have a pretty good collection of obsolete lab skills myself. These days I'm rarely ( okay, never) called upon to do rocket immunoelectrophoresis, take blood from a rat's tail, culture tumor cells in the anterior ...
Drug Monkey has an interesting take on an article that I wrote the other day about publishing in biology. I find it amusing that in some fields it's the most important to be first author and in others, it's the most important to be the last author, and sometimes we ...
Is the case for open access truly "open and shut"? Will open access impede science by limiting genetic studies with families? tags: Microsoft's brave new world The April ALPSP conference began with songs for the open access choir. Microsoft's Lee Dirks painted visions of a utopian future where everything will ...
Last night we went to a pub to hear about some new technology for diagnostic testing. A wonderful speaker, Karen Hedine from Micronics came and told us about the work that her company is doing. She brought along a demonstration machine and passed the machine and several plastic test chambers ...
Okay, watching some of the other movies makes me realize that I've been very negligent in not uploading ours. Without further ado, here it is. Can you guess the age of the person who made the movie? I'll give you a hint. It wasn't me.
One of my all time favorite books is South: The Last Antarctic Expedition of Shackleton and the Endurance (The Explorers Club Classic) . It's an amazing adventure and an incredible story. It's a comfort to know that any challenges I face will be easier than those conquered by Shackleton. Luckily ...
Some of my fellow ScienceBloggers have been hotly debating the role of male science faculty in perpetuating a climate that's chilly and hostile to women. From one end of the ring, we've heard the classic complaint " It's not my fault, I didn't do it." From the other end, we ...
is coming home and flying into Seattle. I took these pictures with my phone (in Airplane Mode, of course). In the first shot, you get to see Mt. St. Helen's and all the interesting geology around it. Can you tell which way the volcano blew? Mt. Rainier is in the ...
Yesterday, I posted a memorial for Ron Mardigian, an enthusiastic champion of science education at Bio-Rad. Today, I scanned RPM's blog and what do I see? A choir! Bio-Rad has produced a really funny music video. It reminds me of the music video from "We are the World," except some ...
Have you ever wondered if creationism was intelligently designed? Most of my colleagues tend to dismiss creationism as generally nutty and not worth bothering about. But, every now and then, we did get the odd situation with a few students who disagree or state legislatures that get a little confused ...
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 ...
Long ago, I worked in a large lab that was divided into several small rooms. For part of that time, I shared one of the small rooms with a graduate student from Taiwan. She was a wonderful person who taught me that many cultural norms are not normal in other ...
Jonathan Eisen (@ phylogenomics) shared this wonderful Lady Gaga lab spoof on Twitter the other day. It rocks. And, it makes me wonder if my pals who've been thinking about getting students interested in careers by having scientists talk on camera might be going at this the wrong way. Sure ...
