Science Education
sciencewoman | October 31, 2007Today Minnow and I are flying home to Mystery City and she'll be wearing her costume on the plane.
This picture is fulfulling another request for MamaScientist, who writes a great blog Mother of All Scientists, whose Bean is just six months old, and who made a contribution to my DonorsChoose challenge.
Speaking of DonorsChoose, today is the very last day of the challenge. From where I'm sitting I can't see whether or not we've made our goal. But if you look over on the sidebar, you'll see that we've either made the goal or are very close to it. DonorsChoose will kick in a 10% completion…
terrasig | October 30, 2007I chose not to plague you with incessant reminders to contribute to our drive to raise funds for projects at DonorsChoose.org - where public school teachers propose class projects and you decide which ones to fund. Just one post at kickoff and another halfway through. We just completed the drive for our local NPR station so I know that badgering can grow on you no matter how worthy the cause.
But you readers have been incredibly responsive and generous in donating to the Terra Sig "Save the Science" projects. With a total of $2,806.47 donated thus far, we are 70% of the way towards our goal…
sporte | October 30, 2007 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 need $83) or
The Questionable Authority (His teachers need $88), or A Blog Around the Clock and click the right links.
You know you want to.
clock | October 30, 2007There is just a couple of more days left and my challenge is still at 50% (just 6 donors!) so I am panicking. There are several projects that are completely funded and several others that are still far away from the goal, but lots and lots of small donations can make it happen.
Every challenge that reaches its goal gets additional 10% from DonorsChoose. The chances of getting one of the Seed prizes, including the iPod Nano, are very, very good! Chances of getting a prize from me are even better! All the relevant information is here.
Just click here on the thermometer. Please! And…
tsmith | October 29, 2007Edited to add: we've reached our goal! Thank you so much to all who participated; if others would still like to donate, Janet has a list of other blogger challenges--and remember that every completed challenge gets a 10% completion bonus from DonorsChoose, stretching your donation farther. Finally, donors--don't forget to register for prizes!
The Scienceblogs DonorsChoose challenge is wrapping up--the contest officially ends at the end of the month. So far readers here have donated $1,590 to help out teachers and students, largely in districts with high poverty levels. I want to first…
sporte | October 28, 2007Metagenomics 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 who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used metagenomics when he sailed around the world and sequenced DNA samples from the Sargasso Seas.
In this…
sporte | October 27, 2007The simple fact is this: some DNA sequences are more believable than others.
The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad."
All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable.
So, for awhile anyway, I'm making a…
sporte | October 26, 2007We 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.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
clock | October 24, 2007My brain is fried. My flight home was horrifying - the pilot warned us before we even left the gate that the weather is nasty and that he ordered the stewardess to remain seated at least the first 30 minutes of the flight. Did the warning make the experience more or less frightening? I think it made it more so. Yes, the wind played with our airplane as if it was a toy, but knowing that the pilot thought it was nasty made it less comforting that he is confident himself in his abilities to keep us afloat. The scariest was the landing - we were kicked around throughout the descent until the…
sporte | October 24, 2007Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?
This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.)
We are going to do a bit of metagenomics by using FinchTV and blastn to identify the soil bacteria that were sampled from different biomes and then use an SQL query that I…
sporte | October 23, 2007It'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 (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs.
There are certainly advantages in…
sporte | October 21, 2007Welcome 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 subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and we…
sciencewoman | October 19, 2007I'd imagine you are probably all sick of hearing about the DonorsChoose challenge by now, but I'll admit that I'm a bit disappointed by the lack of response I've gotten from you guys. Sure we've raised almost $500, but all of that money has come from just 7 people, including me.
Feedburner says that this blog has 116 RSS subscribers. If each of those subscribers donated just $5 (less than two Starbucks drinks), we'd easily reach the goal and help dozens of students.
Apparently handprints from Minnow and the chance to win prizes from Seed aren't enough to entice you to donate, but maybe this…
tsmith | October 17, 2007The DonorsChoose drive here at ScienceBlogs is just over halfway finished. My challenge is almost 50% funded, with $952 raised so far as I write this and donations from 10 of you out there (and thank you very much for that). There's still quite a ways to go, however, and many incentives to get there. For one, DonorsChoose will kick in additional money for anyone who meets their challenge goal, so that's great for the kids; and second, Seed is offering a number of prizes for donors (and especially for donors to my challenge, copies of "Vaccine" by Arthur Allen). If you've donated already…
clock | October 16, 2007When I went to the Lawrence Hall of Science with Janet, I wore a PLoS T-shirt, of course. The volunteer at the museum, a high school student (you can see her here attaching a harness on Janet), saw my shirt and said "PLoS! Awesome!"
I asked her how she knew about it and why she seemed to like it so much and she told me that they use it in school all the time because it is full of cool information, it is free to read and free to use in presentations and such. Obviously, for her and similar students, the material in scientific papers does not go over their heads, no matter how dry the…
clock | October 15, 2007Perhaps you did not like the shirt. Or do not care for the mug. But if you qualify for one of the prizes by donating to a Scienceblogs challenge on DonorsChoose, you may get a much more appropriate piece - a wall clock:
clock | October 15, 2007Just watching someone give a talk is often not enough to remember it later. As they say, a picture is worth a thousand words. And certainly, seeing is believing. But, this presentation is impossible to forget, even if one would rather not remember it so vividly. Oh, and it was absolutely NSFW!
Obligatory Reading of the Day.
sporte | October 15, 2007This morning Bora and I both gave talks in Second Life. Since this was a pretty new experience for me, I thought I'd share my thoughts on it.
Ever since the days when I watched cartoons on Saturday mornings, I thought it might be fun to be in one. But when I tried it this morning, truthfully, it was a bit scary. I haven't experienced stage fright like that for quite awhile. Perhaps it was the setting. I was really nervous and I hadn't practiced with Second Life enough to know what to do.
Watching a talk in Second Life
Moving around in my avatar felt awkward. It was strange not to be…
sporte | October 14, 2007I'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 for Austin Community College, so this seemed like a good time to find out what the fuss is all about.
Tomorrow, Bora Zivkovic (A Blog Around the Clock) and I will be the first ScienceBloggers (that I know of) to give poster presentations in Second Life. Our talk will be at 4 pm GMT, 12 noon EDT, and…
sciencewoman | October 13, 2007In case helping preschool special ed students by providing materials for science exploration isn't rewarding enough, the Scienceblogs overlords at Seed Media have made two really enticing offers.
First, Seed is matching the first $15,000 donated by scienceblogs readers during the challenge. I think we're really close, and your donation could put us over the top. Even if you only have $5 to donate, with Seed's match, you're really giving $10.
Second, it's not just about the altruism. There is something in it for you. Seed is giving prizes. details below the fold.
Donors can win:
⢠1 fresh,…