Tag Archives: education

Ancient Genomes: Neanderthal

So, yesterday was the 200th anniversary of Darwin’s birth. Lots of festivities and NPR stories surrounding that day including a few announcements like UCSC announcing their v200th browser code a day early so as to coincide (they couldn’t resist the coincidence :)). Another announcement that was apropos was the announcement that researchers at the Max Planck Institute for Evolutionary Anthropology have finished the draft sequence of the Neanderthal genome. Since only about 63% of the genome is actually covered (3.7 billion bps covered of the 3.2 billion bp genome, with duplications), when one announces a “draft” can be a bit arbitrary, so the 200th anniversary of the of the man who wrote “The Descent of Man, and selection in relation to Sex” is as good a time as any. And we are learning a few things like, Neanderthal’s might have had the physical ability for language, but couldn’t stand milk as adults (didn’t agree with their digestion). It is expected a draft and research will be published at the end of this year. We’ll report on that of course, and link to any browsers they might be setting up :D. Ancient genomes are teaching us some things.

Speaking of which, the Exploratorium, an excellent science museum in my fair city, has a great exhibit (on site and online) on the ‘how we know things’ and how science works. This exhibit is specifically on the origins of humans and Neanderthal DNA and the research at Max Planck figures prominently.

Teaching and annotating at the same time

plos teaching paperA recent paper (couple weeks ago) in PLoS Biology from Hingamp et al. had me intrigued. Entitled Metagenome Annotation Using a Distributed Grid of Undergraduate Students, the lecturers put together a system to teach bioinformatics to undergraduates that uses new unannotated sequences from metagenome projects. As stated in the announcement,

This method asks students to randomly pick and analyze unknown metagenomic DNA fragments from a real research sequence stockpile. The student’s mission, using Internet tools only, is to figure out from which organism the DNA comes from, and what biological function it might have. As well as gaining confidence and proficiency in bioinformatics, students experience the authentic research process of weighing the arguments, establishing prediction reliability, building hypotheses, and maintaining rigorous disourse.

The lecturers have put together  a teaching-annotation procedure in a publicly accessible “annotation environment” they call “Annotathon.” This web interface walks the student through the annotation process in a procedure as you see in the figure here. Since you can join and use this interface, I thought I’d give it a test drive.

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Nerd Girls

From the Boston Globe I was led to a local blogger, who brought my attention to the Nerd Girls. Apparently this is a local group of engineering students who are trying to make engineering “cool” for girls. I’m not sure I’m psyched on luring them as chemical engineers for make-up, but if that’s what gets some smart young woman interested in the field, so be it. So far we aren’t doing that well with our current outreach strategies.

So have a look at the Nerd Girls. I think their confidence is great, and the social networking approach is worthwhile. Kudos to IEEE for their support of this. But mostly congrats to the Nerd Girls for the courage and the effort.



science blogging conference

We are here at the science blogging conference this morning. It starts in 30 minutes. I’m looking forward to attending several sessions. First one im attending is on “open science” or how the Internet has changed science. I just wrote a post about that :). The next session I’m going to will be on teaching science online. Then there is the making your blog more interactive. Last are the general sessions. I’ll report on them all later. Right now I’m testing out my iPhone blog posting interface :)

EDIT by Mary: I’m watching this conference remotely on UStream.tv from this link: http://ustream.tv/channel/waynesuttontv

Basic Biology Concepts

You have some non-biologist colleagues (attorney? manager? programmer?) you need to get up to speed, or you need to brush up on some concepts yourself? A good place to start is this list from John Wilkins (Evolving Thoughts). It is a list of links to blog post across the blogosphere that explain and expound on various basic concepts in science. The list for the life sciences ranges from basic evolution to clade to biomes to linkage disequilibrium to a lot else. It includes a list of lectures from Bora Zivkovic at Blog Around the Clock in basic biology. Additionally, make sure to read the comments to the first link, commenter contributed a lot of their own. A wealth of information out there in the blogosphere.