Science Education
sporte | January 30, 2007"How much do I love you?
I'll tell you no lie.
How deep is the ocean?
How high is the sky?"
- Irving Berlin
The other installments are here:
Part I: Introduction
Part II: Sequencing strategies
Part III: Reads and chromats
Part V: checking out the library
We all know that sequencing a genome must be a lot of work. But unlike love, it is something we can measure. In fact, an important part of genome sequencing is estimating just how much work needs to be done. This is especially important if you're the one paying for it or the one writing the grant proposal.
Coverage depth: or why do we…
clock | January 29, 2007The 'Basic Concepts in Science" list is getting longer and longer every couple of hours or so, it seems. Try to keep up with it. You may even want to Google-bomb (by linking using the same words as Wilkins does) some or all of the posts if you think they should come up on top in Google searches for these terms. Dan adds his own contribution on Cell Migration and Jennifer makes a wish-list for the Top Ten Physics Concepts that need to be included. To those, I'd add the series on statistics by ECHIDNE OF THE SNAKES: Part 1: Samples, Part 2: Probability, Part 3: Sample Statistics, Part 4:…
sporte | January 29, 2007The University of Nevada in Las Vegas is looking for a few good undergraduates to come do research this summer in environmental microbiology. Environmental microbiology goes way beyond hot springs bacteria and Yellowstone Park. At UNLV, you can do science in the desert.
It almost makes me wish I was an undergraduate again.
The Microbiology faculty at the UNLV and the Desert Research Institute are looking for inquisitive and eager undergraduates to participate in a 10 week summer research experience in the REU (Research Experience for Undergraduates) program.
Projects involve studying…
clock | January 28, 2007In the series of "Basic Concept And Terms" (yup, I know, John is well known for misspelling people's last names, including mine), several people have already chimed in with their own definitions of the "gene", demonstrating how unclear this concept is and how much disagreement there is among the practitioners depending on the type of research they are doing (e.g, molecular biology, developmental biology, population genetics, evolution, etc.).
See how the term was defined and explained by PZ, Sandra and Greg so far and you'll see those differences in emphasis.
Now Larry Moran joins the fray…
sporte | January 28, 2007Shotgun sequencing. Sounds like fun.
Speculations on the origin of the phrase
I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique to Minnesota, though. When I moved out west for graduate…
sporte | January 27, 2007Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from 407 phage.
Much of the methodology used for sequencing DNA is designed to confront one big technical hurdle.
That is, we can only determine the sequence of small pieces of DNA at a time. This means that you must break a larger…
clock | January 25, 2007When I was a kid, there was no such thing as "do it yourself" biology for home. Sure, you could do observational stuff, like go out in the woods with a butterfly net and a magnifi\ying glass, or plant some seeds, or look at stuff under the microscope, but it was hard to do real experiments in biology.
My favourite trio of childhood science books (recently reissued) were "Between Play and Physics", "Between Play and Chemistry" and "Between Play and Mathematics" - see, no biology there!
But the world of science has changed since then and there is much more stuff that one can do at home that is…
clock | January 25, 2007The latest re-post of my BIO101 lecture notes (this one originally from June 05, 2006). I know I will have to rewrite everything about the Three Domain Hypothesis, but you also tell me if I got other stuff wrong or if this can be in some way improved for the classroom use.
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BIO101 - Bora Zivkovic - Lecture 4, Part 3
In the first two parts of this lecture we tackled the Origin of Life and Biological Diversity and the mechanisms of the Evolution of Biological Diversity. Now, we'll take a look at what those mechanisms have produced so far - the…
clock | January 24, 2007Most of our anti-Creationist battles are over efforts to infuse Christian religion into K-12 education. One common battlefield is the courtroom where our side has (so far, until/unless the benches get filled with more clones of Priscilla Owen) won. But another place where we can stop them is the college admission office.
Sara Robinson of the Orcinus blog (which everybody should read daily) revisits, in more detail than I ever saw on any science blogs at the time this first started, the legal battle between the University of California and the Calvary Chapel Christian School over what…
sporte | January 24, 2007Tired of waiting for congress and you don't want to move to California or out of the US? Attila Csordas shows us in a few photographs how to isolate placental stem cells at home.
His series brings back memories. My very first paid technician job in college involved visiting the maternity ward, collecting placentas, and starting primary cell cultures from umbilical epithelial cells. I would tie one end of umbilical cord, squirt a bit of media with some trypsin, and incubate the thing for a while so that the trypsin could digest some of the proteins that held the cells together. After a…
clock | January 22, 2007In the wake of the conference, I suspect that my blog is getting checked out today by many a science teacher, so I thought this would be a good time to point out all the posts written so far by my science-blogging friends on 'Basics Terms and Concepts' in math and science. Here they are:
Good Math Bad Math:
Normal Distribution
Mean, Median and Mode
Standard Deviation
Margin of Error
Uncertain Principles:
Force
Fields
Pharyngula:
Gene
Discovering Biology in a Digital World:
Gene
How do you sequence a genome?
Sandwalk:
Evolution
The Central Dogma of Molecular Biology
Evolving Thoughts:
Clade…
sporte | January 22, 2007About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught.
I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question:
How do you sequence a genome?
Before we get into the technical details, there are some other genomic questions that you might like answered.
How much does it cost to sequence a genome?
I remember in 2002, when we were at the O'Reilly bioinformatics conference and we heard Lee Hood challenge the DNA sequencing community to lower the costs of genomic…
sporte | January 21, 2007In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong.
The definition from…
sporte | January 21, 2007I read about this in Science and immediately had to check it out. Instant gratification on the internet is such a wonderful thing!
The Ed Kravitz lab has made movies of fights and even put them on the web for your viewing pleasure.
You can see the following fly fights that might suit your fancy:
Fighting flies
Male Drosophila melanogaster aggression (with music)
Female Drosophila melanogaster aggression page
Or if you prefer battling sea life, you can watch the lobsters duke it out. Now I know why the lobsters in the grocery store tank always have rubber bands around their claws.…
sporte | January 19, 2007The American Society for Human Genetics is sponsoring the second annual DNA Day Essay contest. If you are a high school teacher here's your chance to combine an interesting assignment along with a contest.
This year's essay questions are:
If you could be a human genetics researcher, what would you study
and why?
In what ways will knowledge of genetics and genomics make changes
to health and health care in the US possible?
The rules are here at GenEdNet.org
I also have an animated tutorial at Geospiza Education that might be of some help. The tutorial is titled Allelic Variants of…
clock | January 18, 2007Part 12 of my BIO101 lecture notes. As always, click on the web-spider icon to see the original post (from June 04, 2006). Correct errors and make suggestions to make this better. Perhaps this entire series can be included in the "Basic Concepts" series.
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BIO101 - Bora Zivkovic - Lecture 4, Part 2
In the previous segment of the lecture, we looked at the Origin of Life and the beginnings of the evolution of biological diversity. Now we move to explanations of the mechanisms by which diversity arises.
Although traits can be inherited by non-DNA…
clock | January 16, 2007 *N.C. Museum of Natural Sciences
/Downtown Raleigh/
**Thursday, January 18
"Flock of Dodos" screening with filmmaker, Randy Olson
7:00 p.m. Museum Auditorium
Free
*Filmmaker and Evolutionary Ecologist , Dr. Randy Olson, presents his
new film */Flock of Dodos/*: /*The Evolution / Intelligent Design Circus.*/
"Flock of Dodos" is the first feature-length documentary to present both
sides of the Intelligent Design / Evolution clash and tries to make
sense of the issue by visiting Olson's home state of Kansas. The film
digs below the surface of the debate by examining the language being
used by…
clock | January 13, 2007The 'Basic Concepts' series has started. Here are the first two, defined and explained:
Evolution
Clade
We are thinking of a way to store all of these posts in one place for easy reference. I'll let you know when that happens.
clock | January 12, 2007I know I kinda burried that at the bottom of the previous post, but now that I see that a number of my SciBlings are trumpeting it loudly (see Chad, Tara, Janet, Afarensis and Mark, so far), I guess I'll make a little bit louder call myself.
When you are immersed in a scientific field for a number of years, it is easy to forget that not everybody undrestands the basic concepts and terms of your field. While I always try to keep that in mind, I am sure I baffled you on occasion. Does everyone know the difference between phase, period and amplitude, the difference between phase-delay and…