sporte | December 19, 2007In which we're reminded that database searches are experiments, too.
One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes even a day later, is a different database. And, if you query a different database, you may get a different result.
The series that I'm currently posting is one that I started working on a couple of years ago. Originally, I was…
sporte | December 18, 2007How do you go about researching a genetic disease?
This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio.
A bit of background
Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the conversation turns to Woody, and someone asks the question that no one wants to touch. Does Arlo's girlfriend know about Huntington's? ...dead silence... Now, I did see the movie quite a few years ago, so my…
sporte | December 17, 2007No, you can't have a glow-in-the-dark kitty.
But never fear, the SciBlings and I have other ideas for holiday gifts.
If you really have your heart set on glowing animals, and you don't live in California, you can get a tankful of lovely glowing fish, genetically engineered with a different version of the protein (GFP) used to make the glow-in-the-dark cats.
If you prefer clothing over pets, there's the pathogenic line of formal wear.
If you've got a child on your list, Janet wrote about these last year, but hey, building sets are always fun. Or, if your kids like other kinds of toys, Janet…
sporte | December 16, 2007Maybe there's something a little bit odd about having a gingerbread construction contest to raise funds for researching juvenile diabetes.
Maybe these gingerbread houses aren't environmentally proper or particularly sustainable.
But they are impressive.
If you're in Seattle over the holidays, you can see them at the Sheraton Hotel until Jan 2nd and even help fund research on juvenile diabetes.
Some more examples are below.
sporte | December 14, 2007Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species.
You gave me some interesting answers.
DAG made me clarify my question by asking what I meant by "similarity." I was wondering whether I would be likely to find a statistically relevant match by doing a BLAST search and I hadn't really thought about the cutoff values. I decided to guess and say that that the protein would be about 30% similar and the nucleic acid about 60%.
Paul gave me some answers…
sporte | December 13, 2007Reposted in honor of the "glow in the dark" kitty clones.
Last year, I wrote about photographs of jellyfish that were altered by newspapers, scientific publishers, science education companies, and me (for the purpose of the article) to make it look like the jellyfish glowed.
Those jellyfish do NOT glow. Those images lie or at least misrepresent the truth.
But that doesn't mean that glowing animals don't exist. These pictures were taken under natural light and came from GloFish®.
Normally zebrafish are white with black stripes, but these zebrafish were genetically engineered to…
sporte | December 12, 2007This is a-mewsing.
(Photo Credit: Gyeongsang National University)
When Genetic Savings and Clone shut their doors it looked like wishful cat owners were going to be out of luck and short of kittens.
Never fear, the South Korean scientists at Gyeongsang National University have come to the rescue. I couldn't find all the details in the news articles but it appears that they inserted a gene for red fluorescent protein into a somatic cell from a cat, transplanted the cell into an egg cell, put the egg into a female cat's womb and a few weeks later, voila!, lovely white Angora cats that…
sporte | December 10, 2007And I was. It was the dreaded Seven Random and Weird things meme! It's on the loose and I've been tagged.
The rules are:
Link to the person that tagged you and post the rules on your blog.
Share 7 random and or weird things about yourself.
Tag 7 random people at the end of your post and include links to their blogs.
Let each person know that they have been tagged by leaving a comment on their blog.
1. Who tagged me? Greg Laden of the kingdom of Linux.
2. 7 random or weird things about me.
Random thing #1: I unconsciously memorize song lyrics and they pop into my head at random times.…
sporte | December 9, 2007These people have dogs and won the contest.
What contest?
I suggest you take a look.
sporte | December 8, 2007Lots of new and curious gift selections are available this year for those of you who had a dog or know a dog owner. All kinds of interesting doggie presents are showing up, like doggie DNA tests and special nutrigenomic doggy diets.
And of course, nothing tops the gift of fake testicles for the dog who's never quite recovered from the big operation.
It's true, the Bleiman brothers were the first to bring up the idea of presents for pets by suggesting the kitty toilet trainer as a holiday gift. Really, though, is that kind of gift that you give to the cat? or the owner?
I just don't think…
sporte | December 7, 2007This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid.
If I gave you the amino acid sequence of this protein, or the nucleotide sequence of this nucleic acid, what is the probability of finding a similar sequence in a different species (picked at random)?
A. High
B. Medium
C. Low
D. It depends on the database that you're searching.
You can have more than one answer.
Now, here's the hard part. Explain why you think your answer is correct.
sporte | December 6, 2007I know it's strange! I never thought I would actually go to web sites (intentionally!) to watch computer ads. But the Mac guy is so cute! And the ads with Mac and PC are sooo funny!
I think these little film clips rank right up there with Steven Colbert and The Office.
What think you?
sporte | December 6, 2007or E. coli, or perhaps a little Giardia (just to loosen things up, of course), or maybe even Herpes.
All these scary pathogens become works of art, when Infectious Awareables puts the images on neckties.
And what could be funnier than a pair of boxer shorts full of Gonorrhea?
sporte | December 5, 2007If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner.
According to GenomeWeb, the test identifies both the breed and origin of the animal.
The university and the company said meat traceability is necessary to ensure consumer safety, particularly in cases of infectious disease outbreaks or accidental feed contamination.
No more doubts about the home of your Jamón.
sporte | December 5, 2007Judging from their groans and moans, I think sometimes that it's hard for kids to grow up with two scientists as parents. Still, over the years our kids have come to accept (and ignore) that we seem to babble in some kind of strange code peppered with discussions of DNA, software, and lately something called "Next Gen."
We'll cook dinner and start reminiscing about PV=nRT.
Our youngest daughter will try to mix water and oil for brownies and one of us will contribute cheerfully: "Like dissolves like."
Now that our oldest daughter is taking freshman chemistry, she gets to hear some new…
sporte | December 5, 2007Do you wonder what the SciBlings drool over during the holiday season?
Here are some gift ideas from Janet, Shelley, Greg, Ed, Mo, the Bleimans, and me.
And you can probably guess what Steve suggests.
sporte | December 4, 2007How do you use science outside of the lab?
People say that transferring knowledge and skills from one subject to another represents one of the highest levels of learning. They also say that it hardly ever happens. Perhaps this explains some of the more astounding things that we hear from Nobel Prize winners, like when Francis Crick proposed that Earth was settled by sperm from outer space, or when Watson, well, we'll leave that subject alone for now.
I admit, I don't always think to apply my scientific training to things that happen outside of the lab. When those moments do happen, I relish…
sporte | December 3, 2007'Tis the holiday season and, according to ancient lore, the time when miraculous events are most likely to take place.
One of those well-known and miraculous events of ancient days was the birth of a son to a young girl, who, although she was married (Okay, I'm not sure about this part of the story) she was said to be a virgin and the birth to be a miracle.
Hmmm.
How do you think the news would be received if that sort of thing happened today?
Certainly, if the young girl were to produce a grilled cheese sandwich with a burn spot that vaguely resembled a woman in a robe, someone might be…
sporte | December 2, 2007Usually, 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 gifts with those you like and love.
I've compiled some of those suggestions here and I'll keep adding new ones as the month proceeds and people post them.http://scienceblogs.com/dispatches/2007/11/get_your_larry_craig_doll.php
Before we indulge the material world though, I'm going to…