Happy Sun-Earth Day!

photo from NASA's image gallery.

I guess there was a live webcast from Turkey this morning (2:00 am PST) of a total solar eclipse. Needless to say, I missed it due an earlier appointment with my pillow.

But it doesn't matter. You can satisfy any urge to see an eclipse over the web at NASA's video gallery. There are 5 short videos of past eclipses that are lots of fun and even one of my favorite technologies, podcasts! I haven't listened to any yet, hopefully they'll be as good as the Stardate radio shows on NPR.

The video gallery includes animations that describe what's happening during an eclipse. Personally, I still like the old fashioned method for teaching these ideas. Outside of seeing an eclipse in person or watching the eclipse videos, nothing beats making an eclipse with a flashlight and a couple of oranges.

Subject: Web resources

technorati tags: astronomy, eclipse

Sugar, Sugar ...

As of March 24th, over 186 people have tested positive for the avian flu virus (H5N1) and 105 are dead (1).

This is a nasty kind of flu.

Luckily, most of the cases, so far, have been in our avian friends and their human companions. Health professionals all over the world, though, are warily watching web sites and looking for signs that people are catching flu from other people. Everyone wants to know the point when it's no longer strictly for the birds.

But for the moment, we're okay, it seems like the avian flu doesn't spread easily from one human to another.

And now we know why.

Two reports this week, in Nature from Shinya, et. al.(2), and in Science from van Niel, et. al.(3) provide the answer.

Avian flu, it seems, likes to stick to a certain kind of sugar. That modified sugar, is a sialic acid with an alpha 2,3 link to galactose, and is joined through other sugar residues to the surface of special kinds of cells. At one time, flu researchers didn't think humans had these specific kinds of cell-surface sugars. But both of research groups found extra-special sugar coating on the surface of cells, deep in the lungs, and confirmed that these were the cells that got infected.

Van Reil and colleagues found this result by mixing inactivated viral particles with tissue samples. They used fluorescent antibodies to see where the virus stuck and which kinds of cells it liked.

Shinya, et. al. stained infected tissues with lectins to see what kinds of sugars could be found on different cells. They also stained infected tissues (epithelial and alveolar) to look for viral particles.

Since the cells that get infected are located deep in the lungs, any new viral particles produced through an infection have to travel a long distance in order to get out of the mouth and infect someone new. This would make it harder for the virus to infect a new human because it doesn't escape the body through a simple cough or casual sneeze.

How is this different from the current human flu?

The influenza strains that are doing most of the damage, in humans this year, bind to a different kind of sugar than the avian strain. The human flu sticks to a sugar with an alpha 2,6 link to galactose; unfortunately for us, this sugar is found on cells in the nose and upper respiratory tract. This makes the human flu more infectious (for us) since it can travel long distances with a good strong sneeze.



Click the drawing to make it bigger. But be warned, I took some liberties here. Influenza is usually drawn like it comes from outer space. Typical images show lots of spikes to represent the hemagglutinin and neuraminidase molecules on the surface of the particle. Also - the cell and the virus are not drawn to scale.

What does this mean? Are we safe?

No one knows. Some experiments earlier this month, by Stevens, et. al.(4) found that it only took two mutations, in the right positions, to change the specificity of a hemagglutinin from one kind of sugar to another. No one knows how many mutations would be needed to change the specificity of the H5 hemagglutinin. Neither do we know much about the probability that this will happen (although I'm sure this is something that could and should be examined by mathematical modeling).

It could happen.


References:

1. World Health Organization. WHO Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO. (www.who.int). (accessed March 24, 2006).

2. Shinya K, Ebina M, Yamada S, Ono M, Kasai N, Kawaoka Y. 2006. Avian flu: influenza virus receptors in the human airway. Nature. Mar 23;440(7083):435-6.

3. van Riel, D., Munster, V., de Wit, E., Rimmelzwaan, G., Fouchier, R., Osterhaus, E., and T. Kuiken. 2006. H5N1 Virus Attachment to Lower Respiratory Tract. Sciencexpress. www.sciencexpress.org

4. Stevens J, Blixt O, Tumpey TM, Taubenberger JK, Paulson JC, Wilson IA. 2006. Structure and Receptor Specificity of the Hemagglutinin from an H5N1 Influenza Virus. Science. Mar 20; [Epub ahead of print]


Subject: Microbes

technorati tags: virus, avian influenza, bird flu, influenza

Look at the wee animalcules!

A new Animalcules has been posted. This week's issue contains stories on Plasmodium, papilloma virus, antibiotics, influenza, and other interesting bits.

Stop by and take a look. And, consider submitting a story to one of the next issues. It's a low pressure way to share subjects that you enjoy.

Read away and wash those hands!

Sequencing a Genome: the video

Have you ever wondered how people actually go about sequencing a genome?

If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?

Wonder no more!

You too, can take a virtual tour of the Washington University Genome Center.

I found this really excellent series of short videos that follows two genetics students, Libby and Bryce, as they meet on the bus to the Genome Center and learn about all the steps involved in sequencing a genome.

A kindly tour guide takes Libby and Bryce through an amazing number of core labs, where they see gallons of media getting made. Among other things, they watch robots pick colonies of bacteria and inoculate broth. They see capillary tubes transport sequencing reactions into genetic analyzers and they see lots of people sitting in front of computers. All the steps are presented nicely and there a number of short animations to help visualize concepts such as growing E. coli that contain BACS (Bacterial Artificial Chromosomes), restriction mapping, and PCR.

Not only are these videos helpful for students who want to learn about biotechnology, these videos are helpful for bioinformatics groups and software companies like ours. Although some of us grew up sequencing DNA, a large fraction of the programmers and software engineers at Geospiza, did not. We routinely send our development team on field trips to a local genome center so they can learn what technicians do. Now, we can refer developers to the genome video to see where the samples go and learn how people work with all those robots.

I like this video, too, because it shows scientific careers that do not require a Ph.D. All too often, people think the only jobs in science involve heading up a laboratory, and they forget that industrial-scale science requires many different kinds of abilities and offers several different opportunities. In fact, a large number of the people working in facilities like genome centers have bachelor's degrees or 2-year degrees from community college biotechnology programs.

Even if you've done some sequencing yourself, it's still interesting to see how the Wash. U. genome center has turned DNA sequencing into an industrial scale process.

I, for one, never knew that so many genome technicians wore baseball caps at work.


Subject: Web resources

technorati tags: biotechnology, genomics, DNA sequencing

When Mt. St. Helens moves her bowels ...

brown water flows out of faucets in Arkansas.

A simple little earthquake on March 7th, 2006, and 22 hours later, there were calls about brown water in the Feliciana Parish.

“People don’t want to believe me when I say an earthquake caused their brown water, but it’s true,” John Hashagen said.

Hashagen said he began looking into the possible effects of seismic waves on the Laurel Hill wells after reading an article in WaterWorld, a magazine for the municipal water industry, on the effects the March 1964 Alaskan earthquake had on water systems across the country.

Not only did the utilities chief uncover a possible connection between west coast earthquakes and discolored water, he found a way to use that information.

Apparently there are only two wells in the area that are sensitive to seismic activity.

Hashagen said he and water district employees can prevent the wells from pumping the discolored water if they learn about an earthquake hundreds or thousands of miles away in time to temporarily shut down the wells.

So, he signed up for earthquake alerts, via e-mail, from the U.S. Geological Survey. Whenever a quake occurs that measures over 5.0 on the Richter scale, he gets the message and shuts down the wells.

The brown water happened on March 8th because the March 7th earthquake was too small to trigger the e-mail alert (only 3.1 on the Richter scale).

I think if Dave Barry were a science teacher, this is the kind of stuff he would love.

Thanks are due to the WSTA for sharing the fun!


Subject: Weird Science

technorati tags: geology, earthquake

3/39/2006 Update: It should be noted that the geological jury is not convinced that Mr. Hashagen is correct. He might be right, Mt. St. Helen's movements might truly be connected with the funny colored water, but a bit more science needs to be done before geologists will believe that the connection is real.

How would you test this? What sorts of data do you think need to be collected and analyzed in order to test Mr. Hashagen's hypothesis?

Doing the cross-species hop

What allows a virus to begin infecting a new species?

This question concerns many people these days as we anxiously watch the skies. When will avian influenza obtain the capacity for human to human transmission?

It seems in the case in parvovirus, that a rapid mutation rate may be a key. If a virus can quickly mutate, some of the progeny might be better adapted to the new host.

HHMI news has a nice description of a fascinating study, recently published in the Journal of Virology, that extends work published last year in PNAS (1).

The authors look at the evolutionary changes that occured when the feline panleukopenia virus made the switch and began infecting dogs. Once the virus began to infect dogs, mutations began to appear more rapidly, paving the way for dog to dog transmission. It's an amazing and nicely done piece of work that helps illustrate why evolutionary studies are important.

Or perhaps it's just a case of the cats getting their revenge.

References:
1. L. Shackelton, C. Parrish, U. Truyen, and E. Holmes. 2005. High rate of viral evolution associated with the emergence of carnivore parovirus. Proc. Natl. Acad. Sci. 102:379-384.


Subject: Microbes

technorati tags: virus, microbiology

When will students do science with computers?

Two puzzling streams of thought have merged lately, leaving me in an eddy of confusion.

In the first stream, swim my observations of the kids in our house. We bought computers for both of our kids with the naive parental notion that they would be important for school.

I still think they are important. And both kids do use their computers routinely.

But, do they use them for school?

Not much. Computers, it seems, are all-purpose entertainment centers for watching DVDs, working with digital photography, communicating with friends through instant messaging, Skype and e-mail; and for organizing music.

None of their classes have the kids use their computers, with the exception of language arts or history classes where they mostly use them for writing papers.

As a scientist, parent, occasional community college instructor, and someone who writes instructional materials for science students, I'm mystified by this observation. Why don't our kids use computers for subjects like science and math? They could be making cool graphs and doing statistics or writing algorithms with programs like Excel. Their science classes could have them looking at GIS data, working with Google maps, searching DNA sequences, or doing fun things with molecular modeling.

I felt like a subversive when I showed my oldest daughter how to use the NCBI Taxonomy database to identify kingdoms and phyla. There are so many wonderful resources out there and I know some high school and community college teachers do use them, but I also know my kids do not.

Why don't our kids use computers for science and math?

The answer to that question lies floating in the second stream but it's a tricky one to catch hold of.

• Is it lack of training?

• Is it lack of money? Are the school districts short on computers?

All of these are at least partly true.

This report and quote from the National Science Foundation certainly implies that lack of computing experience could be a factor.

America's Pressing Challenge - Building a Stronger Foundation, Feb 23, 2006

Technology has its separate challenges. Teachers must shift from being "familiar with" computers to being able to more effectively use computers in support of their instruction. Most of their students are already entering school computer literate, but "do not have a grasp of the science and engineering that underlie that technology."

Lack of money could be another factor. Many science teachers share a computer lab with several other classes, so getting the lab requires a combination of advance-planning and finely-tuned negotiation skills. Still, many teachers will do an activity or two in the computer lab, and never assign outside computer work except for writing papers.

But when I ask teachers, "Why don't high school or community college students learn how to use the computer as a scientific tool?"

I get a different answer.

The teachers, I know, say they won't use computers for science assignments because there are students who don't have home computers.

Admittedly, my sample size is small and non-random, but I've heard the same answer, verbatim, in different parts of the country.

I understand being reluctant to add assignments that require computers that students don't have. But aren't there any other options? I find it strange that this reluctance (as far as I know) only appears in the science and math classes. Language arts teachers require typed papers. Do they ask if kids have computers first? Are science students the only kids in the world still using typewriters?

Universities and private high schools don't seem to have this problem. They just require all students to get computers.

The report above indicates that the NSF believes it's important for kids to learn how do science with computers. Five years ago, in 2001, 70% of the households in Seattle had on-line access, causing it to rank 2nd in the nation in terms of wired cities. Given the large fraction of households in Seattle that have computers, and the number of parents who say they buy them for their children, it seems like parents want their kids to become adept with technology.

But how will kids acquire these skills? If their teachers won't assign the technology, the kids will have to work to learn it on their own, and somehow manage not to be distracted by all the entertainment opportunities that computers offer instead.

Personally, I don't think many public school students will be able to teach themselves how to use computers for scientific research. At least, not until they have guidance from their teachers and access to computers beyond the occasional day in the computer lab.

So right now, judging from what the teachers say, the only kids who will learn computer skills in school will be the kids whose parents can come up the 20K per year for private school tuition.

What is the best answer to this puzzle?

The ideal situation is one where every student has a computer. But how do we get there?

Perhaps high schools, and maybe community colleges, could start loan programs, like they do with graphing calculators. True, laptops are more expensive, and more difficult to maintain, but I think, given the choice between no computer assignments and helping out with a loaner program, parents would help out. It's far cheaper for parents to buy a computer and help chip in for additional loaner computers than to pay $80K for four years of private school.

If all kids had computer access, science teachers might give computer assignments and all our kids might have a chance to learn how to use computers for doing science.

Until that day, it seems that public school science classes just won't compute.


Subject: Education

technorati tags: bioinformatics, education, science
science education

Hunting for huntingtin V: BLASTing on forward

This is the fifth article in our series on using digital biology to investigate Huntington's disease. Right now, since we know that extra glutamines are linked to Huntington's disease, we would like to know if other genetic diseases can result from extra glutamines.

If you wish to learn more about the story, the previous articles are described below. Or you can jump ahead and go straight to today's episode.

• Hunting for huntingtin, part I Background, reviews, biochemistry of glutamine, and a bit of comparative genomics


• We were quite busy in part I. We learned about Woody Guthrie, found an interview with Dr. Nancy Wexler, and got a bit of background information on the huntingtin gene.


• We used the UCSC genome browser to see if other creatures have the huntingtin gene and a similar gene structure.


• We asked if the extra glutamines caused the disease and looked at experiments where the Jackson Labs tested this idea in mice.


• Last we looked at the structure of glutamine and mused about why lots of glutamines might cause problems for a cell.

• Hunting for huntingtin, part II In which we're reminded that database searches are experiments, too.

• We discover that the polyglutamine regions are missing from structures with polyglutamine and we are unable to find polyglutamine sequences in GenBank


• Hunting for huntingtin, part III Our continuing search for proteins with polyglutamine


• In which we learn what happens to low complexity sequences in a blastp search.


• Hunting for huntingtin, part IV: What did you expect to find?


• In which we learn how to adjust the blastp parameters so that we can find proteins with polyglutamines

************************************************************

Enough of the recap, on with the experiment!

It took a few trys to figure out how to do the experiment. Now that we know how to do it, what should we do first?

We should learn a bit more about blastp. Nothing scary, mind you, but it's nice to have an idea how the information we put into a program is related to the output. So, before we go on, we're going to do a little experiment with blastp and see what happens when we search with different numbers of glutamines.

(We could also read about blastp, but hey, experimenting is more fun!)

Here is an image compiled from our colorful results:

I stopped at 50 since the scores didn't really change after that point.

Notice, how the length of our query sequence (lots of glutamines, abbreviated as Q) is related to color code. The color code, as shown in the color key above each alignment, is based on the alignment score. Scores in certain ranges are colored certain ways. You can see as the length of the match increases, the color changes, too. Our polyglutamine sequences give us a nice way to look at this relationship because we're using the same amino acid.

Why is that important? Keep reading and wonder no more!


I'll give you 10 points for a good match!

Did you ever think that calculating blastp alignment scores might be kind of like a game?

Indeed, it's a great game.

You get different amounts of points for matching different amino acids. And if your amino acids don't match, you get a penalty. The scoring table (also called a "matrix") is shown below. Click on the image to see it appear a bit larger, if you like.

I highlighted the value that's assigned when a glutamine (Q) matches another glutamine (Q). If one glutamine matches another, we get 5 points. Yeah!

Our final score is calculated by tallying up the points for each position in two aligned sequences. If we match 10 glutamines in a row, we get 50 points. We multiply by some mysterious factors (that may be discussed later) and finally, we end up with a score around 24.


Can I use my alignment points like frequent flyer miles? Who made the score sheet?
Why does matching another glutamine get 5 points and having a C (cysteine) match another cysteine get 9 points? Or when a W (tryptophan) matches another tryptophan, it gets 12 points?

Steve and Georgia Henikoff came up with these scores by looking at blocks of aligned sequences and determining how often a particular amino acid was replaced by a different amino acid (1). If the same amino acid was almost always found at the same position, it was assigned a higher score (i.e. W, tryptophan).

Notice, too, that our table has a row with a *. The * represents a position in a sequence where one amino acid is missing. Missing amino acids get assigned a negative score (-4) because they're are less common. This is probably because amino acid changes, in important regions, would harm the protein structure and impair the function.

We also get points if an amino acid is replaced by one with similar chemical properties. For example if we replace a lysine (K) with an arginine (R), we still get 2 points, because both amino acids have a positive charge. (If you want a key with chemical structures, or a key to the abbreviations, you can get them both here).



How do different numbers of glutamines affect the blastp results?

The graph below shows what happens when I do blastp searches with different numbers of glutamines. It only takes 10 glutamines to change the E value from 33 (not very significant) to 0.0001 (very significant).

The scores change a bit more slowly. I was surprised to see the relationship between the number of glutamines and the number of hits. Intuitively, it seemed to me that a smaller number of glutamines should match more things in the database. But the results contradict that notion.

Why did that happen?


When in doubt, look at the data

Looking at the sequence alignments shows why we see more hits. The results (below) show that when we we're using a repetitive sequence like QQQQQQ ... etc. and we use a longer query sequence, the query can start aligning to a database sequence at a greater number of points (and still have enough matching amino acids match to score as a hit). See how the alignment starts at 1, then 2, 3, and 4? This means that our query sequence can align to the same database sequence in multiple ways.

Longer query sequences can also tolerate gaps and more amino acid changes; yet still match enough amino acids to register as a hit.



So, in this case, a greater number of hits doesn't really mean that we're finding more sequences in the database. We're just finding the same sequence more times.

Do we only care about the number of hits?

No. Of course not. We do learn which proteins contain lots and lots of glutamines.

Stay tuned, next time we look at results.


References:
1. Henikoff, S. & Henikoff, J.G. (1992) "Amino acid substitution matrices from protein blocks." Proc. Natl. Acad. Sci. USA 89:10915-10919. (PubMed)


Subject: Doing biology with bioinformatics

technorati tags: biology, blast, , genetics, DNA

Birth of the Biotech Boosters

Many years ago, long before my kids were high school age, I joined the steering committee of a brand-new biotech program that was starting at a local high school. A local company (Immunex) had pushed the Seattle school district to start the program and provided start-up funding. There was a brand new lab, additional money from another local company (Zymogenetics) and a strong feeling of energy and optimism for the future.

In the early days, funding was good. Immunex and Zymogenetics helped provide funding, and a grant from the Stewart Foundation gave teachers time for curriculum development and working on the program.

But corporate sponsorship can be a fickle thing. One of the major supporting companies, Immunex, was sold to Amgen and we all learned that Amgen was a different sort of company. Former Immunexers tried to maintain local outreach programs but many of the outreach activities were still lost. Former Immunex employees do continue to volunteer in the community, and Amgen still funds some community activities, but unfortunately, much of the support for high school programs has gone. Corporate sponsorship disappeared along with former student internships.

This left the biotech program in a quandry. Biotechnology is a laboratory science and science labs require consumable supplies, like enzymes and agarose and buffers. These aren't items that can be picked up at the local grocery store and they're expensive. If students are going to learn how to clone genes and work with DNA, they have to have equipment and supplies.

Our steering committee was composed of people with scientific backgrounds and little experience in fund-raising. Writing grants was a possibility but it's easier to get money to start something new than money to maintain a program.

About the same time, my oldest daughter started high school and I gained a new appreciation for the reality of funding anything at the high school level. In her first year, she joined both the soccer team and the biotech program. Instantly, we were bombarded with fees and funding requests. There were $50 activity fees for participating in sports, donation requests from the sports boosters starting at $150, yearbook fees, picture fees, all kinds of fees. Here a fee, there a fee, everywhere a new fee. Still, when you contrast these fees with the cost of $20,000 a year for a private school, public education at a good school is a great bargain. Our school district has serious money troubles, so none of the fee requests were really too surprising.

The surprise was the lab fee for the biotech program. The program asked for a lab fee of $8. As a parent, we had paid more than that for individual elementary school field trips. This was a shock! If I estimated that there were about 180 kids total in the program, the lab fees would bring in less than $1500. This wouldn't even cover the costs for a couple of field trips, much less allow the school to replace broken glassware, pay for supplies, fix broken pipettors (that cost $200 each), or purchase any new equipment. Our community college program had cost about $8000 per year for supplies and we had ten times fewer students than the number in the high school program. It was clear that the lab fees weren't going to be enough.

We realized it was time to learn from the sports boosters and make our own appeal to the biotech parents. We wrote a letter requesting their help and followed it with phone calls to all the parents. Not only were the parents supportive, they were surprised to learn that the biotech program needed funds and their help. In response the parents started the biotech booster group.

Since that time, the biotech boosters have helped out in many ways, including:

• Donating funds
• Finding mentors for students
• Helping to find internships for students
• Finding scientists and biotech professionals to judge student talks

The Biotech Booster help has been very worthwhile. We still can't take adequate funding for granted, but now, at least, there's a way to ask for help. A yahoo e-mail group keeps parents more informed about happenings at the school and gives teachers a more convenient way to transmit information. Communication between parents, steering committee members, and teachers has increased. Parents know more about the different milestones that occur in the program and can find out what their kids are going to encounter. Events like the Biotech Expo, the bioethics presentations for scientists, field trips to SBRI, mentor events, and applications for internships, are no longer mysterious things that happen under parental radar.

All too often, I think, parents become less and less involved once elementary school is over. Having a booster group has helped open a door and made it possible for parents to become more active in supporting their child's academic education. It gives parents a way to show that academics are valued at least as much as the extracurricular activities like football or band.

Subject: Education

technorati tags: biotech, education

A Birthday Celebration with Goofy Minnesota Limericks

GrrlScientist invites you all to attend a surprise virtual birthday party for PZ Myers.

While I've never met PZ, I have enjoyed reading his blog, Pharyngula, and learning new things about embyros and the mysterious things that go on when cells divide and develop. Plus, PZ's brainchild, TangledBank is always a wonderful collection of fun things to read.

It's hard to know where the party is beginning or ending, but if you've ended up here, imagine yourself eating a piece of chocolate cake with pink amaretto frosting, while you can enjoy these goofy Minnesota limericks. Don't worry if they don't make any sense, I try to avoid sensible poetry.


There once was a young man from Morris
whose head was extreme-i-ly porous
his thoughts just leaked out
as he typed them about
and we're all waiting now to hear more o' this


Our fishing is fancy year round
the loon makes a strange erie sound
the canoe is a leaking
so when no one is peaking
napping is where we'll be found


You betcha by golly, it's fun
playing cribbage and waiting for sun
we've got cabin fever
in the lodge like the beaver
we'll come out when the winter is done


The snow is abundant in March
in August we all start to parch
we get eaten by mosquitoes
while we're chomping on fritos
Would it help if we all used more starch?


I once lived near Lake of the Isles
and skated around the goose piles
In my city of green
with the unearthly sheen
I rode my bike on the trails that went miles


In St. Paul every year there's a fair
whose size there is none that compare
we've heard some say "Texas?",
but most they say "not this!"
Minnesota's the place, that we'll share


Subject: Silly items

A day at the Biotech Expo

Today, I'll be your tour guide on a journey through Biotech Expo. We'll begin our trip in creative writing with the exploration of complicated family ties and genetic entanglements.


Next, we'll look at some modeling activities. The gentlemen on the right used an ecology program with sheep, wolves, and bushes, to simulate what might be happening inside your nose. The sheep represented bacteria or viral particles, the wolves, our immune cells, and the bushes, were the nose cells. These students examined the impact of changing the number of immune cells or the numbers of bacteria on the overall health of the nose.

Another modeling project is shown on the left. This model was made by cutting out shapes from some kind of squishy material and sticking wires through them. Very colorful!



On the right is one of our high school researchers describing her project to some of the judges. A winner in two categories, her project compared methods for isolating DNA for genotyping and the reproducibility of the different methods. She put her AP statistics class to good use!


"And when you smile for the camera..."

Serious drama students are always up for an interview with reporters, especially when they bring a film crew.



Today's tour will have to bypass the popular musical performances, and exceptional projects on journalism, multimedia, teaching, website design, and histology since a day at the Expo passes by quick and our tour is running out of time. Fortunately, we will not miss out on biotech art. Below, on the right we see a beautiful painting of yellow Trypanosoma gambiense swimming around in a pool of red blood cells. On the left, we see a drawing with both the science and consequences of multiple sclerosis.

The yellow busses are lined up and ready to depart. If you listen closely you can hear hands clapping from thousands of parents, thanking the dedicated organizers at the Northwest Association of Biomedical Research, and all researchers and biotech people who volunteered to be mentors or judges.

The tour is over

. . . until next year.


Subject: Education

technorati tags: biotech, education
science education

What's that stuff?

Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?

Chemical and Engineering News, published by the American Chemical Society, has a wonderful section that you will certainly appreciate.

"What's that stuff" is a collection of entertaining stories about the stuff we encounter in everyday life. Each article combines chemistry with history and fun facts in a way that entices the reader to stay awhile and read every one.

Since the stories are written for non-chemists, they make a perfect companion to chemistry courses ranging from high school and beyond.

Many of the articles would be great in non-chemistry courses, too. For example, the articles on chocolate, Jell-O, ice cream, margarine, MSG, licorice, and chili peppers would be great assignments for any nutrition or cooking class. Microbiology students would enjoy reading about food preservatives and pasteurized foods. Environmental science students could read about bug sprays, plastic bags, cement, asphalt, and artificial snow.

Even artists, cosmetology, and fashion students would find something here to spark their imagination. Stories on sunscreen, ink, fireworks, hair coloring, self-tanners, and lipstick are sure to appeal.

With articles on topics that range from Silly Putty to Lycra, and catnip to champagne, this site is sure to answer some questions along with raising a few new ones.

What is kitty litter anyway? Now, I'm going to have to find out.


Subject: Chemistry

technorati tags: teaching-carnival, chemistry

Build your own virus

Build your own virus! is a simple, quick, and fun game that provides a good way to introduce students to features that are used to distinguish viruses.

The game works like this:

• First, you choose whether the virus has an envelope or not.
• Next, you choose whether the genome is single or double-stranded.
• Then you pick your favorite kind of nucleic acid - RNA or DNA
• Last, you decide if the viral particle should be small, medium, or large.
• And the site tells you what kind of virus you built (computer is not a choice!).

A good memory game is to pick a virus and try to remember it's characteristics to see if you can get it built.

Subject: Web resources, Microbes

technorati tags: virus, microbiology