Oh, the memes bloggers play now

I'm a bit new to this sort of thing and it still seems to smell like a chain letter.

But instead it's a meme that I was tagged with by Hedwig the owl. It seems easy enough, but I keep thinking that I should emerge from a nice hot bath and find that I've solved a puzzle and can move on to the next part of the contest. Will I get to fly with dragons, swim with mermaids? Maybe during bedtime stories.

Well, here goes:

1. Go into your archives.
2. Find your 23rd post.
3. Post the fifth sentence (or closest to it).
4. Post the text of the sentence in your blog along with these instructions.
5. Tag five other people to do the same thing.

It's hard to believe that I've posted 23 items, but I have. And here's the fifth sentence:

Only, in my case, I'm not a graduate student thinking like a thief, I'm a biologist trying to think like a programmer.

Here's the chain letter part:

I'm supposed to spread this meme by adding some some blogs that I find interesting. Dr. Mom is one, I know what it's like to negotiate who drives to soccer games when you have a late night in the lab (or teaching the lab class). It's always good to know that others share those challenges. Jane is busy out trail-blazing through the computing field, so it seems appropriate to tag her in a blog where I discuss an attempt at thinking like a programmer. Science Goddess wins a tag for letting us know about interesting things going on the classroom. She's not in Seattle, I guess, 'cause I heard our school district has filters that block blogs. The people at Headrush deserve a tag, even with their software-company style title. Not only do they write well about writing, but their stories are fun to read. Last, I think Stew deserves a tag, and a "get well soon" note from all the people searching for Lollipops, lollipops, ooh lolly, lolly, pops.


Subject: Silly items

Don't forget Intimate Strangers debuts Tuesday

It sounds a bit risque, but nothing gets closer than the microbes that share our immediate residence. They live on our skin and in our guts, and leave no part of personal ecosystems uninhabited.

"Intimate Strangers: Unseen Life of Earth" begins on Tuesday, Jan 31st, with a search for the inhabitants of a larger ecosystem. You too, can join the mission to learn about the first life on Earth.

Getting the podcasts is easy, too. If you have iTunes it's mostly a matter of clicking the link at the MicrobeWorld Radio web site. One of our neighborhood middle-schoolers told me that the equivalent program on Windows, works too.

Check it out! The video podcasts are free and, having been a member of the American Society for Microbiology for almost twenty years (gasp!), I know it's a great organization and well worthwhile looking into.


Subject: Web resources, Microbes

Diversity in science: will we ever see a rainbow?

It rains all the time in Seattle; we should have plenty of rainbows

But we don't. And the rainbows we do have are getting harder to see. This year, the University of Washington had only 118 black students in a class of 5,000 freshmen (1).


Somewhere, over the rainbow, way up high

These appalling kinds of numbers bring occasional guilt attacks on the scientific establishment and institutions of higher education. They belabor and bemoan the all-white faces that appear in the University classroom. They stomp around and give a bit of lip service to the idea of bridging the gap and recruiting. But, after a few mass mailings to garbage cans around the country and some fancy new web pages, they throw up their hands and declare that they tried but the students are nowhere to be found.

Whatever the problem, somewhere down the line, someone isn't trying hard enough.

The Seattle school district enrolls roughly 46,000 children (2, 3), shouldn't we be able to find more than 118 black kids, who want to go to UW, in Seattle alone?

Let's do the math. Only 41% of the kids enrolled in Seattle schools are white; 22% are black (2). With a few crude estimates, we can calculate that, if 1/13th of the kids in the district graduate every year (probably a high estimate), and 22% are black, that would be almost 778 black kids. If even 25% of those kids were eligible for the UW, that would give us 194, or almost 200 black freshman, almost twice as many as the number that started at the UW this year.

Of course, even if all 194 potential black freshmen did go to the UW, only some would major in science. Still, if we don't start filling the pipeline, there will never be rainbows appearing in the lab.

What happened to all the black students from Seattle?

Maybe we could find out by working backward. We know students are more likely to get accepted into college if they take challenging courses in high school. That makes sense. So black kids should take challenging courses in high school, right? Got it. But do they? Can they?

It all depends on middle school.

Entrance into advanced high school courses requires that a student must do well on the eligibility tests. Entry into some of the science programs, like the acclaimed biotechnology academy at Ballard High School, requires that a student be eligible for advanced math.

That makes sense, you need to know math to do science. All kids have the same opportunity to take the advanced math in middle school and learn the material for the test, right?

Wrong.

As a parent of a Seattle middle schooler, I've become acutely aware that kids can get recommendation letters from their teachers, meet the standard on the WASL, and place above the 97th percentile on the math portion of the Iowa Test and not be able to get into honors math in middle school because of limited space and a single Spectrum test. (Spectrum is an advanced program for kids with above average intelligence. Achieve is the McClure Middle school version of Spectrum. Seattle has another special program for really smart kids (APP) but I won't discuss that here.)


Blocking the rainbow from view

Part of the problem comes from block scheduling. Since kids are grouped in schedule blocks as Achievers or non-Achievers (is this a slight language problem or am I imagining things?), they cannot take advanced math unless they score well on all portions of the Spectrum test.

In one fell swoop, kids who are weak in spelling but strong in math are rendered (potentially) ineligible for advanced high school math programs. Kids can catch up. At least one of eighth grade teacher is trying to help, but why not let kids who want to take advanced math, take advanced math to begin with? Why leave kids bored and hanging and make them repeat 4th and 5th grade math all over again?

If kids could take one higher level class, rather than the double-barreled, homework intensive, combination of Achieve Language Arts and Achieve Math, maybe more kids could enroll in one or the other. Maybe this option would even minimize some of the stress and anxiety that some kids in the Achieve program experience.


Oops, you're at the wrong end of Spectrum

Honors math at McClure Middle School, and most likely other Seattle middle schools, as well, is mostly limited (at least in 6th grade) to kids who are in Spectrum. If there is space, after filling the class with the Spectrum kids and kids who do well on the Spectrum test, other kids are allowed to join the class. Most of the kids, though, come straight from Spectrum classes in elementary school. Those kids, who are already in Spectrum, do not have to take a test. They are automatically in. As for the kids who do take the test, it gets more challenging at every grade level. The 5th grade version is far beyond than the test most Spectrum kids took in kindergarten.

Non-Spectrum kids have an opportunity, but only if there is space. Spectrum kids automatically have first dibs on all spots.

What's the problem? you might ask. Don't all kids get an equal chance to be in Spectrum?


Why is Spectrum at one end of the rainbow?

Let's continue our journey back in time and see what we find.

How do kids get into Spectrum in the first place?

The Spectrum track begins in kindergarten. Sometime in October, only a few weeks after school begins, really savvy parents fill out an application to have their kids tested for Spectrum. Once kids are in the program, they stay in.

Most of the kids are tested before they can read?

Right. The kids are tested in kindergarten.

Don't all kids take the test?

No. Kids only take the test if their parents know about the deadlines and they apply for it. If a family doesn't have a stay-at-home parent who can attend school meetings and volunteer at the school during the day, they might miss this bit of insider information. Some Seattle PTAs even hold their meetings during the day, when it's more convenient. Like the fraternities of old, some modern day PTA's could be called the secret societies of the school system.

Roughly half of the kids who attend McClure live in single parent households (3). Needless, to say, those single parents are probably not staying at home. It would be interesting to know how many of those kids ever took the Spectrum test, in kindergarten, or later.

Other parents have commented that kids in the middle school version of Spectrum (called "Achieve" at McClure) are almost all (if not all) white; where slightly over half (51%) of the kids at McClure not. It seems plausible, to me, that at least a few of the 100 non-white kids in the McClure 6th grade class, might be interested in advanced work, if they had an opportunity to try.


Aren't teachers supposed to encourage students to take the Spectrum test?

Maybe, but I've never known this to happen. I have two children in Seattle schools and I've never seen high scores on the ITBS, or Direct writing assessment tests, translate into recommendations to try Spectrum. I saw quite the opposite. High stakes WASL testing and No Child Left Behind are a strong disincentive. No elementary school wants to lose a kid who might pass the WASL.

Elementary schools are also friendly nurturing places. Not all parents (or kids) want to change elementary schools, even if it means the opportunity to be in Spectrum.

Still, parents have a few years to figure out that Spectrum tests are in October and if kids miss the test one year, they can take a harder test the next.

In fact, some kids do exactly that. There are parents who have their kids take the Spectrum test every year, as a matter of practice. These parents may opt to keep their kids at the nearby elementary school, but they're not going to have their kids face the determining factor for middle school opportunities, unprepared. Especially, since the Spectrum test is the one test that will be used to determine if kids are eligible.

I've heard it argued that the assorted rainbow of kids wouldn't do well on the Spectrum test anyway, even if all kids took the test. Perhaps the non-verbal, kindergarten, version of the test might be fraught with cultural bias and other scary things.

I'm reluctant to arrive at conclusions, though, when the experiment has yet to be tried.

Certainly, it's wrong for the school district to exclude kids from opportunities based on a single test.

But what do we do when there are limited numbers of spots in advanced classes? How do we give all kids an equal chance to work up to their potential?

Here's one idea:

We could tweak the registration system. A limited number of spaces in advanced classes might not be as great a problem if the middle schools could work together. Kids could register for advanced classes in either math, Language Arts, or both, as their first choice (rather than the middle school) and list their middle schools second. That way, if one school's advanced class filled up, kids, who want opportunities, could go to an advanced class at another school.

No doubt there are other, and perhaps better, solutions. Somehow kids who want to work harder and take classes like advanced math in middle school should have that chance.

After all, it's sure bet that if you don't take the opportunity to look, you'll never see a rainbow.

References
1. Nick Perry "Bigger black enrollment still only a dream for UW"
Seattle Times, Jan. 16th, 2006

2. Washington State Report Card. Accessed Jan 27th, 2005.

3. Seattle Schools, 2004 Demographic Survey, McClure Middle School Accessed Jan 27th, 2005.


Subject: Education

technorati tags: education

Time for iMicrobe?

The American Society of Microbiology is doing Video PodCasts! If that isn't cool, I don't what is.

I'm really glad to see the microbiologists taking the lead in reaching out the public with cool new technology. My 11 yr old daughter showed me how to subscribe to podcasts and watch them with iTunes. Now, I'm all set for next week when the fun begins. (We also had a good language lesson, too, i.e. define the word "explicit." Luckily, at 11 she's not likely to search with that term and since she was properly horrified, she immediately deleted all the explicit podcasts that she'd already downloaded to her computer).

For years, I suffered as my husband and I took the kids to see IMAX movies on subjects like beavers, coral reefs, space, Mount Everest, and Jane Goodall. The kids were always a bit puzzled. How come scientists in the movies go to interesting places?

Yep, here's the rest of it: but you and dad sit in the office with computers?

Right. We don't even do cool things like run gels anymore or play tricks with pH indicators and dry ice. This change of venue is too bad in some ways. Our kids would enjoy the lab now and we wouldn't be so paranoid about bringing them through the door. When they were younger, our respective laboratories were places of peril filled with brightly-colored attractive boxes of radioactive waste and interesting glass objects always stacked precariously next to the sink.

So, I was really excited a few years ago when ASM debuted the "Intimate Strangers" documentary on PBS. And really disappointed when the children pronounced it "boring."


I liked it, but even a friendly coccus with sunglasses didn't interest the under 10 set.

Now, there's another chance. We've subscribed to the videopodcasts. When they begin on Tuesday, Jan. 31, we'll be ready.


Subject: Web resources, Microbes

Biotech Expo - coming in March!

Bootstrap analysis wrote a wonderful story capturing the essense of a middle-school science fair. Now those of you in the Puget Sound will get your chance to see science in the trenches.

Biotech Expo happens March 6th at the Meydenbauer Center in Bellevue, Washington.

I know that's a few weeks away still, but some us need more advance notice than others.

The Biotech Expo is a wonderful sort of high school science fair where students do amazing things like present their own research, sing about telomeres, design web sites, perform skits related to biotechnology, and exhibit works of science art. It's great fun! True, it's a bit more advanced than a middle-school fair, but it's equally entertaining.

The Northwest Association for Biomedical Research has taken on the mission of organizing the Expo and recruiting judges. If you would like to help out or simply want to attend and learn what kids in Washington can do in biology, it's great fun and you might even learn something.

Subject: Education

Thinking like a programmer, searching like a fool

A recent news report told the story of a woman who was robbed and lost her entire thesis project because it was on a memory stick in her purse. The sensible part of me cringed when I read that she didn't have her master's thesis backed up somewhere on a hard drive, but the other part was intrigued by the way she solved the problem. She found her thesis in a green dumpster by trying to think like a thief.

I have to admire her method. I can make better guesses about searching for things, too; when I try to think like I'm someone else. Only, in my case, I'm not a graduate student thinking like a thief, I'm a biologist trying to think like a programmer.

This approach doesn't work with everything. Like, why do GenBank records give the mRNA size in basepairs? And why do so many people think "data set" is one word? And why does the chicken cross the road?

Some questions just don't have a good answer, no matter how you think about them.

Nevertheless, it does seem that programmers use one kind of logic and biologists use another. Neither is ideal, but thinking like a programmer can help when you encounter puzzling results with bioinformatics tools. Microbes and biological systems may follow biological logic, but web server applications and software packages follow logic of a different kind.

One of these unexpected moments arrived just the other day. I began my quest at the strangely-named OMIM database by searching with SOD1. (I say "strangely named" since OMIM is a database of human genetic disorders, not just those found in men.) Notice below, in the image, the link, creatively named "Links," on the right-hand side of the page.



Normally, I ignore Links since I use Safari (by default) and clicking Links doesn't do anything. But for the sake of completeness, I thought I should give Links a try, so I opened the page with FireFox, clicked Links, and selected PubMed. Then I sorted by Date and looked at the results.

Whoa!

Those results couldn't be right! The most recent paper was dated 2004. Surely people are still researching ALS and publishing articles on SOD1!

My biologist's intuition was piqued. Naturally, I redid the experiment under slightly different conditions. This time I searched for SOD1 directly from PubMed. I found articles in PubMed that date a couple of weeks in the future.

Why were the PubMed links from OMIM so far behind?

Time for another experiment.
What would happen if I chose Links again, but started from a different database?

This time I found SOD1 in the Gene database and selected the PubMed link from collection in the side bar. Now, the most recent paper was from Oct. 2005. Still a bit behind, but closer to current than 2004. You can see the results from all three searches below.



As a biologist, results like these are really kind of disturbing. I expected (erroneously) to get the same results no matter where I started searching. Could this be a problem with link rot? Not link rot at the NCBI! With my biologist hat firmly on my head, I did another experiment to look at Links to a database other than PubMed.

Links to Structures
This time I clicked Links from OMIM and chose the Structure database (MMDB). Only four structures appeared for SOD1. Searching directly from the Structure home page, I found 19 structures. Very worrying. Worse yet, I've used this method! : (

A quick flashback to software testing
Sometimes I get recruited to help out with software testing. These episodes give me the opportunity to read interesting test plans with puzzling questions that ask if the program showed the expected behavior. (Expected by who, I wonder?) Needless to say, it's not always the behavior I expected to see (thinking as a biologist, remember) even though it's often the behavior expected by someone.

That night, I had strange dream about previewing filters and running lost through large pipes and complicated pipelines. In the morning I decided to tackle the problem by thinking like a programmer.

Maybe the software was working the way it was supposed too. Maybe there was another explanation and I didn't do the experiment that I thought I did.

Could I test that?

Fortunately, yes. Clicking the Details tab in the PubMed results lets you see the search that you really did, not the search you thought you did.

Here's what I really did:




But what did I search for?

It turns out that a straight search from a database home page, like PubMed or MMDB, occurs without filters. That is, you search all the records in the database and find the ones that match your query.

But, if you begin searching from a different database, like OMIM and you select Links, you see the world through a database-colored filter. Instead of searching of all the PubMed records with SOD1, you only search the subset of PubMed records that are linked to OMIM.

Rather than searching all the records in the PubMed or Structure database, with SOD1, as I thought I did, when I chose Links from OMIM, I searched a filtered database with only 1% of the records from PubMed (147,450 out of 15,896,470).

The take home message
Links did behave in (what I assume) was the expected way. (I wish I hadn't sent that bug report! Sorry!)

It just appears that no one has added any PubMed or Structure references to OMIM for the past couple of years.

Did anyone expect that?


Subject: Life

technorati tags: bioinformatics, DNA, OMIM

Instructions in ethics for instructors

Every now and then I read laments about student plagarism and the problems with increasing amounts of information floating about on the web. I suspect that some of the problems might result from college students modeling the behavior that they see from their instructors. Even things that are done with the best of intentions, like copying parts of books for students to save them some money, might be misconstrued by the students as examples of acceptable behavior. If their teachers do it, it must be okay.

So, I've compiled a set of ethical guidelines for college instructors. Feel free to comment.

Ethical guidelines for college instructors

1. If you use lecture notes that you found on the Internet, ask the author for permission before removing someone's name and posting them on the net yourself.



(After all, you never know when the original person who wrote them will discover them posted on the Internet under your name or get the spam mail about the new course from your organization. It happens.)



2. If you use materials that someone else developed, credit the source. If you make modifications, you can always say, "based on an activity by so and so."
   

   (Many people have done this with materials that I wrote. Thanks!!!! I always appreciate this.)



3. Do not retype instructions from a book that you purchased so that you can avoid trouble from the school copy center.
   

   
   (One instructor, that I worked with, used to give students a 30-page handout that I thought was a pretty impressive piece of work. As least I was impressed until I looked at the lab manual we were using and realized that her hand-out was identical, down to the word.)



4. Materials can be copyrighted even if someone forgot to put a statement to that effect at the bottom of a web page.
   

   (Believe it or not, this rule comes from an audience question at a conference where I was invited to speak. One of the attendees had compiled an interesting curriculum from materials they found on the Internet. They were surprised and miffed because a program officer told them they couldn't just put other people's materials on a CD and sell them overseas, without permission from the authors.)



5. Assume that everything you didn't develop is protected by copyright. Images are copyrighted too, unless it's explicitly stated that they are not.


6. Materials that are developed at a college are governed by the faculty agreement at that college. If you are paid by the college as a contractor, the college may own the materials that you develop.


7. Even material produced by companies should be considered copyrighted.
   

   (I have found that some people in education apply different ethical standards to crediting academic materials and things that they use from companies. I had the amazing experience of asking an outreach educator why his course web page didn't reference Geospiza as the source for one of our tutorials. They did list sources for other materials. He told me, without even blinking, that they only reference academic groups, and never anything from companies.)

Subject: Education

technorati tags: education

Tangled bank 45 is up!

Check out the carnival at Greythumb for some wonderful stories on biology, medicine, and education.

In true carnival spirit there's even a Believe it or Not! section with stories that do almost seem unbelievable. Why would people use frogs for pregnancy tests anyway?

Some of the other intriguing topics are:

Internal clocks and Seahawks,

Parasites and plague,

Biology classes and bigger --- well, that's an article on portion sizes, you can fill in the rest.


I can hardly wait to read the story on the Donner party. Or maybe we should call it the party that wasn't.

For those of you new to blog carnivals, the Tangled Bank carnivals are wonderful collections of science stories. Watch out! If you enjoy reading about science, the stories can keep you away from work for a long time.


Subject: Web resources

iSpecies and Google games

This morning I read about a neat tool, in a BioIT world update, called iSpecies and couldn't resist giving it a try.

The idea of iSpecies, and the possibility of gathering all kinds of information together on a single page for any species, is really appealing and I'm looking forward to further development. You can read the story behind it at the iSpecies blog.

When iSpecies is a bit further along, I think it will be great. Right now, though, iSpecies is more like a new kind of Google game - except maybe funnier.

Here are the results from two searches that I did.

First I searched with Finch and got these results:


Yikes! Imagine if Darwin had seen those guys flying around the Galapagos islands. No one would confuse those finches with magpies. I'm not sure how the articles relate to finches either. Maybe I'm just not ready for the semantic web.

This worked a little better when I searched with Penguin. I'm not sure how the documents relate to penguins but this time the search found a couple of real penguin images and some drawings of Tux. Surely, the Linux guys will be pleased about that. That penguin with teeth is a bit much, though. I'm going to have scary dreams about that one.


Maybe next time I'll try the latin names.

Subject: Web resources, Birds

technorati tags: biology

DigitalBio wins Red Hot Blog of the day

I don't know much about RedOrbit but I guess Discovering Biology in Digital World was chosen as one of their Red Hot Blogs of the Day.

Here's my award button:

I guess they liked Every Structure Has a Story. It's about amazing DNA structures and the fun I had researching wild DNA for the Exploring DNA Structure Instructor Manual.

It must be true, I read it on the Internet!

Wikipedia vs. Britannica
Nature recently published a special report comparing the accuracy of Wikipedia, the on-line encyclopedia, with the Encyclopedia Britannica. Surprisingly, the Nature researchers found that accuracy of science entries in Wikipedia is close to that of Britannica. To me, the most interesting part of this finding, wasn't the result about Wikipedia, it was the result about the Encyclopedia Britannica. According to Nature, researchers found that an average science entry in Wikipedia contained four inaccuracies, while the average science entry in Britannica contained three. It's been many years since I looked at an encyclopedia but an average of three errors per article is still higher than I would have predicted.

The telephone game
I think the reason the error rate, in information sources like encyclopedias, is so high derives from the same phenomenon we see when children play the telephone game.

For those of you who never played, the telephone game begins with one person whispering information to second. The second person whispers the information to a third, and so on. The game ends with the last person sharing the (very different) information with the group.

I used to have my students play the telephone game in our Biotechnology and Society class as an experiment to help students understand why newspaper reports on scientific discoveries can be quite a bit different from the original research finding. I would go out in hallway with a student volunteer and relay a couple of sentences that contained the words "AIDS" and "mosquito."

Usually, I said something like this:

The realization in the 1980's that HIV could be transmitted through blood and cause AIDS caused quite a scare. One of the first questions that researchers had to answer was whether or not HIV was transmitted by mosquitoes.

Then I would return to the classroom and send another student out into the hall to retrieve the information from the first. I didn't do a rigorous study but in general, it only took one or two students before we'd all get reports that students had heard that "mosquitoes cause AIDS."

As the informaticists say, spoken information is "lossy." Every time information travels from one person to another, something gets lost.

This lossiness of information even presents problems in places where it really shouldn't. Genetics Home Reference at the National Library of Medicine, is a case in point. GHR provides summaries of information for different genetic diseases found in humans. It's kind of a newer version of the Genes and Disease section at the NCBI. At first I thought this site was really great.

A is for Alanine
Then I found a mistake, quoted below from GHR, in the entry for the SOD1.

The most common change, which occurs in 50 percent of Americans with type 1 amyotrophic lateral sclerosis, replaces the amino acid arginine with the amino acid valine at position 4 in the enzyme. (This mutation is written as Arg4Val).

Well, I've been working a bit with SOD1, both because I know someone whose brother died from ALS, and also because I developed a tutorial for researching genetic ailments with ALS as a model system. So, I was pretty certain that this statement was wrong and that fourth amino acid was not arginine.

To check the statement, I got the reference sequence for the
human superoxide dismutase I protein from GenBank. You can see it below:

>gi|4507149|ref|NP_000445.1| superoxide dismutase 1, soluble [Homo sapiens]
MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEG
LHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHV
GDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKA
DDLGKGGNEESTKTGNAGSRLACGVIGIAQ

Each letter in this sequence represents a single amino acid. The quote from GHR said that the normal amino acid at position four is arginine (abbreviated R). But the GenBank Reference sequence shows the fourth amino acid to be lysine (abbreviated K).

Well, sometimes the first methionine is processed and cut off of the final protein sequence. If that were true, then the A (alanine) would be the fourth amino acid.

Since the GHR reference stated that a change from Arginine (not Alanine) to Valine was the most common mutation in SOD1, I decided to cross check the information in OMIM, too.

To quote the OMIM record for a mutation at position 4:

Deng et al. (1993) found that the ala4-to-val mutation in exon 1 of the SOD1 gene is the most frequent basis for familial amyotrophic lateral sclerosis (105400)

My guess is that someone on the NLM staff thought (by mistake) that A stands for Arginine instead of Alanine.

Maybe the National Library of Medicine should start a Wiki
I suppose mixing Arginine and Alanine up is a simple mistake but it bothers me for two reasons. First, this is a site that claims a high standard of accuracy, and has a large group of outside reviewers, so even small nitpicky details like amino acid names should be correct. Second, I tried to help out by using the "customer service" web form to let the Genetics Home Reference people know about the mistake. It's been at least a month and I haven't seen the mistake corrected or even received an automated response saying that they got the information.

Alright, we all make mistakes from time to time (yes, me too!) and Wikipedia isn't perfect. The advantage of Wikipedia and other wiki sites, though, is that they can draw on larger numbers of people to help review and correct misinformation. Rather than ask for detailed reviews from a small number of busy people, who might easily miss this sort of detail, a genetic information wiki could, in theory, benefit a larger number of researchers and students if groups like the NLM would allow them to help out.

If the GHR site were a Wiki or had some wiki or even blog capabilities, I would have been able to post a correction, an automated e-mail could have been sent to someone in charge, the posting could be tracked, and someone might have looked at it and checked my contribution. As it is, the information might never be corrected.

I don't want to sound completely negative, because I do like the GHR site. The information is organized well and new conditions are added to the stite on a regular basis. Plus there are links to lots of good sources for additional information. It's just that, now, every time I recommend the site, I have to add a qualifier that students should crosscheck the information with OMIM just to be sure it's correct.

Or maybe I'll just advise them to use GHR for the link list and read the review at GeneTests instead.

Articles referenced:
1. Jim Giles. Internet encyclopaedias go head to head. Nature 438, 900-901 (15 December 2005) | doi:10.1038/438900a

1/17/2006 PostScript: I guess it's not just GHR that's a little off sometimes. I just realized that size of any reference mRNA sequence, in GenBank, is given in bp (base pairs). Sigh.


Subject: Life

technorati tags: education, DNA, genetics

Evaluating website information

Dr. Hsien Hsien Lee from Genetics and Health has proposed that all science bloggers have an obligation to answer 10 questions that she derived from 10 Things To Know about Evaluating Medical Resources on the Web, a web page from one of the NIH institutes, The National Center for Complementary and Alternative Medicine. This provides kind of a disclosure statement so that readers can understand our biases and better evaluate the information in our blogs.

I don't claim to provide any medical information, but I like this idea, so here are my answers.

1. Who runs this site?


Part of the answer is Blogger, a free (so far) blogging service owned by Google.

The other part of the answer is that I run the site since I write the content. My Ph.D. is in microbiology and I've been involved with digital and molecular biology and biotechnology for about twenty-five years, both as a researcher and tenured instructor in a community college biotech program. I currently divide my time between developing instructional materials and doing a bit of digital research. If you're interested, you can read more about it in our papers, abstracts, or posters.

Our paper page is labeled "white papers." Not all of the publications on this page are white papers. But I've learned that most people in the software industry do not know or care about the difference between a white paper and a peer-reviewed publication. Definitely a topic for a future blog (or rant?).

2. Who pays for the site?


Once again, part of the answer is Blogger (and Google) since they provide the blogging tools and site free of charge. But, of course it's more complex than that. The other part of the answer is that I do, by donating my time and writing content. I don't receive any income from the site at the present time, nor does my salary fund this activity.

I think the purpose of this question is to enable readers to determine if a writer is providing unbiased information. To answer that question, since I'm not anonymous, I do have to be sensible about what I write. If I write about Geospiza, or our education projects, my writing will probably have a positive bias. Okay, you've been warned. Read with a critical eye.

3. What is the purpose of the site?


I started this blog because it provides a quicker and easier way to share information about Geospiza's educational materials and report on our NSF-funded project in bioinformatics education. Geospiza does have an official education section, of the company web site, where many of our instructional materials are located, but it's still easier to post new articles through Blogger.

In summary, the purposes for this site are to:

a. Help students and teachers learn about biology by providing examples that show how biological research can be done with digital tools

c. Disseminate instructional materials from Geospiza's NSF-funded education project and provide information about instructional materials that we've developed and published.

d. Obtain feedback on new materials.

e. Share my humble ideas on science and teaching. ; ^ )

4. Where does the information come from?


I write about the instructional materials that were developed through Geospiza's NSF education project, my research experiences (some serious and some just for fun), and about research published in scientific journals. Some topics are based on current news. Citations and references are provided wherever I can. When I write about digital experiments and instructional activities, I often provide sites and references so that others can repeat the experiments for themselves.

5. What is the basis of the information?


This site will discuss my experiences and results plus experiments and findings that have been published in scientific journals. I will do my best to distinguish between objective information and my own opinions.

6. How is the information selected?

Topics are chosen for many reasons. The topics are largely centered around instructional materials and activities but they also derive from my interests, suggestions from others, and questions that people ask.


7. How current is the information?


Blogger adds a timestamp to every article showing when the information is posted. Articles that are related to instructional materials are likely to be updated.

8. How does the site choose links to other sites?


I pick links to sites that I either use for research or simply enjoy reading. The sites that I reference in articles are usually sites that scientists use, like the NCBI. Sites listed in the blogroll are mostly chosen because I enjoy reading them.

9. What information does the site collect, and why?


I measure web traffic so I can report this information to funding agencies. If you subscribe to our quarterly newsletter, I store your e-mail address. The Geospiza Education e-mail list is not provided to others and you can unsubscribe at any time.

10. How does the site manage interactions with visitors?

Visitors are welcome to send e-mail or post a comment. I do moderate the comments and will not post comments that inflammatory or comments about grow lights, discount pharmaceuticals, refinancing, or developing new and unusual body parts.

Visitors can also subscribe to RSS feeds and/or sign up for our quarterly newsletter by submitting a current e-mail address.