Tuesday, December 30, 2003

I am like so smart!



Aw shucks....

Back From Christmas Vacation

Yes, my friends, I'm finally back from Christmas vacation. I traveled about 2500 miles in total through sunshine, snow, and ice. The trip to SLC was uneventful, but traveling from SLC to Las Vega for my brother's wedding was quite an adventure. There was a huge blizzard the day after Christmas and many of the mountain passes we drove through were icy. Near Parowan (in UT) I started fishtailing on the ice, but managed to bring the truck back under control. It was pretty scary, though, and my husband decided to take over driving at that point. I was shaking for ten minutes after that. He drove the rest of the way to Las Vegas white-knuckled until we got past St. George where the roads were clear. We drove back to Dallas on Sunday and it looks like we left just in time since now there's snow in Vegas!

It was nice not to talk about science for a week. The only science-related things I remember saying was briefly explaining my thesis project to a couple family members. After that, they would nod their head and move quickly on to another topic. Feel the love.

I took quite a few pictures, but as I don't have a digital camera, the film will probably languish in my camera bag for months until my husband gets fed up and insists I develop the pictures. He's much better at stuff like that than I am. I do have one finished roll, so I'll try to develop it this week so I can post some pics on this site.

Some of you may have noticed that I went to Las Vegas for my brother's wedding. No, it was not an Elvis-chapel-o-love type wedding if that's what you're thinking. It was a traditional Mormon (LDS) wedding at the Las Vegas temple with the traditional reception at a local LDS chapel afterwards. There are actually quite a few Mormons in the Las Vegas area. They make up about 12% of the population of southern Nevada (for perspective Mormons make up 1-2% of the population nationwide). Brigham Young sent settlers to Las Vegas in 1855 to build a fort there, the first non-Native American settlement in the valley. More history of Las Vegas here.

Anyway, in an LDS marriage ceremony, you'd better make sure you're marrying the right person, because we don't marry "until death do us part," but "for time and all eternity" i.e. even after death. Really, I think this is a beautiful, romantic concept for those of us with good marriages. But if the thought of being with your spouse forever seems horrifying to you, then LDS temple marriage is not for you.

Friday, December 19, 2003

Merry Christmas Blogosphere!

I'm off to visit the family in Utah, so I won't be posting again until Dec. 29th. Everyone have a wonderful Christmas and/ or Hannukah. I'll leave you with some beautiful pictures of my "hometown" Salt Lake City, Utah. If you ever happen to be in SLC during the holidays, I recommend going downtown to see the Christmas lights at Temple Square. With the lights and the Christmas concerts every evening, this is the perfect holiday date.



This week's New Weblog Showcase

Here are my pick's for this week's The Truth Laid Bear's New Weblog Showcase:

My Word: The Politics of the Lord of the Rings
Politics plus Lord of the Rings commentary? We lovesss it, yes we do Preciousssss.

Pragmatic Conservatism by Dan K. O'Leary: Bush, Saddam, and Howard Dean
Dan is a fellow Alliance member and I also enjoyed his commentary on Howard Dean. This guy is fearless in the face of Deanbots.

Spam Town: Spam of the Week
At first I was thinking, who wants to read a blog about spam? But then I read a few of his posts, and there's quite a bit of useful info for avoiding spam. The entry post also had an amusing bit of spam where the sender was looking for stuff like a warp generator and a series time transducing capacitor. Wacky stuff!

Thursday, December 18, 2003

ROTK Review

Well my friends, I stayed up all night on Tuesday, Dec. 16th to see The Return of the King at midnight. I went to sleep at 4 a.m., woke up at 11 a.m., lurched into lab around 2 p.m. and little work was done. But boy, was it worth it!

Unfortunately my husband, who has a real job, was unable to attend so that means I get to see the movie at least two more times. Yay!

Let me begin the review by saying that those that haven't read the books and even Tolkien purists (like myself) will enjoy this movie (given you've seen the first two). The acting is superb, the cinematography and special effects are stunning, and there's plenty of action for the guys and some romance for the ladies (there could have been more, see below).

MAJOR SPOILERS BELOW!!!! I WARNED YOU!!!
The movie starts out with Smeagol and Deagol fishing in a boat. Deagol finds the Ring by chance and Smeagol kills him to get it for himself. We see the physical and mental transformation of Smeagol into Gollum over th 500 years he has the ring. Gollum is twice as evil in this movie as in TTT as he leads Frodo to the gluttonous spider Shelob. I really think Andy Serkis deserves some recognition for his superb work. Sean Austin and Elijah Wood are also excellent in their depiction of Sam's fierce protectiveness and Frodo's exhausted determination to destroy the ring.

We then pick up the story with Aragorn, Gimli, Legolas, and Gandalf arriving at Isengard. The fellowship splits up again after Pippin looks into Saruman's palantir, and he and Gandalf rush off to Minas Tirith. The Rohirrim gather their forces to journey to fight the armies of Sauron at Minas Tirith. Aragorn receives his sword Anduril (Narsil reforged) from Elrond and decides to follow the paths of the Dead to recruit an army of spirits that are in debt to the heir of Isildur for desertion.

I love the depiction of Eowyn's character by Miranda Otto. She goes from joy to complete despair and then the flatness of depression as she discovers that Aragorn doesn't love her. She disguises herself and rides to war with Merry. She kicks major butt in the battle of Pellenor Fields as she takes down an oliphant and the Witch King.

Unfortunately, two of my favorite scenes involving Eowyn were cut. The first is the scene where Eomer discovers that both Theoden and Eowyn are dead (he thinks). I saw this scene in the trailer and the depiction of Eomer's grief as he hold is sister is heart-rending. I don't know why it was cut because it's one of the most emotional scenes in the book.

After the battle, the scenes in the House of Healing are also cut out and we go right to the scene where Aragorn decides to take their armies to the Black Gate. It's a little disjointed because we don't know what happens to Eowyn or Faramir. We just see her at the end with Faramir, but we don't know how they get together. All I can say is that BOTH of these scenes had better be in the extended version, or I will be most seriously displeased!

The rest of the movie is pretty true to the book except the plundering of the Shire and the death of Saruman are not depicted. I expect to see more of Saruman in the extended version.

The battle at Pellenor Fields is awesome, but at times too busy to see all that's going on. Perhaps Jackson wanted to give the audience the same sense of frantic helplessness that the warriors probably felt as their comrades are falling by the hundreds around them.
I know how the book (and thus the movie) ends but at times I was wondering how are the characters going to make it through all this.

One final comment: do not drink a Mr. Pibb (don't tell my bishop) an hour or two before the movie even if you think you need it to stay awake! Towards the end, I didn't know if I would make it to the end. The ending is quite drawn out, but I think it works well.

On a scale of 1-10 (10 being the highest), I'd give ROTK a 9. I'm docking a point for leaving out my two favorite scenes. If it were up to me, I'd give ROTK the Oscar for best picture, Miranda Otto for best supporting actress, and Sean Astin or Andy Serkis best supporting actor. But it's not, so some lame artsy fartsy movie will probably get all the honors. Humph!

Tuesday, December 16, 2003

Geekfest - ROTK

Only 13 hrs. and 15 minutes until the 1st showing of ROTK in Dallas!

Let the geekfest begin!

For reviews, check out Rotten Tomatoes. The tomato-meter is still holding steady at 100%.

Monday, December 15, 2003

On Being a Female LDS Scientist

So where do I begin? First of all, there are not many LDS scientists to begin with and I’m not exactly sure why. There are approximately 2000 LDS scientists currently according to this link. I don’t know how many of those are women. What’s interesting is that Utah produces more scientists per capita than any other state for the last 60 yrs, 75% of whom are LDS. Of these, 83% percent classified themselves as strong believers and 90% of these felt that their religious beliefs and science theories could be harmonized. I think these statistics show that there is a great love for learning amongst LDS people and that most don’t believe that science and religion are mutually exclusive. Here’s a great paper on science & LDS scientists by Robert L. Miller.

Recently on Times & Seasons, there was an entry that posed the question of why there are few LDS women in the “hard” sciences and philosophy. I think LDS culture and theology play a large role. At an early age, it’s drilled into our heads that as women, our primary role is mother. We are told by our leaders over and over that we should stay at home with our kids and not work outside the home unless we have no other choice. So we have to plan ahead while we’re in high school for an education that will prepare us for employment that is family-friendly should we have to work.

I believe that most LDS women, if they attend college, plan for careers that involved only a 2 or 4-year degree. A woman can graduate with a bachelor’s by the time she is 21 or 22 if she attends full-time. This is the prime age for marriage and raising a family. I was almost 23 when I married, so I had a year to work after getting my degree. I was planning on going on a mission, but I met my husband before I submitted my papers. The majority of LDS women are getting married either before or right after they get their bachelor’s degree. And then most have children within a year or two of getting married. There simply is no time for graduate school.

It’s very difficult to attend school, even part-time and care for young children. I’m unique in that I had some health problems that prevented me from having children right away. I decided to use the time I had to further my education. Science is not a family-friendly (or female-friendly) career area. In order to get a position as a professor at most universities, one must have a Ph.D. and a post-doctoral fellowship or two. It can’t be done part-time either because it’s like having a full-time job plus overtime. Typically one takes classes the first two years while working the rest of the day and then one work full-time (and then some) in the lab until the thesis is complete.

The problem isn’t just that there are few LDS women in science, but there are few women in general in science (at least at professor levels). Only 10% of tenured professorships in the U.S. are held by women (link here) even though 25% of PhDs are awarded to women. Most of the women’s advocacy groups claim this is because of discrimination, but I’m not so sure. There may be some institutions where sexual discrimination is a problem, but I have never experienced it. I think the reason is that most women, when faced with choosing between family and a career in the sciences, choose family.

When looking at first year graduate students classes, there are about as many women as men, but over the years, many drop out. Some get married, some have children, and some decide they don’t want to do science anymore. When one finally gets to the post-doc level a lot of women have decided that they don’t want to go further. They might branch out into other fields such as science writing, technology transfer, patent law, etc. These are the prime childbearing years and once one steps off the academic career track, it’s hard to get back on. If a woman stops to have a child or two, then she has to choose to either stay at home with them until they are school age or shuttle them off to daycare at a young age and go back to the lab. The latter alternative is out of the question for most LDS women.

But things are getting easier. There are now day care centers on most campuses. There are more part-time post-docs available. I have met a few female professors that are able to juggle running a lab and caring for their children. But they have had to make big sacrifices. Either their research or their time with their children suffers. Mostly, the children grow up in daycare. If I were unmarried, none of these things would be an issue and I could pursue a position as a professor without any guilt.

Besides the issue of family, some LDS people wonder how one reconciles LDS theology with the theories of science, especially the theory of evolution. I’ll talk more about my ideas about evolution later. But to me science and religion, at least Mormonism, are not incompatible, but rather complementary.

Believe or not, most biological research has nothing to do with evolution directly. I could think the theory of evolution is totally bogus and finish my thesis project with no problems from my committee. Evolution is usually only an issue when relatedness of genes or fossils are being studied. For instance, biochemistry as a discipline involves taking apart a biological machine like a cell and trying to see how all the different parts work independently and then trying to reconstitute the cell. The evolutionary history of all the components is not that important. But the relatedness of an uncharacterized human protein compared to a well-studied homologous mouse protein can give insight into how the former protein functions.

I personally favor intelligent design in part because of LDS theology, and also because living things, even single-celled organisms, are incredibly complex. There are thousands of different enzymatic reactions that take place in various signaling networks that can have hundreds of different component proteins. These networks are robust to perturbations, but are also highly sensitive to targeted mutations. This is a strong indication to me that life did not evolve randomly, but was somehow organized by an outside force.

I’m fascinated by the complexity of nature. To me, science is like taking apart the little machines God has put together, and then trying to put them back together. Scientists are always trying to duplicate what God (or nature) has done. It makes me laugh when some Christians accuse LDS people of blasphemy because we believe we can be like God one day when that’s exactly what we as humans are doing every day. We are creating, organizing, and re-engineering things to make them better, to cheat death, and explore beyond our small planet. No other creatures of God do what humans do.

Yet, there seems to be a significant bias in the scientific community against those that are religious. Most scientists I know are agnostic or atheist and treat religious people as less intelligent and sophisticated. Scientists, who are supposed to be objective and deep thinking, can be just as bigoted and shallow as anyone. We all bring our unique worldviews with us. There was a time when it was unusual that a scientist did not believe in God. I hope that one day religious scientists will be the

Sunday, December 14, 2003

The Butcher of Baghdad Has Been Nabbed!

American 4th infantry division forces caught up with Saddam near Tikrit (hat tip LGF).

It's an early Christmas present for the people of Iraq and freedom-loving people everywhere. Merry Christmas!

My picks for this week's New Weblog Showcase

For political blogs, I cast my votes for:

Anti anti war: The War in Iraq will be a success
I liked their style of commentary, although it had an odd layout for a blog. What really impressed me was their spanking of a competing left-leaning blog. That's pretty gutsy.

Locke, or Demosthenes?: Iraq contracts
This blog looks great and is well-written.

I didn't vote for any non-political blogs because none of them interested me and one was in German, so I couldn't read it anyway!

Cast your own votes at The Truth Laid Bear's New Weblog Showcase.

Friday, December 12, 2003

How Geeky Are You?

No biology-based blog could be complete without a Geek Test. I scored 22.87968% - Geek. I was kind of disappointed that I was only a geek as opposed to a super geek. I think I would have scored higher if there were more science-related questions. See how you do (hat tip geeklife.com).

Science Journal Round-up

Science News

Berkeley accused of biotech bias as ecologist is denied tenure
Nature 10 Dec 2003 - Apparently Dr. Ignacio Chapela, an anti-GM ecologist, is upset that he was denied tenure. He claims that it's because Berkeley is biased (towards research that generates money as opposed to research that generates zilcho dinero). Gee, could it be that he didn't get tenure because he published diddley squat?! Sorry, buddy, in science being a nice guy just doesn't cut it.

Hot Research

Molecular Memories That Survive Silicon Device Processing and Real-World Operation
Science 28 Nov 2003 - Chemists from UC Riverside and N. Carolina State have developed an organic molecular method for storing information. They show that porphyrin-based molecules fused to Si(100) can withstand the extremes of temperature (up to 400 degrees C) and ~10^12 read-write cycles. Also, multi-bit information storage is possible with these molecules since they can undergo multiple redox states.

A Protein Interaction Map of Drosophila melanogaster
Science 5 Nov 2003 - For fly biologists out there, this group has attempted to map all the protein to protein interactions in the fly proteome. The main problems I have with this paper is that the resolution of the figures in the paper is poor and that they used two-hybrid experiments to test for interaction between proteins. Two-hybrid experiments often elicit many false positives. But they did assess the reliability of the interactions based on experiments done on yeast orthologs. The results may be useful for finding novel protein-protein interactions and then lead to more extensive testing.

MICROBIOLOGY: Chemical Warfare and Mycobacterial Defense
Science 12 Dec 2003 - Researchers from Cornell University have discovered a key component of how M. tuberculosis, one of the deadliest pathogens, eludes destruction by the body's immune system. M. tuberculosis is typically inhaled into the lungs where it is taken up by macrophages, immune cells that typically engulf and kill foreign cells. M. tuberculosis avoids destruction by blocking fusion with lysosomes (organelles fill with acid and digestive enzymes) and resisting the toxic effects of nitric oxide (NO) which is produced as part of the immune response.

The proteosome of M. tuberculosis was shown to be the primary component of NO resistance. Proteosomes are macromolecular protein structures found in prokaryotes and eukaryotes. They function in the turnover of cellular proteins by degradation of misfolded or damaged proteins. In M. tuberculosis, the proteosome detects damaged proteins and is also able to repair them, conserving resources. If some proteins comprising the proteosome are mutated, M. tuberculosis is less virulent and easier for the macrophages to fight off. The M. tuberculosis proteosome may serve as an important target for development of additional tuberculosis drugs to treat drug-resistant strains.

Viewpoints: Tragedy of the Commons (a.k.a the sky is falling)This week's issue of Science has a special issue on managing world resources to commemorate the 35th anniversary of the publication of Garrett Hardin's essay, "The Tragedy of the Commons." Dr. Hardin was a zero-populationist. I'm sure what he said back in 1968 seemed radical, but now his views are eerily commonplace. I'll save a fisking of his essay for a later time, when I'm feeling particularly grumpy. Anyway, this collection of viewpoints on Hardin's theme may interest those of you that may wonder where the U.N. gets their policies on reproduction, global warming, management of global resources etc. It appears that scientists from Hardin's school of thought are making international policy and it should scare those of us that value freedom and personal responsibility.

Thursday, December 11, 2003

My first Precision Guided Humor Assignment as a member of the Alliance of Free Blogs

Campaign Slogans

Well, it seems that the Alliance of Free Blogs has lots of assignments. Usually, I'd be too lazy (and supposedly busy with lab work) to do them, but this one has lots of humor potential.

Here's my campaign slogans for the 9 Democratic candidates:

Joe Lieberman Vote for me! Only the jolly Emperor Palpatine can save the Republic!

Howard Dean Vote for me, the irrationally exuberant Grumpy dwarf.

Dick Gephardt I like corn AND NASCAR, vote for me!

John Kerry Vote for me and there will be a ketchup bottle in every kitchen! (Oh, there is already?) Nevermind, I fought in 'Nam!

John Edwards Vote for me because I'm the best-looking of them all.

Al Sharpton There's actually no reason why any of you crackers should vote for me, but I DID host SNL.

Wesley Clark I couldn't lead a herd of monkeys into battle, but I'd make a great President.

Carol Moseley Braun I'm the best candidate you haven't heard of!

Dennis Kucinich Vote for me! Only I can defeat the evil brain-sucking greeyons from the planet Smee!




Wednesday, December 10, 2003

Oh no! What have I done!

So I joined the Alliance of Free Blogs because it seemed like the thing to do. Also, it appealed to my sense of mischief-making.

And I just learned how to do blockquotes.

Healing Iraq Posts Pics of Bagdad Demonstration Against Terrorism

Go Iraqis! Although this demo won't do much to stop the fedayeen and Al Qaida thugs, at least it shows the world that the people of Baghdad support the coalition and want to be a free nation. Read the whole article.

Healing Iraq

Science and the Middle East

I was under the impression that the science community was supposed to act as unbiased, objective observers. You know, just focus on our nerdy little projects and refrain from injecting politics into our research. Unfortunately, some scientists feel the need to mix politics and science when it comes to the Israeli-Palestinian conflict.

Last year a group of scientists from Europe (mostly the UK) organized a boycott of Israeli researchers. One of them was Richard Dawkins, a famous evolutionary biology (and one of my least favorite people). Here's the letter they published in the Guardian. They also tried to persuade the E.U. to boycott Israel, but luckily the E.U., in the interest of invested money of course, declined to participate.

Nature magazine, published in the UK, was a primary battleground in the debate. Here's a link to the web focus page that lists all the numerous letters and articles on this subject. In the October 2 2003 edition of the magazine, the cover (seen below) featured the Israeli wall.



Hmmm... based on this cover, what side do you think Nature is on? I thought this cover was completely inappropriate because typically the cover of a science journal is reserved for the hottest research of that issue i.e. something scientific, NOT political. But in reading Nature's commentary on science policy, I've noticed a decidedly left-leaning and sometimes anti-U.S. tone in their commentary.

However, in that October 2 2003 issue, the article about the challenges facing Palestinian and Israeli scientists was surprisingly even-handed. Here's an excerpt:

Many Palestinian researchers reject the idea of boycotting Israeli science. "It's counter-productive," says Abdeen. Even among Palestinians who support the idea of an economic boycott on Israel, there is unease about the idea of extending protests into the scientific arena. In towns such as Nablus and Hebron, however, some researchers support the actions of those foreign academics who have refused to work with Israeli scientists. Despite his own willingness to work with Israelis if the collaboration strengthens Palestinian science, Khatib is among their number. "Pressure must be exerted on Israel," he says. "I support the boycott because it can enhance movements in this direction."

Such comments are distressing to Israeli academics, especially those involved in collaborations with Palestinians. There is a saying in Israel that reflects the country's love of debate: "put two Israelis in a room, and you'll get three opinions". But this definitely does not apply to discussions about the call for a scientific boycott. "You're not going to get three opinions on that," says Jonathan Gressel, a plant biologist at the Weizmann institute. "I don't think it ever helps to keep scientists out of science for political reasons." His colleague Geiger agrees: "This breaks with one of the most cherished and important features of science: that it is international and non-political (emphasis added)."

Science magazine, published in the U.S., had a more low key approach. No covers. No barrage of letters. They printed two small articles, both on efforts of Israeli and Palestinians to collaborate despite the political conflict.
ISRAELI-PALESTINIAN RESEARCH: As Mideast Peace Process Lags, Science Endures
ISRAELI-PALESTINIAN COOPERATION: Building Bridges in a Battle-Scarred Land

Now, I'm not saying that scientists shouldn't be involved in politics and state their opinions openly. I've got strong opinions myself that regularly conflict with those of my coworkers. However, these political views should be set aside when you do science and interact with scientists from other countries. To me, what Dawkins and his buddies have done is nothing less than bigotry. It smacks of the same sort of anti-semitism that infected German science during the rise of the Nazis. Also, I think boycotts do more harm than good. Look what happened in Iraq. Saddam lived like a sultan, while his people starved and non-military research ceased.

Anyway, incidents like the science boycott are what happens when smarty-pants experts in one little area, e.g. evolutionary biology, think that they are also experts in everything else, including foreign policy. Dawkins et al. should try to look at both sides of the story, write their whiney little letters to al-Guardian (not Nature), and get back to work!!!!

Axis of Weasels Gets Their Just Desserts

FOXNews.com - Politics - White House Backs Limiting Iraq Reconstruction

I just have one comment about this. Hah, hah (a la Simpsons)!

Update:
On a more serious note, it looks like Saddam and his cronies will get their just desserts.

Iraq War Crimes Tribunal Established

The tribunal has said they may try Saddam in absentia, but they have not decided on whether the death penalty will be reinstated.

Tuesday, December 09, 2003

Time for Some Furry, Asia Cuteness

I just realized that I haven't posted any pics of my kitty, Asia. So I give you Asia, Queen of the Pants and all she surveys.



Here she's just helping herself to some Cap'n Crunch.


While Vision of Weblogs Danced in My Head

You know you're addicted to blogging when you start having dreams about blogging. It's almost scarier than dreaming about vengeful giant fruit flies ripping your limbs off one by one, and then gouging your eyes out. Almost.

Thanks everyone!

I guess my blog was voted the best non-political blog in last week's New Weblog Showcase. I'm stunned and humbled by that honor. I thought for sure that Tiffany from Blown Fuse would win. She is really funny.

Anyway, many thanks to those that voted for me. A special thanks to Denita from Who Tends the Fires for her kind words and encouragement. I added her to my sidebar under Fly Friends. I would have posted links to everyone that voted for me as a thank-you, but I'm not savvy enough to figure how to find those links from last week's competition. I guess I should have thought about this yesterday. Drop me an email if you can help me out.

Monday, December 08, 2003

Biology Lab Primer - Of glowing green-eyed flies, calcium, and brains

So I said I'd talk about how my research on fruit flies has a practical application. The eye of a fruit fly is very different from mammalian eyes. They are basically arrays of tiny motion detectors, designed to sense movement of a predator rather than to discern the intricacies of color and form like human eyes. The electrical responses of fruit flies are 100 times faster than those of human eyes. That's what makes them so darn hard to swat with a fly swatter.

While insect vision is interesting in itself (especially if you want to be able to swat them effectively), what I'm really interested in is how nerve cells or neurons function in all animals. The photoreceptors in the fly eye are actually modified neurons. They receive an input (light) and transmit an output (histamine) at their synapses. Flies are ideal model systems to use to study neurons because they have simple nervous systems, they are easy and inexpensive to maintain, there are many mutant flies that can be tested, and you can do experiments on them that you couldn't do on humans. Yes, ripping the eyes off a human being and jabbing electrodes into the freshly dissociated eyes IS unethical and illegal in case you were wondering.

The fly photoreceptor cell signals in a way that is similar to certain types of neurons in the mammalian brain. This pathway contains a receptor, the protein rhodopsin (also found in mammalian eyes) in this case, on the surface of the cell that responds to an external stimulus, light. Once light activates rhodopsin, rhodopsin then turns on a whole cascade of other signaling proteins. The proteins in the signaling cascade had different functions. Some turn on other proteins, some turn others off. Some breakdown certain biological compounds, while other synthesize new compounds. Some proteins undergo conformational changes that allow them to transport other molecules into or out of the cell. These proteins are called ion channels. The end result of light stimulating rhodopsin results in ion channels opening and allowing high concentrations of calcium from outside to rush into the cell. High amounts of calcium are eventually toxic to cells so it is then pumped out of the cell at the end of the signaling event.

But high calcium inside of cells is needed for other signaling events that help make vision and other neuronal processes more efficient and dynamic. Adaptation, which occurs when you enter a darkened room, is a calcium-dependent process. Memory is also calcium dependent. And more and more research is showing that its not just the amount of calcium that's important for neuronal signaling, but also the location of the calcium influx. Localized calcium influxes (also called calcium microdomains) have been shown to occur in the inputs and outputs of neurons. There are billions of neurons in the human brain, and each neuron can have thousands of inputs and outputs. Now combine that with localized calcium signals and the dynamic range and computational power of the brain is enormous. Memories are probably stored by the coding of various inputs and outputs along with the localization of calcium signals.

Proteins in the inputs and outputs of neurons are organized into little signaling complexes so that they can respond to local increases in calcium. In fly photoreceptors, there are scaffolding proteins that bind together ion channels and calcium-dependent signaling proteins. If you disrupt the complex by mutations in the scaffolding protein, the ion channels still function and calcium flows into the cell, but the calcium-dependent proteins don't function properly. We think this is because they need to be close to the source of calcium, the ion channels, in order to do their job right.

So my thesis project involves testing this idea by measuring the calcium microdomains in normal flies and in flies where the protein signaling complexes have been disrupted. I've made flies that have calcium "detectors" fused to different proteins in the signaling complex. The calcium "detector" is a protein that fluoresces in the presence of calcium. I can image these "detectors" inside a fly photoreceptor cell with a microscope and a camera. The brighter the cells, the more calcium is near the "detector."

Falling asleep yet? That's your biology lab lesson for today. Here's a picture of me taking images of fly photoreceptor cells in the dark.




101 Uses for Science magazine

Use #12 - fly swatter
This is very handy in the fly room where gazillions of flies can get loose.

Use #34 - coaster
Since we don't have any real coasters in the break room, science journals work great. They're also good for placemats (use #44).

Saturday, December 06, 2003

Which Founding Father Are You?

Take this quiz to find out. I am:

Support the People of Iraq in Their Fight for Freedom

Visit this site if you want to get a banner for your blog that shows your support for the people of Iraq as they fight against the Saddam loyalists and their terrorist buddies. I added one to my sidebar. Sign the petition too. My all time favorite picture that represents my hopes for the Iraqi people is below. I just love the sheer joy and hope expressed on this little girl's face.




101 Uses for Science magazine

Use #27 - doorstop
Yesterday I saw that the lab next door was using Science magazine as a doorstop. I guess their paper got rejected by the editors. Bummer. I'm sure they can put Science to a better use, such as toilet paper (use #54).

Friday, December 05, 2003

Microbes on Parade: The New Weblog Parade

So I entered my modest little blog in the New Weblog Showcase from The Truth Laid Bear's as a desperate bid for at least one or two readers to give me some useful feedback. Apparently you start out as a lowly microbe and then as you get more links, you rise higher on the evolutionary blog scale. I was at least hoping to get as high as a fruit fly, but today I'm apparently a slithering reptile. Sssssssspectacular, my precioussssssssssss!

I've been putting off voting for my favorite new weblogs so I could see all the candidates, but I know I'll forget to vote if I don't do it soon. So here are my picks:

For best political weblog, I vote for dangerous liberty: Al Franken on Book TV Anybody that bashes Al Franken so enthusiastically is ok in my book. I've never thought Franken was funny, even when he was on SNL. He's a loudmouth braggart, and I just can't stand him. I really tried to keep an open mind and vote for the blog with the best design and writing style, but I couldn't get past some of the left-leaning rhetoric without blowing a gasket. So I'm biased, sue me.

For best non-political blog, I vote for Blown Fuse: Bestiality is a no-no. This blog is highly entertaining and has a dizzying variety of topics. The title of the sample post worried me a little, but it was an amusing, if not disturbing anecdote about an oversexed cocker spaniel.

My second choice is Times & Seasons: What Power? although I thought they could have chosen a more interesting post to represent the blog. It's main focus is Mormon theology, so like the good little Mormon that I am, I'm giving them my support. However, I haven't had a lot of time to read all the articles in depth, so I'm not saying I endorse their representation of Mormonism. However, they have quite a few people that seem to be quite knowledgeable about wide variety of topics. But I would recommend that those not familiar with Mormonism start out with the basics here before diving into this blog.

Update:
Also, don't forget to vote for your favorite blogs here in the 2003 Weblog Awards.

Thursday, December 04, 2003

Science Journals Round-up

BIOTERRORISM: Anthrax Powder: State of the Art?
Here's a disquieting article about the origin of the spores used in the 2001 anthrax attacks from Science magazine (subscription required, hat tip LGF). Basically, the theories on the origin of the anthrax fall into 2 categories: it's a homemade crude extract or it was made in a state-of-the-art (read state-sponsored) facility. I remember when the analysis of the spores found in the Senate offices revealed that the anthrax contained a milling agent, silica, and electrostatic charges. These results seemed to indicate it was a high-tech job because of the spores' high aerosolibility.

Then for some reason the FBI denied that the sample contained silica and seemed to think that the culprit was a "lone-wacko," Dr. Hattfill. This article discusses in more detail the analyses of the samples and the attempts of the government to reproduce the samples. Basically, Army experts were unable to reproduce the sample by using a crude, lab-in-the-garage (without silica) approach, but got really close when they used silica and a top-secret ingredient (probably a coupling agent that gave the spores electrostatic charge). So what's up with the FBI? They led a wild-goose-chase through Dr. Hatfill's home and a nearby pond. Why? What advantage would they gain by covering up the fact that the spores were produced by a highly sophicated research facility?

Personally, I never bought the "lone wacko" theory. As soon as the I heard about the anthrax, I thought "from Iraq with love." I don't have any evidence for my hunch except that we know Saddam had an anthrax weaponization program at one time. Those spores can sit around in storage for decades maybe even hundreds of years without losing potency. The spores sent through the mail were probably a test run. Fortunately, although a lot of people were freaked out, few people died, and our nation did not grind to a halt. People exposed to the spores were given antibiotics, a mail screening process was developed, and a vaccine was already available.

If I were the conviving little terrorist(s) who did this, I would say the test run was a failure. The next step would be to either develop a better method of spore dispersal (e.g. aerial release) or use a more communicable pathogen like smallpox. Both possibilities are rather frightening. So basically, this article leaves me wondering who's responsible for the anthrax attacks and will we ever catch them?

Update: Here's a website that lays out all the evidence in the anthrax case. A lot of it I haven't heard about before (via LGF).

Update: I doubt that the info from the above site is that reliable. In his profile of the anthrax sender he states, "the refiner/mailer probably watches Bill O’Reilly on the Fox News Channel." What evidence supports that assertion? Come on! At least he has an exchange with the author of the above article, Dr. Gary Matsumoto that's kind of interesting.

And now for something completely different....

Jokes activate same brain region as cocaine
A study at Stanford University showed that the same brain centers that are activated by cocaine are also stimulated by funny jokes or comic strips. Functional magnetic resonance imaging (fMRI) showed that one particular brain region, the nucleus accumbens, is stimulated by the release of the neurotransmitter dopamine. Looks like laughter is the best medicine (or dope) after all.

Wednesday, December 03, 2003

Geek-o-rama - ROTK

Only 14 days until the release of Return of the King! If only the actor playing Aragorn, Viggo Mortensen, wasn't such a loser. Personally, I'd rather have brains than beauty. But Legolas (a.k.a. Orlando Bloom) is rather nice to look at.





Why I Hate Pop Science

Now I know I'm going to sound like one of those elitist intellectuals that I despise when I say this, but the science you read about in most popular magazines and newspapers ain't science, baby. The very worst pop science ideas are ones that try to scare you into doing or not doing something based on flimsy evidence.

Here's an example that I just made up, but I wouldn't be surprised to see it in this month's issue of Ladies's Home Journal or Reader's Digest. The headline of the article would blare something like "Twinkies Can Cause an Early Death!!!!!!" The article will open with an interview with a thoughtful young mother who says, "I never thought that something so tasty and delightful to my adorable children could cause so much damage to their fragile little bodies."

Then the article will site a study in some obscure medical journal where out a group of 50 people, those that ate a twinkie every day were 20% more likely to die of a heart attack before the age of 50 than those that did not eat a twinkie every day. Of course, some people might conclude that twinkies are harmful to your health and will cause you an early death.

However, this study would show, like most of the studies in JAMA, a correlation, not a causation. There may be a correlation between eating a twinkie every day and dying of a heart attack before age 50, but there is no evidence that twinkies actually cause heart disease. First of all, I would look at the size and composition of the sample group. If the sample size is small I wouldn't trust any conclusions the researchers came up with. Also, the sample group should accurately represent to whom the study would apply. Does the sample group contain a representative number of males, females, racial types, age groups, body types etc.? In the imaginary twinkie study for instance, I could have stacked the cards by selecting all the young, healthy, athletic people for the control group(non-twinkie-eating), and all the overweight, old people with bad hearts for the twinkie-eating group.

Also, how can one control for just the twinkie eating behavior? I think it would be nearly impossible to select a sample group that had everything in common except for the twinkie-eating behavior. The twinkie-eaters are more likely to engage in other unhealthy behaviors like not exercising, eating 3 bags of potato chips daily, and super-sizing their McDonald's combos while the non-twinkie-eaters are more likely to eat tofu and practice yoga. But that shouldn't affect my decision to have one lousy twinkie today.

And of course, there's always the possibility that the researchers or the magazine editors tweaked the statistical results to favor their position: that twinkies are bad for you. So then the food police decide cite the twinkie study and lobby for higher taxation or outright banning of twinkies and other "dangerous" foods.

Now I don't have a problem with clinical correlational studies. They are useful for showing trends in conjunction with other studies, such as combining a more representative twinkie study with studies on many different types of foods to show that in general a healthy diet is better for you. But I think that many lobbying groups and media sources use studies like my phony one to promote their own agendas.

Here's some examples:

Study shows 9/11 cause heart attacks.

Center for Science in the Public Interest Issues list of "Better and Worse" Snacks for kids

California to Sue EPA over Global Warming

All three of these article were written by Steven Milloy who runs a website called JunkScience.com. He does a great job of exposing the flaws in many of these studies and the motivations behind the groups that use these flawed studied for their pet causes.

Another webpage that might be of interest to those of you who want to be able to eat your dingdongs and twinkies in peace is The Center for Consumer Freedom. Now I'm going to get a Snickers bar. Just try and stop me, you food Nazis!

Tuesday, December 02, 2003

Oh No! Not again, Jimmeh!

Since I really didn't want this to be a political blog, I've been trying to refrain from bringing up politics. But alas, I am a news junkie, and with LGF and others to keep me informed of all the pols' shenanigans, I just couldn't resist. Our illustrious ex-Pres Jimmeh Carter has once again opened his mouth and inserted his muddy peanut-farming foot (via LGF).

In a interview with the NYT "Mr. Carter, defeated in his quest for re-election by Ronald Reagan in 1980, speculated that "had I been elected to a second term, with the prestige and authority and influence and reputation I had in the region, we could have moved to a final solution."

Um, I don't think Mr. Carter realized how bad that sounded. I mean, come on: Israel, Jews, final solution, Adolf Hitler. Ring a bell, Jimmeh?

Monday, December 01, 2003

Viva les comments!

Since I'm trying to get back into my work at school this week, I thought I'd start by adding a comments section to this blog instead of working. Yay! Now I'll see if anyone will have something useful to say.