In need of narration

I'm a molecular biology nerd so I got a huge kick out of this movie. It's an animated look at some of my favorite proteins, including those important for cell motility and structure. There's also a sequence on protein translation, including vesicle transport to the cell membrane! Unfortunately there is no narration!! I've been thinking about making a cytogenetics movie but I quickly realized it would be very difficult to explain anything sub-cellular without diagrams (and animation to keep things moving). And here's someone who really has a handle on the animation stuff completely skipping the part where anyone can learn from what they're seeing. Argh. I hope they make more with optional captions at least.

On a semi-related note, scientists have converted amino acids to musical notes creating a signature song for each protein. Check out the sound of your favorite protein here.

UPDATE: This video is part of a textbook package, when you buy it you get narration.

Reflectance Detectors (aka Eyeballs)

Color blindness may be more troublesome now than ever due to our reliance on computers and graphic images for conveying information. But, according to this article in the Boston Globe, Tenebraex Corp. has come up with a relatively simple solution. The company designed a computer program that allows users to interact with the colored areas in an image in a variety of ways. Here's a flash animation of the program.

On the other side of the spectrum, researchers may have located women that are able to perceive more than the normal range of colors. Normally humans are able to see well in three areas of the light spectrum (blue, green and red) using three types of cones (light-detecting structures in the eye).

Color detection genes reside on the X chromosome which is why color blindness is much more common in men. Men have only one X and therefore only one copy of each gene. Check out this great post over at damninteresting.com.

I've always wanted to be on the same wavelength as the birds and the bees and the flowers and the trees- all of them can communicate using ultraviolet signals. Birds have feathers that reflect in the ultraviolet range and receptors to receive those messages. Flowers also display UV-reflectance to lure insects (including bees) for pollination.

Two can play at donkeys.

A Distinction with a Difference

My lab recently got a sample of a mystery animal from another campus lab. Well, not completely mysterious. The sample was from the baby of a donkey. But they weren't sure if it was a hinny or another donkey. Hinnys are hybrid animals produced by breeding a female horse and a male donkey. Mules are the opposite of hinnys, their mothers are donkeys. Like many other hybrids, mules and hinnys are typically sterile because they have an odd number of chromosomes (see chart). Hinnys and donkeys can usually be distinguished by appearance but if the animal is too young they can be distinguished by counting their chromosomes. Donkeys have 62 chromosomes and hinnys (and mules) have 63.

Zedonkey

The liger is probably the most famous hybrid animal. But it also has an lesser known "opposite" called the tigon. People went crazy with zebras as well creating zorses, zonies, zetlands, zebrasses and zedonkys.

I don't know what this one is called though.

Mom	Dad	Offspring	# of chromosomes	Sterile?
Female Horse (Mare)	Male Donkey (Jack)	Mule	63	yes
Female Donkey (Jenny)	Male Horse (Stallion)	Hinny	63	yes
Female Horse (Mare)	Male Horse (Stallion)	Horse	64	no
Female Donkey (Jenny)	Male Donkey (Jack)	Donkey	62	no
Female Mule (Molly)	Male Horse (Stallion)	?	?	?
Female Hinny	Male Donkey (Jack)	Dragon Foal	?	?

Willy Wonka and the Space Elevator

To tell the truth, the first time I heard about space elevators it kind of blew my mind. I couldn't get away from the image of launching a tethered object to just the right height and then having it stay there. For some reason it was a lot harder to wrap my mind around that than plain old satellites even though floating should seem more unnatural.

The space elevator has been proposed as a permanent route to space. Instead of launching rockets over and over to get people and things into space, the tether will acts as a road vehicles to climb, carrying people and materials.

The space elevator is way cooler than a base on Mars or more star wars defense projects but as I was looking around for fresh abstracts to link to this post I didn't find anything newer than 2005 in Google scholar. However, I did find a competition planned for fall 2007 to improve the design. The prize is $1 million.

There are several technological hurdles to the creation of the space elevator. Most importantly is the design of the tether which must be miles long and incredibly strong. Most groups are focusing on carbon nanotubes and a ribbon-like tether. Nova has a GREAT video on the subject with nice graphics and some video of the creation of nanotubes.

Autistic/Artistic

Autism and autistic spectrum disorders are among the most heritable of mental disorders as demonstrated by twin studies and family histories. Some of the heritability may be related to super genetic traits like expanded number of repeats in certain segments of the chromosomes as opposed to inheriting a gene for autism. The Autism Genome Project has been investigating some of the genes involved in autism and has come up with a few according to this news article.

Prevalence
Recent studies have disputed the perceived prevalence of the disorder. Some believe thr increasing incidence can be explained by better measures, better reporting and the expansion of the definition of autism into the autistic spectrum.

Savants
Check out this amazing video (5 mins) in which an autistic man takes one helicopter ride over Rome and then accurately reproduces a huge swath of the city on paper (Originally hosted by the Wisconsin Medical Society.)

Besides having some autism in the family [[ UPDATE: Diagnosis changed!]], I've read a few great books on autism: Oliver Sacks' An Anthropologist on Mars and Temple Grandin's Thinking in Pictures. I have to admit, Sack's book is a collection of essays on different interesting neurology cases, one of which is Temple Grandin, so they are two closely related tomes. Sacks writes about autistic adults and children and Temple Grandin writes about her own experience with autism. Both focus on the special talents that come with the deficits of autism. Grandin believes her experience of the world is closer to that of animals, not that she lacks intelligence but that her emotions are more like those of species other than humans.

Finally, here's an article on a group show of works by autistic artists.

Which came first, the lazy chicken or the lazy egg?

Abstract ahoy.



This study looked at the relationship between fitness and urban or suburban living. Not surprisingly, urban-dwellers tend to be in better shape. It could be because of all the 24-hour gyms they have in those big cities. But there is a possibility that people move to the suburbs so they can drive their cars everywhere. It's not location, location, location it's parking, parking, parking.

... these associations don't prove that sprawl causes laziness or weight gain. Most of the studies provide only a snapshot of different people at a single time. Such studies can't prove that living amid sprawl leads to inactivity; it may also be that inactive people choose to inhabit areas where driving is the easiest way to get around.

(from Science News)

While I was expecting city dwellers to be healthier it is a little weird. When you go to the suburbs you see parks and trees and bikes all over the place. When in the city all you notice are cars and buildings.

Fruity

This week's abstract is in honor of the news of the closure of PEAR.

PEAR, or Princeton Engineering Anomalies Research operated for almost thirty years. PEAR's studies looked at the ability for human consciousness to interact with the physical world. In some cases they used machines that use various schemes to create random numbers. The researchers asked people to influence the outcome of binary events controlled by these random machines. Using statistics to analyze extremely large samples, they came up with some indications that the conscious intentions of their subjects could affect the physical world. There are a lot of objections to these experiments, both methodological and theoretical.
















The main objection to these experiments, beyond their methodology, is the idea that scientific research should build on what came before; new experiments and hypotheses should be formed in the context of current understandings. However, others argue that we don't have to accept the idea that these are paranormal phenomena, and the rejection of all evidence and study on these topics is based on certain beliefs that also cannot be proven.

An article in today's New York Times on Carl Sagan brings up some interesting points on the intersection of science and religion but somehow tows the line that investigation is more important than confirming our beliefs.

“It goes with a courageous intent to greet the universe as it really is, not to foist our emotional predispositions on it but to courageously accept what our explorations tell us.”

That's a sexy selection

Since the abstract isn't up yet:

In this Committee Opinion, the American College of Obstetricians and Gynecologists' Committee on Ethics presents various ethical considerations and arguments relevant to both prefertiliztion and post fertilization techniques for sex selection. The principal medical indication for sex selection is known or suspected risk of sex-linked genetics disorders. Other reasons sex selection is requested are personal, social or cultural in nature. The Committee on Ethics supports the practice of offering patients procedures for the purpose of preventing serious sex-linked genetic diseases. However, the committee opposed meeting requests for sex selection for personal and family reasons, including family balancing, because of the concern that such requests may ultimately support sexist practices. Because a patient is entitled to obtain personal medical information, including information about the sex of her fetus, it will sometimes be impossible for health care professionals to avoid unwitting participation in sex selection.

This statement is in reaction to new types of pre-implantation selection. One can now use sperm sorting to decide the gender of their baby (females always donate an X chromosome, males can donate either a X or a Y). Or, embryos created through in vitro fertilization can be selectively implanted.

After implantation, the sex can be determined either through ultrasound or cytogenetic analysis of amniotic fluid or villi (amniocentesis). Cytogentics is the study of chromosomes.

Because of the risks involved (although recently downgraded by quite a bit) amniocentesis is typically only used when the mother is of advanced maternal age or there is a history of chromosomal disease in the family.




I personally doubted a lot of sex selection is going on in the US, mostly because of the stigma attached to what's going on in India and China. But, then I found this site. The writer argues for using sperm sorting to choose the gender of children for family balancing reasons, exactly what the American College of Obstetrics and Gynecology is arguing against.

Should we do things just because we can? It seems like a skewed sex ratio would be bad for society but there's always a chance people won't all choose the same gender.

Toothy Smile

Abstract for the day.

Why do orthodontics keep coming up here?

Anyway, this study looked at how getting braces improves or doesn't improve your life. In Britain, the researchers found there was no significant difference between people who had braces as a kid and those that didn't in terms of "well-being and self-esteem."

There were minor correlations between getting "necessary" tooth fixin' and later satisfaction but all in all the best predictor of "well-being and self-esteem" 20 years down the road was self-esteem at a young age.

I will make no comment about the generalizablity of this study beyond the following:

The authors didn't control for culture so you can't expect the same to hold true here in the US or in other countries because how people feel about their appearance depends on social norms.

Environmentally-Friendly Chem Labs

I totally want to take this class at the University of Oregon.

The EPA defines green chemistry as:

"...the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances."

The 12 Principle of Green Chemistry.

I have often thought about how to make labs more eco-friendly. In a lab, throwing away gloves, metal, glass and gallons of chemicals is a daily habit. You forget that the lab isn't a sealed environment. Whenever you leave you wash your hands and take off your lab coat, you're clean. But what all the trash the university or company has to deal with?

Part of the problem is that if you are working on a basic science problem or in a clinical situation you feel like your work will be doing some good down the road, so the waste will be justified in the end.

Green chemistry focuses on ensuring chemical processes are efficient in their use of material, make things that are better for the environment and preserve energy. The focus is twofold: invent chemicals and processes that are cleaner than what we have now and do the inventing in an environmentally-friendly way.

I looked around MSU's Web site for some clues as to what's going on here. I found one lab that mentions green chem but no overreaching campus initiative to make things better.

Reading this makes me want to make my lab safer.

Oobleck

I thought I would join the YouTube bandwagon for this post. I used "science" as a search term and came up with one pretty cool example. (I do hope it's real, I found some fake science experiments in my search. The best by far is the Look Around You series.)

Here's a second video with a much bigger vat of cornstarch.

I looked around for some cornstarch articles on Google Scholar and PubMed but most of them had to do with eating cornstarch instead of walking on it.

Oobleck behaves as a non-newtonian fluid. Newtonian fluids react in a fixed proportion to pressure. If you push twice as hard, there's twice as much resistance. So when you try to step on water you push right through, there is nothing special about the molecules near your foot.

Non-newtonian fluids can have non-proportional reactions due to their sensitivity to gradients in flow speeds.

Oobleck gets incredibly viscous over small areas when strong pressure is applied. Oobleck molecules do care about their neighbors, a lot. If your foot is creating a change in the flow gradient, pushing one area of the liquid around a lot faster than the neighbors are being pushed, they stiffen up and push back. The reaction of the liquid isn't proportional to the pressure applied, it's complicated by the locals.

Okay, that hurt my brain so I'm not even going to attempt to explain what's happening in the video up top.

More fun with cornstarch (or sand or sugar). Sorry about the noise.

Now, let's combine crazy liquids with art (video). These artist/scientists used magnetic liquid in their sculpture. The magnetic fields are controlled by a computer that detects sound in the room. As a result, you get crazy movement when there's lots of noise. One of the artists, Sachiko Kodama, has a new solo project using magnetic liquids.

Magnetic liquids can be used in inkjet printers so that text or patterns can be read by machines.

Dampening is more common use for these liquids. Magnetic liquids can be manipulated by applying magnetic fields. When the field is off, the substance behaves as a liquid. With the application of the field the substance becomes thicker and resists motion. Some car shocks use this property to adjust stiffness depending on road conditions.

Can You Say "Tipping Point"?

Abstract number two.

President Bush plans to weigh in on the healthcare debate tomorrow during his state of the union address. Hillary Clinton is proposing legislation to expand the federal health plan for children. And of course, Schwarzenegger is doing his best to pass his own pet insurance plan.

But, as you probably know, these are not the ground breakers.

Way back in the day, 1989 to be exact, Oregon had a plan: the Oregon Health Plan or OHP.

Basically, the Oregon plan expanded Medicare to cover more of the state's uninsured. They started out by providing enrollment in managed healthcare plans to residents that earned 100 percent of the federal poverty level. But in order to expand the number of people they covered, the plan limited the services provided. When the OHP budget was drawn up, all the treatments would be prioritized and then the line was drawn.

“Every two years the state legislature would literally draw a line in the list, with Oregon Medicaid paying for all services above the line and no services below it,” Jonathan Oberlander wrote in his study on the failure of the plan.

None of the current state proposals have this rationing built in. But the plan didn't fail because of the controversial line drawing, instead the state tried to enlarge the plan even more in the beginning of this decade. However, complicated enrollment rules, changes in co-pays and deductibles and substantial premiums for the new members, caused many people to drop out of the program. Add an extreme economic slump and the OHP stopped accepting members in 2004.

The message to states going down this path is a basic one: don't change a bunch of things all at once (also, don't provide a tax kicker, but that's another story).

Other States
The newest plan on the horizon is from Gov. Ed Rendell of Pennsylvania. This plan is so new the legislation hasn't been written yet, but it has a couple of shiny new ideas tucked inside.

Rendell noticed what a lot of other governors are noticing these days: uninsured people use medical services anyway and the state ends up paying, a lot. So since the state's already paying, let's reduce the cost of medical care.

The proposal suggests saving money by reducing medical errors, preventing hospital-based infections, outlawing smoking in the workplace and increasing the tasks that can be performed by nurses. And that's just the "cost-cutting side." On the "where will this money come from side," we have an increase in the cigarette tax and a payroll tax for businesses that don't provide health insurance to their employees.

I haven't seen the details yet, but Bush's plan sounds awfully confusing to me. It goes something like this- we will make people who pay a lot for health insurance pay even more by taxing their plans and then we will use that tax money to subsidize the purchase of less expensive insurance for others.

I get that part where money from rich is supposed to go to poor (except that most people who work and get insurance through their employer don't have a lot of choice in coverage). But this is also supposed to be some kind of mechanism that will reduce the average price of insurance over time. Hmmm. Well, if we assume that the most expensive plans are purchased through employers that don't offer options to employees and probably switch providers once in a decade, I really don't see how this will work.

Massachusetts, the first state to require that residents purchase health insurance has had their plan in place since April 2006. Residents earning less than three times the federal poverty level can get a subsidized plan with no deductible (that includes dental!).

I'm excited about dental because dentistry is neglected by many insurance plans and many, many people visit the ER with dental issues.

California is still in the midst of the heath insurance battle. Schwarzenegger proposed, the assembly passed but the senate is on the fence on the $12 billion dollar plan. One of the fights is whether the money will come from taxes or fees. Fee are the magic word here, if you say TAXES, Schwarzenegger will have gone back on campaign promises.

The Robert Wood Johnson foundation is tracking state plans.

Not that kind of organ.

I mean organ (see number 6) in the sense of an information outlet.

My first abstract.
One thing that we need to get out of the way: if you look at the origins of the study, its lead author belongs to the department of onchology according to the Pub Med abstract. However, "onchology" is not a real word, but there is an oncology institute in Sheffield. I looked it up to make sure onchology wasn't the study of the urge to vomit when goo is introduced into the oral cavity.

That's what this study is about, the goo, or alginate, dentists and orthodontists use to take impressions of your teeth. I recall when first entering the world of orthodontia at the tender age of 11, I was offered a choice of flavors by the technician in the fancy scrubs. But no matter what kind I chose, strawberry or mint, I always felt ready to throw up after about 2 minutes. Apparently this is a common problem. So, these acupuncture-dentists try to solve it with needles.

Alginate is also used for life casting and making Hollywood masks.


This study by Palle Rosted and associates looked at the effectiveness of acupuncture in preventing dental patients from gagging when the alginate is placed in their mouths. They were surprisingly successful.

The dentists needled the patients in a spot directly below the lower lip, in the center of the chin at a spot denoted CV 24. CV24 stands for Conception Vessel 24 in the Chinese medicine map of meridians.

The Process
They first tried to get the impression tray in the participants' mouths, then the tray plus goo. Meanwhile the acupuncture-dentists collected information on the patients' gagging feelings. Next they applied the needle. Then they gave it another go with the goo.

Problems
The patients were chosen because they were unable to undergo normal dental procedures because of gagging, so people with a less severe problem with the process might not benefit in the same way. However, the goal of treating people with a serious difficulty receiving dental treatment was met and how widely it can be applied might not be so important.

Everybody got acupuncture. There was no comparison group to show that having someone spend an extra amount of time fussing over you won't cure your gagging issues.

The Last Part
I chose this study because it rates high on my gee whiz scale, mostly. I didn't know that gagging during dental procedures was common. I didn't know what alginate was. I didn't know what acupuncture point they were using and when I found out I wasn't sure why. Actually, I'm still not sure why they chose that point. Finally, I like that they took a very practical problem and used an unusual tool to solve it.