Scientist Barbie.

"Scientist Barbie comes complete with a white lab coat, map of the human genome, pictures of fetal defects, and 2 books (Sigma catalogue, and How to lie with Statistics). HIV, Hepatitis, H Pylori, and pregnancy tests can be ordered from Sigma. Pull her chord to hear her say: 'Who cares if math is hard when you have a TI-85', and 'There's REALLY nothing dangerous about radioactive materials'. Scientist Barbie drives a classic 1979 'vette......chevette, that is, because everybody knows that academia doesn't pay. Microscope, transgenic mice, and dissecting scalpel needed to undercut fellow researchers and stab collaborators in the back sold separately. Small animal surgery kit includes coupon for Dominatrix Barbie accessories."

Er, not so much. I'm not sure Barbie could handle it. But Barbie does come in Slutty Nurse Barbie, 'coz you know, hot pink heels are my go-to shoes for work.

Watch your language!

I started reading some of the Nature news articles this morning and came across this:

"It's not easy making a human. Getting from a fertilized egg to a full-grown adult involves a near-miracle of orchestration, with replicating cells acquiring specialized functions in just the right places at the right times."

Let's stop calling scientific facts miracles, ok? Seriously.

The cutest gel

Hello again

I just got linked to "The Best Science Blogs" and #1 is pharyngula, a self-proclaimed godless liberal who spends all his time talking about how dumb religion is and no time at all talking about how cool science is. Lame. Let's talk about science again!

I'm spending a lot of time thinking about protein structure these days.


I'm trying to model mutations computationally and see how it changes the packing volume inside the protein! I wish I had learned more geometry than just what they taught me in 9th grade.

I'm also doing real experiments finally! Look, a western blot!

Jerry Woodall, a Purdue University engineer, has developed a method to generate hydrogen from water using an aluminum alloy. He discovered this in 1967 working as a researcher in the semiconductor industry.

"I was cleaning a crucible containing liquid alloys of gallium and aluminum," Woodall said. "When I added water to this alloy - talk about a discovery - there was a violent poof. I went to my office and worked out the reaction in a couple of hours to figure out what had happened. When aluminum atoms in the liquid alloy come into contact with water, they react, splitting the water and producing hydrogen and aluminum oxide."

The gallium is critical to the process because it hinders the formation of a skin normally created on aluminum's surface after oxidation. This skin usually prevents oxygen from reacting with aluminum, acting as a barrier. Preventing the skin's formation allows the reaction to continue until all of the aluminum is used.

He envisions a future where we drive cars with tanks of water. When we need hydrogen for our fuel cell powered engine a small pellet of aluminum alloy is dropped into the water tank to generate the hydrogen on demand. Sounds nice.



On a personal but blog-related note, my ability to report on podcasts will be severely impaired over the coming 6-8 weeks. My iPod, which has been sickly for over a year now, as some of you may have known although I doubt most would notice because he hides the pain so well, has begun what I am afraid are the last throes of his ultimate demise. (If only I could get Dick Cheney to announce it to the nation my iPod might actually last another 3 years.) The lapse in coverage is due to the time it will take to raise funds (spending money for Ecuador takes precedence) and to find a suitable replacement. I apologize for an inconvenience.

Farewell iPod. I loved you and then you broke.

Bomb-A-City

This is a "game", if you will, that a post-doc in my lab found today. FAS gives it the catchy name Bomb-A-City. Basically, you input your city, method of delivery, and tonnage of nuclear weapon, and the Bomb-A-City calculator shows you a map of what the destruction would be. Useful for, you know, all those arguments you get into at parties about what the total incineration radius would be of a 2 megaton nuclear weapon detonated one mile above Reno. Note the odd inclusion and exclusion of certain cities from the pop-up menu...

This is fucking weird.

telekinesis for real

Ever wanted to move things...with your mind? Soon you can: Hitachi has devised a "brain-machine interface" that measures small changes in blood flow in various parts of the brain. These changes can be translated into electric signals, such as ones that cause your TV to turn on or off, or that cause an electric train to start or stop.

Widespread applicability? I'm skeptical - but it's pretty damn cool in any case.

Adults aren't the only crazy ones!

In typical fashion, like Erin with her podcasts, Dave and Christina with their blogs, and Cressida with her, uh, ear to the ground, I read the following in the newspaper. (I love print media.)

"We need to treat these children. They are in a desperate state," Biederman said in an interview, producing a video clip of a tearful mother describing the way her preschool daughter assaulted her before the child began treatment for bipolar disorder. The chief of pediatric psychopharmacology at Mass. General, he compares his work to scientific break throughs of the past such as the first vaccinations against disease.

In the past, bipolar disorder was reserved for only those who made it through the unpleasantries of puberty, but recent research has suggested that children as young as 2 (!) can require treatment for the agreesive behavior. However, in December a child died from an overdose of drugs used to treat her bipolar disorder and attention deficit hyperactivity disorder. These drugs were NOT approved for use in small children.

We take a step back: Aren't kids that age wildly agressive one moment and giggling the next? I thought that was expected of your infant child. While I have seen the diagnoses of ADD and ADHD increase dramatically over the last 10 years, this seems to be the latest increase in pre-pubescent behavior disorders.

I would never say that people with behavior disorders shouldn't be treated with appropriate drugs, obviously. But I am more conservative when it comes to children.

How conservative should we be? There is significant debate on whether such young children should ever be diagnosed as bipolar. How do we draw the line? Should children be protected/prevented from the sometimes agressive treatments that adults receive?

I would argue that the standard for aberrant behavior in children must be significantly higher. There is an increasing culture of The Average, originating from the educational system that has leaked into medicine. My child doesn't perform as well on exams. They must not be below average, there must be something clinically wrong - and treatable - with them. Let's medically fix that lower performance and reach the level of The Average. Yes, some people benefit from it. But medical treatments have led to less of a focus on educational treatments. I say this with my limited experience with teaching students with dyslexia and ADD last year, my mother's work with SpEd children, and working with Melissa's teachers to design her curriculum. The difference between the attitude and energy applied to the educational program of children with medically treatable disorders vs non-treatable is amazing. Melissa's teachers were forced to design entirely new curricula for her, whereas my mother's and my hands were tied working with kids with ADD, as they were expected to be drugged and perform like their peers. It is not effective for everyone, despite it certainly working for some.

Good, I think I've managed to complain about both medicine and education.

Do men fear the end of patriarchy? Apparently!

Are you familiar with Mandrama? It's this super-embarrassing thing dudes do when trying to pretend not to be agitated. And then - oops! Out it comes! Comments like "You made me cry you evil bitch!" This website documents such outbursts. Fu-nny. I almost peed myself. Can someone put it in "stuff to look at"? I'm website illiterate and can't figure it out...

Moon Dust Saves Us From Global Warming

Wow this is the dumbest idea I've heard in a long time.

Curtis Struck at Iowa State University in Ames published an article in the Journal of the British Interplanetary Society (vol 60, p 1) suggesting we mine the moon for dust to generate a gigantic cloud to shield us from the sun. Lunar dust particles are the right size to scatter sunlight. If we put dust at two precise positions along the Moon's orbit, they will form a pair of stable clouds that would each pass in front of the Sun once a month, blocking sunlight for about 20 hours each month. This would reduce the amount of heat reaching the earth and thereby help alleviate the affects of global warming. I should say that I have not read the article because I can't get my hands on it but here is what I think from what I have read and heard on a podcast.

Not only is this ridiculous in its extremity but I'm pretty sure blocking out the sun will hinder plan growth, which help reduce CO2 levels, and potentially insulate the Earth from radiating heat back out into space (not to mention the logistics of mine on the F-ing moon). And what happens when we don't want the dust cloud anymore, do we build a gigantic vacuum cleaner? Other criticisms have included that the clouds may act as mirrors when not directly blocking the sun thus adding heat, and at night will act like massive full moons increasing the amount of light reaching the earth at night, which may also have deleterious effects on plant and animal life. This would also devastate ground and earth-orbit based astronomy. In the end this is only a band-aid, if we don't stop living in an unsustainable manner, no cloud will be big enough to save us from self-destruction. (Ok, that was a little dooms-day-ish, but you get my point.)

Gigantic dust clouds...I mean really!

Hens and Bucks?

So I got up this morning and heard something on the radio that made me stop what I was doing. “I’m sorry to say it but most of the lesbians are more aggressive than homosexual men.” My disclaimer is that I couldn’t get the transcript of this interview from the BBC website so I’m quoting from memory and I am not entirely sure if the guy said heterosexual or homosexual men, but either way it made me stop and say WTF. As it turns out a pub in Australia has won the right to exclude patrons based on their sexuality. The claim is that the heterosexual men and lesbians were creating an environment uncomfortable to the gay men by treating them like entertainment or as if they were “zoo animals”. This pub is the only one (out of 2000) in Melbourne geared toward gay men. So the pub owner/manager would like to limit the number of heterosexuals and lesbians to help keep a safe balance. I do sympathize with the notion of creating an establishment where gay men can feel comfortable as apposed to a freak show. However, I don’t see why the owner couldn’t have implemented a policy of asking groups of people to leave when they start making other patrons uncomfortable. It would be as if a group of men hung out in Victoria’s Secret to ogle the women while they picked out thongs. A manager would be perfectly justified in asking the group to leave without getting a court to declare that the store can exclude men. It seems to me that this is how it will have to be enforced anyway. I can’t image the pub prohibiting gay men from bringing straight and lesbian friends, or asking men if they are gay or straight before entering. So why did the owner feel it was necessary to take the matter all the way to The Victorian Civil and Administrative Tribunal? It seems to me that the pub has put itself in a position of favoring discriminatory practices, even if it is with good intentions, as well as set a legal precedent for discrimination in the future. Or, maybe it was necessary to take legal action to effectively protect the rights of a group being discriminated against and harassed. Any thoughts?

science in the blogosphere

Not that I wasn't excited about the Tasmanian Devil cancer, but I'm kind of glad I found something to push that...aesthetic...picture out of the top of the page.

An analysis article in the latest issue of cell discusses scientists in the blogosphere: how there are so few of them, what their impact is, and varying opinions on how to present ideas depending on the audience. If you get a chance, read it and tell me what you think. Think we could make it onto scienceblogs.com? Then maybe we'd have a real public audience!


EDIT: I have decided to make this post longer, as I discovered that the original length was not quite enough to push the DFTD picture out. So please enjoy this random picture of calculus chocolates. Mmmmm.

Tasmanian devil facial tumor disease

OK, I had to share with everyone one of the coolest things I've come across in a long time. Maybe you've heard about it on NPR, if you're in one of those labs that plays NPR all day (God knows I am).

The Tasmanian devil population has fallen by 90% across large parts of Tasmania. This is due to a recently evolved illness, Tasmanian devil tumor disease (DFTD). And holy cripes people, it looks painful. Just Google "Tasmanian devil cancer" and be horrified. It's a tumor of neuroendocrine origin that causes awful ulcerated lesions on the head and face of Tasmanian devils, usually starting in the mouth. If the tumors don't kill the devils by secreting hormones or impinging on essential organ function, then the devils typically starve to death or suffocate as the tumor mass in the face and throat increases. Once it's visible, it's 100% fatal within 4 months.

But here's the cool part: it's an infectious cancer! Seriously! Devils are really violent, especially when gettin' it on, and when they bite and scratch each other during sex, the cancer is transmitted by inoculation with the cancer cell line itself - basically an allograft. It's not a virus causing the cancer, which is what I totally thought it was gonna be when I heard this on the radio. (One of the articles I read called DFTD a "rogue cell line", which just sounds bad-ass.) The tumors do not have the same genotype as the affected animals - in fact, they all have identical chromosomal defects, indicating that the cancer is clonal throughout the population. It's basically a cancer that's somehow "learned" to be transmitted between immunologically different individuals of a species. As you may know, this is not how cancer usually works. If I got a big nasty facial tumor and made out with Scott, Scott would not get Cressida tumor popping up all over over his face. His immune system would be all like, WTF? And kill that shit. DFTD has found a way around that, which totally blows my mind.

I was really interested in this story, since I'm interested in anything infectious, especially eukaryotes. As it turns out, DFTD is the second example of a cell line that's become infectious, the first being the appetizing transmissible venereal sarcoma, a disease of doggy hoo-haa's and wee-wees. As it turns out, this disease is studied by my favorite evolutionary biologist, Armand Marie Leroi.

So in terms of organisms colonizing other organisms, we have:

1. proteins (prions)
   
2. viruses (HIV)
   
3. bacteria (tuberculosis)
   
4. traditional eukaryotic parasites (malaria)
   
5. helminths (tapeworms)
   
6. cell lines (DFTD)

What happens to the Tasmanian devils? From what I've read, biologists aren't too optimistic. The problem is that it's sexually transmitted, which means that even if very few individuals in a population have it, it will still be transmitted effectively (see HIV for an example of how that works). It's not clear yet how infectious it is, although it's thought to be poorly infectious as it's taken DFTD like 10 years to get half-way across Tasmania. If it were highly infectious, it would have moved more quickly, as devils travel great distances on a regular basis. Resistance has been slow coming; I saw one report that said that 3 female devils had been found that were partially resistant, but there are no reports confirming that. And the population's already been so decimated that other factors, like feral species or loss of habitat, become more able to drive devils to extinction. Several "insurance" colonies have been set up off shore, but you all know what that means: no more genetic diversity. This has been a problem in populations like cheetahs and ne ne geese that experienced severe bottlenecks in their evolution, leading to essentially clonal cheetahs. So one good infectious disease, and they're gone.

How can this happen, the evolution of a rogue cell line?? (Makes you look at those HeLa cells with a little more respect, eh?) It's obviously a very rare event, but what's going on immunologically to allow this? Cancer people, what gives?

Some cool resources for DFTD:
Save the Tasmanian Devil
FAQs from Tasmania's DNR equivalent
The Nature paper proving DFTD is a parasitic cancer
NPR story
Tasmanian devil movie

crack is whack

So I couldn't figure out how to embed this video right on the page, so a link will have to do. It's a video a friend of mine sent me about the effects of drugs and alcohol on spiders. Fantastic.

It's Science

As I was searching handy dandy PubMed for sequence based approaches to mapping breakpoints in translocations I found this article. I don't think it'll be useful in my research but I do think it's useful in life.... in general...

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16413181&query_hl=2&itool=pubmed_docsum


Sorry for the ugliness - I can't figure out how to name the link. I'll make it up to you all with this picture:

PS - This is supposed to spark conversation about "worthwhile" research.

And if you say worthwhile a bunch of times it totally loses its meaning...