DIY DNA Extraction

This is awesome

One summer years back I worked in a plant genetics lab doing something not completely unlike this to isolate DNA. I guess the main difference would be in the purity and integrity of the DNA collected - you certainly couldn't use this method to get analyzable samples. The kits we used in that lab contained lots of buffer solutions, enzymes, and other chemicals to break down the cell walls, remove the proteins, and precisely isolate the DNA. At the end, you get a few micrograms of the stuff. I'll stick with the stovetop method from now on. It's probably not hard to modify this to get DNA from other things - certainly other plants - but what about animals? You would have a hard time getting a big enough sample to collect a visible amount of DNA, and it might be more fragile. I've never done that, so I'm not sure how the procedure differs.

Maybe one day I'll be outside poking around in the dirt and come across some fossilized amber with a mosquito inside. I'll take it back to my kitchen, pull out the blood from the mosquito and...

DINO DNA!!
Continue reading "DIY DNA Extraction"!

Visualizing science

This article from the Boston Globe on opening up science* pointed me to some really exciting online resources that are free and open for anyone to access. Most interesting is the Journal of Visualized Experiments (JOVE). This site publishes videos of experimental protocols submitted by researchers. Each is reviewed by a panel of experts, so quality and relevance are ensured. The videos range from basic wet-lab techniques and equipment-care tips to highly specialized imaging and brain recording methods. It's all free and open from the start, you don't even need an account.

This is extremely useful for other scientists, particularly those attempting to learn a technique for the first time. It's also a great example of transparency and camaraderie within the scientific community - a group that unfortunately, faced with trickling grant money and declining job prospects, are often forced to be quite competitive and opportunistic.

I see sites like this, however, as really important for educational purposes, for getting the word out on what scientists do day to day. Videos are especially useful for this because they get around technical learning curves that prevent most from comprehending scientific journal articles. You don't need to have an extensive background knowledge to understand what a scientist did in the methods section of a scholarly paper if you can see it. Ever wanted to know how scientists image individual neurons within a living brain? How stem cells are collected and analyzed? Now you have videos with pretty pictures to watch.

Any effort to remove some of the secrecy and mystery associated with research, to help the public see that science isn't just for stuffy Ph.Ds and nerds, but rather, can be an interactive, dynamic, and open exchange of ideas among researchers and everyday people, is worthwhile and necessary for progress.

*I plan to comment more about the open science movement. The linked article discusses some of the reservations old guard scientists and journal publishers have about giving everyone access to their data (so read that too), along with several web 2.0-esque science resources new to the internet. I think it's an interesting generational issue, sort of the Napster debate of science.

Continue reading "Visualizing science"!

Internet Memes

Check out this cool internet meme timeline. It's interactive! Zoom down to the month scale to see them all. After the jump.





This makes me nostalgic for those *simpler* days when I had to sign into AOL with my 56.6K dial-up modem to see the internet. My family was a little late to adopt internet usage, our first serious computer purchase was around 1996, if memory serves. I definitely remember the Dancing Baby meme, though that memory might be from something similar in an episode of Ally McBeal. Notable high school memes included the Blair Witch Project, Hamsterdance, Homestar Runner, and (unfortunately) Bonsai Kitten. From college, the Ashlee Simpson lip-sync snafu, Chuck Norris facts, Ask a Ninja, I Can Has Cheezburger, and (again, unfortunately) OK Go memes stand out in my mind.

I feel both young and old.

Continue reading "Internet Memes"!

For Your Consideration: Media recommendations

Book

The Drunkard's Walk: How Randomness Rules Our Lives by Leonard Mlodinow. Mlodinow is a Caltech physicist and author of several popular science books, notably, Feynman's Rainbow and (with Steven Hawking) A Briefer History of Time. This new book explores probability in everyday life, emphasizing how humans misunderstand randomness. We (read: primates) are especially evolved to form patterns and associations, to build heuristics that confer us some ability to predict future events. In other words, we seek out non-randomness in the world, a quality that was helpful in a simpler time, before modern civilization, but one that can lead to bad probability judgments when applied to modern scenarios. I've only gotten a few chapters into this, but so far it's highly entertaining and informative.

Pastoralia by George Saunders, is a collections of short stories and a novella. As the book jacket notes, Saunders is an author in the tradition of Mark Twain, Thomas Pynchon, and Kurt Vonnegut, sharply satirical and smart. The title story, "Pastoralia" is a swift and punchy, but utterly disturbing riff on the absurdity of modern America. After reading this, I'm going back to get all of his other work.

Magazine

SEED Magazine has been around for a couple years, along with its blog network Scienceblogs (Something else I would recommend as a great place to read about science/politics/culture/etc). I've been a subscriber and reader online for a good chunk of that time. Their motto, "Science is Culture," reflects the focus on the confluence of science and society, what really interests me about the magazine. Great art design too.

Podcast

The Naked Scientists is a podcast by several young Cambridge, England researchers, distributed by the BBC. It covers a wide swath of popular science stories, from public health to space exploration. Each episode includes a review of the week's science news, Q&A with listener email, interviews with prominent researchers, and a "kitchen science" experiment reminiscent of Mr. Wizard. Add in a bit of cheeky Brit humor, and you've got a great show. What makes it really entertaining, in my opinion, is the hosts' enthusiasm for the subject matter and interest in promoting public scientific literacy. The science is presented in an accessible way, but it's never dumbed down.

Philosophy Bites is a great little podcast by two British authors. Each week they interview a philosopher on a specific topic - such as, for example, evil, forgiveness, infinity, and human rights. This week's episode discusses the paradox of tragedy - that is, how we seemingly take pleasure from tragic literature and film, even though such things are filled with pain and suffering. Most of these discussions are 10-30 minute segments, so it's easy to stay engaged.

Continue reading "For Your Consideration: Media recommendations"!

New Gadgets

Last Friday I turned 24 years old (nearly a quarter century!), and I ventured away from Ann Arbor for some fun with family and friends. I was given several nice gifts, but I want to highlight two that satisfy some of my greatest interests: technology and coffee.

First, the Flip Mino, a miniature camcorder.

It's about the size of a pack of cigarettes and holds up to an hour of video. The best part is the flip-out USB adapter; all I have to do is plug it into my MacBook and upload, or connect the TV Out cable and display images on a bigger screen. I've recorded a couple short ones, but nothing yet worth posting. There may be an opportunity to record and post video of some of the more visually interesting things I do in lab. YouTube, here I come!

Second, a Bialetti mukka, a stovetop device that allows you to make cappuccinos and lattes without an expensive milk steamer and espresso machine. It works great, like magic actually, as you can see in the demonstration video at that Williams Sonoma link.



This mukka is going to save me so much money. Every morning I get coffee at the Espresso Royale outside my building. Every morning. And not just coffee, sometimes I get fancy drinks, like a soy chai latte. This amounts to $2-4 a day. Just this summer, I've spent over $200 on coffee. Continue reading "New Gadgets"!

Do you want to be an astronaut?

I'm really interested in what the Mars Phoenix lander is doing. You probably heard that it recently discovered water ice, a huge finding that lends a lot of credence to the theory that Mars used to be much more like the earth - warmer, wetter, greener - and potentially habitable for life. The news about ice was first announced on Twitter. The lander has its own account, and the posts are written from the perspective of a robot on another planet. It's fantastic.

Today Phoenix posted a link to a job announcement on NASA's website. The job? Astronaut, class of '09. Here's the announcement:

RELEASE : 08-158

Deadline Approaching to Apply for New NASA Astronaut Class

HOUSTON -- NASA's deadline for accepting applications for the 2009 Astronaut Candidate Class is July 1. Those selected could fly to space for long-duration stays on the International Space Station and missions to the moon.

To be considered, a bachelor's degree in engineering, science or math and three years of relevant professional experience are required. Typically, successful applicants have significant qualifications in engineering or science, or extensive experience flying high-performance jet aircraft.

Teaching experience, including work at the kindergarten through 12th grade level, is considered qualifying. Educators with the appropriate educational background are encouraged to apply.

After a six-month period of evaluation and interviews, NASA will announce final selections in early 2009. Astronaut candidates will report to NASA's Johnson Space Center in Houston during the summer of 2009 to begin the basic training program to prepare them for future spaceflight assignments.

To apply to be an astronaut, visit:

http://www.usajobs.gov

Really? According to this, I will be a legitimate applicant for the position of astronaut in a couple years. Bachelor's degree, significant experience in science, teaching experience, yeah, that's me. If I can somehow commandeer a jet and learn to fly it, I am totally in. Seriously though, do real astronauts, those people that actually go to space, apply for their jobs this way? The image of some rocket scientist/top gun sitting at his or her laptop, filling out an online application to enter the space program is so hilarious to me.

There's more information at the NASA Astronaut Recruitment site. With a job like this, some travel is involved, they say, including "Texas, Florida, California, Russia, Kazakhstan, the International Space Station and the moon." HAHA

You know, it couldn't hurt to apply. I'm still not sure what to I want to do after getting a Ph.D, and it's probably smart to keep my options open, stay open minded. If you're interested, time is running out to get into this year's class. Deadline is July 1st. Continue reading "Do you want to be an astronaut?"!

SPORE

I just downloaded the Spore Creature Creator, a limited version of the game that will come out later this year. There is a free trial version, which is what I got, and a $9.99 full version, which I will probably get later. Okay, so, this game was MADE for me. The only part of the Sims that I ever really liked was building/outfitting houses. Maybe it reminds me of earlier times, when I seriously considered becoming a engineer. With Spore, they add in this awesome biology element - which greatly appeals to me - in that you can "evolve" a creature from single celled to civilized.

Well, okay, so there isn't much basis in actual biology and evolution. I guess it's not inconceivable that a creature would evolve a horn growing out of its ass, twelve legs, and beard, but variations of those traits would have to confer some advantage to individuals in the local environment for a long long time before they developed. Nevertheless, this is still going to be an awesome game, scientific accuracy or not. I spent a few minutes building a creature, Arthropodiculous, shown below in dance-party mode.

Continue reading "SPORE"!

Wednesday, with some bonuses

Long day, busy organizing for an experiment that starts tomorrow morning. It was also hot.

When I got home, two surprises awaited me. One was my latest Netflix movie, I Am Legend. I never got around to seeing it in theaters, even though I wanted to, and now I know a lot of spoilers about the plot, but I'm still interested. One question does remain, however. Does Will Smith say "welcome to earth!" or "get off my car!" to the vampires? I doubt it, but haven't given up hope. Will Smith never lets me down. The second main character appears to be a dog. That's also good.



The second surprise was my new Western Digital My Passport 250 gb portable hard drive (hat tip James Foreman). I've never been responsible about backing up the information on the computers I use. I don't have a system, just data strewn about. Now, with this tiny new drive, I'll have no excuse not to back up often. My back up anxiety stems from an irrational fear of accidently erasing everything, permanently, in the process. I know this isn't as easy as it is in the movies, where people sit down at a computer, hit ENTER, and suddenly a dialog box appears, displaying FILES DELETED. Regardless, I'm getting back up for this backing up. Nick, brother, soon to be world traveller, and, importantly, knowledgeable tech person, has promised support. If I'm not spotted on the internet for a few days, it means my computer exploded and someone should send help.
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UPDATE: I Am Legend is really good, though the third act is a bit discombobulated. Will Smith is excellent. Oh, if I'm ever stuck in NYC in the aftermath of a worldwide viral epidemic, I want a highly trained German Shepherd beside me. No humans necessary. Humans get in the way. Continue reading "Wednesday, with some bonuses"!

Windy City Excursion

I'm traveling to Chicago this weekend to attend a conference with some grad-student friends. Chicago is one of my favorite cities, so it should be a good time. I'll post about it while I'm there, hopefully with some decent pictures.

In preparing for the trip, I searched Google Maps for my hotel's location. Has anyone noticed they have added Wikipedia to the maps of most areas of the country? If you toggle the option on, dozens of tiny W's pop up, each representing a Wikipedia page corresponding to that location.


View Larger Map

Most of the articles relate to architecture and geography, but one can assume Google is adding more every day. This is such a useful idea. Along with street view and the photos option, you can get a pretty realistic account of a place, beyond simple geography. It's one thing to read about local attractions in a book or on a website, but integrating that information into a map allows you to see at a glance where in space it's located. When I visit a new place, I try to form a map of it in my head, based on the real map, and refer to it as I go. This just makes that easier. Information association and merging of this sort is really powerful, and it seems like a lot of new web applications are going in that direction.

Aside from conference talks, I plan to spend some time at one of the main museum campuses.


View Larger Map

I've been to the Field Museum multiple times, but wouldn't mind going back, it's so good. The Shedd Aquarium, however, I haven't been to, so that's on the list of things to do. Continue reading "Windy City Excursion"!

Media wallz

Sensory tables are often used in elementary schools to provide children, especially those with developmental disabilities like autism, something to play with and focus on. The're filled with things like small blocks, stones, sand, popcorn, buttons - great for providing tactile stimulation. That's nice, and I'd sure like to have one, but it's sort of a stone-age solution. The sensory table of the future will look a lot different. Echoing something out of Minority Report, this interactive media wall is now on sale at Neiman Marcus. Only 100,000 dollars! Check out the demonstration video, it's so cool. Here's another one from Youtube.



Oh, I want one. I'm used to the touch screen on my iPhone, but this thing recognizes some really complicated hand gestures. Imagine having one on every flat surface in your house.

If things pan out as they do in Minority Report, we'll be doing our computing like this, by 2052.

Continue reading "Media wallz"!

Elements of a good evening

Finals are approaching. I studied all day and rewarded myself.



Otherwise busy with more end of term nonsense. Frak! Undergraduate interviews, experiment planning, conference scheduling, advisory-committee forming, meetings...

Some quick notes.

Today is the 76th birthday of Cheeta (aka Jiggs), the oldest non-human primate. Cheeta appeared in some of the Tarzan movies, Bela Lugosi Meets a Brooklyn Gorilla (which sounds amazing) and the original Doctor Doolittle. There are plans for a ghost-written autobiography.

This article from The Atlantic critiques the state of education in America and offers some suggestions in the spirit of Horace Mann. It's one of those problems without a clear solution and I don't think we're to see any change soon. At least not until unscrupulous, out of touch baby boomers are gone from local school boards and teacher unions. Study your maths, kids!

There is a vacancy at the post of London Underground announcer, and people want David Attenborough to fill it. The woman who has provided the vocals for the "mind the gap" and other Tube voice overs years past was sacked a while back, partly over spoof announcements posted on her website, such as "We would like to remind our American tourist friends that you are almost certainly talking too loudly" (its true, the gits).

Cheers Continue reading "Elements of a good evening"!

Cells and Easter wrap up

On this day in which the American death count in Iraq passed 4,000, I offer a visual distraction. Check out this video from Harvard and the Howard Hughes Medical Institute. It's a handsome depiction of some basic cellular processes.



In reality, the action of these molecules isn't so graceful; at that atomic level, movement is messy, frenetic, and quite random. An accurate depiction would have made for a seizure-inducing video, so we'll let that one slide. The specific physics don't really matter, just keep in mind that most of those processes are going on in your body trillions of times a second. There are a bunch of other videos on YouTube of course, but also here.

Yesterday was Easter Sunday. Not unlike any other Sunday for me; I watched Food Network over breakfast, went to lab, blogged about cereal. I also ventured to Best Buy to return a wireless-internet router, only to arrive at an empty parking lot. Best Buy gave their employees the day off to hunt eggs and eat chocolate bunnies, it would seem. This was irksome, sure, but luckily the adjacent Borders was open. I bought two books (that I have no time to read).

More disturbing was the "CNN Presents: The Mystery of Jesus" special I viewed when I got back. In an attempt to delve into the controversial history of the life of Jesus, CNN interviewed several religious scholars on his prophetic exploits. What is pretty certain are the main biographical elements like his place of birth, teaching, and crucifixion. What of the rest, such as the purported miracles and resurrection? Well CNN took a less than critical line on these events, concluding that "science can't account for them" but never questioning that they happened in the first place. (Just like science can't account for, ahem, the Easter Bunny?) The lone source material for all of this deep inquiry - the four gospels of the Bible. No mention of the myriad other accounts of Jesus' life, nor the contradictions implicit within the New Testament. To put a big disturbing cherry on top, CNN gets Liam Neeson to narrate. He might as well have been proselytizing the midi-chlorians.

Oh, I'd hate to end on such a cynical note. Here's another video (cell wars).

Continue reading "Cells and Easter wrap up"!

Kinetic Sculptures

Theo Jansen is a kinetic sculptor. He creates moving skeletal structures out of very light materials. Once placed in an open area and given a push, the animari walk along, powered by the wind.



I haven't seen a video of one of these structures stopping, so if you are ever on a beach in the Netherlands, look out. Continue reading "Kinetic Sculptures"!

Baby Mammoth Found

Researchers have discovered a baby mammoth in the permafrost of northern Siberia. The body remains almost completely intact, with even its eyes and some hair preserved. With such a complete specimen, some scientists are going to attempt to extract DNA. The ultimate goal is to create new mammoths or mammoth-elephant hybrids through cross-fertilization and nuclear cloning techniques.

Of course, impeding this process is the black-market selling of mammoth remains. Local people have horded scientifically-viable mammoth remains for the past few decades, and the Russions government has done little to stop them. Mammoth hair, for example, can go for as much as $50 an inch.

That said, I think it is likely that we will be cloning a mammoth pretty soon. Northern Russia is ripe with remains, mostly because a population of mammoths lived there until only 5,000 years ago. If scientists succeed, then they can overcome the negative effects of hunting and climate change that originally pushed the animals to extinction. Continue reading "Baby Mammoth Found"!