Last year I did a co-op placement working on some medical imaging software. Looking back, I definitely needed more C++ knowledge, but I ended up walking away with from the job with many crucial linux development, programming, and pasta boiling skills.

Wait, pasta boiling?

You heard me correctly. Here's a short video of some zitoni we imaged in real-time using the software I was working on. Note that the quality is butchered because it was originally captured in an unusual resolution.

You can see me frantically moving the slice plane and rotating this view in 3D. This branching pasta creation was made to to be similar to the branching vasculature found in the body so we could easily test our software and catheter tracking.

I made this fantastic creation by first obtaining zitoni, a long tubular pasta, from Masellis Supermarket in Toronto (it's a great Italian market). Then I boiled the pasta until al dente in water and Gadovist, which is a commonly used contrast agent for MRI. I carefully sliced holes and wrapped the pasta joints in Saran Wrap. I then suspended the pasta abomination in Agar. All credit goes to my graduate student supervisor Kevan Anderson who came up with the idea.

Near the end of the video, in the cross sectional slice of the pasta tube, you can see some horrible black mess within the pasta. That's an air bubble due to my sloppy joint wrapping. It shows up as black, an area of zero signal, because air has no magnetic properties. 

In the making of the pasta phantom I used enough contrast agent to make the pasta appear gray under MR, but what if I wanted more precision to have the pasta appear identical to human tissue? 

New research in Nature last week outlined the fabrication of magnetic particles for use as contrast agents in MRI. By engineering your own magnetic particles you could tailor their characteristic spectral signals to show up exactly how you'd like them to. The precise control of contrast with magnetic particles has great implications in imaging from cell tracking, to micro fluidics, to realistic pasta arteries. 

Sure, Improbable Research has a Luxuriant Flowing Hair Club for Scientists, but what about those of us normal people with luxurious beards? If the Smithsonian Institute's Flickr gallery can teach us anything, it's that todays scientists can learn a lot from the fine beardsmanship of our forefathers.

We cater to all audiences here at Jacks of Science. If joining the Luxuriant Beard Club for Scientists isn't your cup of tea, you may be interested in purchasing some Jack Black Beard Lube.

Here's an unedited transcript of my difficult interview with George, the Jabberwacky AI chat bot, on the topic of artificial intelligence. I chose George because he learns entirely by human interaction as opposed to a chat bot like A.L.I.C.E. which just uses specific pattern matching conversation rules. Even then, it was really hard to get him to stay on topic, especially near the end...

Read the rest of this entry »

WNYC's Radiolab is a masterpiece of radio science. I'm a late joiner to the "Jad and Rob" party but I've finally caught up on season 4 during my bike rides to and from the lab. The whole series is free to download on their website and I highly recommend listening to it.

To justify this recommendation I've decided to post some of the great things I learned from listening to Radiolab, in reverse chronological order, to whet the knowledge appetite of the reader:

• A study of laughter found 85% of laughing is proceeded by stuff that is not a joke (Laughter)
• You can engineer an E. Coli culture can smell like Wintergreen when it's growing, and Bananas when it's completed growing (So-Called Life)
• People who admit to thinking about raping or being raped by an individual make worse athletes (Deception)
• Our brains produce opium (Placebo)
• Harvard professor Robert Stickgold got a cover of Science thanks to Tetris (Sleep)
• Scientists have erased memories in rats (Memory)
• Lobsters are immortal (Mortality)
• The number of the beast, 666, was once 616 (Detective Stories)
• In Mandarin, there is a single word that means mother, hemp, horse, and reproach depending on the tone it is enunciated (Musical Language)
• A study found killing 1 person by a lever to save 4 people is accepted whereas killing 1 person by pushing them off a bridge to save 4 people is not acceptable, regardless of age, gender, or education level (Morality)
• Some people have a condition where they lose all feeling within their own body (Where Am I?)
• Dr. Peter Diamandis funded the X-prize for the first private-sector manned space flight by making a 10 million dollar "bet" with an insurance company that it could be done (Space)
• It is not known how thousands of fireflies shine can in synchronization (Emergence)
• The author of Peter Pan, J.M. Barrie, may have had psychogenic dwarfism (Stress)
• Monkeys have no introspective consciousness (Who Am I?)
• Your brain activity to wiggle your finger spikes before you "decide" that you want to wiggle your finger (Beyond Time)
• The people of the Andaman Forests in India have a scent calendar where they tell the seasons based on the scent of various fruits and flowers (Time)

The Gonzo Scientist, in this weeks Science, describes the gruesome tale which occurred on May 11th during the conference "Convergence of the Real and Virtual" held in the World of Warcraft MMORPG:

As we made our way south into the Barrens, we tried to clear away the more aggressive beasts, particularly the crocodiles along the riverbank. Even in the vanguard, things got hairy. At one point, a croc charged toward an undergraduate student on our fringe. I drew my bow and squeezed off three arrows, killing it before it could reach her.

The stragglers were not so lucky. Lutters, a computer scientist at the University of Maryland, Baltimore County, tried to reach the rock-art site on his own. He drifted off the road somewhere near the mountains. A pack of hyenas found him and tore him apart. That's a horrible way to die.

Unfortunately, the full article requires an institutional subscription but it's a very enjoyable read. It wouldn't be the first time that a science conference has been held in an online community, but the possibilities for united Horde raids in the name of science are too awesome to be ignored.

Most people agree that owning a poofy kitty or a slobbery poochie can be extremely rewarding. Companionship, pre-warmed furniture, a lap-full of shedded fur...the list of pet benefits is both long and heart-warming.

However, it is really moral to keep animals locked in our houses, mostly for our own enjoyment? Furthermore, is it moral to genetically alter (i.e. breed) animals to look "cute" or "handsome", even if that means creating in serious health risks for the animals?

Based on the picture above, I'm inclined to say that the moral risks are well-worth the hilarious pet-wig payoffs. For the sake of argument, here's a run-though of the various moral justifications I've heard from pet-owners, along with my zoological retorts:

1. "Pets live much better/more comfortable/longer lives in human homes than they would in the wild."

This one is tough to defend. It rests upon the anthrocentric idea that humans, being all-mighty, must know what's best for animals and how to give them the most fulfilling lives possible. But how can you ever know whether or your dog is truly better off in your house versus the lush woods?

2. "Dogs and cats have been selectively bred to enjoy the company of humans. My dog loves it at home!"

The problem with this that is assumes that the behavior the animal has been selected to express (amicability to humans) is truly reflective of the animals thoughts/"feelings" (i.e. that they really do enjoy the company of humans, rather than simply behave that way).

3. "Working animals, such as seeing-eye dogs, increase the owner's quality of life dramatically."

This is probably true. However, it doesn't change the fact that the animal is born into a life of servitude.

4. "It has been suggested that dogs may have domesticated themselves. They've got themselves into this mess, they can get themselves out."

I haven't thought of a clever response to this yet. I was thinking about using "Its only a theory!", but we all know where that leads.

So, it seems that the keeping of animals as pets is, at least in some ways, difficult to defend from a moral standpoint. In spite of all my zoological musings, Chris sent me the following video that blew my arguments to smitherines:

Lost is over until 2009 and Battlestar Galactica followed suit last Friday. So what the heck am I going to watch on TV for the rest of the year?

Most likely J.J. Abrams new Sci-fi series: Fringe. The 2 hour premier, leaked 2 months ahead of time, with a 2 x 5 million dollar budget, so I thought I might as well give it my 2 cents. Especially since the "Fringe" in the title refers to ...FRINGE SCIENCE!

As noted on Wikipedia, fringe science is a bit classier than the pseudoscience which science bloggers love to hate. It's supposedly "legitimate" research using the scientific method but in a context which deviates from the mainstream beliefs. Not generally a crowd you want to fall in with but you can't argue that it makes good television, just look at the success of Heroes and X-Files!

Speaking of those shows, if you've watched them, then you won't be surprised by the premise of Fringe. There's some ___insert shady organization___ covering up ___insert controversial research___ and it's up to ___insert protagonists here___ to unravel the mystery.

I hate to spoil anything plot-wise, but, I have yet to see a major difference between this show and your standard X-Files episode. It just seems like an updated X-files with a less likable cast. Some notable differences include:

• Weird giant floating 3D letters instead of classy typewriter-style letters.
• Introduction has words like "Dark Matter" and "Nanotechnology" instead of "Paranormal Activity".
• Lead actress character isn't as hot as Scully, Lead(?) actor isn't as hot as Mulder.
• Larger special effects budget means more goriness, but less creepiness.
• Aliens replaced with mad science experiments gone wrong (just a theory).

At least they got one thing right about the stereotypical scientist, they sure love their coffee! 

Based solely on J.J. Abrams work with Lost and the words that fly by in the introduction of this show I'd say this show has some serious chemical potential energy. I'll reserve judgement until I see the first season, but Sci-fi fans should be all over this.

Taking Control of Mathematica was posted on the Wolfram blog about 10 months ago. That just shows you how how far behind I am on the blog schedule because I finally got a chance to try it out.

Mathematica 6 has built in support for input devices with the Manipulate function. So, you can use a number of controllers to adjust any 2d or 3d plot parameter. You can imagine the possibilities!

Support for controllers includes support USB gamepads, joysticks, IR remotes, and, last but not least, the Apple sudden motion sensor built into your Macbook or Macbook Pro. 

You knew about the sudden motion sensor (SMS), right? It was originally intended for the practical use of preventing damage to your hard drive if your laptop hits the floor but it has a variety of additional uses.

I took it upon myself to whip up SMS controls for some existing 3D examples in the Mathematica documentation. The main problem I encountered was that the SMS values changed so quickly and I didn't have the CPU power to re-render my object when the values changed. I'm not really a Mathematica master, but I settled on nesting my Manipulates in a Dynamic so I could set an UpdateInterval. You can download my Sudden Motion Sensor Controlled 3D Plots Notebook.

You may notice how exceptionally swift and dextrous I am. This unexplained speed doubling is surely due to my roommate's Dell, but the point remains.

Did you know that scientists have created artificial DNA? Just for the record, that's only one step away from inserting the DNA into a cell and bringing it to life. However, this area of research is still in it's infancy so we won't have any soulless synthetic human puppets for very much longer a long time.

Most recently, the synthesis of a meager 500,000 base pair bacterial genome was explained in detail by the researchers at the J. Craig Venter Institute. The size of the bacterial genome pales in comparison to our hulking 3 billion base pair human genome of champions but it's a step in the right direction. Naturally, stepping in said direction is a cause for bioethical concern but I'm more interested in the new possibilities for biocrime!

It has been 20 years since DNA evidence was first admitted in court which lead to a death sentence. Similarly, it has been a recurring plot device for television crime drama for just as long. Being exposed to such shows, today's criminals know better than to leave saliva, blood, or semen at the scene of a crime if they can help it. Although, with the advent of synthetic DNA, bodily fluids may be making an unexpected comeback...

Everyone knows that planting DNA evidence like hair or fingernail clippings is a straight forward way to frame someone for a crime they didn't commit, but let me walk you through a more intriguing scenario:

1. Almost half a billion DNA profiles of offenders are contained in the FBI's CODIS National DNA Index.
2. A crooked cop or hacker mastermind leaks criminal DNA profiles to the internet. 
3. A regular joe (RJ) obtains a DNA profile of regular criminal (RC) on parole in his area.
4. RJ has DNA synthesized en masse and inserted into cells by a private lab.
5. RJ commits his crime of choice, stealing a rhubarb pie from a windowsill, without leaving any trace of his own DNA (easier said than done).
6. The forged DNA is left at the scene of the crime.
7. Forensic scientists find a direct DNA match with RC using the CODIS National DNA Index.
8. Assuming RC has no significant alibi, he is considered a repeat offender and found guilty of grand theft pastry.
9. RJ, pretty hungry at this point, consumes pie and sends an anonymous thank-you card to J. Craig Venter Institute without ever having made contact with RC.

This scenario may seem far fetched but it's undeniable that the validity of DNA evidence relies on the fact that people assume DNA cannot be tampered with. Much like the questionable admissibility of digital photography and digital video in court due to computer forgery, DNA evidence will one day be under high scrutiny.