I recently listened to the Systems Biology Nature podcast.

Systems biology is mathematical modeling of biological systems (even at the molecular/gene level) with the intention of reproducing emergent properties in complex living systems. These mathematical systems could  combine everything from gene regulatory networks to crazy metabolic networks into one glorious approximated abomination of biology. This research could lead to at least two great things:

1. Spore 2 (check out local guest blogger Kate's Spore creature gallery)
2. Accurate evolution simulations, ie. new opportunities for creationist bashing

Systems biology is a perfect example of a new multidisciplinary field. It combines the work of mathematicians, computer scientists, physicists, bioinformaticians, biochemists, molecular biologists, cell biologists, and geneticists. Even a philosophy major could probably slip into the team undetected for a little while!

As grad school selection approaches and life decisions loom above like an angry sun, it really begs the question: Should one be specializing or diversifying ones skill set?

Sure, you could diversify (your bonds) and learn about computer science and physics like me, or you could specialize the old fashion way and join some miraculous science collaboration dream team to work on cutting edge science.

The case for diversifying is argued nicely in a PLoS essay entitled: "Antedisciplinary Science". (Hat tip!)

It turns out that antedisciplinary science aligns nicely with the ideal Jacks of Science "Jack of all trades" blogging philosophy:

Perhaps the whole idea of interdisciplinary science is the wrong way to look at what we want to encourage. What we really mean is “antedisciplinary” science—the science that precedes the organization of new disciplines, the Wild West frontier stage that comes before the law arrives.

The essay was written by a computational biologist and the topic really hits home for me. By next April I'll have graduated with equal amounts of physics and computer science credits thanks to University of Waterloo's free-spirited computational science program. But I'm kinda doomed. I don't have the expected skillset of a physics major or of a computer science major if I choose to go to grad school for either.

I should have specialized in something!

Why am I currently researching computational chemistry!?

Why do I plan to study polymer physics next term!?

Who am I!?

Have you ever had been frustrated because you have a great idea but so-called "time commitments" or "lack of qualifications" prevent you from executing it?

Look no further than the internet. It has literally been staring you right in the face this entire time! (Unless you're like me and you get your RSS feed dictated to you by robot servant while you close your eyes in bed each morning).

The internet is an undrank milkshake worth of people who have a lot of time on their hands. You don't have to look very far to be convinced of that [link to Digg comment flame-war here]. For that reason alone I implore all idea hoarders to go out on a limb and release their conceptual burdens in blog form for the joy of others.

• Best case: someone does a great job with your idea and gives you credit.
• Worst case: someone gets rich off your idea and doesn't give you credit. Good thing it's time-stamped on your blog! You may not get any credit, but you get to be bitter that they stole your idea and you get to learn the lesson that money isn't everything in life, money can't buy happiness, happiness is a warm gun, or something along those lines.

So make the internet a better place and blog your ideas! If you need some encouragement check out the great work being done at the Free Idea Factory. But what's with all this art stuff? What can art retarded scientists do?

Don't look at me. I have no time to make a "Free Science Idea Factory" (time-stamped on July 31st, 2008), but here's a nice idea I had recently.

In the same vein as the Molecule of the Day blog, an Equation of the Week blog written by a savvy mathematician would be fantastic! I've noticed that Built on Facts has a Sunday Function, but I was thinking something a little more elaborate...

Every week an equation could be chosen and profiled with any of the following:

• Using it in a worked through example
• Linking to current popular science articles which rely on it
• Discussing what makes it unique
• Explaining its applications in different fields
• Discussing social significance (Perhaps an equation that made the moon landing possible)
• Mentioning it's history, first time it was published, or story of discovery
• Fancy graphical depictions and plots
• Discussing it's limitations (Where it's relevant and where it's not)

What's the best way to bypass expensive conference fees as an undergrad? Volunteering of course!

This year I'm volunteering at the ISMB 2008 conference in Toronto, which, for a minor time commitment, entitles me to hear fascinating presentations on all aspects of computational biology and bioinformatics. One of these was a tutorial on ncRNA (noncoding RNA) gene finding, given by Jan Gorodkin and Ivo Hofacker.

First, a quick intro.  Most of what we know about the genome deals with coding sequence:

• DNA that's transcribed into messenger RNA (mRNA) 
• mRNA that's translated into proteins

But only 1.3-1.6% of the (human) genome codes for protein!  The rest, despite the popular misconception, is not "junk DNA".  DNA and the transcribed non protein coding RNA have many functions, a few of which we know about [PDF].  The recent ENCODE pilot project estimated that as much as 97% of the human genome is transcribed into mRNA at some point. But what does it do?

There are many different classes of ncRNAs.  First, you've got transfer RNA (tRNA) and ribosomes, which have functions in translation of mRNA to peptides.

Another type of ncRNA are MicroRNA, or miRNA.  These are short sequences of RNA that are complementary to (protein coding) mRNA.  They act as downregulators (suppressors) of genes, by attaching to the mRNA and getting in the way of the translational machinery.

Discovering ncRNA genes can be tricky! This is mostly due to the fact that ncRNA function is in many cases tied inextricably to the structure of the transcribed RNA.  RNA, being single stranded, can double up on itself and form loops and helixes (as pictured below).  These crazy loops are called the secondary structure. The secondary structure of RNA is what results from the first pass of folding, and serves as a simplified (but useful) model for the 3D structure of the RNA.

Because the secondary structure results from the pairing of bases, any of the so-called canonical base pairs (C-G, A-U, U-G, and the reverse of all three) can occur.  Mutations can occur that change the sequence, but keep the bases paired in the same way, leading to structures that are the same, but with sequences that are very different.  

However, a single nucleotide that no longer base pairs the same way can produce a completely different secondary structure.  In the world of bioinformatics this can make it difficult for computer algorithms relying only on nucleotide data to align sequences that are too dissimilar.  There are algorithms that can align sequences based on conserved structure, but they are computationally expensive both in terms of memory and CPU time.

That said, sometimes alignment based only on sequence are good enough.  Sequence alignment tools are fairly common, and alignment data across many species is available for downloading.  Algorithms can use these alignments to discover the genomic locations of new ncRNA genes.  Because the sequence (well, structure) of an ncRNA gene will stand firm while the sequence around it mutates, functional genes will stand out as regions with high conservation across an evolutionary tree.

The alignment of multiple sequences is used in a few different ways to discover ncRNA genes.  Some of them use the known evolutionary tree in a probabilistic way (how likely is it that this nucleotide mutated from A to U?  What if it's part of a base pair?) to try and find a consensus structure.  Others calculate the stability of the stuctures formed.  Sequences with the most stable structures tend to be functional.  There are algorithms that combine the two approaches.

The sets ncRNA genes predicted by these different matches have little overlap.  This may be due to lots of false positives being predicted, or it may be because certain approaches are more likely to find ncRNA genes of certain types or with certain properties.  Improvement of these methods, as well as secondary-structure based sequence alignment and prediction of RNA structure and function, remain areas of ongoing research.  It's clear that we've already begun to crack the genetic code.

The secondary structure of ribosomal RNA from E. coli.

The FADER called it. LA Times called it. Random blogs have called it. Just like gold and fluorescent are the new black, hypercolor clothes are about to replace acid wash jeans as the nerdiest textile. It's about time! What's more stylish than wearing micro encapsulated PH indicators?

I guess I'm kinda fashionable but I was never on top of the hypercolor fad of the 90's. If only I had realized the chemistry involved in these garments I'd probably be dressed in a hypercolor unitard through public school.

How does it work though? Gordon Nelson gives you the summary in his paper "Application of microencapsulation in textiles": 

There are two major types of colour-changing systems: thermochromatic which alter colour in response to temperature, and photochromatic which alter colour in response to UV light. Both forms of colour-change material are produced in an encapsulated form as microencapsulation helps to protect these sensitive chemicals from the external environment. Today manufacturers are able to make dyes that change colour at specific temperatures for a given application, e.g. colour changes can be initiated from the heat generated in response to human contact.

Wikipedia breaks down the science, albeit unsourced, in greater detail:

The liquid [inside the micro capsules] is a leuco form of a dye (in this case crystal violet lactone), a weak acid (1,2,3-benzotriazole), and a quaternary ammonium salt of a fatty acid (myristylammonium oleate) dissolved in a solvent (1-dodecanol). At low temperatures, the weak acid forms a colored complex with the leuco dye, interrupting the lactone ring. At high temperatures, above 24-27 °C, the solvent melts and the salt dissociates, reversibly reacts with the weak acid and increases the pH. The pH change leads to closing of the lactone ring of the dye, which then regains its colorless (leuco) form.

At least it should tie me over until the wearable computer fad comes back into style...

Now that I'm finally The Dread Zoologist Roberts, I feel a need to help the people. The confused people. People confused about wives tales, folk taxonomy and poorly researched news stories. People confused about whether the appropriate short form of Charles Darwin's name is Chas D, Char Dar, or Chuck D (in fact, all three are acceptable, along with "Charwin").

But as my first order of business, I'd like to demolish some zoological misconceptions I commonly come across. I hate zoological misconceptions! Let's begin:

1. Assuming you live in the New World, honey bees are not your friends. Nor are they friends with your true bee friends, the native bumblebees. Honey bees were introduced to the Americas by European apiculturalists, making them an ALIEN/INVASIVE species. So, it shouldn't be any wonder that they are "declining", given that they didn't belong here in the first place (OH SNAP).

2. Daddy Long-Legs are not spiders, nor are they poisonous. They are harvestmen. Also, check out the weird pro-harvestmen science bias in the Wikipedia article:

Because they are an ubiquitous order, but species are often restricted to small regions due to their low dispersal rate^{[citation needed]}, they are good models for biogeographic studies^{[dubious – discuss]}.

Indeed! Dubious!

3. Polar bears are not a distinct biologically species, separate from grizzly bears and brown bears (which themselves are not biologically distinct). In other words, polar bears, grizzly bears and brown bears are in fact all the same (biological) species, and hybridization is possible!

4. Monkeys and Apes are different things! Chimpanzees, Bonobos, Gorillas, Orangutans, Gibbons and Humans are apes. Apes, I say! Monkeys are things like Tarmarins, Capuchins, Owl Monkeys (above), etc. So, next time your esteemed associates say "Humans are descended from monkeys!" you can say "That statement is incorrect, associates! They are descended from, and still are, apes!".

5. Killer whales are oceanic dolphins, not whales. Similarly, Koala bears are not bears.

Do you feel informed? I have many more such facts, stay tuned!

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.