Jacks of Science is a bit of an experiment.

I hypothesized that the site would become a flourishing group science blog as far back as 2006.

To observe this desired blog state I devised a simple theory. I would mix a solution from a staff of student bloggers in different fields such as Physics, Biology, Geology, and Chemistry.

Would I be able to find reactants that formed a homogeneous mixture or a highly reactive substance on the brink of explosion?! Even if I found writers that worked coherently together, would I continue to get decent results over time? 

I figured that the greatness of Jacks of Science would be directly correlated with post diversity. Many authors would lead to diversity in post subject matter, writing style, humor, complexity, geekiness, and length. However, in theory, things are much different than in experiment. As you may have noticed, this diversity of authors ended up just being a diverse range of posts authored by me. I didn't follow through on my original plan of finding other writers since I was busy trying to become a better blogger myself.

The original intention of the site has been lost but, 102 posts later, as my domain renewal date draws nearer, you're looking at the results of the Jacks of Science experiment. Full of random art doodled on my class notes (which now includes my 1st and 2nd year!), to pro-piracy open science discussion, to science DJ mixes, to my most popular article: Science Valentines.

So I'm trying to draw some conclusions about the data so far. As far as the traffic indicates the site is growing in popularity but I'm just not sure if things are working out. Blogging is a lot of fun, but the Jacks of Science initiative, as originally imagined, has been stagnant for some time. It doesn't seem to be going anywhere for a variety of reasons off the top of my head.

• No clear audience that I'm writing for!
• No incentive for new writers to be part of the site!
• I can only post once a week by myself (quality over quantity)!
• Science is boring (and thus cannot reach a wide enough audience)!
• My single column blog theme is too narrow!

I'm out of Ontario on a co-op placement this summer. I've had to dust off my first year chemistry brain synapses because I'm researching small clusters of water molecules. Like in any research project, one must ask oneself, and be able to explain to ones family, why is my research important?

From nuclear reactors filled with heavy water to pouring out some Bling H2O on the concrete for our fallen homies, we need be able to accurately understand water in any context. 

By computing how water molecules interact with each other on a small scale one may be able to gain insight into the bigger picture. An interesting property of a group of 2-5 water molecules is that they are most likely to form a ring structure. However, this is not the case for 6 or more water molecules as more stable structures are available (Xantheas). One might wonder if this small scale phenomena has macro consequences leading to the watery characteristics we have come to appreciate and adore. 

For example, starting from just 2 hydrogens and an oxygen, would it be possible to predict that ice floats at the top of your glass of water instead of sinking to the bottom? The ab initio techniques I use on my daily grind are designed to do just that. I input a list of electrons and protons into my computer and it outputs a fantastic amount of data on that system (but not the ice density in particular). Computation is a powerful tool in understanding properties emergent in chemical systems.

This study of emergencies has been an ongoing battle for all flavors of scientists in understanding nature. Physicists want to understand how the classical laws of our daily lives are emergent from quantum mechanics (subscription required). Some biologists want to understand the sociality emergent in bee colonies (or ant colonies). Chemists want to predict crystal structures [PDF] emergent in clusters of molecules. Computation is an essential tool for understanding many if not all of these situations.

My work brings up an interesting philosophical question about the scientific theories we use to describe the world. Are our theories of biology, chemistry, and physics really discontinuous? Desiraju [PDF] argues that our current model of chemistry is incompatible with biology and that there exists a new model of chemistry on the forefront which cannot be expressed in terms of physics and mathematics. The thought is this a little disconcerting to me. Not being able to compute everything implies that we would never be able to build The Matrix! 

Anyway, call me a reductionist computational scientist but I'm pretty sure computation will one day be able to fill in the blanks of our models of science. Admittedly, it hinges on the discovery of a grand unified theory to build upon, but I'll leave that to the theoretical physicists. From there on out, it's all computation baby!

A grayscale range of hats are often used to qualify moral standing of computer hackers. There are the virtuous white hat hackers who discover and patch holes in security systems but not surprisingly there are malicious black hat hackers who hack for profit and spite!

In between lies the ambivalent league of grey hat hackers who dabble in both affairs. They aren't afraid to break a law to get a point across about security to administrators. This edgy type of hacker anonymously creates far more social impact than the white hat hacker, advancing security nonetheless. 

Similarly, in between the everyday scientist and the mad scientist lies a new breed of researcher with similar objectives to the grey hat hacker. They aren't afraid to break a law or an ethical norm for the advancement of science.

Allow me to illustrate a scenario where grey hat scientists could make significant impact.

As we speak, hackers are in control of millions of home computers in botnets. Not to alarm you, but there's a chance that your computer compromised and being rented out for password cracking, spam, and other nefarious online business.

It has been speculated that the magnitude of computing power distributed across these zombie computers is enormous! Meanwhile, distributed computing projects such as Folding@Home, a project where people donate computing cycles to fold proteins, is slowly making progress. I agree that it's unethical to access another persons computer and install Folding@Home without their permission, but should a breakthrough in the understanding diseases caused by mis-folded proteins, wouldn't your idle screensaver time be worth it? 

Forced computation has been attempted before. A SETI@Home virus began to spread in 2003 to put unused CPU cycles to use in home computers. If you aren't familiar, the SETI project aims to discover extra-terrestrial life by analyzing radio telescope data. Sign me up for that virus!

Although distributed computing is a rather tame example compared to the ethical boundaries that will have to be crossed in order to advance fields like bio-engineering. There will surely be an uprising of grey hat scientists who choose to loosen their moral obligations, perhaps anonymously as hackers have done, in order to make scientific progress. 

The grey hat scientist follows a consequentialist philosophy. Put simply, that the ends justify the means. I'm not saying I subscribe to this philosophy, but I'm curious, especially in biology, as to if our culture will be able to keep up with the breakthroughs in research. Otherwise scientists will be forced to undermine laws and ethics to continue research and the age of the grey hat scientist will be at hand!

PirateBay is the Paris Hilton of anti-copyright organizations. Somehow, mainly due to the lenient copyright laws, they are still serving up the hottest uncensored videos even after a constant barrage of publicity. Well, to be more precise, PirateBay doesn't actually serve up any copyrighted material they simply host and track torrent files.

Torrent files are instructions to find other people on the internet with the latest Radiohead album (bad example) that you want to download. A torrent application of your choice assembles chunks of the files you get from others and simultaneously sends those chunks to others in the same boat as you. Before you know it you have "the gentlest, prettiest Radiohead set yet" (Entertainment Weekly).

It's hard not to weep a little for the directors, producers, musicians, actors, and technicians which I am indirectly stealing from but I reverse-weep when I think of the percentage of money that goes to said individuals when I purchase a CD or DVD. So, I go back to weeping, but with joy, as I witness Cloverfield in the theatre and The Roots live in concert.

However, the real question is, who would I be weeping for if I could download scientific literature on a site like PirateBay without having to pay expensive journal subscription fees (subscription required) that Universities are required to pay?

I might weep for the niche journal publishers and some peer reviewers for a little while, but my tears would instantly evaporate at the thought of the greater good. It's no question that the merits of open-access science are hotly debated but who actually stopped to consider a business model for downloading TV shows on the internet before just doing it?

It's called piracy! It's not really a complicated thing. What you do is go ahead and download using your new and innovative distribution method like Torrents and 12 months later companies realize this and adapt in order to stay in business. They advertise online, they sell shows on iTunes, they stream shows with commercials on their websites, ...whatever! The same should be true with scientific publishing. 

This idea was already started by Joanna Karczmarek in like 2005. With permission from Arxiv, she grouped up entire categories of Arxiv as torrent files and hosted them at UBC. Of course, Arxiv is free to begin with but the concept is the same.

Having a local copy of all high energy theoretical physics papers (a mere 9GB at Arxiv) would be mind boggling for a researcher in that field. One could research entirely offline, free from any institution, with search speeds as fast as ones hard drive could read. Journal subscriptions could be automatically synchronized to a local copy and scientists across the world could all be on the same page (an electronic page).

So, with Arxiv already dealt with, one has only a few more journals left to go! Of course, you'd want to specify what journals are relevant to your field, but I'm estimating that all of Nature in PDFs will be 143GB (20mb per issue with 7193 issues). Similarly, I expect Science will be 117GB (20mb per issue with 5878 issues). With disk space costing about $200 for a single 1000GB drive this isn't so unreasonable.

Of course, there are minor technicalities in obtaining 100's of gigabytes of science papers, but putting that aside, pirating science is entirely PloSable. It may be just the shady underhanded approach to open-access science that people are looking for.

Thank goodness for Sweden! 

Edit: Lots of great comments on this article at http://reddit.com/r/science/info/6jmij/comments/

For some people clothing is just a formality (where's all the nudist laboratories at?). For others people clothing is an expression of ones individuality. For me it's just a clever way to draw attention away from my hideous face.

Goblin face or not, even I acknowledge that some garments are just off limits. For example, I can understand how designer sunglasses and a purple fur scarf aren't acceptable in the lab because it literally becomes a safety issue when you are that hot. Thankfully, I've prepared a list below of stylish clothing alternatives with much more nerd credibility.

We just have to accept the fact that not all of us can dress like Nobel prize winners.
 

If you play any video games from racing to first person shooters to plain old pinball, you'll appreciate realistic physics simulation. "Serious business" gamers often fork out wads of cash for top of the line video cards for their PCs, but would it be worth it to fork out a few more Benjamin's for improved game physics? Graphics card developers aren't afraid to take the chance that people will...

Last year, Intel decided to acquire Havok, the developer of a toolkit called Havok FX which designed to make special use of ATI and NVDIA graphics processing units for optimizing physics. Not to mention, Intel is rumored to be moving into the graphics card business in 2008.

Last February, NVIDA decided to acquire Ageia Technologies, the developer of PhysX physics acceleration cards, to incorporate their technology with GeForce graphics cards. Simply put, the standalone PhysX cards act as a dedicated physics processor for computer games which are intensive on all the things we love about games, like realistic explosions, pretty looking water, and precise car crumpling as you collide at 160 into a road divider. To add to the excitement, NVIDIA recently opened its PhysX platform to all graphics card developers! Sweet, sweet physics for all.

As processing power increases, it makes sense that as games develop richer lighting and textures that the physics should also have improved realism. I believe that it's only a matter of time until similar attention will be given to calculations for simulating complex chemical and biological systems.

It is bound to happen with games like Spore on the cusp of release, which incorporates at least some form of evolution from multicellular organism to land creature. The educational merit of such games has been noticed by NASA who is exploring the possibility of a massively multiplayer online game where:

Virtual worlds with scientifically accurate simulations could permit learners to tinker with chemical reactions in living cells, practice operating and repairing expensive equipment, and experience microgravity.

I can't wait for some sweet science games to play, because Peggle is only fun for so long...

Photoshop CS3 Extended is a powerhouse. Beside the usual support for making fake celebrity nudes and airbrushing out your blemishes for Facebook profile pictures, did you know it has support for a wide selection of image measurements?

Simple image processing can be fun and easy with Photoshop. Various books have even been published on the use of Photoshop in forensic science!

I recently watched a Lynda.com tutorial on using Photoshop for Biomedical research and Photoshop for Research Methods and Workflows. The latter included a step-by-step guide for image processing techniques from analyzing protein expression in microarrays to obtaining penetration data in tissue sample. But I think it's safe to assume that most reader's aren't concerned with biomedical research, so I decided to take the measurement idea and run with it.

In this post I'll outline some applications of Photoshop's measurement tools which should not be missed! Note that this tutorial assumes you already have basic knowledge of opening images, working with layers, and making selections.

Read the rest of this entry »