harnessing the power of the gamer

There are many things in the world of science that we just can't figure out. Not because we don't have the math, or the theory down but because we simply don't have the computing power available. It's a well known fact in my lab that I'm a bit of a video game geek, my boss regularly jokes that if they could some how find a way to make downloading research papers be controlled by a dualshock and have a snazzy graphical interface (possibly with a J-pop soundtrack) I'd probably never leave the office.

He also thinks this is the key to solving most problems of computation: to code the problem into a video game and have the processes required to solve it be related to actions taken within it. He's talking "massive scale, solving the problems of the universe which are possibly not for human consumption" that would require large amounts of obfuscation before being turned over into the hands of gamers of course, so there's no way we could implement it in the near future. But it's nice to see that a program named FoldIt has actually taken the first steps.

The game involves trying to figure out different ways in which proteins can be folded. As a biochemist this is a fascinating topic for me, protein folding is ludicrously complex and defined by a whole host of factors: the order of amino acids making up the primary chain, the secondary structure that the polypeptide takes, stabilising interactions between individual residues, the points at which water interacts with the molecule (I won't go on but if you're interested the Wikipedia page on protein structure acts as a fairly good crash course). Calculating all the different possible configurations is a mammoth task, but using human interaction could make it solvable much, much quicker.

Right now they're testing out the accuracy and efficiency of the game using known protein configurations but if it works well enough we're not just talking about solving the structures of existing proteins but also determining novel structures. One of the biggest problems facing drug design has long been the inability to isolate the perfect protein structure for the desired function. This is especially important in treating viral diseases such as HIV where interaction between the drug molecule and the virus' structure is absolutely vital to correct function. Computers so far aren't capable of determining completely novel protein structures from scratch and so if this technology actually works (and is fun enough to convince people to play with it), we could certainly see protein science, if not medicine advancing in leaps and bounds.

More information is over at Science Daily and Kotaku. I don't know about you guys but solving 3D puzzles and helping humanity? Sounds pretty spiffy to me.

a note on the ungrateful

Many thanks to the fabulous Girl With Curious Hair for the call to arms on this issue...

So, science is inherently evil is it? You know what? Fine. I give up. There's no point arguing with a statement like that. I could cite advancements that have been life saving, revolutionary. I could point to dear friends who are currently in the care of the medical profession, people the world would be a worse place without. I could start talking about engineering allowing international travel and reliable water supplies, architecture providing us with shelter from the elements, maths and physics explaining the world around us. I could talk about space travel, genetics, communication, crops being farmed with improved yields, AIDS medication, water purification, computers, printing presses, heart bypasses, bionic limbs, cameras, telescopes, video games, sunscreen, decongestents, cars, clock-radios, MRI machines, cinema, electric lights, mass produced clothing, canned food, electric shavers, CAT scans, pencils, the notion of gravity, post-it notes, life as we know it. But I won't. Instead I'm going to say this:

All scientific discoveries are the work of Satan and we'd be much better off crawling around in the muck and dying from poisoning brought around by eating foraged food. Same goes for animal testing, that's bad and totally unnecessary. Yep. Absolutely. While we're on the subject of things that are important to me being crap I'm also totally going to admit that all feminists are evil too. That entire political movement was a pointless waste of time and should never have happened.

Just a couple of points:

re: Feminism. I'd like everyone holding the above view to raise their hands. OK, Ladies would you kindly stop voting, driving, owning property, wearing trousers, having any control over your medical care, getting an education, working, earning money, enjoying a life without violence as standard, going into pubs and bars, eating alone in restaurants and having orgasms. Gents, you're going to need to head right back out the door to work because, guess what? You have seven kids to feed (contraceptives, what? Never heard of em) and a mortgage to pay. Alone.

re: Animal testing. Please stop taking aspirin, paracetamol, morphine, vicodin... oh screw it, you know what "medicine", yeah stop taking that. Oh and could you also stop having surgery. Of any kind. Although especially heart surgery. Anything life saving. Although you can probably still have your appendix taken out. You just can't be anaesthetised while we do it. It's cool though, here's a rag to bite down on. Hope you don't get a post surgical infection cause we really can't help you with that.

re: Science. Well, if you managed to survive this far without medical care, heating, electricity, transport, living in a building, eating processed food, eating organic food, hell - eating cooked food, defending yourself or you know, having fire to provide light and warmth could you please move it out to the mountainside, possibly into a cave, you're going to have to walk there though. Barefoot. And wearing some sort garment fashioned from leaves and bits of twine that you've hand woven from tree bark. Actually "weaving" that's a bit advanced, maybe you could just sort of hold them on or something. You also might want to stay in the shade, I hear skin cancer's a bitch without access to treatment. Don't bother packing either, we all know that suitcases are the work of the devil. You won't need that laptop you write your charming anti evolutionary screeds on either, and leave that bible where it is. The printed word really isn't for folks like you. OK, now could you just sort of sit still for a while. Don't move. You might discover something. That would be bad. Sit very, very, very still.

Oh yes, and get the fuck off our internet you ignorant, anti-intellectual, narrow minded, Luddite wanker.

mumbo jumbo for thursday

Wow. Just wow.

Slate online posted the peer review guidelines for a Creationist journal as its hot document today. And I've got to say that the concept of Creationist peer reviews fucking terrifies me. Why? It means that these nutjobs take themselves seriously. I currently work in academia and peer review is a massive part of getting any scientific paper published. It acts as an internal system to prevent wildly speculative, falsified or just plain wrong data from being published as scientific fact. The reviewers are accredited scientists, at the top of their field. They do not, however, agree with the viewpoint of the paper's author by default. Peer reviewing is an arduous (and often insanely political) process that is the bane of most serious scientists' lives.

I immediately forwarded the link to co-worker M who finds this stuff as horrendous as I do. His response was to spend the rest of the morning reading the journal and forwarding me links.

Taking a random example: Dinosaur Nests Reinterpreted

Highlights include: overusage of quotation marks around the word "nest", scientific figures drawn representing how the authour imagines how the eggs dinosaur nests were arranged, several sections citing academic(ish) evidence for stress conditions followed by the section headed "Evidence of Stress Conditions from Scripture", the entirety of the "Acknowledgements" section (including praising the Lord, classy move guy) and the entire thing being written in a style that would have gotten me kicked out of my undergraduate degree course.

Read and enjoy.

I weep for humainity...

I was flicking through the Guardian today when I came across the "notes and queries" section in the G2. One of the queries rendered me actually, literally speechless - no mean feat (I learnt to talk at the age of one and apparently "haven't stopped since"). Alas, the query isn't up on the website yet so you'll have to take my word for it:

"Evolution is now well-documented and accepted, so if people kept jumping off the roof of a tall building, how long would it take before we developed wings to fly?"

Seriously?

Ok. A deep seated hatred of the kind of people who write into newspaper editorials actually prevents me from writing in to the section in question with my response, however it doesn't stop me from passive-aggressively ranting about it in my blog. Here is a highly simplified crash course on how evolution works:

Evolution is in its simplest form "survival of the fittest". The best adapted members of a species are more likely to survive and/or be chosen as breeding partners - meaning that they are more likely to pass on their genes to the next generation. This makes those favourable genes more common in each successive generation. As the process continues through the generations the "favourable traits" that led to the first individual's evolutionary success become more and more widespread until eventually they become "normal". I'm aware that my hastily noted ramblings may be confusing so let's use a totally fictional and rather extreme disease model to simplify things:

On planet Alex there are millions of bunnies (why bunnies? Because it's planet Alex. Deal with it). The bunnies all live in harmony on planet Alex, which is plentiful in food and free from predators, and are free to interbreed at will. Because of this there is a large amount of genetic diversity. Some of the bunnies have spontaneously mutated so that they carry gene X (note the "spontaneous" part. This is random people). At the moment gene X has no general effect on the population and so it is passed on from parent bunny to baby bunny with no real consequence. Until the plague comes.

(The plague has been brought to planet Alex by evil toad overlords who came for a two week holiday and then buggered off again)

The plague is fatal to the bunnies on planet Alex, however it just so happens that gene X makes the bunnies that carry it immune to the plague. This is a total coincidence. Pretty soon the entire bunny population has been wiped out by the plague, leaving only the bunnies with gene X alive. Because they are bunnies they set about repopulating planet Alex pretty sharpish. The result? Every in bunny in the population now carries gene X.

That was a very simplistic and entirely unrealistic scenario (in actual fact there are no bunnies native to planet Alex) but the basic point I'm making here is that evolution is a process that happens by chance not by design. It is caused by the selection of existing genetic traits that have become favourable for survival due to a particular environment. It is not caused by the actions of individual members of a species over time.

Taking the above example: people continually leaping from a roof top would not cause other members of the population to sprout wings, it would merely serve to remove those idiots who jumped off of buildings from the breeding pool.

And that ladies and gents is why I'm going into science journalism.

The worst thing is when I told one of my co-workers that I'd seen something truly depressing in the newspaper our resulting conversation was as follows:

"You mean the thing I sent you?"
"Erm, what thing you sent me?"
"The thing with the scratchcards."
"What thing with the scratchcards?"
"The thing I sent you with the....Jesus, Alex. Try checking your work email."
"Ok, ok..... Oh, crap."

The little gem awaiting me in my inbox was this. My favourite line of the piece?

""I phoned Camelot and they fobbed me off with some story that -6 is higher - not lower - than -8 but I'm not having it."

I'll be out back, researching tall buildings with roof access in my local area.

wednesday geekery

I'm feeling the warm and glowy love for my subject today. Mainly because of this article. Seriously, if it were possible to marry a piece of journalistic writing it would be this one waiting for me in the registry office. The author puts into words exactly what I want to scream at some people on a daily basis. The gist of the article is this:

The past 30 years or so have been an age of endarkenment. It has been a period in which truth ceased to matter very much, and dogma and irrationality became once more respectable. This matters when people delude themselves into believing that we could be endangered at 45 minutes' notice by non-existent weapons of mass destruction.

It matters when reputable accountants delude themselves into thinking that Enron-style accounting is acceptable. It matters when people are deluded into thinking that they will be rewarded in paradise for killing themselves and others. It matters when bishops attribute floods to a deity whose evident vengefulness and malevolence leave one reeling. And it matters when science teachers start to believe that the Earth was created 6,000 years ago.

It's a well written piece and well worth the read, I may be a little biased as creationists were the bane of my religious studies A-level (I did it for the ethics course which, incidentally was a super fun experience. I was the only person in the room who didn't think that aborting your heroin addicted half sibling was going to earn you a one way ticket to the land of fire and brimstone. Try teaching situational ethics to that crowd. Here's a hint: you can't.) but this is not an anti religion thing, people are perfectly capable of combining science with belief. I've seen it happen. And whether or not I see the rationale or point behind it is an entirely off-topic issue.

The way I see it the essential problem is the death of the questioning mentality. The general public isn't educated enough in the basics of science to question what the newspapers and their so called "experts" have to say. And so we live in a society where potentially famine-solving research into GM crops is put on hold because "We'd be eating DNA!!!!", people give their life savings to psychics and mothers endanger the lives of their children because they want them to be treated "naturally". It makes me ill.

Here's my dirty little secret: I own two decks of tarot cards. I can also read I-ching. I have an oracle book. But and I really must stress this I do not believe that they will answer my problems or tell me anything I don't already know. Dividing yarrow stalks or dealing cards gives me the time to think over a problem and by the time I'm done it doesn't even matter what the outcome is. I think horoscopes are a bit of fun, I read them as I flick past the page and then immediately forget them. These things are diversions at best and quite frankly anyone who thinks they're anything more needs a fucking straitjacket.

I think magazine psychics are a sick joke - especially the ones who pass on messages from dead loved ones or give life advice based on their spirit guides. Live psychics are frankly, con-artists. Anyone who's looked at cold reading will tell you so. But still this isn't where my problem lies.

My problem is when they call it science.

Skepdic makes for an enlightening read on the subject especially if you don't have a scientific background, there are some fantastic articles on the ways that studies using "scientific methodology" can be deliberately misinterpreted, skewed or simply explained away. Most people don't understand scientific terminology so if you have an agenda to push then it's easy to twist things your way by throwing out some jargon and hoping the public bites.

I honestly believe that critical thinking should be on the curriculum as standard. But what do I know?


Well now that the ranting and raving is over with I'll give you something amusing to look at while I get on with the business of packing up my soap box.



Now that's dedication to the cause. There are more tattoos for the thoroughly geeky here, and I must say: it did indeed brighten up my day.