Distracted Driving

This is kind of brilliant. It's a video summarising an article published in the New England Journal of Medicine, about distractions which affect novice and experienced drivers.

 
Link to the original journal article.

The animators obviously had fun (love the brick joke with the ninjas), but what's more pertinent is that the study was presented in a manner which could be easily understood by anyone. I think it's important for journals to reach out to common man, because their staff actually understand the subject matter and know how to discuss it in an accurate manner (Dr Jeffrey Drazen, who narrated the above video, is actually the Editor-in-Chief of NEJM). Media such as reputable newspapers and news programs are better sources of scientific information that, say, certain celebrities who are not qualified to discuss vaccination, but may still unintentionally misrepresent facts or make exaggerated claims. While we're discussing it, science textbooks aren't perfect sources of information either. Especially the ones which present tongue maps as being accurate.

I'd like it if journals articles became more accessible to the public. Open access is a step in the right direction, and easy-to-understand summaries are helpful when the original article is too technical for a lay audience. Perhaps this is a maverick proposal, but I'd like secondary school students to have some experience reading real journal articles. I think it's important to expose students to the terse, specific style of scientific writing as early as possible, get them used to the idea of reading primary sources and not the rehashes presented in textbooks and newspapers, get them used to writing in a succinct yet informative manner. Maybe I'm overestimating the attention span of the typical student, but I only learned - properly learned - to write scientifically when I was doing my Honours degree, thanks to my supervisor's patient tutelage. What would have happened if my supervisor was less than ideal?

I guess I'm just sad that there's a substantial proportion of the population who lack the capability to keep up with the very cutting edge of science. Knowledge should be for everyone.

Concerning Science

[...] This mistake is why many people think they can argue about science the same way they argue about relationships, politics, and all the other imaginary human entertainments. They think that a single verbal counterpoint can undo what went before. But science is based on reams of data. Saying "That's just what they say" doesn't discount reams of empirical proof; it just announces who shouldn't be allowed in the room when the grown-ups are talking.

 - Luke McKinney, Cracked.com, from 5 Mind-Blowing Scientific Mysteries Solved Without Computers

Quoted for extreme truth.

Leptospira interrogans

After another long absence... Spirochaetes.

Leptospira interrogans is somewhat hard to draw, on account of being helical and having hooked ends. These MSPaint sketches were the result of trying to get a feel for this bacterium's unique topology. (It still isn't quite right - I neglected to include the periplasmic flagella - but we progress.)

Mirror, Mirror

The title text to this xkcd comic describes a famous trick question:

"When you look at words in a mirror, how come they're reversed left to right but not top to bottom? What's special about the horizontal axis?"

The answer is fairly obvious (they're reversed left to right because that's how you flipped the text around in order to face it towards the mirror), if slightly counter-intuitive, because it is easy to confuse the idea of a reflected image with a reversed image. It's also easy to prove that the premise of the question is incorrect - write a word on a sheet of paper, and then turn it top to bottom to face the mirror. Oh hey, the word is now upside-down, but not remotely flipped from left to right!

The question of what's special about the horizontal axis needs to be taken separately from the mirror. Or rather, why do we feel compelled to turn a sheet of paper or a book from left to right when turning it towards a mirror, rather than top to bottom, diagonally or any other angle out of the three hundred and sixty available? 

I thought it might something to do with the way we read horizontally, and therefore someone accustomed to reading top-to-bottom would turn the paper in that direction instead. My father contended that, since our feet are stuck to the ground by gravity, we are accustomed to move along the horizontal axis.  If you're in a dressing room and want to take a look at the back of your outfit, you twist yourself left or right about your waist - it never occurs to you to bend forward or backward until you can see your reflection, possibly because you're simply not flexible to do that anyway.

It's a bit funny though, how we don't even stop to think about such things. Or about astronauts in zero-gravity environments who might have a different perspective on things.

Western Blot (The Movie)

Haha oh my goodness.



Gilsons are indeed the workhorse pipette. Not as comfortable as an Eppendorf or as simple as a Finnpipette, but they're rugged and they get the job done. Just what a mercenary needs. (Incidentally, the multichannel shown in the video was a Finnpipette F2.)

I also just noticed the dry ice on the floor, for dramatic effect when Vitto steps into the lab. These chaps sure were having fun!

Science and Creepiness

I have mentioned the SCP Foundation before, and perhaps hinted as to how much I adore the series. It is only recently, however, that I have begun to understand why made-up reports about fictitious entities, contained by an equally-fictitious organisation, have such a draw for me. It's because of when I sit down to write a report about my lab-work, or plan an experiment, I could just as easily be writing about a SCP object.

I wouldn't say all researchers in all scientific disciplines could say this, but in my case, working with infectious disease, it certainly applies. We have physical containment levels for what we work on. There are often special requirements for different organisms, pertaining to handling, containment and maintenance. While there is usually enough information to culture the organism, and prevent it or modified strains from escaping into the environment, there is frequently a lot which is not known. That, of course, is the reason for experimentation.

We often have to do things we would rather not in order to find answers. I have infected and then killed several mice in the course of my experimentation. Did I enjoy it? Of course not. But it had to be done - there's that ugly phrase again - for the greater good. It's not on the level of utilising Class D personnel, or any sort of human experimentation for that matter, but it is still unpleasant, and often difficult to morally justify.

There are always the nasty surprises - the person who breaks a flask of infectious bacteria and acquires the corresponding disease shortly afterward, the person who ends up in a room with a leaking nitrogen dewar and suffocates before they know it - all the times when a mistake was made during the most unfavourable circumstances. There are incident reports, and they are every bit as impersonal as the artificial ones in the Foundation's collection.

Perhaps most pertinently, these organisms can be utterly terrifying. Look up bacillary dysentery, or meningococcal disease, or gas gangrene. These are real-life horrors.

In handling a pathogenic organism almost every day, when the precautionary measures are known by heart, it all becomes routine. When it becomes routine, one stops imagining the worst that could happen. Why imagine, when the worst has never happened, and when paranoia leads to a waste of resources?

Horror fiction on the other hand, makes it a point to explore the worst that could happen, in the process exposing the fallacy of considering a dangerous object, which hadn't done anything harmful yet, to warrant no more caution than a harmless object. When I mentally wrote out a SCP entry for the bacterium I work on, and realised it would qualify for Euclid class, it was a shock. Had I truly become so familiar with a dangerous, dangerous pathogen, that I no longer considered it threatening? Did I really think that it could not have any nasty surprises hiding up its prokaryotic sleeves, even there are many things about it which are poorly understood? Was I so really so arrogant, that I no longer feared a bacterium which causes an often fatal disease?

The entries in the SCP series are written to be entertaining, which is why their properties are so exaggerated. It's understandable, that the more dangerous objects have to have such bizarre, obviously undesirable effects in order to be accessible to a lay audience. But if you think about it, a bacterium like, for example, Clostridium tetani doesn't need to liquefy a patient's insides or cause projectile haemorrhaging. It's already frightening for what it does naturally. 

The SCP Foundation showcases the creative fiction of some excellent writers. Are we really so arrogant as to think that Nature can't possibly be more creative?

Scale of the Universe 2

Or, how to feel small and insignificant.

Humans can't comprehend large numbers. It's only when a bigger and a smaller number or objects are placed side by side that the differences are obvious, and even then it can be hard to comprehend. The creators of the Scale of the Universe series have done a great thing here.

(The Large Hadron Collider is bigger than Vatican City? Seriously?)

(Actually it's bigger than Uluru as well. And the Titanic looks quite comfortable sitting next to the International Space Station.)

(I need to think a little.)

Update XXX: Thirty Posts Titled "Update"

Quick check in here - been stupidly busy. SO MANY EXPERIMENTS. I am a fiend of science.

Whatever that means.

There was a great short story in Nature last month. Go take a gander. (Make sure that you're not eating anything, or intending to eat anything. There's a fair amount of squick.)

G-T-C-A

BioRad did it again.



So...catchy!

That's Certainly What I Said

A computer which can accurately use innuendo may not sound productive at first, and spending time to develop the necessary software seems like a waste of resources...until you realise that this actually furthers our understanding of how humour works. The essential ingredients which make a joke funny are difficult to distill, and often we may laugh without understanding why. Programming a computer to be able to generate a funny statement in 22 out of 28 attempts is really quite impressive. This sort of research may someday lead to  improved artificial intelligence, and a better understanding of communication.

Also, I suspect the focus on this particular class of humour was not because it was juvenile, but because it was easier for a computer to replicate. Sophisticated humour is harder to spin, even for a human.

In other news, my plant is doing well.

Geek Graffiti

Dear Esther is a gripping Half Life 2 mod which is really more akin to a film which you can walk through. If you don't have Half Life 2, I recommend, at the very least, watching a playthrough video on Youtube. It takes away some of the subtle horror when watching someone else play it, but you do get a feel of the atmosphere.

What I'm really here to talk about, however, is the cave graffiti. Specifically, the one that appears at 7:52 on this video, and which is visible at multiple areas.

It is probably a bad thing that I immediately recognised it as this image of a Helicobacter pylori cell.

Yup, I'm doomed.

Patrons of Truth

"You don't use science to show that you're right, you use science to become right."

- xkcd

Scientific research is something of an idealistic profession. You're constantly testing your own observations of the reality around you, and you're always aware that you may have to re-evaluate your current explanation for any phenomena you may encounter. That means having an open mind, and while you must always be prepared to defend your own theories, you also have to be able to accept and account for conflicting observations from another person. In essence, you are never trying to prove yourself right, but rather trying to find out what the truth is, no matter how it may invert your beliefs.

Working in science as a job complicates things. Here, you are expected to produce results. Getting results does not necessarily mean accurately predicting the outcome of an experiment before doing it; it can also mean getting an unexpected result and then figuring out what it means, and then doing a second experiment to show that the revised theory is plausible. However, the whole figuring-out process is long and painful, taking shots in the dark, as it were, so most of us would like to be correct from the beginning.

That creates a lot of pressure to "get things to work." You have a theory that something should do something you expect, and so you spend months proving that it does, even while all your experiments methodically keep failing. And it is upsetting, because you have ownership over that theory - the need for it to be right, for you to prove it - although, technically, you should have no ownership. You are supposed to be impartially seeking the truth, and therefore should be prepared to discard unsupported theories.

But it is hard to be impartial when you are working for a salary, or when you are a student on a time-limit, and when you urgently need data to publish.

It is a tough thing to balance out. And once you've discovered something important, and have been acknowledged for it, it is even harder to accept conflicting evidence which may appear later. But you have to. As a scientist, you agree that seeking the reality of the truth matters more than receiving adulation over a lie.

If you don't, you aren't a scientist. You're an attention-seeker.

Green Jelly Beans Linked to Acne!

This comic made me laugh out loud.

And then the alt-text killed me.

Thank you, xkcd. You have made my day.

And an Anniversary

Also, I'm a bit late with this, but my PhD anniversary passed a couple of days ago. I spent it, among other things, running 72 PCR samples which promptly failed.

How very apt.

I like the assonance of this post title. [/random]

Writer's Block

Best published journal article ever.

I think this even tops the article describing how to make an origami model of a DNA strand. There used to be all sorts of wonderful articles by people who not only worked in science, but also played in it.
...

Update XXVII: For Science

So. We haven't spoken in a while.

I've finally experienced a researcher's worst nightmare - finding out that someone else is doing the same thing you're doing, only better. Also, they are based in Hawaii. Hawaii.

It's not too bad. Science is ultimately an altruistic pastime, and if you go into it hoping for fame and wealth you are going to be severely disappointed. Your contribution as an individual means nothing compared to the contribution to the overall picture - and it doesn't particularly matter who makes that contribution.

It is a noble, harsh thing, to be a scientist.

But Hawaii, goshdarnit.

The "Dance Your PhD" competition has recently come to my attention. It has to be the single most bizarre method to be recognised by the Science magazine. (For those who have not been exposed to the cut-throat world of publications, getting published in Nature or Science is akin to an article about you being printed on the front page of your national newspaper, complete with full-colour photographs.) It probably would be quite challanging to express a PhD topic by dance.

...

...

I want to do it.

What does everyone think of Google Instant? While potentially annoying to slower typists looking up obscure topics, I can see how it would be intuitive to the impatient among us. I actually didn't notice anything different for the first thirty minutes or so, until - "Hey, why is the page loading before I can hit the Enter key?"

I like how they put up an actual graph to prove that Google Instant is faster. A graph with no axes.

Look! Jurassic Park the Musical!

...
...

Sequencing Perfection

Anyone who has ever done DNA cloning knows how hard it is to get the sequence you want without accumulating any mutations, especially when amplifying the insert via PCR. Anyone who has ever done DNA sequencing knows how hard it is to get a clean, readable sequence with no bizarre misintepretations by the sequencer's software, or a chromatogram which looks like the frequency plot of a heavy metal track.

I have just looked at the results from sequencing the insert of the vector construct I made. 970 base-pairs of pure, untainted perfection.

Shh, let me enjoy this moment.

Been a While

It's been a busy week.

I've been doing restriction digests. It seems that's all I have been doing, setting up the same reaction again and again until it actually works. Turns out the first attempt was actually the best one, and fortunately I still have purified products from that one. Going to use it and move on.

Then yesterday I had a poster presentation. There's the paradox with poster presentations. On one hand you want a lot of people visiting your poster and asking you questions, because it means you did your job and your work is actually interesting. On the other hand, practically everyone asks you to "talk me through your poster." I had to tell the same story at least six times, with varying levels of detail to account for differing familiarity with the subject field. And differing character.

"Tell me about antigenic shift," says one visitor.

I stare at him. He was my lecturer for Molecular Virology last year. He was the one who taught us about antigenic shift.

"You have to be joking," I say.

Wednesday was April Fools' and nothing of note happened, which was sad. On Thursday, my co-supervisor's lunch went missing from the common refrigerator, which attracted an undue amount of attention.

Today is Saturday.

It's just another day.

Update XX: Cool, Useful or Plain Funny

So, one of my friends recently picked up a 1 terabyte hard drive for about $200. That's 20 cents per gigabyte, people. And to think that a few years ago, a 1GB hard drive would have cost $100. Meanwhile, Seagate promises over thirty thousand times that capacity in a mere two years.
Computers are moving altogether too fast these days.

I've been trying to figure out for some time what makes things funny...It's sometimes incomprehensible, how some things make us go "ha-ha" while others get nothing more than a bored stare...
Anyway, today's xkcd was undeniably funny, though if it was because of the entirely everyday manner in which the character failed to escape, or because of the subversion of what I expected would happen, I cannot say.

Something which does seem to be almost universally funny are mistakes. Other people's mistakes. CakeWrecks is dedicated to the professionally-made cakes which follow instructions too closely, are incredibly creepy, do not look remotely edible, or are simply... beyond words.
I spent a few days browsing the archives. I don't think I've laughed so many times in my life.

This amused me. Not the vehicles themselves - they are clearly M3G mobile bridges - but rather the various suggestions concerning Decepticons (that one navy gunboat was getting lonely, apparently), Allied Troop Carriers, Universal Soldiers, aliens...

It's been a while since I found a nice time-waster... Cursor10 is a neat little game. You have 650... well, they're clearly not seconds, so I'll call them "units of time." You have 650 time-units to reach the sixteenth floor, and ten cursors to help you accomplish this. If you run out of time, you control the next cursor out of your ten while the previous one simultaneously copies every single action you made it do when you had control of it. In essence, you have to "programme" the ten cursors to reach the end. A very original idea for a game, and fun to play too.

Trapped 5 is a vastly superior puzzle game to its predecessors, and well-crafted. The best part is that it is not possible to get a Game Over, which removes a lot of potential frustration. Other puzzle-game creators, take note.

And finally, something useful. If you've never checked that your desktop clock was synchronising correctly with an Internet time server, it may not actually have been doing so... Recently, I checked mine and found, to my utter horror, that it was four minutes slow. To think I had considered it accurate.
Anyway, I was unable to fix the synchronisation by changing the server or opening a port through my firewall, so I got hold of this nifty piece of software. It's a very small program, and can be set to automatically synchronise the desktop clock with any Internet time server. Worth the minuscule bandwidth cost required to download it.

And now, have a pretty picture. Ta and later.

(Edited on 21 October 2008 for a broken link.)

Cool Things

Mozilla aims to make a record for most software downloaded in 24 hours, with the release of Firefox 3. It's somewhat silly, but hey, why not? The Download Day site is here.

You fail... orchestrally. (The music makes it seem sillier.)

Braainsss... (I should try this recipe...if I can find an appropriate brain mold.)

In other brain-related news, a monkey hooked up to a robotic arm successfully fed itself with said arm.