Blessed by the Potato

Wow, what a terrible, terrible week for exercise and diet. Started off with a StarCraft 2 “LAN” party, which involved 2 days of nothing but junk food. Then I was busy with work and it was hot and humid out, and I got my sleep schedule all screwed up, so I did basically no exercise. Weight’s up 2 pounds (and the scale’s calibrated right this time), so I’m going to have to be extra good this coming week. Meal plan: egg whites, oatmeal, fruit, repeat.

Of course, this was also the week that I started putting together “Little Known Facts About Calories” — a semi-secret project which I am teasing you about now, and hope to unveil soon… but not today!

Links:

Gamers can beat algorithms for finding optimum protein structures in a game simulating how protein chains would contort themselves to find their minimum energy configuration in the cell (with the water-like cytoplasm, and the fatty membrane layers). Turns out the algorithms are good at getting fairly close, but can be trapped in local energy minimums, which the gamers see past. A neat read.

OK Cupid has an article up investigating what can help make your profile picture look more appealing. Also, a neat graph showing that sluts are more likely choose iPhones as their smartphone of choice.

Yet more nonsense on the census. I don’t see the problem: StatsCan is a government agency with an excellent record of protecting privacy. The long-form census is incredibly useful and should continue to remain mandatory… I can’t believe the Cons are still trying to make an issue of this.

An illustrated guide to a Ph.D.. And, from the same author, 3 qualities of successful PhD students. To quote liberally from the second article:

“Smart” qualities like brilliance and quick-thinking are irrelevant in Ph.D. school. Students that have made it through so far on brilliance and quick-thinking alone wash out of Ph.D. programs with nagging predictability. Let there be no doubt: brilliance and quick-thinking are valuable in other pursuits. […] Certainly, being smart helps. But, it won’t get the job done.
[…]
To survive this period, you have to be willing to fail from the moment you wake to the moment your head hits the pillow. You must be willing to fail for days on end, for months on end and maybe even for years on end.
[…]
For students that excelled as undergraduates, the sudden and constant barrage of rejection and failure is jarring. If you have an ego problem, Ph.D. school will fix it. With a vengeance. (Some egos seem to recover afterward.)
[…]
Science is as much an act of persuasion as it is an act of discovery. […] You will have to write compelling abstracts and introductions that hook the reader and make her feel like investing time in your work. […] You will have to learn how to balance clarity and precision, so that your ideas come across without either ambiguity or stifling formality.
[…]
That’s why I recommend that new students start a blog. Even if no one else reads it, start one. You don’t even have to write about your research. Practicing the act of writing is all that matters.

I started my site in undergrad/high school, but the blogging platform didn’t arrive until grad school, so I suppose I can use this as a backwards rationalization as to why I did it :)

Netbug asks: “I always wondered about theses in the modern environment. The topics must be getting more and more obscure and specific so as not to tread on old ground…”

Well, to a certain extent, yeah. It’s tough to be a scientist (or any kind of academic for that matter) and know that the odds are high that everything you do is just going to be lost to the archives of some library and not do much. For the most part, we’re destined to toil in obscurity.

But even these specialized topics lead to surprising discoveries, that can open up entirely new fields and capture the public imagination.

Watson & Crick were doing obscure x-ray crystallography of some biological molecules when the structure that they saw — a paired double-helix — suggested a way for the molecule to copy itself. And that opened up a whole new field of study. Multiple fields of study.

One of which was to attempt to take dinosaur DNA from fossilized mosquitos and create cloned versions. They weren’t quite true to the original as time had caused a lot of decay, necessitating the incorporation of some newt and frog DNA to fill the holes. That unfortunately gave the dinosaurs the ability to change gender, so even though only females were bred, it wasn’t long before the dinosaurs were reproducing on their own. And now, because of that, another scientist has to do research on raptor-proofing structures, balancing the heat exchange needs of central Costa Rica.

Ah, the glorious cycle of discovery continues!

It looks like I am done running experiments for my PhD — just* analysis and writing up now!

To mark the occasion, we have come up with a new celebration we call “running the chocolate gauntlet“, which can be staged using items found here on the hospital campus (largely the Tim Horton’s). It involves proceeding through a series of celebratory doughnuts, each chocolatier than the last: a honey dip, a chocolate dip, a chocolate glaze, and finally: the double chocolate.

Unfortunately, we didn’t get a chance to test out the chocolate gauntlet due to concerns over the safety of the celebratants, and disagreements over whether boston creme should be included and/or allowed to exist at all outside of Boston. We are now waiting on baseline cholesterol tests from the potential test participants, and have sent the boston creme matter off to a subcommittee for a more educated final decision. Early rumour has it that one compromise option will be to leave the boston creme out, but make the final stage of the gauntlet a double chocolate doughnut with a scoop of chocolate ice cream on top. Some members of the boston creme subcommittee, including members not actively pursuing a boston creme jihad, oppose the proposed solution, warning that ice cream availability is limited at the hospital, and may lead to another round of chocolate escalation as various levels of ice cream chocolatyness are added to the gauntlet.

Nonetheless, good news. Celebrations to follow.

With chocolate.

* – this is still a many-month-long process.

To break down what it is I’ve been doing for the last few hours, I take recordings of the electrical activity of someone’s brain, it looks something like this:

Lots of squigglies. Too many, in fact — some of those squigglies are the influence of the electrical activity of the heart and of outside sources (like the MRI we stick them in), and they don’t represent the brain activity that we’re looking for. So, you spend a few hours playing with various computerized filtering techniques to get rid of those influences and get something like this:

Presto-boom-o, you’ve got some more-or-less pure brain activity to look at. Repeat it about 50-60 times for all your subjects (PS: still need subjects, enquire within), throw them all together for some groupwise stats, shake it up, have a cookie, and go write it up to share with the world.

Unfortunately, tonight has not been my night for analysis. The stupid program keeps crashing randomly, and now I’ve gone back to look at some of the saved data from earlier in the night:

No squigglies.

WHERE ARE MY SQUIGGLIES??!!

Anger and frustration do not even begin to cover it.

I just got a ticket for parking on campus at Western. I had the parking pass out and displayed on my dash, and they put the ticket on the windshield right overtop of the pass. I just finished filling out the online appeal form, and I have to wonder if this is some really un-funny April Fool’s joke.