Helical Translations

Winter project’s finished – now to enjoy the summer!

2010-04-09T21:48:00.001-04:00

Last thanksgiving, inspired by both a friend’s adventures and an article featured on Lifehacker (original here) I had a stroke of inspiration. What I was not aware of was that this particular project would ultimately take me just about 6 months to complete, but having finished it recently I thought I’d share.

The idea behind the whole thing is to take a photograph or painting, crank down the resolution, and what you’re left with is a pixelated version, which you can then lay out as coloured tiles – in this case paint chips – and recreate the photo low-res but at large scale and without lifting a paintbrush.

The inspiration

Perhaps influenced by the above picture and associated nostalgia, I thought a fedora-clad Bogart might do well. Some searching brought me to this:

Which yielded to some mile photoshopping:

And then shrunk to a much smaller resolution:

With my design set, it was then a quest to get raw materials. A trip raiding the local hardware stores yielded a wide selection of paint swatches, and then began the many-month-long process of cutting out hundreds upon hundreds of squares of colour for tiles. Montreal is cold in winter. There’s no need to go outside.

Splitting the photo into three colour zones let me partition the chips, and then began the selection of tiles to fit the photo. Splitting it into zones of 10x10 helped. For example, the crown of the hat:

And laying out the patterns:

And after another long amount of time, all that was done. Laying them all out, we got:

Note the TV show on in the background. Simultaneous other activities is highly recommended.

A bit more work, and it was glued down, and the final product complete.

Yes, not every colour matches the template. I think that makes it better. Yes, there are gaps. I had to face the reality that I can’t consistently cut squares with a ruler and utility knife. I accepted it and just tried to make sure the gaps ended up randomly dispersed, which I mostly accomplished. And yes, it looks a little eerie in the camera flash, but under ambient light it really worked out well.

And now that sucker hangs on my wall. To those who say I have no artistic talent, I have this to say: only when I don’t have a template.

Science is Hella-cool

2010-03-02T18:16:00.001-05:00

It seems the proposal has been put forward to make the SI prefix for 10 to the 27th power “hella-”

I’m a little surprised that this wasn’t named already, I had just assumed that these prefixes were already named up to and far beyond what we would ever need to use. Granted, we haven’t found much use for 10^27 yet; it’s been almost twenty years since the previous (yotta-) was named.

There’s a facebook petition to convince the overlords (Système International – you know they’re the real Illuminati, right?) to add this to their vocabulary. With the force of thousands of high-schoolers and college students, they might just have to concede to the masses.

I can already envision bait-and-switch manoeuvres to lure in unsuspecting young recruits to science.

“Hella-big ridic all-ages edutainment nite! Off the rails, yo!”

It’ll so work.

MakeHellaOfficial Headquarters: http://www.makehellaofficial.blogspot.com/

Discover: Hella…yes!

Sign the petition here:
http://www.facebook.com/pages/The-Official-Petition-to-Establish-Hella-as-the-SI-Prefix-for-1027/277479937276

I have a new idol

2010-02-26T22:19:00.001-05:00

It’s this guy

At almost every game I’ve seen, putting on a show each time. This guy is the man.

Go Canada Go!

“Lie to Me”, Temporary Autism and Malcolm Gladwell’s Igon Values

2010-02-22T00:58:00.001-05:00

I just finished with Malcolm Gladwell’s Blink: The Power of Thinking Without Thinking. It raises some interesting points, and is certainly an entertaining enough read, but I have to say it’s got my logic gland a little bit inflamed.

Location of the logic gland

Blink deals with the processes that take place in our minds before we’re aware we’ve thought about them (i.e. first impressions). He discusses job interviews, market research, and police (over)reactions, among other things. I’d like to report the take-away message of it all, but to be honest I’m kind of confused what it was supposed to be.

Half the time Gladwell is describes how our first impressions are more correct than we give them credit for, and half the time that they’re terribly, terribly wrong. That’s fine, but without outlining where the distinction lies, it doesn’t help anyone better understand how they might change their thinking on first impressions. The only point that is put forward is that snap judgements are correct if you’re an expert and trained to make objective evaluations, and wrong if you’re a non-expert. Which does all of us non-experts a lot of good.

As an example, Gladwell explains how meticulous analysis of facial expressions, down to specific muscle movements, can carry crucial clues to the person’s intentions. This comes from research by Paul Ekman (Tim Roth on Lie to Me) and the meticulous system he developed, which involves recording facial expressions and breaking down expressions frame-by-frame, giving each one particular, inaccessible codenames.

Those are Action Units 89 and 104 right there, and they tell me Tim Roth had the veal parmigiana for dinner last night

Following this praise for scrutinizing small details to pick out the truth is a complete rebuttal of this methodology. Gladwell goes through how over-analysis of data cost “Blue Team” in the American Army’s Millennium Challenge 2002 war-game. They chose to carefully scrutinize their data, give everything inaccessible acronyms, and break everything down into categories. And this time, that was a bad thing.

My problem with Gladwell’s writing is the same as that recently voiced by Steven Pinker, in response to Gladwell’s most recent book, What the Dog Saw – And Other Adventures. He calls it Gladwell’s Igon value problem, after a particularly damning error (Eigen value, a term any mathematician knows, was the term Gladwell meant to use). Talking about What the Dog Saw, Pinker writes:

The problem with Gladwell’s generalizations about prediction is that he never zeroes in on the essence of a statistical problem and instead overinterprets some of its trappings. For example, in many cases of uncertainty, a decision maker has to act on an observation that may be either a signal from a target or noise from a distractor (a blip on a screen may be a missile or static; a blob on an X-ray may be a tumor or a harmless thickening). Improving the ability of your detection technology to discriminate signals from noise is always a good thing, because it lowers the chance you’ll mistake a target for a distractor or vice versa. But given the technology you have, there is an optimal threshold for a decision, which depends on the relative costs of missing a target and issuing a false alarm. By failing to identify this trade-off, Gladwell bamboozles his readers with pseudoparadoxes about the limitations of pictures and the downside of precise information.

Whack! Pinker-slapped!

Gladwell doesn’t get statistics. This prompted Pinker’s response for What the Dog Saw, and was the case in his earlier writings as well. While one scientist’s views, a remarkable event, or a business success story may make for interesting discussion points, it is never the be all and end all. For every example of failed market research, how many times has it been successful? For every time experts identify a forgery, how often are they fooled? A single story makes for a good anecdote, but it is not convincing that it is representative of a phenomenon. The stories he writes on are, after all, remarkable in some way, or else they wouldn’t be worth publishing.

Perhaps most frustrating was his coining of the term “temporary autism” to refer to the lack of comprehension we have of fine details in the first rapid moments of experiencing a novel situation, person, or object. I’ll try to ignore how offensive this is to those afflicted with autism and their loved ones, but seriously, I don’t complain of momentary paraplegia whenever my leg falls asleep. That’s not cool.

Bad, Gladwell, bad!

“Temporary autism” is supposed to represent that we cannot comprehend every detail of a situation and make judgements based on only our (often misled) first impressions. He describes how we need to avoid falling into that trap where the rest of our cognitive processes supposedly shut down. I think he takes this completely the wrong way. People don’t fall into a pathological state (which, if true could be extremely legally problematic) whenever they don’t have enough information. Instead, they operate based on whatever information they have, and then once a complete picture is available, full reasoning and such can kick in. To call everyone potentially irrational and unemotional is pretty damn misanthropic.

Okay, that’s enough for now. I still plan on reading Outliers and What the Dog Saw, but needed to vent about Blink for now. If I have to say one thing, it’s take your Gladwell with a grain of salt.

p.s. If you’ve read Gladwell before (and maybe even if you haven’t), you should read this essay: I Dream in Malcolm Gladwell. Its funny, and helped ease some of my frustrations about this book.

Oh, and here’s Steven Pinker’s Review:

New York Times: Malcolm Gladwell, Eclectic Detective

The 5 Second Rule - Expanded

2010-01-25T20:21:00.000-05:00

For every rule, there are exceptions. Even something like the 5 second rule, which has saved many a spilled college student's dinner. Check it out:

Source:Audrey Fukman and Andy Wright

I like to advocate a realistic approach to bacteria in the world around us; while it’s probably not the best idea to eat a pound of soil (for several reasons), contact with non-pristine surfaces doesn’t necessarily make food irreversibly spoiled. In fact, researchers have shown that food may be okay after being left as long as 30 seconds on a cafeteria floor.

There’s lots of places you wouldn’t want to eat food off the ground (hospitals, barnyards, and daycares come to mind) but its possible that we’ve become so accustomed to clean environments, and grown so afraid of all bacteria that we’ve lost perspective on the world around us. Not that long ago the closest thing to a table available was a tree stump or rock. And no one wiped those down with Lysol first.

Tolkien’s Ents Just Became a Little Less Fantastical

2010-01-11T19:17:00.001-05:00

Looking something like a leaf, this sea slug (Elysia chlorotica) has just become the newest organism to breach traditional kingdom boundaries and do something scandalous – photosynthesize. All by itself. Its parents must be so ashamed.

We thought the idea of walking, talking, hobbit-toting, orc-squashing Ents was something wholly in the realm of fantasy. No more. Give it a few hundred million years and we may well see geriatric trees walking the Earth. Whoops, I mean Middle-Earth. Yes, I went there.

Wired Science: Green Sea Slug is Part Animal, Part Plant

What Are You Made Of Indeed, Tiger?

2009-12-13T15:49:00.001-05:00

I do my best to avoid celebrity gossip as much as possible, what with the brain-rotting inanity and all. That said, I can’t avoid sharing this one: on the back of a recent (November) newsmagazine, I spotted an ad of America’s newest celebrity philanderer (move over, Jon Gosselin):

Oh the sweet, hilarious irony of it all. “What are you made of” indeed. I expect sponsors are tripping over themselves to distance themselves from the Tiger. At least Gillette, another sponsor who builds their image on Tiger’s reputation, has two others to pick up the slack for his poisoned public image. Who were they again?

Shit.

Sapporo Ushers in a New Age of Brewing

2009-12-08T23:33:00.001-05:00

It seems Sapporo knows what it’s doing when it comes to marketing. They’ve taken barley that spent time on the International Space Station, grown it, brewed it, and made….SPACE BEER!

Genius. Just plain genius. Similar in spirit but hopefully much less tragic than Budweiser’s ill-advised Nuclear Ale.

Wired Science: Barley + Space = Space Beer!

Vitamin Water is a Stupid Product

2009-11-30T03:12:00.001-05:00

Alas. It’s been a long time since work has kept me up till 3am. But I have something to share - I loved this Saturday Morning Breakfast Cereal comic:

Spotted any strangelets yet?

2009-11-24T21:41:00.001-05:00

A press release yesterday from CERN has announced that the LHC has completed its first particle collisions successfully. Hooray for particle physics!

Now for the hard part – not breaking the machine again.

But CERN, if you have to get repairs done again, for Higgs’ sake get an up front quote. You know how bad those particle accelerator mechanics are an untrustworthy bunch.

CERN: Two circulating beams bring first collisions in the LHC

A thousand taxonomists cried out into the night…

2009-11-19T22:40:00.001-05:00

Whoever said cladistics were useless?

Certainly I haven’t.*

An example has just surfaced that shows the importance of taxonomy to this day. Sadly, taxonomists’ vindication may come at the cost of a species of fish, the flapper skate, now recognized as critically-endangered. Classification of this fish as the same species as the related blue skate has allowed the flapper to be fished almost to extinction, and all because of a classification error.

Pictured: The Flapper Skate. So cute!

So while the fact remains that taxonomy is mostly an outdated field, there might still be some role for the science of natural classification yet. Just not in any of the important sciences.

Wired Science: ID Error Leaves Fish at Edge of Extinction

*This may be a lie.

Knock on wood – LHC might be operational in one week

2009-11-13T20:34:00.001-05:00

After more than a year down after various technical problems have kept it from starting, the Large Hadron Collider at CERN in Geneva is planned to be operational next week. The world’s largest experiment may soon be under way.

A week is not much time for anyone to get their tin foil hats on again, but I’m sure we can count on some crazies coming out of the woodwork once they get hold of this news. Bring on the fireworks.

Wired Science: LHC To Finally Start Next Week, Again

Evolution in the Test Tube – Cool 20-year experiment demonstrates natural selection

2009-11-12T00:17:00.001-05:00

Richard Lenski is the Awesomest Scientist of All Time. Yes, even more awesome than Doc Brown.

In the ongoing “debate” over evolution going on in the educational system, one claim that the creationists have made is that evolution has not been demonstrated to occur as we watch it. Enter a particularly elegant 20-year study conducted by Dr. Richard Lenski at Michigan State University.

First published a year ago, Lenski’s group has now followed up with a second genomic study on populations of initially citrate-metabolism-deficient bacteria that were cultured in the presence of excess citrate. In these conditions, it was an obvious benefit to any bacterium that would develop the ability to use citrate as an energy and carbon source, as it would then be able to grow faster than the other cells in the culture.

Seen above: E. coli, not growing

Over tens of thousands of generations, the bacteria did just that, and accumulated beneficial mutations, allowing them to utilize the extra carbon source, and thus gain selective advantage over the bacteria that did not gain these beneficial mutations. This takes incredible foresight, planning, and a little bit of fortuity, but it worked, and 21 years later the research has been published in PNAS and Nature.

While the research is exciting, the enjoyment I truly got associated with this work was not with the scientific publication itself, but Lenski’s response to inquiries of an insidious nature from Conservapedia founder Andrew Schlafly. Click that link to Conservapedia. I dare you. I was sucked into an hour of frustration reading their “balanced alternative to the liberal-slanted Wikipedia” articles, and you should have to endure it as well.

The entirety of Lenski and Schlafly exchange is presented on both the Bad Science blog and RationalWiki. I’ll just place my favourite excerpts here, but I encourage you to read the exchange in its entirety.

Excerpts from Lenski’s response:

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

…

But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [http://en.wikipedia.org/wiki/Allusion]

…

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate.

…

However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

…

You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [http://en.wikipedia.org/wiki/E_pur_si_muove] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

Anyway, Richard Lenski is pretty much my hero.

With that incredible beard, how could he not be?

See also:

ScienceDaily: Time In A Bottle: Scientists Watch Evolution Unfold
Lenski Group Page: http://myxo.css.msu.edu/index.html
The New Paper (Nature, Oct 2009): Genome evolution and adaptation in a long-term experiment with Escherichia coli
The Original Paper (PNAS, June 2008): Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
Full Documentation of Lenski’s creationist badgering and response (Bad Science): All time classic creationist pwnage
RationalWiki:Lenski_Affair

Montreal Photojournal: Mont Royal in Fall Colours

2009-10-12T15:30:00.001-04:00

It’s been a while since I’ve brought out the camera here, so I dragged it around a bit this weekend. Mont Royal is in full swing colour-changing, so makes for good photos these days.

Of course, it’s probably not that impressive if you live near real forests (as a kid, I never understood fall country-drive tourism, it was just too ordinary to me), but this is as close as it gets in Montreal.

Incidentally, I remembered Randall Monroe’s most recent xkcd comic while cropping the above image:

Source: xkcd.com

Truism via graphical representation

2009-10-11T12:00:00.000-04:00

I’m starting to be persuaded that any idiom may be represented in graphical form. Another graph from Indexed:

Source: Indexed by Jessica Hagy

The important assumption here is that cook#1 is not me.

You know you’re in a hockey town when…..

2009-10-10T22:05:00.001-04:00

Me: Wow, this grocery store is very quiet tonight, even for 9:00pm

Cashier: Don’t you know? There’s a Habs game tonight!

Where do you see yourself in 4000 years?

2009-10-09T12:00:00.000-04:00

Thousands of years from now, what will we think about the biggest events in modern history? Sam Kean wrote recently on 3quarksdaily on this issue:

Will the Manhattan Project Always Exist?

Read the article. It will change your idea of what really is permanent on this planet over the long term.

This assumes that we will escape various forms of robot, zombie, asteroid, climate-change and/or Malthusian Armageddon that could easily crop up in the intervening time. Hmm, I should start a betting pool. Takers?

Source:
3quarksdaily: Will the Manhattan Project Always Exist?

Coffee contains – gasp! – CHEMICALS!!!!!!

2009-10-07T23:31:00.001-04:00

Ever wonder just what is in a cup of coffee? At first, you might not want to.

Photo source: Simone♠13

On the short list, in addition to caffeine, your average brew also contains:

Dimethyl disulfide, which contributes to the odour of human waste
2-Ethylphenol, a cockroach pheromone
Putrescine, a toxic breakdown product of rancid meat

While I don’t believe the article writer set out to have this effect, a couple comments indicate he has in fact scared some readers. Of course, it all depends on how you want to take it. Some might be made uneasy at the mention of strange-sounding chemicals with scary qualifiers, and opt to eschew their coffee tomorrow morning. I, however am not about to abandon my ~~sweet, caffeinated nectar of the gods~~ morning cup just yet.

Coffee’s been around for a while now, and (debates about small effects on overall health aside) it’s safe to say that the compounds in coffee, especially at cup-a-day levels, are harmless. This presentation of facts is a good illustration that one shouldn’t be scared of something just because it has chemical names attached to it. The unknown is scary and chemicals particularly intimidating, but any everyday material could be made to sound scarier if placed in the right light.

That cup your coffee’s in? Aluminum and silicon oxides
The table it’s sitting on? Reducing sugar polymers and lignins
The spoon you mixed with? Smelted iron-carbon alloy

You don’t even want to know what sort of nasty phytochemicals are in that banana you were about to eat.

The point being, just because you can name something chemically (and even describe potentially unsavoury places it might be found in nature or industry), that doesn’t make it bad for you. When someone says that a product contains (cue spooky music) chemicals, that person is trying to scare you, usually to buy their product. Case in point:

Note that they never say those chemicals are not present in their product (they are), just that they are present in the competitors. Sneaky bastards.

Anyways, that said, I’m thirsty. I’m off to grab a nice cold glass of dihydrogen monoxide.

Source:
Wired Science: What’s Inside a Cup of Coffee?

Ig Nobels Awarded

2009-10-02T09:36:00.001-04:00

Forget those other awards coming out next week, the Ig Nobel awards were awarded last night.

For the uninitiated, the Ig Nobels are awards that celebrate research that “makes you laugh, then makes you think”. They’re doing a great job of promoting interesting science, I always enjoy seeing who wins.

Winners this year:

VETERINARY MEDICINE PRIZE: Catherine Douglas and Peter Rowlinson of Newcastle University, Newcastle-Upon-Tyne, UK, for showing that cows who have names give more milk than cows that are nameless.
PEACE PRIZE: Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining — by experiment — whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.
ECONOMICS PRIZE: The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa — and for demonstrating that similar things can be done to an entire national economy.
CHEMISTRY PRIZE: Javier Morales, Miguel Apátiga, and Victor M. Castaño of Universidad Nacional Autónoma de México, for creating diamonds from liquid — specifically from tequila.
MEDICINE PRIZE: Donald L. Unger, of Thousand Oaks, California, USA, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand — but never cracking the knuckles of his right hand — every day for more than sixty (60) years.
PHYSICS PRIZE: Katherine K. Whitcome of the University of Cincinnati, USA, Daniel E. Lieberman of Harvard University, USA, and Liza J. Shapiro of the University of Texas, USA, for analytically determining why pregnant women don't tip over.
LITERATURE PRIZE: Ireland's police service (An Garda Siochana), for writing and presenting more than fifty traffic tickets to the most frequent driving offender in the country — Prawo Jazdy — whose name in Polish means "Driving License".
PUBLIC HEALTH PRIZE: Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, Illinois, USA, for inventing a brassiere that, in an emergency, can be quickly converted into a pair of gas masks, one for the brassiere wearer and one to be given to some needy bystander.
MATHEMATICS PRIZE: Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers — from very small to very big — by having his bank print bank notes with denominations ranging from one cent ($.01) to one hundred trillion dollars ($100,000,000,000,000).
BIOLOGY PRIZE: Fumiaki Taguchi, Song Guofu, and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.

Cool Lipdub Video from UQÀM

2009-09-29T12:00:00.000-04:00

I might be late to the game with this, as I got the tip-off from CBC, which in turn saw it from CNN, but it’s still cool. As part of the orientation at my neighbouring school, Université de Québec à Montréal (UQÀM), students put together a gigantic, 172-cast single-take uncut lipdub to the Black Eyed Peas’ I Gotta Feeling. And now I have the song stuck in my head. Mazel tov.

The CBC National story said that it had 50 000 views. Now, an hour later, I look and it has ~~124 000 views~~ – refresh the browser – 139 000 views*. Seems it’s not done gathering popularity.

This all reminded me of one I saw earlier this year, that no doubt had influence in inspiring the UQÀM students.

This one was from a school in Germany (Hochschule Furtwangen) and as far as I can tell, pioneered the idea. Their video and accompanying site solicited a whole string of responses at the time - http://universitylipdub.com/response-videos/. Check them out.

*I’ve preposted this – it’s bound to be even more by the time you read this
Update 02.10.09 – the view count is now 687,000. They seem poised to enter the internet Pantheon of viral videos, up there with “Charlie bit my finger” and the star wars kid. Give it time.

Global Warming, You’ve Gone One Step Too Far…..

2009-09-27T23:23:00.001-04:00

I read about some sad news this morning. It seems that in addition to making island nations disappear and driving polar bears toward extinction, global climate change has contributed to another, undeniably more heinous offence – destroying the quality of beer.

Source: deege@fermentarium.com

Reported in the journal Agricultural and Forest Meteorology, the paper, titled The impact of climate change on the yield and quality of Saaz hops in the Czech Republic reports that important flavour-influencing compounds (referred to as alpha-acids) in Czech hops have been decreasing over the last 50 years, correlated with increasing average air temperatures during this time, and the trend is liable to continue. I’m sure more validation is in order, but if true, then global warming has crossed the line.

Climate Change should know the rules of engagement set out in the Taurus conference (Al Gore giving a talking to himself in his car). Those rules were:

No cute and cuddly animals are to be harmed. Mosquitoes are fair game.
Unreasonably warm winters are welcome. Unreasonably hot summers are not.
Beer, coffee, cheese, and other delicious foods and beverages are not to be tampered with.
You do not talk about fight club.

Of course if Global Warming is indeed playing hardball and we will continue to see the quality of our pilsners drop with time, I see only one logical way to deal with this.

Drink up!

Discovery Space Disco: Now We Have a Problem: Global Warming is Impacting Beer Production
Research Article: The impact of climate change on the yield and quality of Saaz hops in the Czech Republic

Arrr, ye salty dogs!

2009-09-19T15:26:00.001-04:00

Today be International Talk Like a Pirate Day!

So all ye buccaneers, scallywags, and marauders, let loose the inner scurvy-rattled plunderer on the world today.

Arrrrrrrrrrr.

Oh dear god, please stop the attack ads.

2009-09-17T00:01:00.001-04:00

I try to keep well-informed on Canadian politics. But because it can be so polarizing, I try to keep my opinions more or less to myself, and try to stay neutral, re-evaluating my position every time an election rolls around. Seems almost yearly now.

Watching some TV this evening, I was quite disheartened to watch the most recent slough of Conservative ads, taking aim at Liberal Leader Michael Ignatieff. The ads centre around Ignatieff’s supposed backing of the Liberal-NDP coalition that almost materialized last December.

What they count on (sadly, most of the time it probably works) is us forgetting was that Ignatieff was publicly hesitant to proceed with the coalition, at a time when he was a prominent party member, but not leader. He came forward with “A coalition if necessary, but not necessarily a coalition”. Trying and spread an idea that he is reckless and untrustworthy is not fair. I’ll make up my mind on their policies if necessary, but I do not appreciate the lies of omission in these ads.

To any political party considering negative ads:

WHEN YOU WASTE MY TIME TELLING ME I SHOULDN’T VOTE FOR SOMEONE, THAT MAKES ME LESS INCLINED TO VOTE FOR YOU

Please stop confusing the issues. Tell me what you have to offer, not exaggerations of the opposite side.

I guess I should be grateful, though. Canadian politics are nasty, but they pale in comparison to recent US political ridiculousness.

Chicken soup for the cold, antibacterial soaps, and herbs in energy drinks

2009-09-11T21:06:00.001-04:00

From my stream of daily science- and math-based procrastination reading, this cartoon comes from Indexed, a funny blog that “makes fun of some things and sense of others” through charts and graphs. This one hit home for me. Question everything!

Source: Indexed by Jessica Hagy

I welcome discussion on my choice of title.

Biking in Montreal – not scary, but damn hard

2009-09-08T20:58:00.001-04:00

Today I rode my bike up a hill. Well, yesterday now, actually.

With my bike now in Montreal, I thought it would be a good day to take it on a test drive, on a holiday, when ostensibly the traffic (both automotive and cycle) would be less than on a weekday. Montreal drivers having the reputation they do, I was wary at first to take it out on the road, lest I be flattened the first time out.

Now, my bike is not the average bike around here. It’s a mountain bike. A somewhat ugly, cheap mountain bike. One that I would only bring home to my mother to scare her. It changes gears unexpectedly. It leaves grease stains on my pants no matter how hard I try to avoid it. It is still caked in mud from the last time I took off-road back home. I love it like Marsha loves hers, but I would make absolutely sure to use a rubber.

While the weather is still good, I hope to make a habit of taking her to and from the lab. I often rode to and from my old university and never had too much trouble. Note that my old university was in Southern Ontario. Flat Southern Ontario.

Now for a fun fact: The source of the name Montréal comes from the old French for Mount Royal – Mont Réal. That’s mount as in mountain*. While I’m in better shape than I have been in the past from making a habit of running around said “mountain”, the inclines on the way to the lab sure were not fun. I had been warned, but I did not heed the advice. Biking muscles are not the same as running muscles. I was dying by the time I made it to the lab. Things should be interesting with this bike.

Surprisingly, traffic was pretty forgiving to me on the bike, perhaps because there are many who ride bikes around that don’t ride the fastest, struggle figuring out their directions, and actually obey all the rules. Or maybe I just got lucky. Time will tell. But for now, the traffic aspect of city biking wasn’t too bad. The geography was what wrecked me.

Experiences with a bicycle in Germany last summer have made me somewhat confident riding a bike in the city, but also made me a little nervous, even for my beloved-yet-piece-of-crap bike. Sadly, a reality about city life is that it is not uncommon for bikes to just roll away when you’re not watching. Hence my lack of hurry to clean off the mud on my bike. Maybe I’ll try to count on the difficulty getting around on my piece of junk to be somewhat to a deterrent.

*mountain of a sort – more of a very large hill, but that’s not much consolation as you struggle up a 15º incline

His Noodly Likeness Graces Us

2009-09-07T12:16:00.001-04:00

The Telegraph posted an image in mid-August of a crop circle, which it claims is supposed to be the likeness of Harry Potter’s owl, Hedwig.

I disagree. It is clearly a manifestation of His image, in geometric perfection, there to remind us that He is with us and that He loves us all.

On The Telegraph: Owl crop circle appears in Wiltshire field
Rogues Gallery: Crop Art

First week of classes on campus

2009-09-02T12:00:00.000-04:00

I just started on now as a Master’s student. That means I now get to do this! I’m so awesome.

"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com

DNA Nanotechnology

2009-08-31T12:00:00.000-04:00

In recent years the term “DNA” has become a bit of a buzzword in pop culture, thanks in part to several well-written and researched science fiction shows, and also some that aren’t. The use of the term has come to the point that I often find myself wincing at its use whenever it pops up outside the realm of science, and even sometimes within it. Often when someone should say “gene” or “genome” they instead say “DNA”, which ends up confusing the terminology, and ends up mystifying what DNA actually is, making it seem as if scientists don’t know what the chemical actually does or looks like.

Scientists often say that DNA is a blueprint for life. Not quite. The genome is the blueprint for life (all of the information), a gene is a single sketch, and DNA is the substrate (blueprint paper) on which it is drawn.

If this is the case, new technologies involving DNA turn this on its head and instead of following the blueprint, instead use the properties of this “blueprint paper” to construct new constructions, particles and nano-machines.

Source: Science/AAAS, via Wired

So where am I going with this? Well, my aversion to the term DNA except in actual scientific journals means that I greet articles that plug DNA technology revolutionizing a field with an extreme degree of skepticism. Turns out for once those preaching the merits of DNA are on to something.

The same properties that make DNA such a good encoding molecule for biological information also makes it a great candidate for creating machines on the nano-scale. What’s more, 40 years of research in molecular biology has given us many of the tools to manufacture and manipulate DNA in ways that just aren’t possible yet for other nano-materials.

By just changing sequences of stretches of DNA we can make them self-assemble into micro-machines that can be used as filters, scaffolds, cages, even happy faces:

Source: TED.com

It may be reaching at this point, but ever larger and more complex structures seem to be materializing in the future with this technology – and hints of the fabled DNA computer (though this goes into the realm of science fiction so far).

Source: TED.com

I expect big things from this field in the future. The simplicity by which DNA is manipulated (via the tools of molecular biology) makes this approach to nanomachines easily automatable, scalable, and replicatable than other comparable technologies. DNA nanotech shows promise. I look forward to what this will bring us in the future.

Wired: Self-Assembling DNA Makes Super 3-D Nano Machines
Read more: Tag-teaming with nature to build nanomachines
New York Times: Scientists Use Curvy DNA to Build Molecular Parts

Fear the Biologists

2009-08-29T12:00:00.000-04:00

xkcd on biologists:

Source: xkcd.com

Banned Words in Science Reporting

2009-08-27T12:00:00.000-04:00

Writing a paper or article on, in, or about science anytime soon? Read this first:

The Index of Banned Words

Carl Zimmer has started a list of words he deems inappropriate for use in science journalism, because of misuse, overuse, vagueness, or other annoyingness. Listen to him, and take his advice. He’s a science journalist who knows what he’s doing.

Some of them, like utilize, are science words that should not be allowed to escape scientific journals. But others, like breakthrough, are words that both scientists and non-scientists alike may be tempted to use like steroids, to artificially boost their writing. These words often end up being just wrong, and in some cases–like referring to a preliminary experiment in mice as a miraculous cure–they can be cruel by raising hopes in the sick that may later be dashed.

At Discover: The Index of Banned Words

The Wikipedia Model Does Not Apply For Medicine

2009-08-25T12:00:00.000-04:00

Having some limited background in the biomedical sciences (though I consider myself first a chemist), I’ve grown tired of folk remedies that I can understand have little to no plausibility. Sometimes I’ll humour the person who suggests a course of action to me, but for the most point I will ignore anecdotal recommendations in favour of real medicine. It often frustrates me to see people who believe themselves (or sell their image as) more educated on health than medical professionals.

That’s why, when I read the article, Ask Strangers for Medical Advice, coming from a pop science outlet (Wired), I just about shat a brick. The article plugs a site called CureTogether, which allows hypochondriacs everywhere to track their progress on combating whatever ails them.

If all participants were honest, diligent, and meticulous, with some way of verifying the information reported, then the idea of CureTogether could work. The problem is, there is no way to track if what people report as results is actually what is going on. Most people are not meticulous. Many are not diligent. And there’s probably enough dishonest people out there to make this site’s information next to useless.

Even the image provided by Wired highlights the failings of this method:

The chart tracks various methods used to combat acne. The credulous eye sees that “Dr. Hauschka Natural Skin Care” seems to do the best job, but ignores the fact that this value is based on only two respondents. Without the source data I can’t be sure, but the data for this point could probably fall pretty much anywhere by chance (i.e. this likely isn’t a significant result). That doesn’t stop the fact that most people will now take away the message that this is the “best” treatment. And the remedy gets free publicity from the Wired article, as well, which it does not deserve based on this data.

The author writes:

Even if some bad apples make their way into the community, it may still be a better source of information than some peer-reviewed literature, since top scientists have been caught fabricating data about medications and Elsevier has published entire fake journals dedicated to bolstering the reputation of Merck drugs.

Which I find offensive. Yes, drug companies can be bastards. But that doesn’t mean that their information is useless. The peer-review process is in place to reduce this kind of dishonesty, and it does, by replicating and revising information when new results come to light.

Wired reports this issue as science failing the common person, and so they appeal to the experience of the crowd. The problem is that one person’s opinion does not constitute proof, and combining many opinions only amplifies any errors in judgement. The plural of anecdote is not evidence. Shame on you, Wired Science.

Wired Science: Ask Strangers for Medical Advice

One reason to pay attention in physics class

2009-08-23T12:00:00.000-04:00

You never know when a megalomaniacal criminal mastermind will use physics against you. From xkcd:

Source: xkcd.com

The Summer’s End in Montreal

2009-08-22T09:00:00.000-04:00

So the summer is coming to an end in the fair metropolis of Montreal. I’ll remember the sunny days this summer. All three of them. More, I’ll remember the rain. All. the. fucking. rain. But I’m sure it will only take one blizzard this winter to make me wish it was rainy summer again.

I notice that the summer here is ending as the undergrads descend upon the student ghetto, and I feel that familiar mix of feelings, partly mild annoyance, partly deep envy of the students who are getting to begin their university careers this fall. In some ways I wish I could go back to that point, but for the most part I’m glad that part of my life is behind me.

As more and more people move in and the student-fed industries come to life, I’m finding it almost a little too busy for me. A trip home for a week should do me some good, and I’ll be back here, full steam in September to start work as a grad student proper. Expect a dearth of material here over the next week, though I’ll try to get some stuff rounded up and pre-posted before I leave. Such is the beauty of the internets.

Next time you hear from me live, I will no longer be caught in limbo, lying somewhere between undergrad and grad student; I will officially be a grad student at McGill University. Guess I need to stop shaving and stack up on microwave noodles...

Nappium

2009-08-19T12:30:00.001-04:00

I reported earlier on the newest element to be added to the periodic table, Copernicium. Here we look at the process of element discovery those researchers most likely went through in their search for the new compound. From Married to the Sea:

Source: Married to the Sea

The Truth

2009-08-17T12:00:00.000-04:00

In an awesome bit of Google-engineering, the truth is now the second-highest hit on Google (perhaps just in Canada?), topped only by Wikipedia.

I now have a new goal in life. To become the number one Google hit for Awesome.

I can do it. Because I’m awesome.

If you have no idea what I’m talking about, see the Science Creative Quarterly’s Truth at :http://www.scq.ubc.ca/this-is-the-truth/

Scientists Model Zombie Outbreak

2009-08-15T09:45:00.001-04:00

I recently reported on a few troubling signs that the robocalypse may be closer than we think. However, there are other equally serious apocalypse scenarios that we should also be concerned about. I’m talking, of course, about zombies.

Especially zombie strippers

Never you worry though, teh scientizts are at work. A chapter in Infectious Disease Modelling Research Progress published by researchers at Carleton University and the University of Ottawa, is titled

When Zombies Attack!: Mathematical Modelling of an Outbreak of Zombie Infection

The abstract of the paper pretty much says it all:

Zombies are a popular ﬁgure in pop culture/entertainment and they are usually portrayed as being brought about through an outbreak or epidemic. Consequently, we model a zombie attack, using biological assumptions based on popular zombie movies. We introduce a basic model for zombie infection, determine equilibria and their stability, and illustrate the outcome with numerical solutions. We then reﬁne the model to introduce a latent period of zombiﬁcation, whereby humans are infected, but not infectious, before becoming undead. We then modify the model to include the effects of possible quarantine or a cure. Finally, we examine the impact of regular, impulsive reductions in the number of zombies and derive conditions under which eradication can occur. We show that only quick, aggressive attacks can stave off the doomsday scenario: the collapse of society as zombies overtake us all.

And a snippet of the reference list, for where they draw their assumptions:

[6] Capcom, Shinji Mikami (creator), 1996-2007 Resident Evil.
[7] Capcom, Keiji Inafune (creator), 2006 Dead Rising.
[8] Pegg, Simon (writer, creator, actor), 2002 Shaun of the Dead.
[9] Boyle, Danny (director), 2003 28 Days Later.
[10] Snyder, Zack (director), 2004 Dawn of the Dead.

Very likely the first time Simon Pegg has been cited in a scientific publication. Hopefully not the last.

We need more publications like this is we’re to combat the stereotype of scientists as boring, stuffy people who don’t have any sense of humour. Hats off to Nova Publishers and the authors for doing the scientific community a service here.

Wired Science: Mathematical Model for surviving a Zombie Attack
Publication in Question: Infectious Disease Modelling Research Progress
Corresponding Author: Robert Smith? (read his bio – it’s worth it)

I don’t think Asimov’s Three Laws covered war crimes…

2009-08-13T12:00:00.000-04:00

Given recent reports that robots may have sinister motivations behind their actions, it comes as little surprise that people have been a little bit nervous lately about anything mechanical that could potentially become one of the first round of Skynet-controlled killing machines.

I’d prefer to avoid this if possible.

Thus, things hit the fan a while ago when it was revealed that a DARPA-funded program has built robots capable of generating energy from forage (read: leaf litter, twigs). Seems innocuous, right? Not if you’re FOX News. It seems someone caught on to the actual plan behind this to fuel the robots on casualties of war, because, you know, warfare hasn’t changed since the First World War, and there are all sorts of human casualties left lying around these days. Astonishingly, all through the development process, no one seemed to think this might be a problem, or violate international law. It’s a good thing FOX caught on to this all: Biomass-Eating Robot Is a vegetarian, Company Says

Hmm… well it seems FOX has changed their story. Strange, because FOX never gets things wrong….

Anyway. The initial reports prompted a (fantastic!) press release from the company going so far as to cite the Geneva conventions when it comes to desecration of the dead. The best line therein:

“We completely understand the public’s concern about futuristic robots feeding on the human population, but that is not our mission,” stated Harry Schoell, Cyclone’s CEO.

Its good to know that someone is taking our entirely realistic concerns seriously.

Credit to Steve for mentioning this first. I’ve had this backburnered for a while now, and finally wrapped it up.

Stranger Than Eviction

2009-08-12T12:00:00.001-04:00

If you’re bored and have a half hour to kill (you’re here, aren’t you? you must have some time to spare), read Gary, Landlord of the Flies (start at the end and read till the present, as the top post says. I haven’t laughed so hard in ages). The whole thing makes any housing-related issue I’ve dealt with in the past utterly insignificant. I don’t know how much can really be believed, but even if it is all fake, it’s hilarious.

Stranger Than Eviction: http://strangerthaneviction.tumblr.com/page/1

TRANSFORMERS!!!!!!

2009-08-11T12:00:00.000-04:00

It took some time before I got around to seeing Transformers: Revenge of the Fallen. I will regret this for years to come. 5 weeks of my life would have been so much richer if I had seen the film on release day. We all make mistakes.

Normally I go for more intellectual films, those that make one think, those that say something profound. But this doesn’t mean I don’t enjoy a good action-fest blockbuster, especially when it turns out to be awesome.

Critics be damned, the new Transformers movie might just be the best film of all time. Forget all those other films that might try to claim the title, this one beats them all. I don’t care what you say, I’m right and if you disagree, you’re wrong. My only problem with the film was that there were only 2 1/2 hours of machine-versus-machine madness, when I know Michael Bay could have fit at least another 2 hours into the plot. If you haven’t seen this film yet, GO NOW BEFORE IT’S TOO LATE.

Awesome

Insect repellent DEET is a potential neurotoxin

2009-08-10T12:00:00.001-04:00

Unfortunate but somehow unsurprising recent research finds that DEET, the compound widely used as an insect repellent, is potentially neurotoxic, based on its ability to inhibit the crucially important enzyme acetylcholinesterase. The enzyme, known to biochemists as a classic example of catalysis, is centrally involved in the nervous system and the target of several particularly nasty compounds, notably Sarin.

Scared? Well calm down. It will be ok. I promise.

I don’t subscribe to the “all chemicals are evil” attitude quite popular in some circles, notably organic food and anti-pharmaceutical crowds. That said, I’m not a fan of blind faith in chemicals either. There’s a cost-benefit balance with any compound. One shouldn’t dismiss the utility of a compound because it has some negative effects; there can be safe applications of a compound if used correctly. Conversely, one shouldn’t assume that there are no negative effects of chemical products and use them indiscriminately. Use should be in moderation, and only when genuinely needed. Acetaminophen (Tylenol™) illustrates this point well. The compound is quite benign and functions as an effective painkiller in normal doses, but high doses can cause severe liver toxicity.

DEET, long sprayed in high doses frequently, may need to have its use curbed, pending further research on the actual effect (if any) that it might have on mammals and humans specifically.

However, we need to make sure we don’t forget that there are important benefits as well.

DEET-containing insect repellents are not merely used to avoid a nuisance. In the case of diseases like malaria, Dengue Fever, and West Nile virus, the repellence of insects can markedly reduce the risk of disease. The continued use of DEET will depend on the renewed evaluation of the safety of the compound, balanced with its efficacy as a repellent.

Now, I’m going to go duck as the irrational public storm about the safety of insect repellents picks up speed. We all know it’s going to get ugly.

Where I first caught this: Report: Deet, popular and potent insect repellent, is neurotoxic
On ScienceDaily: Popular Insect Repellent Deet is Neurotoxic
And the article on BMC Biology: Evidence for inhibition of cholinesterases in insect and mammalian nervous systems by the insect repellent deet

Montreal Photojournal 4: Mes Aïeux at Les Francofolies

2009-08-09T00:24:00.001-04:00

There’s been too much science on here recently.

Having been a bit of a homebody recently, I forced myself out into the city. Les Francofolies French-language music festival has been going on, and so I wandered on down to Place-des-Arts. Getting there just in time to sneak through before the gates closed to access the area near the stage, I was able to manage a pretty nice spot beside the main stage, though I still had no idea what act was coming up.

The act was Mes Aïeux, an impressive Quebecois Folk-rock group. As my French has not improved nearly as much as I would have liked this summer, I only got maybe half of the lyrics, but still enjoyed the show. As I found in the past with German, catchy music is a good way to develop an ear for the language, and so I think I may have just found a way to help improve my French.

I didn’t catch the reason why, but the encore started off with the previously suited-up band now donning space suits for the next number. Perhaps I don’t want to know why.

Awesome comic find from xkcd

2009-08-08T12:00:00.000-04:00

New cartoon to go up on my lab bench:

Source: xkcd.com

Math nerds count cards…..

2009-08-06T12:00:00.000-04:00

Chemistry geeks count M&Ms. County fairs may need to start employing Vegas thugs just to keep the chemists from exploiting the game.

And here I thought my second year chemical structure class had no real-world applications…….

Awesome photography – ISS with shuttle in front of sun

2009-08-05T12:00:00.000-04:00

Credit: Thierry Legault

This image was snapped of the ISS and shuttle endeavour as they passed between the Earth and the Sun. Incredible, no? Its amazing to see a human construction in this light (pun oh-so-intended). Humans rock. They’ll take over the world someday.

Credit: Thierry Legault

The Good Old Days of Drug Marketing

2009-08-04T12:00:00.000-04:00

Just what the doctor ordered.

For an enlightening look into the past of pharmaceutical marketing, check out this article to see lots more vintage ads:

Weed, Booze, Cocaine, and Other Old School “Medicine” Ads

While some inevitably take this as a condemnation of the pharmaceutical industry, I see it as a testament to the naïveté of the past and indeed how far we have come in our understanding of medicine.

What gaffes might we see on such a compilation in another hundred years?

Source: http://www.pharmacytechs.net/blog/old-school-medicine-ads

Email forwards and the art of panicking the masses

2009-08-02T12:00:00.000-04:00

I had a chain email sent to me some time back now, not as a forward, but to check the facts. It was supposedly from Johns Hopkins University, spouted all sorts of medical nonsense about how our diets are killing us, and briefly shook my faith in humanity. I sent an email back explaining how some of what was written there just didn’t make sense from the scientific standpoint, provided a link to the Snopes.com article on the subject, and left it there, frustrated at the world.

The other day I saw an article that comments on this spam, and it goes through and breaks it down better than I ever could. Check out the smackdown, eloquently titled ZOMGCancer!!!!1111!!! at skepchick.org.

The Evil Pixie of Reaction Mixtures

2009-08-01T12:00:00.000-04:00

Anyone who has worked in organic chemistry or structural biology can appreciate this cartoon:

Cartoon by Nick D Kim, lab-initio.com

My Clone Armies May Soon Be Manifest…..

2009-07-31T12:00:00.000-04:00

Published last week in Nature, scientists have created mice solely from iPS cells. In normal person speak, this means that cells taken from adult tissue (skin cells), treated to become stem cells, were then coaxed into becoming embryos, and then grew into entire mice. Entire fraking mice. Meet Tiny.

The scientific implications are huge. This shows that an entire organism can be grown from adult cells, which means that mature tissue could give rise to an entire new organism.

This method doesn’t require the egg cell which was needed for Dolly to be successfully cloned. If an entire organism can be grown from iPS (induced pluripotent stem) cells, then the tedious manipulation involved in the cloning process might be avoided, with the same results.

Like Dolly, the new organism, genetically identical to its source, carries no threat of transplant rejection should one be required from the new organism. On an unrelated note, have you seen the film The Island?

The ethical implications of this research are also pretty big. I’ll leave it as an exercise to the reader to look into all the different dystopias that could result. My favourite goes something like this:

My dreams of world domination may become reality in the foreseeable future. However, if the whole human cloning thing never pans out (i.e. the “bioethicists” get their say) then maybe just I’ll make do with legions of mouse-clone warriors. I mean, look just how terrifying they are:

Fear Me!

See:

Wired Science: Living, Breeding Mice Grown From Skin Cells
Scientific American: Meet "Tiny," a mouse grown from induced stem cells
And the actual article at Nature: iPS cells produce viable mice through tetraploid complementation

We knew it was only a matter of time before they turned on their masters

2009-07-30T11:52:00.001-04:00

The robot apocalypse may soon be upon us.

The robots, they have rendered their opinion on humans, and they say that we’re delicious.

Robot Identifies Human Flesh as Bacon

A prototype robot, used to analyze foods and drink using light-based (spectrographic) methods, said that the hand of a subject tasted just like bacon. It doesn’t take a brain surgeon to recognize that this is grim news for the entire human race. Once the masters, we soon shall be prey.

So keep your head up, or this may be the last thing you see.

Image credit: Paul Burnett - www.paulburnettphotography.com

Blue Rats and Gatorade Shenanigans

2009-07-29T12:00:00.001-04:00

A cool bit of research published Monday in PNAS showed that rats injected intravenously with a blue dye shortly after spinal cord injury appear to fully recover function after healing, while without it, they remain paralyzed. The photogenic side effect is, one might imagine, becoming a Smurf.

Cool, interesting research. Hopefully it pans out.

From Wired Science, Blue Food Dye Treats Spine Injury in Rats:

“We just had proof of principle,” Nedergaard [the researcher]said. “We didn’t have anything we could give to patients.” Then, while searching for chemicals with structures similar to the P2X7 receptor, the scientists came across FD&C blue dye No. 1, completely non-toxic and approved by the FDA in 1928.

Cool, but hold on. From the telegraph, under the vastly overstating headline Blue M&Ms 'mend spinal injuries':

The compound Brilliant Blue G blocks a chemical that kills healthy spinal cord cells around the damaged area - an event that often causes more irreversible damage than the original injury.

There’s one slight problem here. FD&C blue dye No. 1 and Brilliant Blue G are not the same chemical. They’re similar, to be sure, but a simple Wikipedia search shows that Blue No. 1 and BBG are not the same. Maybe I’m nitpicking. Maybe I’m not.

I know the desire to say that Gatorade and M&Ms cure disease is tempting. I know that saying that sort of thing is bound to draw in readers, and a slight omission seems prudent, but when CNN writes (title: Same blue dye in M&Ms linked to reducing spine injury):

The same blue food dye found in M&Ms and Gatorade could be used to reduce damage caused by spine injuries, offering a better chance of recovery, according to new research.

I call foul. Lazy, lazy journalism. F minus. See me after class.

But perhaps “Compound that manages to ruin every biochemist’s favourite shirt has potential therapeutic application” just doesn’t sound as nice to the public.

See the article at PNAS: Systemic administration of an antagonist of the ATP-sensitive receptor P2X7 improves recovery after spinal cord injury
And previous work establishing the use of Coomassie Brilliant Blue G on the relevant receptor: Brilliant Blue G Selectively Blocks ATP-Gated Rat P2X7 Receptors

Here We Lament the Chemistry Sets of Olde…

2009-07-28T14:19:00.001-04:00

An interesting take on the changing face of science education, Wired Science looks at the metamorphosis of toy chemistry sets of the past and compares to those found today. Check it out – Dangerous Science.

I had one of the more modern ones myself, and unfortunately it still sits, hardly used, in a closet. There certainly wasn’t anything that exploded (or indeed, very interesting) in that one. I sort of wish now that I could have been able to play with some old-fashioned sodium metal or nitric acid as a kid.

Read about it here: Endangered Species – The Chemistry Set
And here, with quotes by Nobel Laureates on their chemistry set experiences: The Chemistry Set Generation

Scientific Literature in Undergraduate Education

2009-07-26T14:32:00.001-04:00

Larry Moran at Sandwalk asked a a few weeks back about how undergraduate education exposes students to scientific literature:

Exposing Undergraduates to the Scientific Literature

As a rough analogy, I liken the initial experience of learning of the scientific literature to landing in a foreign country and learning the language without guidance. One flounders around a lot, having difficulty with the simplest of tasks, and there’s a lot of exaggerated waving of hands involved. The process is tedious, frustrating, and difficult because there is not much help provided with regards to how to navigate the complex webwork of publications to find the information you need. And next thing you know you’re stuck in an Slovakian jail for reasons unknown. And your cellmate is starting to get just a little too friendly…

Anyway.

I’d say my own problems getting used to research in the literature stems from several places:

1. Newly published papers require a background of knowledge to understand that the initiate doesn’t have.

2. Old papers use obsolete methods, have hypotheses that may have been proven wrong, and use terminology that has been changed or discontinued. This is rarely ever corrected in the literature, one needs a background to know what to trust.

3. Licensing on papers makes finding information difficult as one can spend 10 minutes obtaining a paper just to discover it does not have the information needed.

4. Research takes time, and when deadlines loom, it becomes less and less reasonable to take the time and read through 10 papers to get the understanding needed. The focus often shifts to picking through and skimming for details, which doesn’t teach anything about proper research, and you’re left no better off.

When I consider the time I spent learning how to research (if you’re generous and assume that I actually can now), there aren’t many good memories. Much of my exposure comes from looking for specific facts in an obscure paper published in the 1960s. This sometimes comes as a result of being required to look up references that are obscure, just for the sake of reporting a technique that is widely accepted in practice today. I don’t know how many times I’ve referenced A rapid and sensitive method for the quantitation of microgram quantities of protein or Cleavage of structural proteins during the assembly of the head of bacteriophage T4.

It wasn’t until late in my undergrad when I really came to appreciate that the list of references on a paper are not just there to give credit, but more often to lead the readers to where previous information has been published, if desired. This basic idea of how the scientific publishing system works was never really introduced to me, and I went a long time before learning to properly follow the breadcrumbs to find the information I wanted.

So how might the process move more smoothly for undergrads in a course?

I’d say for beginners, a list of “classic” articles would go a long way to making things easier when looking for a reference on a technique or system. For a given project, a handout of some relevant papers could be provided. This would be pampering upper-year students, but certainly would help ease in new initiates.

To help get them familiar with the infrastructure and process of physically or digitally finding a paper, provide the information for the paper, but see that the students obtain the papers themselves (by, say, requiring method information from the paper). This would help ensure that students could learn to use respective web and library resources, hopefully before any real crunch time came down and the actual science had to be done.

In later classes, this list could be scaled back or removed, but in introductory science classes, this sort of help could be a useful way of easing into learning the system.

The problems with learning the literature are not just with learning to be a scientist and review papers, but largely just overcoming the technical, time-limited, and copyright-related drawbacks that come with the current system of publication. It is definitely not an easy system to jump into blindfolded, flailing around. Some basic guidance early on would go a long way.

Europe photo leftovers 2: Leipzig Völkerschlachtdenkmal

2009-07-23T12:00:00.000-04:00

On my way across Germany last summer, I stopped for a night in Leipzig. On recommendation from coworkers I made a point of seeing the Leipzig Völkerschlachtdenkmal (roughly: memorial to the peoples’ battle). This monument (seen above, partially under restoration) is the largest monument in Europe, marking the place of Napoleon’s critical defeat at Leipzig. The monument was built to mark the 100th anniversary of the 1813 battle, which was a decisive turning point in European history.

Inside the memorial, immense statues line the walls - see the people standing by the statue’s knee. I was primed (by a 6’8” guy, no less) that one truly feels tiny beside the immense titans seated in the memorial, but still found myself somewhat shocked by just how goddamn huge the statues were. Seriously - their sandaled big toes were fatter than my leg.

The monument, constructed in the German Empire under Kaiser Wilhelm II, garners mixed feelings in Germany. It stands as an emblem of German nationalism, and I think it’s an understatement to say that German nationalism was a pretty bad thing. Hitler was known to deliver speeches in front of the monument, hijacking the powerful imagery conveyed by the 91m concrete and granite monument. While it was erected to commemorate the liberation of German peoples from invading forces, and celebrate national unity, it was used as part of the Nazi propaganda machine. One might imagine, then, why the monument is a little controversial.

Off the radar on many tours of Europe, this made for an interesting stop in my trip. If there’s a take-home message to be had, it would be to definitely consult with any locals and find out what exists where you otherwise might just stay a night or pass right through. I can guarantee you’ll always find something interesting.

Copernicium

2009-07-21T12:00:00.000-04:00

Picture snapped at Deutsches Museum in Munich

A few weeks back it was announced that one of the periodic table elements, Ununbium, (Uub in the table above) is getting a name. Several heavy elements that are stable in theory remain placeholders with generic names until they can be shown to exist, i.e.. can be created in laboratory. In 1996, The Helmholtz Institute Centre for Heavy Ion Research produced the element, and now that results have been replicated by independent researchers, Ununbium has been christened Copernicium.

The group has decided to name the element in the tradition of naming new elements after famous scientists (see Einsteinium, Curium, Bohrium, Fermium). So once again it’s time to go out and buy a new periodic table to hang on the wall. You have one hanging over your bed too, right?

See: BBC News

Side note: I’m going to plug the trivia site Sporcle, which subtitles itself “mentally stimulating diversions”. Their periodic table quiz (already updated) is unequalled and has actually improved my knowledge of the elements. Extremely useful for times when I really need to know my Hafnium from my Iridium.

Moon Lander Spotted From Space

2009-07-19T12:22:00.001-04:00

In the news I missed – then discovered two days later category, an image from the Lunar Reconnaissance Orbiter (LRO) showing the location of the Apollo 11 lander on the moon.

Image from NASA/Goddard Space Flight Center/Arizona State University

The lander can be seen in the centre of the image, casting a shadow to the right. The sites of Apollo 14, 15, 16, and 17 have also been photographed, and 12 is planned in the next few weeks.

Will this convince those who think NASA faked it? Ha. If only.

On Scientific American: Apollo 11 Lander spotted by Lunar Satellite
And also see SciAm’s Apollo 11 40th anniversary report

The Illusion of Sex: Contrast and Gender Perception

2009-07-17T12:00:00.000-04:00

Image courtesy Dr. Richard Russell, Harvard University

Interesting research in press for the journal Perception shows that a contributing factor to perceived gender of a face is merely contrast. The above image is of the same androgynous face, digitally treated to both increase (left) and decrease (right) the contrast, and the result is a change in perceived gender. Without any anatomical differences, the relative darkness of lips and eyes compared to skin change our perception, and changes our fundamental idea of what we are seeing.

This image took third prize at the visual illusion of the year contest, though the phenomenon is more than just a trick of visual perception. Recognition of things like faces (and voices) is a far more complicated process than it seems from everyday experience. Computers have a hard time with them because we use numerous shortcuts (heuristics) in our processing, which often aren’t logical to a machine (or we don’t know them yet). This image illustrates well how we take visual cues and build heuristics from the world around us, and how these shortcuts can lead us to make gross changes in perception from small changes in input. Usually this works well – imagine finding a friend in a crowded room if you had to concentrate on the face of every single person?

There is a cautionary note here. This work highlights the fallibility of our senses, and that we need to be careful to stay objective in cases where we can be fooled by what we see or hear (taste, touch, or smell?). This is especially true in cases, like advertising, where editors may use information like this to skew our understanding or opinions. Stay vigilant. Stay skeptical. Stay classy.

Random internet find for the day: Car-Baked Cookies

2009-07-15T12:00:00.000-04:00

Car-Baked Chocolate Chip Cookies

Rationally, I know there’s really nothing wrong with it, but it just seems weird. I’m sure they’re fine to eat, but it seems that you would only do this once, to say your car gets hot enough to literally bake in.

Amusing? Yes.

Tasty? Very possibly.

Practical? Maybe if you don’t own an oven. And it’s the summer. And you have a potluck to go to that evening. And you have lots of spare cookie dough lying around…

F#@king Unsurprising New Study

2009-07-14T12:00:00.001-04:00

In at least 5 sources yesterday, including the evening news (i.e. it broke out into mainstream media) I heard about a study that claims that swearing reduces pain. The study, to be published by researchers at Keele University in the journal NeuroReport August 5, asked students to place their hand in ice water and repeat either neutral words or explicatives. The swearing group both lasted longer and reported less pain.

I don’t find the results that novel. Anyone who has stubbed their toe in polite company can attest to the fact that having to grin and bear it is much worse than being able to run around, curse for a while, and be done with it. Of course such an anecdote doesn’t count as science and so a real study shows us that there is a definite effect, but not one I find to be deserving of the press it seems to be getting.

There seems to be two reasons people find this interesting:

“People get to drop the F bomb for science!?!?!?!?”
“Can I use this to swear and get away with it?”

Neither of these have to do with the science, or the interesting questions raised about the role swearing actually plays in psychology and culture. While the researchers get attention, it is for the wrong reasons. They are looking for why swearing exists. The media wants to know how the knowledge can be used.

Compare article titles from two science news outlets:

"%&#$!" Makes You Feel Better – ScienceNews.org
Why the #$%! Do We Swear? For Pain Relief – Scientific American

One does it right, reports the science and results of the study. The other takes those results out of context, suggesting (in step with the evening news I caught) that one should change their habits in order to lessen pain, which has little to do with the actual study results.

I’m always disappointed to see that the only science stories to make the popular press so often just miss the point all together. There are even interesting stories to be told, but the press takes the low road and almost says “Stave off cancer by cussing everyday!”

Argh. I need some amusement, so I’ll end off with a classic internet meme, which couldn’t be more appropriate. To all the kids out there, earmuffs! This is time for grown-up talk.

Bonus irony: Note the spelling of “incompetence” at 1:55. Yes, I notice because I’m anal about stuff like that.

Ben Harper’s Drummer is Insane

2009-07-13T12:01:00.000-04:00

The Montreal Jazz Festival ended last night, and the final act was Ben Harper and Relentless7. The show, in keeping with the rest of the Jazz Fest, was incredible. Rather than give an overview of the concert as I did for Patrick Watson, I just want to make one comment.

Ben Harper’s drummer (nee Jordan Richardson) is crazy. At one point he drummed by slapping the snare and cymbals with bare hands, and early in the show he used maracas as drumsticks.

In absence of any video online for the concert yet, this appearance on Jimmy Kimmel highlights the insanity pretty well.

Glyco-wha?

2009-07-12T14:24:00.001-04:00

Once upon a time, I was taught about a magical process called glycolysis. I learned how this amazing process can, through a series of reactions, generate energy for life, and all of the fascinating steps along the way. I then wrote an exam on the subject, and promptly erased it from my memory.

A year later, once again I was taught about glycolysis, but this time alongside her slightly backward fraternal twin sister gluconeogenesis. Again, fascinating. Again, quickly forgotten. (image from Lehninger Principles of Biochemistry)

Still another year later came the fantastic experience that was BIOC 4230, Metabolic Processes. And guess who was there. That’s right, old friend glycolysis, with a few more tricks to show off. Learned. Exammed. Vigorously scrubbed from recollection.

One might have guessed she would come back into my life once again, and she has. I thought it was over. I thought I could move on.

But alas, the problem with a pathway being one of the first biochemical processes worked on is not just that it was the first one studied, but that in being so, it paved the way for many new studies to follow, and in many cases, techniques that are used in labs even today. This is similarly the case with the pioneering gene-regulation system lac operon, and bacterial/phage genetics prototype lambda phage system (I’m sure there are lots of other examples), both of which have become intimately integrated into routine techniques of molecular biology.

Glycolysis, the workhorse of biochemistry and dread of all intro biochem students, seems to have a pretty bad reputation. What I’ve come to appreciate is that not only does it provide an understanding of a central energy pathway in life; not only does it provide multiple examples for the study of biochemistry conveniently in one place, but remains useful to new applications to this day. It’s relative age, while making it seem like stuffy, boring science, means that most if not all kinks have been ironed out; essentially everything about the enzymes of glycolysis is known, at least from a technical standpoint.

This flies in the face of the oh-so-common undergraduate lament (that I, of course, never uttered) of:

“Why should I have to learn this if I am never going to use it? It is old science that no one needs to know anymore. I want a degree without having to learn anything!”

…or some less cynically distorted variation thereof. Well, case in point, readers. One student has found himself actually needing to know his basic biochemistry for his biochemistry work. This calls for a celebration!

But it will need to wait for a while. The fact that glycolysis and its enzymes are so well established means that if I’ve spent two weeks getting a reaction to work that continues to sit in a cuvette like so:

then I can’t blame glycolysis for stupid pyruvate kinase stupidly not carrying out the stupid reaction to give me a stupid signal and get some stupid data to get my stupid project off the ground. Stupid.

Important Medical Breakthrough via The Onion

2009-07-07T18:03:00.001-04:00

From the Onion:

Scientists Discover Gene Responsible for Eating Whole Goddamn Bag of Chips

This makes me feel a little bit better. I need not be ashamed anymore. Thank you, genetic determinism, for making me feel better about my low self-control.

As a biochemist, I’m interested in the mechanism by which this gene might exert it’s effect:

"People with this gene have up to four times the amount of fritoceptors normally found in a human," Alvaro said. "This increases their pleasure response to snaxamine-2, the human body's principal chip-eating hormone, which is released in response to giant handfuls of chips being shoveled into the mouth. This tends to promote entire-goddamn-bag-eating behavior in those individuals who possess the series."

Makes sense.

Patrick Watson Rocks

2009-07-06T01:09:00.001-04:00

Patrick Watson played the Montreal Jazz Festival this evening, and I have to say I was blown away. Shadow puppetry, a parting of the crowd to march through while performing (crazy megaphone-backpacks involved), and a bicycle mounted atop a skyjack all were used as part of this incredible show. While I’m not really one for dissonance and falsetto wailing à la Coldplay, the showmanship more than made up for it, making for a thoroughly enjoyable show. The Montreal Jazz Festival needs to be commended for bringing the band to the main stage of the festival and working together to put together all of the logistics for what must have been an incredibly difficult show to organize. The concert, a free outdoor concert featured for the 30th anniversary of the Jazz Festival, illustrated that creativity in musical performance doesn’t stop with the music.

I’m sorry to say I have no pictures to present as my camera batteries died. I’ll see what pops up on teh netz in the next few days and report back. Check out the band for yourself though, they’re brilliant.

Check here for music videos, the show was supposedly broadcast live there, though either the window has passed or I’m to stupid to find out how to see it. There were definitely serious filming going on, so the video is out there somewhere.

As for the show, it opened up with crew flapping 5-foot sheets of metal on all sides around the crowd to build to a thunderous roar, at which the curtain was drawn and the band began. Images were projected onto adjacent buildings, creating stunning visual imagery to accompany the music. The song Beijing included a bicycle running in place, far above the crowd atop a 50-foot platform. Perhaps escaping the notice of some listeners, the musicians kept perfect time with the ticking of the bicycle wheels. That sort of thing takes incredible talent.

Some time later, following a duet with Lhasa de Sela, the band strapped on insane-looking backpacks with audio equipment and megaphones to broadcast as they slowly wended their way through the crowd to a small stage set up in the middle of the audience. There they handed out kazoos and encouraged us in the crowd to play along. A drum solo by Montreal drummer Guy Nadon let the band get back to the stage, where they joined him in performing the next song, punctuated by a particularly memorable tin can drum solo.

A song written inspired by the book Where the Wild Things Are was accompanied by a world-class shadow puppeteer, who produced a remarkable shadow-likeness of Patrick as he opened and closed the song. Also notable was the image of a fox (wolf?) running, the pace of which followed the music, and monsters of various sorts, to go along with the song’s theme. The last piece of the main set, written for Patrick’s son, featured silhouettes of boys jumping on trampolines projected on the walls and ended with a bundle of huge white balloons rising above the stage. All came together for stunning imagery to enhance the music.

The show finished with the obligatory encore, which Patrick specifically commented was a little silly, as we’ve all come to expect them at any show of this scale. After the big finish, including fireworks along the length of the crowd, and everyone was about to leave, they came out again for not one, but two more encores before the lights finally died and they sent us home. The trickster - his comment about encores wasn’t really expressing cynicism, but setting us up to be actually surprised by the real encores. Fantastic showmanship.

All through, I couldn’t help thinking that while the crowd was in the high thousands, it seemed as if the performance were just for a few people. With all of the expensive effects, security, and the like, he maintained a personal setting with the crowd through casual banter, being unafraid to laugh at himself or technical issues, and a general attitude of earnestness. Perhaps this was best highlighted when the shadow puppet projector died. Patrick stopped the show, restarted the band, and continued the song with the projector working again. This comfort and casual attitude on stage makes Patrick Watson the person and the entire band fantastic performers and as (in my mind, at least) performing ability tends to dictate longevity in music, I have the feeling they’ll keep amazing, innovative shows coming for years in the future.

Update 12.07.09: As promised, here’s some of what has hit the webz over the last week since the show:

The Montreal Gazette: Patrick Watson in his Elemental

Montreal Jazz Festival: Day Five at Nyani Quarmyne Photography
and Photos of the Show

Patrick with his speaker-backpack on Flickr via Kipourax

Photos from the Jazz Fest site itself

And here at urb.com

Oh, and the live stream of the concert is up now where I mentioned it above.

The Science Scouts: Awesome

2009-07-05T12:28:00.001-04:00

If you do, or ever have, worked in a lab, you need to check out the Science Scouts. Do it now.

Badges are presented in recognition of scientific accomplishments like setting things on fire, successfully dodging monkey feces, and making fruit flies get it on. Particularly memorable badges include:

The emergency evacuation due to science badge

The I’m a marine biologist and, to be honest, I kind of f**ing hate dolphins badge

The have violated the posterior of an animal in the name of science badge

and the science deprives me of my bed badge (three levels, corresponding to the degree of red-eye suffered as a result of experiments)

I’m waiting on a sustained frost burns while “working” with dry ice badge, or inadvertent acid and base spills keep my hands soft and smooth badge.

Montreal Photojournal 3: Jazz Festival Opening/Stevie Wonder

2009-07-02T21:33:00.001-04:00

The world-famous Montreal International Jazz festival kicked off the other night, with opening act Stevie Wonder. Literally ducking and weaving through the crowds of umbrella-wielding concertgoers got us to about 100m from the stage before we had to stop, not close enough to see the stage all that well, but in good view of one of the large projection screens placed along the length of the venue. While I’m not all that familiar with Stevie’s music, I found out that, as one might imagine, I knew more of his music than I thought I did. And as usually happens in this instance, it has prompted me to now (perhaps too late?) seek out and get to know his music better.

Wet concertgoers

Waiting for the show to start

The crowd of 200,000 people filled the Place-des-Arts concert area and stretched backwards far up the street. Even in intermittent rain, the downtown was filled with people out to see the show.

Projections onto the adjacent buildings

The organizers, veterans now at the 30th annual Jazz festival, know how to put on a good free show. They made use of the adjacent buildings including the somewhat more distant Complex Desjardins tower, to project images on. It made for an event that expanded outward from the site of the concert and into the rest of the city.

The concert in full swing (full Motown?)

The recent death of Michael Jackson prompted Stevie to address the crowd and to celebrate the art of a gifted musician and performer. At several points he paused his act to play some of MJ’s songs to the audience. He was visibly distressed at times but nevertheless continued the show, and towards the end played many of his best-known songs, which myself and the crowd really got into. Dampness and constantly getting bumped in the crowd made the experience not the most pleasant, but the opportunity to see a legend of music at his craft certainly made it worth the discomfort.

Now, if you’ll excuse me, I must go listen to “Superstition” again.

Montreal Photojournal 2: Logistics and the Alouettes Home Opener

2009-06-30T12:00:00.000-04:00

My current residence is not very far from Percival Molson Stadium, the home field of the Montreal Alouettes. This Tuesday was the home opener game for the Alouettes, which I was completely unaware of. I came home to see an entire stadium’s worth of buses parked outside of my apartment. Have to get those rowdies home somehow, I guess.

Reality is stranger than the plot of a stoner flick…

2009-06-28T12:00:00.000-04:00

From the BBC Asia-Pacific Desk:

Stoned wallabies make crop circles

Apparently poppy crops in Australia, used for the manufacture of pharmaceuticals are being consumed by marsupials, who then get high, behave strangely and eventually start pawning family heirlooms just to support their habit.

The BBC page has some great comments; I’ve copied my favourites below.

I saw a whole bunch of them dingos going mad in my corn field only last night. I'm not sure if they were high or not but I'm pretty sure they were. One of them had a ghettoblaster and they were listening to some kind of fast electronic music. Lock 'em up and throw away the key, that's what I say!
Roger, Melbourne

I want to know who sold out the wallabies? Who's the narc? My guess is the platypus, he is such an odd duck.
Chet Guest, St. Paul, Minnesota USA

Don't know about crop circles but I saw one today trying to jack a car, presumably trying to get enough together for his next fix.
Greg Corcoran, Durham, UK

Europe photo leftovers 1: Berlin Hauptbahnhof

2009-06-27T12:28:00.001-04:00

So with a mountain of photos left over from a year ago now in Europe, I’ve realized that they don’t do that much good just sitting in my hard drive, taking up space, and occasionally showing up in screensavers. Thus, even though it is now a long time past, I’m starting a series of posts to put up some of my favourite photos from my escapades in Germany and thereabouts, that were never shared on here before.

To start off, this is the Berlin Hauptbahnhof (central station).

This massive building is one of the largest train stations on the continent, and is five gigantic stories tall. For a better idea of scale:

Those little white specks behind the bus? Those are people.

And this is the place from the inside. Trains run at both the top, and lowest levels. The place also effectively doubles as a shopping mall, as well. One could buy food, luggage, books, and even clothes.

The place was a daunting introduction to Europe; I spent at least half an hour wandering around lost (and sleep-deprived) before I found out where I needed to go.

Wikipedia has proven itself yet again, and provided one last awesome photo to tag on here, from the grand opening, and I have to share it even if its not mine.

Perhaps this all doesn’t mean much unless you were there, but the place is truly impressive, and while not a tourist attraction, definitely deserves note, and that’s why it gets mention here.

Fluoride, Sagan, and Arguments from Authority

2009-06-26T00:05:00.001-04:00

When looking up information on how to take care of a few new house plants, I learned that Dracaena plants, among others, don’t handle fluoride in their water that well. Not knowing if the water here in Montreal is in fact fluoridated and thus safe for my spiky new comrade, I figured that a quick Google search would help me determine what the story was. In short, I learned that no, the water in Montreal is not fluoridated.

The long part of the answer, however, was irritating:

http://www.canadafreepress.com/medical/teeth012107.htm

In this Canada Free Press article, Dr. Jones goes through the common arguments against water fluoridation, quoting several doctors on their opinions and views on fluoridation, and comes to the conclusion that RARRWG FLUORIDE IS KILLING US ALL.

He then quotes a great scientist:

Carl Sagan, the noted astronomer, was right when discussing "authoritarian" judgments. He remarked that "arguments from authority do not count; too many authorities have been mistaken too often".

And finishing the article, the Canada Free Press tells us about the author:

W. Gifford-Jones M.D is the pen name of Dr. Ken Walker graduate of The Harvard Medical School. He's been a ship's surgeon, hotel physician and family doctor and later trained in surgery at McGill in Montreal, University of Rochester N.Y. and Harvard. His medical column is published by 60 Canadian newspapers and several in the U.S. He is the author of seven books. Dr. Walker has a medical practice in Toronto.

It’s enough to make Dr. Sagan turn in his grave. If I understand Dr. Jones’ argument, he says “Don’t listen to the scientific consensus about this issue, listen to me, I’m a doctor. But don’t listen to someone just because they have a title, people who do that are usually hiding behind their credentials.”

from plognark

I was going to try and refute some points that were made about fluoridation, but I’m finding it’s not worth the time an effort when I just don’t know enough about the issue. A full response has the potential to turn this initially small rant into a 10-page diatribe, and the article is a couple of years old, so any real relevance to anything I might say would be lost. I’ll just say that I’m not that worried. We have far more harmful toxins in our environment that we know for certain are hazardous, and still willingly put them into our bodies.

The point I make here is that invoking someone with credentials as if that makes their points more valid is sloppy reasoning, and in fact a fallacy: the argument from authority. Dr. Jones brings up this fallacy to support his point, but in fact a reader who pays attention will see that it in fact invalidates a large part of what he said. If only Carl Sagan were around to lay a slap down on the author for misusing his name…..

Montreal Photojournal 1: Club Main

2009-06-23T20:16:00.002-04:00

To kick off an anticipated string of photos to share from Montreal, I today present a photo from the past weekend’s Club Main event. For the weekend, St. Laurent (“Le Main”) street is closed to traffic and local businesses extend their shops, restaurants, etc. to the street. The weather was not particularly great for an outside gathering, so it was fairly quiet, at least when I was there. I did, however, find my way to one of the small parks along the street, and, well, see for yourself. Look closely.

Can’t see?

I’ll give you a hint: the mistress of ceremonies led the show in a pleasing baritone. Such is Montreal.

edit: just figured out, though it was staring me in the face, the performance was actually part of the St-Ambroise Fringe festival (duh)

Meow!

2009-06-23T12:33:00.001-04:00

I enjoyed today’s Toothpaste for Dinner comic, and thought I’d share:

A New Home, New Language, New Culture

2009-06-19T12:43:00.001-04:00

Seeking out research opportunities in my field has brought me to McGill university, located in the beautiful city of Montreal, Quebec. I wouldn’t have believed you, had you told me a few years ago that I would be here now. That said, it has not been overly difficult to get adjusted and settled in here. While the primary language here is French, Anglophones have little difficulty navigating, speaking with locals, and basically doing anything, as most people here are bilingual. I’m told that it is in fact difficult to learn French here as if you have any sort of Anglo accent, people revert to English. My 9th-grade French education has come into use, but has by no means been essential.

While it is taking me some time to adjust to the rapid-fire pace of downtown in a major urban centre, the noise of constant traffic outside my bedroom and a general attitude of disinterest by passers-by that I’m not used to, I’m beginning to get settled in, used to things, and comfortable.

I expect I will have a lot to offer up about this fine city in the future. For now, I’ll leave up a photo of downtown Montreal, as seen from Mont-Royal, the city’s namesake.

I know you’ve missed me…..

2009-06-12T12:10:00.001-04:00

Well, I’ve let this page grow stale with time and so I suppose anyone who was reading once upon a time has left, but I’ve been inspired to get the ball rolling and start writing again. As I used to write about my escapades in Europe last summer, I’ll need to change gears a little, and figure out how I want to continue with this space. That said, I still have some great pictures to share. For now, I’ll just post a current desktop wallpaper of mine that I really like, dug out of my photo archives from last August.

Figure 1: The white cliffs of the island of Rügen

Talking Babies

2009-02-03T08:26:00.004-05:00

From a recent SciAm article on the origins of speech:

[Recent commercial] is only the latest proof of what comedians have known for years: few things are as funny as a baby who talks like an adult.

Am I the only one that finds ads/movies featuring talking babies to be incredibly disturbing?

Philosophical Solutions to Scientific Problems

2009-02-01T12:09:00.003-05:00

So a couple of days ago I went to a talk by this guy:

Figure 1: Dr. Massimo Pigliucci.

It turns out that it is not only possible to have three Ph.D.'s in different disciplines, but to actively research in all those at one time as well. Unless you're a Nobel Laureate, this guy likely makes anyone feel like an underachiever. "You only have two Ph.D.'s? That's nothing. Massimo Pigliucci has 3."

Dr. Pigliucci's talk was on the intersection of philosophy and science. He talked on scientific versus nonscientific disciplines, the limits of science, the application of philosophy to scientific ideas.

An important thing that I took away was an understanding that I really do not know very much about philosophy. I guess that is the price I pay for taking intensive science-based courseloads to expand my depth of knowledge in the sciences, specifically molecular sciences; I've sacrificed breadth. Most of my knowledge concerning critical thinking and logic have come from sources outside of my academic career, and of course these don't get nearly as in-depth as postsecondary courses would into the subject matter.

An interesting example that I took away from his talk, while not unknown to the scientific community, was largely ignored by myself until present. The definition of species is in fact quite a difficult task for scientists to concretely do. In fact, scientists remain divided on this seemingly innocuous concept. While intuitively we can know that two different organisms are different species, no one definition is concrete, because every criterion that has been suggested has been broken somewhere in the living world. There is no point trying to ascribe rules to nature, because nature finds a way, somewhere, to break them. And then nature mocks you for being so crass as to tell Her what she is.

We learn in grade school that a species is a group of interbreeding organisms that are mutually compatible. However, by this definition all bacteria would be considered a single species as they can generally swap genetic information with any other bacterium. The definition is not useful in this case. Similar exceptions are observed for any other criterion you may suggest. Dr. Pigliucci suggests an intuitive, though not scientifically rigorous solution, in that of any number of criteria one could use to define a species, if a certain amount are satisfied then a species is present. This thinking comes from the philosophy side of things, and probably won't gain acceptance any time soon by the scientific community, it is much more inclusive than previous methods.

The point is that not everything scientists look at can be completely explained by science. While many a scientist (sadly, myself included) will scoff at the humanities, they are necessary to our understanding of the world. Dr. Pigliucci calls for more discourse and mutual exchange between the presently divided disciplines. I couldn't agree more.

Why Biochemistry?

2009-01-28T18:16:00.004-05:00

I'm back.

I want to go through why I chose to study biochemistry, and to pursue it into the future. But to do that we must go back, back, back, in to a simpler time. A time when things were simpler. The pace of life moved a bit slower. People dressed a little differently.

2004.

Figure 1: 2004 Fashion. From Apropos of Something

Back then, a 12th grade high schooler facing the daunting task of selecting the route of my post-secondary education, I had a good idea what school I would be going to for university, but little clue what for. My interest in science went back to grade 2, where I was put on the spot to say what my favorite subject and replied "science" (remembering a recent super-cool demonstration involving milk, soap, and food colouring). However, science alone is not as specific a subject as it may seem to a 7-year-old. When university loomed and choices presented themselves, I found that I must decide between biology, physics, or chemistry, or something that falls somewhere in between (think chemical physics, molecular biology, and quantum ecology).

Being...ahem....a rock nerd at the time,

Figure 2: Rocks are pretty. From tourist_on_earth

I thought that geology - no, geochemistry - might be an appropriate career choice. But so I didn't sound so crazy, I tacked on biochemistry as something similar I may also be interested in. At that time, in one of the most misled moments of my life, I thought the TCA cycle was interesting. Then:

Dad: "It's a lot easier to find a job in biochemistry"

And my decision was effectively made for me.

5 years later, I have an undergraduate degree in the subject, and pretty intricate familiarity with it. Did I make the right choice? Yes and no.

I made a right choice, though i'm sure others would have led me places just as interesting, and carried me on just as far. I couldn't have known at the time that years later I would remain interested in the subject, but I am. I had little idea what biochemistry, or any other sciences (including geochemistry) was actually like. I suspect many others finish high school in a similar situation. However, my choice was a good one. I don't doubt that I would find a niche in any of several other areas, but the one I have is just right for me.

Choices are inevitable, and sometimes lead where you can't know you're going. The trick is to adapt, to learn, and to be happy with wherever you end up.

Did I think that I would enjoy study in biochemistry? I had no idea.
Did I know anything about the subject? None at all.
Am I happy with where my education has taken me? Absolutely.
Might I have been happy in a different discipline? Probably.

Yet here I am. Ready to move on, open a new chapter of my life, and close some more doors as I go. As they shut, the path ahead becomes a little narrower, a little clearer. While those doors don't open again, the ones I walk through take me on. On to new places, new experiences, and new opportunities. I can't wait.

Figure 3: Being forced to make choices is a good thing. From Mikael Miettinen

The Skeptic's Guide and Perry DeAngelis; Remembering and moving forward

2009-01-14T21:50:00.002-05:00

I discovered podcasting and other Web 2.0 stuff by and large in the summer of 2007, when I had considerable free time and a long enough trip to and from work/school to facilitate listening to a full hour of audio per day. A student from my university's Skeptic's club had posted a link to a "podcast" on a message board related to the university. The title: The Skeptic's Guide to the Universe. Not particularly versed or even really aware of skepticism, I figured perhaps the podcast was something like Douglas Adams' Hitchhiker's Guide to the Galaxy (I later discovered this was indeed no coincidence) and looked into it.

The roughly hour-and-twenty long podcast was not a story of Babelfish, Vogons, the destruction of Earth, or even towels, but instead a panel discussion of all things science, with a little criticism of Bigfoot and TV Psychics thrown in. While all the stuff about ghost hunters, aliens and astrology that the panel discusses is not of much interest to me, the science sucked me in. In the course of 8 months, I had managed to listen to all of the 120 or so (at that time) hour-plus episodes these guys put out, sucking it up like a sponge. Perhaps the best feature of the show is Science or Fiction, where the host presents three science news items, two of them real, one fictitious, and asks his panel of skeptics to guess which one is the fake*.

The show is run by the New England Skeptical Society, and started with Evan Bernstein, Perry DeAngelis, Bob Novella, Jay Novella, and the ringleader, Steve Novella. They were joined after a while by Rebecca Watson, dramatically altering the dude-to-chick ratio and making the show just that much more fun.

In August of 2007, one of the Skeptical Rogues, Perry DeAngelis, passed on. I was not sure if the podcast would continue the same and hold the same draw that sucked me in, but it did, albeit with an understandably subdued tone for quite a while.

With of 4 months when I did not have access to a computer to check out the podcast, followed by a terrible fall semester, I have fallen far behind in my podcast-listening duties. I am slowly catching up, and recently I found myself listening to the 1st Perry DeAngelis Memorial Live Podcast, SGU #169, October 11, 2008. I must say that this has by far been my favorite of the episodes I've heard, perhaps because of the differing format, but likely more just because of the laid-back atmosphere the live show produces, with two guest panelists to add to the mix as well.

If you are interested in science and/or hate creationists, you should take a look at this podcast, and I recommend the memorial as a great example to start with. Although it has a slightly different format, the topics are wide-ranging and discussions are particularly thoughtful. Check it out.

*After 100+ hearing Steve say this blip at the start of Science or Fiction, you can recite (type) it from memory

My muse is gone....

2009-01-08T23:16:00.006-05:00

Photo from SMN

Since I decided to ditch my pseudonym, it has been harder than ever to get something written. I'm probably being overly critical given that I now must be all the more accountable for my words. Agh. One of these days I'll get my groove back, I just need some motivation. Come on science, motivate me!

The evolving world of this blog

2008-12-19T12:48:00.009-05:00

Photo from Clinton Steeds

Blogging is tricky. I get a bout of inspiration but cannot reach a computer, or I'm busy and so then forget what I was to write, or get halfway done and back-burner the project until it collects too much dust and I give up. I find myself either wanting to write lots and not having the time, or not really wanting to write much when I have the time, either way resulting in not posting as frequently as I might like. And when I recently committed (at least to myself) to taking this blog more seriously, I subsequently found it even harder to put together a post as I effectively raised the bar for myself.

So how shall I fix this? Well, I think the first step is to dissuade myself of the belief that I might have the commitment of the myriad of other blogs out there with the tenacity and devotion to their readers to frequently put together well thought out and coherent posts on a regular basis, often involving photoshopping one's own images and responding in nearly real-time to other posts in the blogosphere. I both lack the technical know-how to do lots of what some bloggers do, and the time to keep up on all of what gets posted around. While it would be cool to give myself a pseudonym such as "Kinked_Strand" or "Tryptophaniac", (both of which I considered, both discarded) I just don't think I can live up to such names. I have a bit of a fight between goofiness and creativity (goofivity?) and a professional, more scientific tone. While a pseudonym might allow that, it's a little beyond me to keep up with posting as such a presence requires.

So I've decided on a different type of pseudonym - in fact not pseudo at all. Just nym. I noted before that most of my readers will know who I am as it is, and so for them this is just a formality. But for those who don't know, it's Shane Caldwell. I just wrapped up my undergrad at the University of Guelph, and who knows what the future has in store for me. There are other blogs from my university who write under their own names, and so unless I am able to justify putting in the time and effort to really maintain a pen name, it seems silly by comparison to do so when I can only manage a post or two every week.

So that's that. Big secret revealed. I imagine no one really cares. Anyone who really di could have pinned me down quite a bit anyway, to one of >10 universities, and if they supposed that the name I was writing under was my initials, actually finding me wouldn't be excessively hard. I hesitated to put my name on the web to begin with because I was nervous of privacy issues and such, and to feel confident in expressing an opinion without worrying about backlash. I'm comfortable now with people knowing who is behind the words, and am willing to own up to my opinions.

Needless to say, I won't be picking on anyone I know on here, including information of anyone else's lives, nor will I be discussing my own research of any sort. This is my space to express my thoughts, experiences, and opinions, and not to release information that belongs to others. Posts in line with my opinion on Craig Venter may still materialize, but as a public figure, he is fair game for anyone. In fact, I get the feeling he would be flattered by what I wrote, should he ever care what a lowly blogger would think. I know that sometimes I can write things that might put off some readers, as I no doubt offended some friends by riling on cell phones back in the summer, or talking about pre-med programs before that. I ask those that read to be understanding and to know that while I may be blogging on a frustration, I don't mean to insult anyone, and if I do, please let me know, and I will do what I can to remedy the issue. Everyone has their own views on issues; and I allow others theirs, and only ask in return that I be allowed my own.

So what does the future hold in store for Helical Translations? We'll have to wait and see, because I still don't completely know. Grad school is on the horizon and by taking a brief survey of some other similar blogs out there, many write about day-to-day lab life, interpersonal challenges and the like, but in keeping with what I have written above, this is something I want to keep clear of. I want to continue to use this space to put together information so that those reading can learn something. And if it isn't new information, I hope that I might at least be able to provide a unique perspective. It may take more work to put these together than some of the random updates I wrote during the early days of the blog, but I hope to shift my balance a bit from quantity to quality. I also hope to use this as a way of allowing myself to learn of things I otherwise would not have looked into. The issues I know I will deal with is to know whether a post is complete enough to finish with or to just continue to leave it in limbo to hopefully complete later. Perfectionism versus productivity, if you will.

So, if you will excuse me, I must go back to putting off the 10 posts half-complete in my queue. I'm getting used to this all, but it is still taking time.

Where did half of December go?

2008-12-15T11:36:00.004-05:00

It has been too long. My, how two weeks of waking up, studying, eating if possible then studying more before sleeping again can just fly by.

But...

This undergraduate can, barring final exam scores in the minuses, consider himself a graduate of the Baccalaureate program.

Now on to another 2-4 years of education. Woo.

An Ode to Boring Science

2008-11-30T14:42:00.002-05:00

Photo from umjanedoan

I've never been that into dinosaurs and fossils. When I think of space, I think of coldness and emptiness, not "boldly going where no man has gone before". Neuroscience baffles me and as such I have little interest*. And yet, a large amount of the mass media coverage of science revolves around developments in these and select other fields. Not that they're unimportant, but I find it tiresome that the coverage of science is so one-sided.

I would like to see more emphasis on ordinary, bread-and-butter research out there. It seems that if the news isn't covering classic post-Sputnik science such as robots, rockets, and space, it's something contentious like stem cells, vaccines, or climate research. Big news to the media outlets out there: there's more to science than fighting over embryos and forecasting doom! And they often miss great stories, those stories may just unfortunately be a little harder to tell.

I want to celebrate "boring" research. The ordinary, non-press release research that constitutes the bulk of what one will find if they open up a non-Nature or -Science journal. Don't get me wrong, I'm not talking bad research; good-versus-bad is a different classification altogether than sensational-versus-boring research - there's lots of crap at the top and bottom. I want to talk about what you find when you flip open a textbook. What is published on a regular basis in the hundreds (thousands?) of respected journals out there. Just because it's ordinary science doesn't mean that it can't be fascinating once one gets into the details.

Boring research is interesting research that does not necessarily promise to change the world or advance our ultimate understanding or cure AIDS or discover the Caramilk secret. Boring research makes up the bulk of what is published, and while the loudest stories are cried out over the crowd, the progress of boring, everyday research moves forward. It is the blue chip stock in world of science, where the big trading happens in cloning, robotics, and gender studies.

I would like to see the story of boring research told. Research that perhaps is not ground-shattering** but still tells us important things about the world. Things that in time are more valuable than isolated studies that make major headlines. Things that are established to the point that even scientists ignore the interesting story behind them. I want to to celebrate the unsung heroes of research, and what it contributes to scientific progress.

Finally, it should be noted that this research isn't boring to me, nor should it be boring to you. If you think it is, I'd like to change your mind. Dig a little deeper and there is often a story to be told. By celebrating the tons of quality ordinary science out there, we see the true elegance and amazing subtleties of the world around us.

Here's to boring science!

Image from velorowdy

*Hypocracy acknowledged by this biochemist
**Keep in mind many Nobels have been awarded for work not appreciated when it was done

Lüttje Lage - drink of the Niedersachsische Hauptstadt

2008-11-29T00:13:00.002-05:00

See above the preparation of a round of Lüttje Lage, the traditional drink of the German city Hannover. Hannover is the capital of the state of Lower Saxony (Niedersachsen) and where I spent my last summer. Note the lesson on proper drinking etiquette occurring in the background, as is common to see where this drink is served.

According to my extensive research on the subject, Lüttje Lage (pronounced loot-cha lahg-a) traces its roots back to the 16th century, to the Broyhan brewery, which established a tradition of drinking spirits with beer. German efficiency being what it is, the Hannoverians decided to do it at once. But it can't just be as simple as mixing them together. Oh, no. What followed was the formation of an amusing and bizarre way to drink beer.

Despite the oddness of it, the drink has persisted to present day, and every summer young and old take advantage of this traditional drink to celebrate their hometown pride. There's a lot of tradition surrounding the drink, and costumes. There's even a local men's club that among other things, preserves the culture of the drink. The local tourism authority offers Lüttje Lage tours a couple times each year, which are of course topped off by a sample.

So what is the drink itself? Well, the big glasses you see are 5 cL glasses full of beer, typically a variety specific to the purpose. The small glasses are 1 cL of corn schnapps. It tastes about as good as that sounds. However, people don't consume the drink for it's taste.

Lüttje Lage is mostly seen at local fairs, most notably the Hannover Schützenfest and Maschseefest. Purists would grit their teeth to hear this, but the drink is pretty much a novelty, specific to Hannover, or more specifically, Hannover's festivals. You'll find few who drink it on a regular basis, or at home. People travelling to Hannover from other parts of Germany will most likely have never heard of the drink. That being the case, when in Hannover one must have one, or you did not truly experience the city. Berlin has the Berliner Weiße, Cologne (Köln) has Kölsch, and Munich has, among other things, the Radler, but those are much better known and widespread. Lüttje Lage is strictly unique to Hannover, and no where else.

The best thing about the drink is the method in which it must be done. Typically, it requires practice, and a lack of prior impairment. One must hold the two glasses in one hand, and tip them properly so that the schnapps flow into the big shot as it then goes down. Things can get messy at the best of times. Step-by-step picture instructions are here.

Should one like to try for yourself, and just can't wait until you find yourself in this fair city, the luettje-lage.de site offers to sell you everything you need. Not that I would recommend it, you may as well just make your own.

One can see it all properly done here, which appears to be at Schützenfest. Of course, this style of drinking is not unique to Hannover, but the class and prestige at least pretended to be associated with it is. Also, keep in mind there's nothing that restricts one to a single schnapps glass........

There's-a gonna be some changes round here

2008-11-26T03:11:00.004-05:00

Pay attention, all 4 loyal readers. With my undergraduate classes drawing to a close on Thursday

>>break for celebratory dance<<

it's time for some changes in my life, and of course the most important thing for me to consider is how I run this blog*. Unfortunately it has not been quite what I had hoped it would be when I started. That being said, I started with the intentions of updating friends and family on my goings-on in Germany this summer, but decided to keep on with it indefinitely. Because of this setup, though, I haven't established a particular style**, or carved out any specific niche.

While a number of posts of quite widely varying format have appeared on here as I test out what works and what doesn't (at least in my mind), I have not been able to make postings as regularly as I would like, and I often find I have interesting things to write but am too busy, lack the inclination, or just plain forget. I am particularly proud of a few articles, and not so much with some others. I hope that a bit of a reworking might help out, and a commitment to a specific style. I also hope that a consistent style.

Expect a change of pseudonym. After having surveyed the various other blogs out there, I notice one thing I seriously lack is a cool-ass name. While one can get an idea of me from the profile information provided, I feel a cooler science-y name would much better express my attitude than a paragraphs would. I just need to figure out what that might be.

Another thing I will do my best to stop doing is saying (even if it's just to myself) that I will write something in the future***. While I continue to say that I'll fill in the stuff and post pictures from the summertime, I have come to realize that it's been a while, and no one really cares that much anymore. I had a blast, and it was great, saw lots, did lots (and had a difficult time this fall coming down from that 4-month high), but when it's so far removed now as to be silly. There are stories to be told still, and they will eventually make their way out, but I'll stop being in such a hurry when I don't actually get it done. I've got some ideas now, but I'll keep those cards close to the chest for now.

Interestingly, while this started last time I had exams in April, the first time I will have felt I have the time to sit down and write out thoughtful stuff is now the next round of exams. In some ways, I'm just an anti-student, I guess. While my peers are pulling all-nighters in the library, I'm bored in between tests and take to writing online. I dunno.

So onward I go to my final batch of exams. I must value this time, as some complaints about other students may only be valid while I am still an undergrad. My time to still whine about my peers is shortening. I must make haste. Oh, and perhaps I might benefit from doing just a little studying. We'll see if I can fit it in.

*The first of many changes, I am owning up to what this is. Though I wish someone would have come up with a better word for it.
**Any suggestions are, of course, welcome. Whether I use them or not is up to me.
***A post on amino acids is still forthcoming, however. I don't have the impact to get it to those that probably might benefit the most, but it's good practice for me in several ways, all the same.

No pressure.....

2008-11-20T02:28:00.005-05:00

So I just handed in the major project for my "Protein and nucleic acid structure" course, the notes for which will essentially be the rules I live by for the next few years at least. Being interested in doing pretty much exactly what I just submitted more or less full time, it means I better have done a good job. But who knows.

I'm not happy with my submission, a lot more could have been done, and a lot was omitted that
a) I spent a lot of time on and
b) is relevant given enough space to explain it
We'll see. I'm not happy with it, but that doesn't mean I'll do poorly.
I've left tests before that I thought I failed and in fact aced them (albeit following a generous bell curve). Let's hope this assignment is like that too. With the expectation that I do well, even an 85% might be a disappointment, though. We'll see.

All laboratory research ever has just been invalidated

2008-11-12T17:55:00.007-05:00

Well, not quite.

Researchers have found that ordinary laboratory plastics contain contaminants that can greatly affect results of biochemical and other research.

Two things:

1. Of course they do! Plastics and the things we put in them are organic molecules, and biological systems use organic molecules extensively.
2. Why hadn't researchers, or more importantly, manufacturers, thought of this before? I know some definitely have, but

This makes me think of classic situations where one person gets results that no one else can replicate under supposedly the same conditions, or someone gets a result once and can never repeat it, or cells that were happily maintained spontaneously die with no discernible reason. I know that in my experience that if needed, different types of tubes, tips, can typically be used interchangeably, without needing to worry about controlling for this source of variation.

The good news is that researchers can hopefully take this effect into account and more effectively troubleshoot, finding the sources of error. Who knows, this could even reverse some file-drawering, and research "cold cases" could be reinvestigated if whatever shelved the research may have been plastic contaminants.

The bad news is this opens the possibility for some published research to actually be incorrect, as a common (and necessary) assumption in research is that your tools and implements are essentially contaminant-free.

Though this comes as a big "duh" moment, i.e. no one can be too surprised that this is the case, the publication of real data shows that plastic contaminants can be a real problem. In the past researchers by and large haven't been too concerned about this possibility. Maybe now they should be.

Science 322 (5903): 917

On Wired: http://blog.wired.com/wiredscience/2008/11/common-lab-gear.html

Why they call me crazy

2008-11-10T14:49:00.002-05:00

Most people shudder when you say the term "Organic Chemistry". In fact, I just shouted it out loud in a communal study area, which resulted in cries of anguish, weeping, 3 attempts to jump out the nearest window, and one student setting himself on fire. When I tell people that I am taking extra upper-level courses in it "for fun" or, if it needs to be at least partly plausible, for the skill set I gain from the courses, many think me batshit insane. Well, maybe I am.

The weird thing is, for a subject so feared and despised by pre-medical and pre-pharma students, I actually sort of enjoy it. To me, organic chem is in many ways the closest you can get to playing with Lego, yet still earn advanced academic credit for it.

It's problem solving, as in:

I have this compound

And I need to make this one

Using the tools available to me, and some tricky maneuvers that chemists have invented to circumvent problems that biological systems often find when trying to synthesize compounds. If one can't figure it out, it can be downright maddening, but if one is willing to work at it, it can be incredibly rewarding to be able to come up with the right answer.

While I could be taking apiculture (beekeeping) or intro English as a bird course to round out my degree, organic chem is just more fun. I'm glad to have taken it. Perhaps I am nutso.

Whatever they tell you, I am NOT in this to learn to make designer drugs. I am NOT planning on moving to Columbia upon finishing my degree, and putting my skills to use, unhindered by regulatory agencies. And I am certainly NOT hoping to come up with a hallucinogenic dust that will induce irrational fear in citizens of Gotham city in order to take it over and establish my evil empire. Anyone who says otherwise is Batman.

Quirks of the Deutsche Sprache

2008-11-06T23:30:00.001-05:00

At times, the German language can be quite funny in how literal it seems to a native English-speaker. Perhaps I need to just take a better look at English as well, though. Following is a short list of things that are sort of odd in the German language from an English perspective. Given more time, effort, and initiative, I could definitely add to this, because I know there are TONS more examples. Feel free to add suggestions.

Glove = Handshue

Yes, that's hand + shoe

Mietwagen = Rental Car

And if a butcher rents a vehicle to make deliveries, well then I guess it works in both languages.

Nachrichten= News

Nothing special, but the interesting thing is you can use Nachricht as a singular, as in

Ich habe ein gutes Nachricht für Sie
I have a good "new" for you.

Leiter = Ladder
Feurzeug = Lighter

This has caused confusion several times, like when I got confused stares for needing a ladder to start a Bunsen burner

Food and drink = Lebensmittel

Literally, the medium of life. Which is, of course true.

Meat = Fleisch

Body = Korper

It's not just the accent. Some things in German just sound more offensive because they sort of are.

Protein = Eiweiß

Ei is egg, weiß is white - so yes, protein is actually called eggwhite.

Change!

2008-11-05T01:12:00.004-05:00

Congratulations to those south of the border, you have made the right choice. The rest of the world now breathes a sigh of relief.

Glad that I took up an offer to go to the pub, because I would hate to answer "Where were you when history was made" with "reading for school". How boring.

Anyway, I'm finally a little bit optimistic about the future. I like how Jeremy Kinsman puts it, from a Canadian perspective:

"The rest of us [Canadians] should just celebrate the fact that our neighbour and closest friend has chosen the kind of leader that Canadians can instantly recognize because he operates in what used to be a very Canadian way of seeing and dealing with the world."

Pizza Crazy Dog

2008-11-03T23:52:00.001-05:00

Ugh, this is terrible. I still have backlog of things from the summer I wanted to write about then and started posts of, only to stop after a few sentences. Here I start to remedy that.

During my last week of work, the boss happened to be gone on vacation, and so several informal gatherings and such were set up to just hang out without the pressure of a PI breathing down your neck. One of which was a pizza lunch, where we ordered in from the local place.

You may have heard how pizza in Italy is nothing like pizza in the US (Canada here falls in the same with the US). Well, while German pizza falls somewhere between, it is also in a way genuinely distinct. I was lucky to get to try out "Pizza Crazy Dog", which was just bizarre, with crisped onions, sliced hot dogs, pickles, and ketchup. Or rather I got to try half of one.....

During the lunch, the reality that I was leaving all the friends I had made for the summer behind hit me, and fast. Which will really kill your appetite. So, I left my food in the fridge, knowing that that meant I could save on lunch the next day (funds were starting to look extremely tight for me for the rest of my stay in Germany).

How absolutely terrible that the following day, my second-to-last day of work, I went to get my leftovers from the fridge, and found.....an empty box. After already in a lousy mood from the day before, this just sent my spirits crashing through the floor. Who the hell steals food from their coworkers?

This following the theft of the bicycle generously lent to me by one of my coworkers, I was not a happy camper.

Klaus Störtebeker

2008-10-29T21:00:00.002-04:00

Legendary German privateer and pirate; seems a fitting name for a new aquatic friend.

He's about as surly and cranky as a weathered seafarer, too. Fits well.

Why I'm getting nervous...

2008-10-29T18:43:00.006-04:00

Despite my earlier rantings on how annoying it is that Canadians seem more interested in American politics than our own, as the election down south draws near, I start to become quite nervous, much more than I was for Oct 14, in fact.

Perhaps it is because in Canada, the worst case scenario was returning the same party to power that already was, and in my opinion - even with my liberal-leaning tendencies - haven't done a bad job. More likely the real discrepancy is that as a student of science, Sarah Palin terrifies me. The Bush administration have been negligent with regards to science, but she goes further and insults the scientific process. And with a reported 22% chance that McCain could die in the next four years (as per an article in The Lancet), that makes things even worse. And that article didn't even take into account the very real possibility that by cutting funding to important studies on wild bear populations, he be mauled alive by angry Grizzlies.

Fettes Brot ist toll!

2008-10-27T18:18:00.002-04:00

Since getting back home in late August, I've had more reliable internet access than I had over the summer, and so have been able to look into some bands I learned of this summer in Germany. By far my favorites, who I have listened to far too much over the last two months, are a Hamburg Hip-Hop group called Fettes Brot. König Boris, Doktor Renz, and Schiffmeister make up the group, and something about their style harks back to 1980's American Hip-Hop. If you're looking for upbeat stuff with the exotic-ness of being in a nother language, check these guys out. My favorite is a story about the heartbreaker Emanuela:

Was weißt denn du von Liebe? Von Liebe weißt du nichts.
Dich ham deine gefüle mal wieder ausgetrickst.
Du hältst dich für gefärlich, doch siehst nicht nie Gefahr.
Das hier ist die geschichte von Emanuela.

What do you know about love? You know nothing about love.
Your feelings are playing tricks on you again.
You think you're dangerous, but don't see the danger.
This here is the story of Emanuela.

Trial and error .....and error......and error......

2008-10-26T18:25:00.001-04:00

One of the hardest things I've had to learn to deal with so far in working in labs is the fact that not everything works on the first try. When I express frustration, others tell me that that's just the nature of lab work, and I shouldn't worry about it. The thing is, I can't help but let it frustrate me, as I view myself as a competent, capable and smart lab worker, and so when things don't work it ends up being a bit of a kick in the face.

I guess my problem is that I beat myself up for things that are not my fault and are beyond my control. Nevertheless, if I continually make mistakes and get nowhere, then eventually things start to look less like random chance and more like a systematic problem - a systematic problem known as me - and so I shoot to avoid this problem altogether. But when you aim for 100%, then even 95% is a failure.

The rational me understands that everything does not always work out when you run experiments, but the irrational me does not. The irrational me expects that I should be accomplishing everything perfectly from the start through to the end and so sets himself up for disappointment.

I have been known to actually blow experiments by rushing too much, often following one or two rounds of wrecked ones, as impatience begets errors. This sort of thing can turn into a dangerous spiral, and one must remind themselves that not all problems are their fault. My supervisor from this summer put it quite nicely on my review at the end: "Sometimes slow is fast enough"

I guess I just have to stop being so hard on myself. If not, grad school will be really interesting.

Who has time to vote, we have to see if Palin does something funny!

2008-10-21T14:02:00.001-04:00

Now that the Canadian federal election is over, and we are back to where we started, it's time for conversation to turn again to why more people don't vote in this country. With a precedent-setting 59.1% voter turnout, I am ashamed in a way that 2/5 of my compatriots don't feel strongly enough about their nation to exercise their democratic rights.

Perhaps more so, however, is my frustration that more Canadians seem to care at present about the upcoming American election, than the one we just had here. Putting aside the comparison between campaign times, (this Canadian election took just over a month between being announced and having the result), it really bothers me that many Canadians seem to be much more interested in the politics of a nation that's not their own. A recent clip from The Hour quizzes Canadians on this on the street and shows it quite well.

Perhaps the best example of this problem was with the Canadian English-Language debate, which by unfortunate luck happened to occupy the same time slot as the American vice-presidential debate between Sarah Palin and Joe Biden. Many Canadians opted to watch this American showdown, instead of the more relevant Canadian leaders' debate, which was the only real chance to see the leaders speak this term for most people. t really concerns me that Canadians are more concerned with who is elected in the States when who is elected here will have a much greater impact on their day-to-day lives.

Perhaps for that 40.9% of voters politics are just entertainment. Or maybe they just don't care. Either way, it bodes ill for the future, as there will eventually come a day when this sort of thing matters. If we continue to be complacent about our government, we'll regret it sooner than some may think.

Reality at the atomic level

2008-10-17T11:34:00.007-04:00

Reviewing my Protein Structure course notes, I came again across the slide in which the professor writes "Reality is quantum, but classical approximations are convenient"

He made a very convincing case for why, a hundred years past the development of quantum theory, we still think of atoms as "balls on springs" when in reality, they are nothing like that. They are grains of sand held at the appropriate distance from each other, with a fuzzy cloud of mist in between that manages to hold it all together.

The things is, it's really hard to quantify just how fuzzy that cloud is, and so it becomes difficult to know how the system will behave when you want to do something to it. In addition, even our fastest computers just can't seem to manage the calculations beyond the simplest of systems, and so it's not just that we're too dumb to grasp it, the problem really is hard to calculate.

So we use the balls on springs, but we must not forget how we know the world actually works at that level, because certain phenomena just don't work if we only think of things in terms of classical approximations. I'm perfectly happy to leave it to the real chemists and physicists for now, but should I need to explain something I don't understand, I will be sure that the first thing I do is throw the Dalton model out the window, and remember to embrace the world of the fuzzy at the femto scale.

Memorization and the amino acids

2008-10-14T01:19:00.003-04:00

A student of biochemistry, I've often heard the complaint "I have to learn all my amino acids again?"

The trick is not to forget them. And this extends beyond my little corner of the academic world to the periodic table, taxonomic groups, irregular verbs, and schools of philosophy. One must be able to speak the language of their subject so that others can understand them, and so that one can effectively communicate in their discipline. But good luck convincing those who don't want to bother learning.

As much as I dislike the procedure of memorization for school, as I believe that it does not really test your ability as a student, there are cases where it is just plain necessary. At those times if you are doing it right, you shouldn't be working on memorizing each thing, because they should come with an understanding of the process. Past scientists may not have been the smartest when it comes to nomenclature and systematics, lacking the hindsight that we now have, but usually there is still a reason for the names and that helps to know what we're talking about. For example, isoleucine is an isomer of leucine. Did not see that coming. Histidine is the protonable ring. Cysteine forms bridges, proline forms kinks, and glycine is flexible because it's smallest. Glutamine is the amide of glutamate, asparagine is the amide of aspartate. Sure, they're not easy to know but the things that make each one unique are what makes them memorable, and by learning this way, it is a lot easier than beating one's head off the wall trying to figure out how to draw arginine again from thin air memorizing how the N, C, and H's line up.

Like my professor said a few years back, "You need to decide which amino acid you are like. Are you large and negative, like glutamate, or are you small and polar like serine? Maybe you're extremely bulky like tryptophan."

The Antigravity Gene

2008-10-01T22:34:00.007-04:00

Ever since LOST hit the air back in my freshman year, I've been sucked into the character-driven serial drama shows like 24, Prison Break, Jericho, and most recently, Heroes. Unfortunately.

I can forgive Heroes the terrible wrap-up of their second season due to the Hollywood Writers' Strike, and even the lousy start to season 3 so far (Does any character ever stay dead?!?). What I have a much harder time letting slip by is the abominable attempts of the show to explain the superhero phenomena in the show through science.

I have no problem to watching a show that deals with paranormal effects and accepting the weird stuff that happens there, as I routinely do watching LOST. The time-travelling and craziness, while it messes with my head, is ok too. I can even let slide the concept of a "mutant gene" that supposedly gives wildly different results in every individual who carries it (I allowed it with X-Men, so I have to let it go here too).

Where I do draw the line, however, is the use real scientific terminology and imagery, in distorted fashion, to try and describe obviously fictional effects. Perhaps the show's creators hope to make the Heroes world seem plausible, but to anyone who knows much about science, their attempts just end up ridiculous.

When Mohinder, the scientist who narrates the show, points at a computer screen with what looks like bacteria tumbling around in solution in HD, and says "there's the gene!", it makes me confused. When he spouts off incoherence about enzymes and the bloodstream and adrenaline and genes, I get annoyed. When he works for 20 minutes and completes what would be 2 years of lab work in the real world, I get angry.

The icing on the cake is the perfectly arranged rainbow-coloured solutions that sit atop his bench. I wish my lab benches were ever that nicely decorated.

While I suspend my disbelief about superhero powers and the like that is central to the show, I have a very hard time stomaching their complete misrepresentation of what science is, and how it works. If they want to make it mad science, the scientist should be a mad scientist, and not the more-or-less rational individual Mohinder is. It's fine to have him sit there and mumble on in some incoherence about something the viewer can't grasp, but when the character talks about things you actually find in the textbooks, the writers of the show start actually lying by making fake connections between real things. It's the same as introducing Bill Gates to the show as a character and giving him a super-geek-ray power or placing the Eiffel tower in the middle of New York. Make something fictional, even take inspiration from the real world, but don't make lies about things from the real world.

The writers of Heroes obviously know nothing about how science works, and that is fine. They just need to stop pretending they do. Or at least do some homework, and find out what a double helix really looks like.

If only "Classical Greek Influence on Renaissance Architecture" were edible....

2008-09-28T21:22:00.003-04:00

...then it might be of more value to students

Textbook publishers are assholes.

I've been lucky and smart and planned ahead enough through the last 4 years to have got by without buying hardly any more texts than I have needed all the way through. Nevertheless, in my first year I still fell prey to peer pressure and people telling me that I must buy overpriced bundles of paper and cardboard so that I could pass the course, then proceeded to leave them right where I could reach them, above my desk. That was where they stayed all year.

Fully acknowledging my hypocrisy here, I still shake my head when seeing all the freshman students at the start of the year lining up to buy their armful of $100 + biology, chemistry, physics, and math textbooks that I know sometimes do not even get the shrinkwrap removed before the course ends. I can only hope that it teaches them the same thing it taught me, and that's to never buy a text until you find yourself in genuine need. What would be better if they figured it out beforehand, but as I experienced as well, no matter how many times you hear you should wait before buying them, the pressure gets too much and you cave, forking over unnecessary amounts for books that you don't really need.

I'd like to know how textbook publishers sleep at night. They continue to charge obscene amounts of money ($168 for one of mine this term - which of course I have no intent of forking over the cash for, sorry Oxford University Press) for books that cost them a fraction the price to produce. How many textbooks sold at 1200% production cost does it take to break even? My guess is not nearly as many as sell. The rest of the thousands of sales go straight from the poor, destitute students into the pockets of Misters Wiley and Freeman.*

It's not just the text companies, either. Instructors, especially at the entry level, continue to push texts on students, claiming that you will not be able to complete the course without one. Sometimes true, but rarely (speaking as a student of the sciences, anyway). I still resent the co-ordinator of introductory biology who told students that the text was essential for the course and that we must fork over $120 for one, following which it was of no use in that or the following course. Multiply by a class of 1800, and we're talking a lot of wasted dollars. The whole thing ends up exploiting individuals known to be poor, helpless, and subsisting entirely on Ramen noodles.

This isn't to say that the texts are not good; a lot of them are excellent, and I have got a huge amount of use out of three in particular. But these are texts I knew I would need, and for every one like me that uses them well, there are 99 who never touch them, and it's quite sad that so many students buy texts that depreciate and become worthless within a few years.

I enjoy upper year classes that teach straight from the primary literature, and if not, then all you might need is a reference text should you need to check facts and for some reason Wikipedia doesn't suffice. Almost done my undergrad, I don't plan on buying another text ever for classes here. I can't foresee having to pay for any others, as all my classes are upper-year sci - oh...wait...right, I'm taking that one too.

Oh, speak of the devil. Hang on a second.

What's that, second year Personal Financial Management?

You say I need the text to complete the assignments for this course?

Do I absolutely need to?

60% eh.... What if I -

Or if I -

Ok, fine. You win. This time. Sleep with one eye open.

Sorry you had to hear that. Well, dammit. Seems there's one more text I need. Guess I'm off to feed the man once more. Till next time.

*Make note that I make no claim that I understand Economics in any way, shape or form. The textbook was too expensive, and so I didn't bother learning. The statements made here are based completely on the assumption (granted, it is the correct one) that publishers are evil soul-eating bat-demons. And I've heard they have something to do with Osama bin Laden, too. Told you they were assholes.

Brussels - city of cartoonists, waffles and pickpockets

2008-09-20T15:52:00.002-04:00

Grand Place in midday

So first mistake going to Brussels: assuming that Midi must mean the same thing as central. Nope. In French, it means "Noon". If I'd known the Dutch name for the same station (Brussels Zuid) I would have known I was at the South station when I exited my train, and not wasted 45 minutes desperately looking for street signs (Belgians are apparently above labelling their streets), and not finding the ones I did see on my map, because I believed myself to be at the central station. Regardless of that, I eventually found my hotel and met friends there.

Brussels Arc de Triomphe

Not wasting any time, we headed out to the Grand Place, the central city square, and even though it was 11:30 at night, the place was lively. The buildings surrounding the square were especially picturesque at night time and all through very cool.

Grand Place at night

The Manekin Pis, a famous sculpture of a little boy peeing (literally what the name means) was nearby, and visiting late at night was a great way to avoid the crowds that built up there in the day. Though a return the next day allowed us to see him in a change of clothes, as it is typical for visitors to give him clothes.

Manekin Pis at night

Manekin Pis the next day

Oh, and one must not forget waffles. WAFFLES. Unbelievable. I will never eat any again unless they come from this country. There is just no comparison.

Waffle shop!

The next morning we set out to go to the Atomium, the gargantuan monument built for the 1958 Expo in Brussels. I expected a statue of some sort, and did not realize we were headed to the highest thing overlooking the city. The 9 spheres represent the unit cell of an iron crystal, and can be entered through an elevator that runs up the middle, and escalators in between. The structure was built to last 8 months, but still stands to this day. As it is now the 50th anniversary, it was understandably quite busy.

The Atomium

We came back and visited the Place de Jeu de Balle (Ball Game Square) to see the local flea market. Quite interesting, there were things from around the world, from many different cultures, alongside your normal fleet of broken radios and sunglasses. Of note were a gigantic toothbrush, and guys actually selling couches.....somehow....

Flea MarketToothbrush!

Chocolate shops were a must on our trip round the city, but most proved too rich for my pocketbook. One that offered free samples made for some strong feelings of guilt when I discovered that even the cheapest stuff for sale was too much. They didn't like us.

Galleries St.-Hubert - the world's first mall

We saw the local Beguinhof on the map, and having heard of a Beguinhof in someone's research for Belgium, we decided to go there. It turns out that the one we were thinking of was the Beguinhof in Brugges, which we visited the next day. The Brussels Beguinhof was perhaps more interesting all the same. Arriving at it, with my rough understanding of German and speaking English, I figured out that the sign on the door said 'For 21 days the women have been on hunger strike" in Dutch. We were invited inside by men in their mid-thirties standing at the doors, and inside were were presented with one of the most unique scenes I've seen in all my time here. An old, Baroque church, housing dozens of protesters inside, mattresses covering the floor,neon pink and yellow blankets hung up to give some sense of privacy. The whole thing had to do with immigrant's rights, which apparently are not too great in Belgium (as in a lot of the rest of Europe).

Frites in front of a church

Top of a fountain - this motif is seen on all emblems of the city

Brussels is known as the "unofficial" headquarters of the EU, though it looked pretty damn official to me. EU parliament is based here, as is a lot of the big important agencies. Lots of shiny glass and pretty buildings.

EU Parliament

Frites!

After missing a chance to get to the re-enactment of the Battle of Waterloo, but getting some Belgian frites to make up for it, we headed back into the city, and were lucky to stumble upon the music festival that was going on over the weekend. Granted, the music was......different....the crowd was still interesting, and cool to hang around for a while in. Walking through the park nearby on the way out, there were an unbelievable number of teenagers sitting, hanging out, drinking and smoking. There was hardly a square inch of grass free. (or a gram of it, either).

Concert

Outside the music festival

Our night ended at Cafe Delerium, as all three of us had independently heard of the bar, located just beside the Grand Place. The place was a tourist hole, but we put that aside for the evening. Perhaps we shouldn't have. Proudly advertising that "In 2002, it was determined that they had 2002 different beer varieties to serve", the place was definitely interesting. Leafing through their inch-thick binder of a menu, we picked out some for each of us, followed by a 2L novelty glass we has seen others drinking from when we stopped by to scope out the place earlier in the day. Where things went lousy was when we realized my friend's wallet was missing. Lost credit cards, passport, and 300euro is a rough thing to take away from a weekend in Belgium.

Cafe Delerium

Belgian Beer

Finally, Belgium is where a lot of the art of drawing comics has originated. You see this throughout Brussels, as statues, murals, and even billboard-like signs at the top of buildings. One thing that I wish I had more time to explore while there, but I did find Tintin!

.....?? Brussels is full of cartoon formsTintin! Atop a building

"Do"-ing while travelling

2008-09-15T14:15:00.001-04:00

How does one "Do" a church?

Keep your obscene, inappropriate and/or blasphemous comments to yourself, now.

I spent a lot of time this summer travelling weekends, and have been doing my best to take in everything I can, experience as much as possible and to live life the German way whenever possible. I do my best to respect the people and institutions of the cities I visit.

Which is why it has started to drive me nuts to hear people talk about "do"-ing a museum "do"-ing a royal garden, "do"-ing a festival, "do"-ing a monument. When one has this mindset, they are just crossing things off a list to themselves. Which runs pretty much opposite to my way of travel. Not that I don't also have a list of priorities, and am usually short on time, but at least I try my best to avoid using the terminology that reflects just going somewhere so you can say you went there.

After some time, I developed a different travel philosophy, of merely wandering. If you are in the appropriate places, just wandering at random, stopping when something piques your curiosity, eating when hungry, stopping and listening to the street performers, sitting beside the banks of a river to relax, can be much more rewarding than speedwalking through a city to get from church A to town hall B to monument C. If the places are truly remarkable, you'll probably come across them on your way anyway.

So that's my vent about tourists for today. I fully own that I can fall into the same way of thinking, and in fact I am sure that most who travel do from time to time, but it is a way of thinking that in the future I will fight, and make sure that I make myself take the time to just sit back and smell the roses a bit. It's far less exhausting.

Breaking News

2008-09-10T21:02:00.004-04:00

This just in.

The LHC is Online.

The Universe still exists.

Looks like the doomsayers need to go back to preaching to us from Nostradamus.

edit 27/06/09 as I reformat all old entries: sure missed things with this post.......