DNA Nanotechnology

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

xkcd on biologists:

 
Source: xkcd.com

Banned Words in Science Reporting

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

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

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

Source: xkcd.com

The Summer’s End in Montreal

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

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

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

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…

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

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!!!!!!

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

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

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

New cartoon to go up on my lab bench:

Source: xkcd.com

Math nerds count cards…..

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

 
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

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

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

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

Cartoon by Nick D Kim, lab-initio.com