Abort, Retry, Ignore, Fail?

On Saturday afternoons in the summers of the 1980s, we'd excitedly enter the Dial-A-Movie, still dripping pool water from our swimsuits. Here was a whole world of choice, a rental store with seemingly every movie ever made displayed on its shelves. What to choose, what to choose. Arguments would ensue - the youngest of the bunch would want to get Pinocchio (again) and the older kids wouldn't want to rent things from the Disney shelf at all, or anything else that's animated, for that matter. While the rest of the gang was debating the merits of Summer School versus Spaceballs, I would notice the poor guy standing in front of the Betamax shelf. That's right - just the one shelf, with its meagre selection of titles. I would wonder why they weren't afforded the same cinematic cornucopia as we VHS people. Back then, videotape was videotape to me. Why would they choose a Betamax tape? Why not simply take a VHS tape home? I had no idea that the machines they had at home would be different, that the tape wouldn't fit. With no concept of incompatibility issues, I was therefore even more unaware of the vicious format war between Sony's slightly superior Betamax and JVC's almost ubiquitous Video Home System. Today, I'm more aware of these things. Primarily because history repeats itself.

You knew it was coming, but you couldn't wait, could you? Now you're stuck with an HD-DVD player that has become obsolete within less than a year of purchase, as well as a shelf sagging under buyer's remorse, instead the weight of all those movies. Sony must be pleased: their format has finally won. With all the major retailers exclusively carrying Blu-ray discs, and the movie studios following suit, the future looks blue for Toshiba and its HD-DVD format. In fact, Toshiba has announced that it would cease production of HD-DVD players entirely. Blu-ray has become the de rigeur sexy upgrade from DVD (or VHS, if you've spent the first part of this century on some desert island). And that's the thing: there will always be format wars, winners, upgrades, disappointments, triumphs, technology. No matter how much the 21st century is moving towards doing everything digitally and downloading your music and movies as zeros and ones from some anonymous entertainment server, people still love gadgets. You cannot wrap a download and put it under the Christmas tree. Well, you can probably wrap a download gift card, but that's just not the same; it's the gift that shows you cared enough to do the very least... And for the afficionados, the quality of downloads is still miles behind. Audiophiles wouldn't dream of polluting their ears with 128kbps MP3s, exclaiming, "There are so many gaps, the loss of information from the sound is a crime. I'd rather listen to something authentic." And then return to their scratchy 78s, implausibly. Personally, I love new technology, the fruit of format wars. I love my collection of Super Audio CDs, for example, another Sony brainchild that makes DVD-Audio sound like 8-track tape. Although, the SACD format has been slightly less well supported than I'd like it to be. History repeats itself.

Forgive me, Father, for I have cloned

Oh, great. Not only am I going to Hell for what I am, I now also deserve eternal damnation for what I do. I can either finish my degree, or drop out and be saved. Hmm... decisions, decisions. Not only is biological research now not helping civilization advance, but the very act of holding a test tube up to the light is akin to stabbing a kitten. It has become a reprehensible act, worthy of the utmost punishment Catholicism affords. Yes folks, the Vatican - being the groovy and happening place that it is - has updated the Seven Deadly Sins of yore (which one is your favourite?):

• sloth


• envy


• gluttony


• greed


• lust


• wrath


• pride
  

to the 21st century 'social' sins of:

• genetic manipulation


• human subject research


• environmental pollution


• violating human rights


• inflicting poverty


• accumulation of excessive wealth


• drug trafficking (and consumption!)

So now I'm not allowed to put plant genes in bacteria anymore (or bacterial genes into plants, for that matter), unless I plan to spend eternity in Dante's inferno. Brilliant. Or perhaps I'll just spend some time in Purgatory instead - after all, I gave up chasing the dragon and injecting orphans with trial size volumes of toothpaste years ago.

Read the full story from Reuters here.

Mouthwash hysteria and protocol mythology

Our society of the 21st century is rather alarmist. I was reading an interesting link on Boing Boing about a single-blind study in which a bunch of audiophiles could hear no difference in sound quality between music conducted through expensive stereo cables and music conducted through coat hanger wire. This led me to the original article at The Consumerist and finally on to this. Briefly, it seems that people are concerned that using Crest Pro-Health Oral Rinse leaves their teeth stained brown. So far, the article has generated more than 150 online comments, most from concerned mouthwash users upset at Procter & Gamble for putting the stuff on the market in the first place. Brown stains in return for practicing good oral hygiene? No thanks!

The comments were really interesting to read. They remind me of a lab phenomenon I call 'protocol mythology'. It starts like this: you're busy in the lab, homogenizing your samples, centrifuging your tubes, cloning your DNA fragments, running your gels, when suddenly... things go pretty much the shape of a pomaceous fruit (hint: it's not an apple). The arduous task of troubleshooting begins. You retrace your steps back to that part of the procedure when things were still working. What came next? Did you precipitate at room temperature, or on ice? What was the pH of the buffer again? Perhaps the restriction enzymes are not compatible with your extraction method. What voltage did you run the gel at? The protocol therefore gets altered, often changing many variables at once in order to save time. Big mistake. And yet, changing it up seems to have worked - the DNA fragments on your gel are of the right size. Hurrah for troubleshooting! This is how the grad lab protocol myth gets born: one student will suggest the set of in-house modifications (which they spent simply months optimizing) to the next student, who then passes it along. Newbies are often intimidated into compliance with tales woe and crying under lab benches. I know I was. Who wouldn't follow the sound advice to rather use that laminar flow cabinet instead of this one, unless you want guaranteed yet unexplained contamination of your agar plates? We can't explain why, all we know is that it works. Don't argue with us - we know what we're talking about. Or do we?

Back to the mouthwash. It seems so much like a snowballing mass hysteria thing to me. Almost everyone has at least some kind of discoloration to their teeth. This is usually in the hard-to-reach areas, like between the bottom teeth, right at the gum line. It's a spot that goes without close scrutiny for the most part - but you're bound to find it if you go looking for it specifically. And what better time to investigate your gumline than after reading a scary report that everyone who has used your new brand of mouthwash was left with stains making them look like champion tobacco chewers? As disinformation gets spread around, the whole thing takes on a mythology of its own. The staining gets rapidly attributed to various things, including the blue dye in the rinse (so why are the stains brown?) and the presence of stannous fluoride (although the Pro-Health toothpaste does contain fluoride, the mouthwash does not and besides, dental fluorosis only occurs during tooth development). Some people spit out blue gunk after using it: how strange and unexpected! Who could have guessed that the active ingredient designed to rupture microbial membranes and act as a detergent to collect cellular debris might actually do its job? We can't be having that! People have poured the contents of their bottles down the drain, or returned them and demanded refunds. The stuff of urban legend. And then there are those who have completely lost their sense of taste after using it. Now that's scary, isn't it? Truth be told, I've never used a brand of mouthwash that didn't extinguish my sense of taste for a couple of hours. Actually, I've never had a gin & tonic that didn't do pretty much the same thing.

We all react differently to different products. Some people are allergic to peanuts, others to tomatoes, some to antibiotics, some to anything that isn't cashmere, Dahlinks! That doesn't mean we should take peanuts, tomatoes or acrylic sweaters off our shelves. Well, maybe the acrylic sweaters at least... The point is that everything we consume, whether it be food or medicine (or both, in the case of nutraceuticals and dietary supplements) has side effects or is toxic to some degree. Yes, even water. The next generation of mouthwash is no exception to this. The brand in question uses cetylpyridinium chloride instead of alcohol to battle bacteria, making it an attractive, non-dehydrating alternative for children, diabetics, the aged... and recovering alcoholics, naturally. The bacterial remnants and salivary proteins disrupted this way can attract tannins from food, and form brown residues in the crevices between teeth. This is will be especially noticeable in only about 7% of people who use the product. And one person out of a million having a bad reaction to one of its ingredients doesn't imply that the product is no longer of any use to the population at large. If that were the case, we wouldn't have any antibiotics left to treat disease with. Or, indeed, food. So there you go. Since stains are not harmful, the rinse has not been slapped with a warning label. Neither are pineapples, which contain enzymes that can cause bleeding, by the way... Is the Crest Pro-Health Oral Rinse responsible for stained teeth? In some cases, probably. Does this warrant all the disinformation-based consumer hysteria? Probably not, although P&G are partly to blame for not explaining the possible side effects and their origins clearly enough. And so fear and ignorance creates a whole 21st century mythology around what is actually a marvelous advancement in human health. From chunky blue saliva to evil fluoride to burned tastebuds... to oral cancer, presumably.

All I know is that once the lab protocol fails again (as it inevitably does) reverting back to the original procedures, presented in Molecular Cloning: A Laboratory Manual by Joseph Sambrook and David W. Russell more than twenty years ago, always gives you the desired results. All that tweaking was just weaving a myth.

Hyaline Hiatus

As you may have noticed, there has been little activity on this blog in the past month. Unfortunately there is much to do in fleshspace. I've been scrambling around in the lab, getting things in order, and preparing for a scientific conference this coming weekend. I'll be giving a talk, and therefore will devote my time to that. More fun-filled musings from the inside of my head to follow soon. In the meantime, I'd like to share this delightful video clip with all of you. It features some of the best ever footage of a most prehistoric looking fish, the frilled shark, Chlamydoselachus anguineus. Although hardly fresh news (the shark was filmed off the coast of Japan about a year ago) it is still quite mesmerizing and an elegant reminder of how little we now about the things that stir in the depths below. Enjoy.