Optimal Tweezers

A group of skeptics in Oxford recently formed a suicide cult in protest of homepathic remedies. Homeopathy is often marketed as a viable medical practice, but it’s actually a form of pseudo-scientific medical treatment based in the (ahem, BS) idea of water holding a therapeutic ‘memory’ of toxins long after the toxins have been diluted out.

Since water doesn’t have a brain–and certainly not any kind of memory–this is of course total bunk. Unfortunately, it’s also very profitable bunk–and this group of charming brits got together to show that massive overdoses of homeopathic treatments have no effects at all, aside from a delicious aftertaste (seeing as they consist entirely of sugar pills).

Their motto? “Homeopathy: There’s nothing in it!”

The concept of being able to patent a gene has always been a preposterous one to a lot of scientists. A gene, after all, is really just a short piece of information–given a specific DNA sequence, you can assemble and replicate it from scratch in less than a week with only basic tools. Which makes it really exciting to hear that a federal judge has ruled that it is not legal to patent the human genes BRCA1 and BRCA2.

These genes (the acronyms stand for Breast Cancer 1 and 2) are important indicators of hereditary predisposition to breast and ovarian cancer, and the company that held the patent on them made its claim with some really shaky arguments–saying that their technique for isolating the genes was transformative enough to merit a patent. Working in a biology lab, I know that these techniques are pretty trivial. I could check whether or not you have a specific mutant of one of these genes in just a day or two, and for probably less than $100.

It’s yet to be seen if this ruling will be upheld, but a lot of people are hopeful that it will be–while it will make some biotech companies have to work a bit harder to set themselves apart, it’s better for everybody in the long run.

Google's got it figured out.

An article in the New York Times this week described a disease threatening to destroy the tasmanian devil population that appears to actually be the second known case of a transmissible cancer. This is bad news for the tasmanian devils, of course–it appears that this disease may wipe them from the wild–but I was intrigued to see the confirmation of a idea that I had been pondering recently: whether or not cancers could act as a transmissible disease.

The only other known example of a cancer like this is in dogs, and genetic studies have shown that the canine one is thousands of years old, so it’s really interesting that this cancer appears to have developed much more recently.  On a fundamental level, it’s really remarkable that both the dog and tasmanian devil cancers are able to actually survive and grow when they get transmitted between individual animals.

Given the intensity of the body’s usual response to the presence of outside cells–think of the drugs that organ donation recipients have to take to keep their bodies from killing off the foreign tissue–it’s really intriguing to see that this can actually occur in these (albeit extremely rare) cases.

This is also an exciting opportunity for cancer researchers, in that the tasmanian devil disease is so young.  Although normal genetic evolution occurs on the scale of hundreds to thousands of years, cancer cells effectively lift the brakes on mutation rates:  biologists will be able to watch to see if this disease develops and changes over just the next decade or two.

Some nasty infectious diseases are believed to adapt to become less deadly over time so they can survive and multiply without quickly killing off their hosts (syphilis is one disease where this is suggested to have occurred), so it will be interesting to see if this cancer can strike this balance before it completely wipes out Taz and his cousins.

I was delighted to come across Microbial Art today, via Easternblot. It’s exactly what it sounds like–a group of biologists who enjoy experimenting with the aesthetic opportunities of cultured microbes. As, in my experience, these opportunities are fairly few in the course of their normal use–mostly they just smell funny and look like yellowish fuzz–I think it’s a worthy effort. Think of it as the biologists’ answer to latte art.

(I humbly submit my own picture of a dried-out agar culture plate that once held E. coli.)

After seeing this video of a slingjaw wrasse getting a meal, I felt inspired to pick out a few of my other Favorite Interesting Critter Videos. Because sometimes natural selection produces some funny results:

(drumroll…)

number 3: The invisible octopus

number 2: Dolphin Bubbles: An Amazing Behavior

number 1: Manatee Squash

Okay, that last one wasn’t so much cool-animal-tricks as silly and immature, but hopefully the others made up for it.

I was intrigued to hear recently that Paul Nurse was a speaker at The Moth, a very cool storytelling collective in NYC. Paul Nurse is a Nobel Prize-winning biologist, who achieved fame for identifying the molecular stopwatches that regulate the timing of cells’ division and growth; I figured that his story would somehow relate to his life in the lab, or some saucy story of academic intrigue, but it turned out that the story–while still quite saucy–was much more personal for him.

I don’t want to give away too many details (it’s really best to let him tell you the story, on the July 27 episode of the podcast) but it involves some surprises in his own genetics. So go check it out!

It’s true that some scientists are rather short on social skills (there are even stereotypes between scientific disciplines–just ask a biologist to do her impression of a chemist…). However, it’s also worth noting that there are many delightful exceptions.

A Berkeley friend’s blog, NCBI ROFL, has recently gained internet fame as a repository of hilarious abstracts available in one of the leading search engines for the life sciences. Their recent success got me thinking about other icons of internet science humor. Here are a few examples:

• Along similar lines to NCBI ROFL, though spanning all scientific disciplines: The Annals of Improbable Research.
• Greg Crowther is a professor studying infectious disease who also writes a wide variety of science songs.
• Naturally, it was a British lab that set out to uncover the world’s funniest joke. (It’s kind of funny…that’s what happens when you try to please everybody.)
• National Lab Mustache Day is exactly what it sounds like: a large fraction of my lab participated this year. I’m on the left edge, second from the top:
  

I’m in New Hampshire at the Proteins Gordon Conference, living it up and learning about all sorts of things. Unfortunately, it’s a confidential conference–I can’t give any details of the work being presented here, so I can’t write at all about the brilliant work I saw today on the ________tonic modeling of the behavior of ___________ ________ation in the _____rqui____ ________some.

So you’ll just have to wait for that to come out in publication.

In hard times, how does a cell quickly search through its own DNA to find the genes that will help it survive? The genomes of even the smallest organisms are enormous, and searching along all of the DNA in a cell to find a single site is a complex challenge if you want to do it in any reasonable amount of time. For a sense of scale: all of the DNA within a single human cell, if you unraveled it and stretched it out in a single strand, would be about as tall as you are! (Now, imagine walking along that strand of DNA with legs that are only a nanometer long…)

A friend Michelangelo D’Agostino recently wrote a review of a French group’s efforts to explain the amazing efficiency with which proteins can slide along DNA strands without falling off or getting stuck somewhere along the strand. It turns out that the proteins take a hovercraft approach: they have evolved to have a strong affinity for DNA, but they have also engineered their interactions with the DNA such that when they bind to it, a layer of water gets excluded between the protein and DNA.

Water molecules in the vicinity attempt to diffuse into this region, and the pressure they put between the protein and DNA wedges them just far enough apart that the protein essentially floats on the DNA. The protein can then slide freely along the DNA with minimal friction while it searches for the DNA sequence that it targets.

This is intriguing because their model is surprisingly simple: the DNA and protein were modeled as very basic shapes, but they managed to extract this behavior in an elegant and compelling way.

(To clarify the title of this post: it’s a quote from the Rolling Stones about how they stayed together for so long.)

Two friends of mine at the Berkeley School of Information, Ben Cohen and Ljuba Miljkovic, have put together a really fantastic final project for a course in user interface design: a redesign of the BART ticket kiosks.

Check out their vastly improved approach, at bartkiosk.com. They’ve created an elegant and simple workflow–and made it beautiful, to boot. I’m hoping that the BART management people hear about it, and realize what a great thing has been dropped in their laps.

Easy to read and navigate--a great improvement!

Some background information for non SF locals: BART is the Bay Area Rapid Transit system, and its current interface is pretty cruddy. Poorly organized information, and lots of unnecessary button-pressing–which gets especially frustrating when you’re about to miss a train!