I was delighted to see an article in the New York Times this week that described how a disease threatening to destroy the tasmanian devil population appears to actually be the second known case of a transmissible cancer. Not delighted for the tasmanian devils, of course–it appears that this disease may wipe them from the wild–but delighted 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:
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:
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!
The trailer for Adam, a ‘New York love story’ between a chipper, attractive lady and a chipper, attractive gent with Asperger’s syndrome, looks interesting (and also chipper, and attractive). It’s hard to find even-handed presentations of people with autism spectrum disorder (ASD) in the media; I lived with a friend with autism, Jessica Park, for two summers in college, and I think the trailer for this movie actually puts forth some effort to capture both the easy and more difficult aspects of living with someone with ASD. (Naturally, it also paints everything with the romcom brush…you take what victories you can get.)
It’s also encouraging that they neglected to mention that the main character has Asperger’s syndrome in the synopsis…it’s brought up within the trailer, but I think that focusing more on his personality in the description helps humanize him. Hopefully, the movie will try to present both protagonists in an equal light (people without ASD have wrinkles too!).
The trailer:
Some related links about ASD:
A March 2009 article about Jessica Park from the Boston Globe, and her website at jessicapark.com
Clara Claiborne Park’s landmark book, The Siege, is a powerful account from her early years raising Jessica–all the more notable because of Clara’s eloquence and her (sometimes brutal) honesty.
Pet peeve: When ASD comes up in the news, people refer to the ‘debate’ over whether or not MMR vaccines cause autism; the answer, of course, is a resounding NO: established with many good, independent studies, and no longer worth discussing. For an in-depth analysis, check out Science-Based Medicine’s recent post on the recent championing of the anti-vaccine campaign by misguided celebrities.
Last March, many scientists were overjoyed to see President Obama’s repeal of a 2001 executive order issued by G. W. Bush. Bush’s order had specified that federal grants for embryonic stem cells research would be provided only for work done with the few currently existing cell lines. Its passage was especially disappointing to many scientists because it was enforced just as the stem cell field was starting to show great promise!
It’s natural to expect that the 2001 executive order probably stifled research in this field within the USA, but I wanted to see something quantitative–whether or not this was somehow reflected in the quality or quantity of our research papers. I went to the ISI Web of Knowledge, which indexes scientific papers across many disciplines, and searched for all papers containing the phrase “stem cells” between 1995-2008. I split the results by whether or not any of the author’s labs are in the USA, and plotted the annual number of papers published by the two groups. Here’s what I got:
G.W. Bush's 2001 executive order correlated with the USA falling behind in stem cell research
Up through 2001, the USA-based and non-USA-based production of papers on stem cells were nearly identical. After 2001–just as international publications went into a steep rise–the USA productivity in this field immediately flattened out. Bush’s executive order correlated exactly with a dramatic stunting of growth in the USA’s stem cell research programs!
I was also curious to see whether or not the 2001 executive order lowered the quality of the publications. I looked at the average number of times that papers from a given year were cited, between the two groups:
USA-based papers get cited about twice as often as foreign-based papers
Here, there’s no clear trend. The papers from USA labs are consistently cited about twice as often as those from non-USA labs, both before and after 2001. (The drop-off in recent years is just due to the fact that older papers have had more time to accumulate citations.)
It’s interesting that this ratio stays at about 2.0-2.5 through the entire range of years: does this mean that the papers published in the USA were able to keep a consistent quality of results, even though fewer cell lines were available and fewer papers were published? Or does it mean that the limited access to cell lines was less important than some other bias towards citing papers from USA labs?
Unfortunately, I don’t have an answer–though I’d love to hear from any readers who have thoughts on this. And I’m definitely looking forward to seeing what happens to these trends now that President Obama has lifted this ban.
p.s. Reader beware: I did this analysis on a lazy afternoon, with lots of cut+pasting and hacked-together matlab scripts. I certainly didn’t do any control experiments. If anybody has seen a more in-depth analysis of these questions, please let me know!
