Taking the best friend thing to a whole new level...dogs will cure cancer

The case is made for dogs as a realistic cancer model for drug development in this month's Nature Biotechnology. The arguments are quite compelling, and given the clinical trial bottleneck currently limiting the development of new therapies, I wouldn't be surprised if the cure for cancer is discovered in someone's pet dog sometime soon.

Computational design of receptor and sensor proteins with novel functions

As cited on the bayblab podcast, a computational based method for engineering receptors that bind a pre-determined ligand of choice.

Synthetic Biology

A number of high-profile researchers and institutions across the US are jumping on to a movement they're calling synthetic biology. The problems are old (biofuel production, cancer therapy, small molecule production, etc.), but the philosophy is new. The aim is to develop a bottom-up approach to assembling, from simple and standardized parts, living organisms that perform defined tasks. Check out the latest in the field - most of the talks from the synthetic biology 2.0 conference are available as online webcasts.

Nobel Rejections

I came across a paper summarizing some of the hostilities and/or manuscript rejections associated with discoveries that were eventually awarded a Nobel prize. Obviously, innovative science is often not appreciated immediately. Here's a few notable examples:

• Hans Krebs, manuscipt on the citric acid cycle. Rejected by Nature. Published in Enzymologia
  
• Kary Mullis, manusciprt on the polymerase chain reaction. Rejected by Nature, Science. Published in Methods in Enzymology
• Hartmut Michel, manuscript on the determination of the three dimensional structure of a photosynthetic reaction center. Rejected by Nature.
• Pavel Cherenkov, manuscript on "Visible radiation produced by electrons moving in a medium with velocities exceeding that of the light". Rejected by Nature.
  
• Burnet could not find any journal to publish his work on the production of antibodies. The work appeared instead in an unrefereed monograph.
  

Nobel prize to Digg users

Of course you've all read about the nobel in med to RNAi. Probably it is deserved? Seems just a bit premature as the mechanism/function is not nailed down. However the discovery certainly is profound.
You've probably read about it on nature news or some other science source. You know that slashdot sucks when almost ALL the comments on this post were non scientific. I think this made me finally appreciate the clear superiority of digg.com. Digg actually has good user comments.
Of course Slashdot and Digg pale in comparison to bayblabs authority.

Home Science Crafts Project

From the "OMG I can't believe someone did that, barfffff" department: A lazy sunday afternoon crafts project for your kids that involves mouse taxidermy. Or do-it-yourself hemroidal surgery on your pet turtle! Warning, you may be scarred for life.

Damn that's a big pipettor!

Check out the macropipette (is that a P-10^12?).
I came across this photo on the Lim lab website at UCSF (pretty cool as lab websites go).

Bet on Nobels

Each year Thompson Scientific, better known for updating impact factors of journals, makes a prediction on possible Nobel Laureates based on their citation counts. They've proven to be quite successful in the past. This year they have for medecine the discoverers of homologous recombination, nuclear hormone receptors, and DNA fingerprinting. And it's a tight race, just look at the polls:
34% - Chambon, Evans, Jensen
33% - Capecchi, Evans, Smithies
33% - Jefferys
So which are you putting your money on?

Spiderman, Spiderman. Does whatever a zebra tarantula can.

In Nature, the zebra tarantula is shown to be the first example of a spider spinning silk from its feet instead of its abdomen. It shoots out adhesive silk to aid in locomotion and climb vertical surfaces. Just like the real Spiderman.

The Allen Brain Atlas

Speaking of cool 3D visualization tools. I highly recommend you try this with your favorite gene. It displays expression data in the brain in 3D at a high resolution. Really impressive! But you'll need a decent computer, my laptop was chugging worse than at a CS LANparty.

Robots - The Good and the Evil

What if those first-person shooter/Counter-Strike robot players were real - ie had a remote-controlled corresponding physical representation in the real world? What if your character also had such a physical representation when you were playing video games? Would you care? Big deal right? Video games aren't real and neither are the physical robots structures. Good clean fun and no (biological) one gets hurt. Except that what you're talking about is a robot war. Sound far-fetched? Maybe, but the US military is taking advantage of the gong show that once was Iraq to test out their prototype robot soldier as we speak. It actually looks pretty wimpy, but hey, it can fire a machine gun like nobody's business. Slap some camo on that thing and all of a sudden it's a bad-ass killing machine. I can't decide if robot wars would be a step forward. Robots killing robots sounds better than people killing people, and we could just settle all our international conflicts at a good old-fashioned LAN party. We could even move the physical representation of the battle somewhere they wouldn't hurt anyone or our environment, like the moon or Pluto (it's not even a planet anyway) and let them duke it out. Hell, you could just eliminate physical war altogther and make them entirely virtual. It just makes you realize how out-dated physical fighting really is - why don't we just divvy up the world's resources over a euchre tournament?

On the other hand, if one side, like the US gets their war-bots online first and no one else has any, than it'll be robots vs. people which is very scary. Maybe it's a good thing that the Japanese and Chinese are leading the way in robotic technology.

Speaking of which, I just heard about this robot that's all the rage in Japan. The robot, called wakamaru, can speak and understand Japanese, remember and recognize up to 10 familiar faces. It can wake you up in the morning, remind you about appointments and even call you up if there's trouble at home. It gets around the house on its own thanks to an internal map, and returns to its charger when the battery's low. Best of all, it runs on Linux. Wired reported back when it was released.

NCI-60

There is a little historical perspectives type article in Oncogene about the NCI-60 cell panel and the standard ways to show data from screens of these cell lines. The article mentions some online tools for looking at data of this type but I haven't spent the time to figure it out (I can't even see how they call it 3D). It is at least interesting to note that the NCI-60 cell panel was origonally set up as a lung cancer cell panel that was in need of negative controls.

IA updates

Yeah more IA updates. As always very good.

PLOS one : a new way to publish

Nature recently started an experiment in open-acess online peer reviewing. The concept is simple, the reviewers, from the same field, are open to critisize and submit comments pre-publication, but they do so under their own name. I think this could lead to greater accountability, and better peer review ultimately. But how many are willing to try this experiment? If the paper is not accepted for publication, everyone is free to replicate your experiments and scoop you. PLOS, everybody's favorite open access journal, is going even further by starting a new journal, PLOS one, which will abide by the same principle : open discourse + access + data = open science?

Fortune telling through science

It seems anti-aging research is getting a lot of press recently with the announcement that the co-founder of Paypal is teaming up with the infamous Aubrey De Grey to match the funds of the Mathuselah prize. Whoever gets his mice to live longest gets the 3.6 M$ jackpot. The evil scientists on their tropical island are collectively rejoicing. Then this paper comes out on PNAS saying that by analyzing every biomarker under the sun you can guess how long you'll live. It seems to me we could use those markers to breed super-mice. I for one welcome our immortal mice overlords. If you are interrested, those are the rules: "The rejuvenation prize deals with peer-reviewed studies involving at least 40 animals, 20 treated and 20 control. Treatment may begin only at mid-life, and the average lifespan of the 10% longest living treated animals is used for the record. As of 2005, this record stood at 1356 days (about 3.7 years); the treatment was calorie restriction."

Even Patry has a Podcast

It seems our beloved overlord, "el presidente" Gilles Patry recently started a podcast of his own. If even Patry has a podcast, it's definately time for Bayblab to develop its own... So tremble in anticipation to our upcoming podcast, featuring fermentation product-fueled discussions of the effect of aptamers on extrasolar planet geology.

Firefox scholar

I am going to wet myself. This pleases both the scientist and the tech geek. Firefox Scholar is a set of extensions to the popular open source web browser that will:

• Recognize and capture metadata from online objects (e.g., author, title, publication information of books)
• Collect documents, images, and citations from the web
• Allow materials to be sorted, annotated, and searched

The program will be free and will replace programs like EndNote, while operating completely within the browser window. A beta of Firefox Scholar will be available in the summer of 2006. Like the Firefox browser itself, Firefox Scholar will be open and extensible, allowing others who are building digital tools for researchers to expand the platform.

Buy cigarettes in bulk!

Forget about your local dealer or even starting your own meth lab... any good scientist knows the best way to score a quick hit is to use your CIHR funding on the good stuff from Sigma. Cocaine, heroin and other drugs are readily available (once you can prove to the DEA that it's for 'research purposes'). Or better yet, just buy one of their Pseudo(tm) scents (now available in 'corpse'!) and sprinkle it in your co-workers luggage next time you go through airport security...

And for those of you not really into the hardcore drugs and your Player's Light just won't cut it, you can buy research cigarettes from the University of Kentucky. Now, I'm not sure what the current price for a pack of smokes is, but 12 000 cancer sticks for $2800 doesn't seem like that bad a deal. Maybe smoking isn't so un-economical after all.

What's cooking?

If you are into extreme cooking you may like these recipes involving high voltage and burninating food. The videos are a must-watch. I wonder if we could come up with recipes of our own involving the drying ovens...

Luxuriant Flowing Hair Club for Scientists

From the annals of improbable research, the group responsible, among other things, for the IgNobel prizes comes a club for scientists who have luxuriant flowing hair. It is a well known fact that the lenght of the hair is correlated to the scientific abilities, just take Newton and Eisntein as examples. "The project was first announced in mini-AIR 2001-02. The initial list, assembled by a subcommittee comprised of seven members of the American Association for the Advancement of Science, was meant as a nucleating seed, from which a larger list could grow." Well Bayman, I think it's time you let your hair grow back!