Milking Snakes

I saw a great doco on TVO recently. It was about novel drugs derived from studying venoms of poisonous animals. It looks as if most of them have a mode of action that relates to neural transmission. Nature from PBS has some links on the subject of venom derived drugs. It looks as if the field is also quite busy since there has been an FDA approved drug based on the cone snail for calcium channel therapeutics. Check out you tube for a vid of a cone snail eating a fish. What is also pretty cool about this research is that work in the field involves cone snail colleting on the great barrier reef. From the PBS article about the doco: "Bryan Fry has milked thousands of snakes during his career." no comment.

A bad case of dumbed-down science

We were recently discussing the perils of analogies in science. This is an extreme example, where the work involves from what I can infer, a reshuffling and/or substitution of protein domains to make new peptide antibiotics. "You have a string of letters and that string of letters reminds you immediately of a sentence, a kind of incomprehensible sentence, and you wonder in that sentence, 'Is that meaning hidden?'" asked Stephanopoulos. He used the example of a sentence: "Dave asks a question." What Stephanopoulos did was the equivalent of substitute different names for Dave and found that the peptide often still beat the bacteria.

Harvard evolutionary biologist Marc Hauser said that using grammar rules to decode genetics and medicine is growing more popular. But he said he worries that too many people are calling grammar what is really just simple code, not nearly as complicated as human language. Berwick said the bacteria-fighting grammar rules are equivalent to the extremely basic spelling rule, "i before e except after c." The grammar rules Stephanopoulos developed are about what 2-year-olds learn on their own by listening to adults speak, he said." WHATTTTT?

How to win a Nobel

PLOS this week has a review of the book "how to win a Nobel" by Peter Doherty. Here's a few pearls:
(1) Learn to write clearly and concisely. The problem with much of science is that the scientists hurt their own efforts by being unintelligible.
(2) Be generous and culturally aware. Acknowledge the achievements of others. Every young scientist needs frequent reminders that it is important to have as few enemies as possible.
(3) Time is precious. Women in particular are vulnerable to “death by committees,” and their representation is sorely needed.
(4) Avoid prestigious administrative roles. This is a major source of destruction, particularly to those from clinical backgrounds. Now a sometimes beleaguered vice chancellor, I can only underscore the importance of this point.
(5) Live a long time. It may take 50 years for the Nobel recognition of a discovery!
Also I warmly recommend Santiago Ramon y Cajal's classic from 1898, Advice to a Young Investigator.

Carl Sagan Center of Astrobiology

For those of us hoping that there will be a spot for a biologist on a future Mars mission, rejoice. While NASA is cutting funds in astrobiology, SETI picking up the slack: " [today] a distinguished panel of institute trustees and staff will announce the formation of the Carl Sagan Center for the Study of Life in the Universe. The center's activities will focus on astrobiology and be dedicated to the memory of planetary scientist and astronomer Carl Sagan." Hopefully this will help restore some credibility to the whole enterprize, that some people dismiss as more faith than science.

Shrimp Running on a Treadmill

science definately needs more videos : run my pretty apetizer run... "A shrimp encountering a bacterial infection has mechanisms to fight this infection, but, like humans fighting an infection, the shrimp may not be as physically fit. In response to the movement of the belt of a treadmill submerged in water, shrimp will walk at slow treadmill speeds and swim at higher speeds. We have used this treadmill system to stimulate shrimp to high levels of activity after they have been injected with a dose of a common shrimp bacterial pathogen, Vibrio campbellii. "

MC Hawking Drops His Music Video Debut

Wow, this is the greatest animated video I've ever seen. MC Hawking, the undisputed king of theoretical gansta astrophysics, just put out his first video for the hit track "What We Need More of Is Science". A must-watch! Also awesome is the trailer for the album, "A Brief History of Rhyme".

From the smallest to the largest genome project

Clocking at a little under 160Kb, the carsonella rudii genome encodes 182 protein. Talk about streamlined. In fact this insect symbiont may be on the way to becoming an organelle. Still this is not as interresting as a free living organism in our quest to find the "minimum genome". Craig Venter (of the human genome fame) is interrested in finding this minimal genome to develop the new field of synthetic biology... "The Synthetic Biology Group is also interested in understanding and thus engineering new pathways ... Most genomes contain hundreds to thousand of genes necessary for adaptive living in complex environments. By synthesizing minimal genomes the team believes it is possible to construct simple cellular life with desirable synthetic properties... the team is dedicated to developing only synthetic organisms that completely lack the ability to survive outside the lab." Craig also recently announced the 10M$ X-prize genomics challenge (the same prize that was awarded for sub-orbital flights last year), to map 100 human genomes in 10 days. All you need is a few thousand summer students and lots of gels.

Organelle-sized fossils?

As we sipped bubble-tea the other night we were discussing how incredible it was to find a 550M years old single cell fossil. When we think about fossils we usually picture bones, which over time are permineralized, meaning the organic matter is replaced by minerals. Recently there has been accounts of soft body fossilization of the bone marrow. But that's still a long ways from intracellular fossilization. Even bacterial fossils are not single-cell fossils, they are usually remnant colony structures such as stomatolites of cyanobacteria or ferromagnetite deposits from magnetobacteria, or evidence of bacterial decomposition or "tunnels" (endoliths) left behind. So how can somthing like a flowing lipid-based membrane of a cell mineralize? Well it turns out the process is called diagenetic phophatization "Early diagenetic phosphatization of the remains probably occurs following shallow burial and in proximity to decomposing phosphate-rich macroaggregates. Depending on phosphate availability, the resulting phosphate layers are deposited on the outside, inside, or enveloping the acritarch organic walls from both sides...under local conditions where pH and activities of P and HCO₃- turn phosphatization on and off"

Cellular Randomness

I vaguely recall a discussion with Bayman about cells being different due to just random fluxuations. A paper in PLOS addresses just that with analysis of mRNA and protein abundance in individual clonal cells. It looks like there indeed is alot of randomness especially when it comes to mRNA abundance (figure suggesting chromatin structure effects above) but it seems (on first glance of the paper) that lots of this effect is buffered and protein abundance is less random. I wonder how OPEN PLoS is and if posting the figure like this is OK?
Summary in Nature Methods (need subscription).

lan-egeddon

The gamer nature of the average bayblab reader should welcome one of their own into the fold.

Pure Pwnage is a made-for-internet TV series about a pr0 gamer named Jeremy whose sole drive is to pwn n00bs.

This is another example of how anyone cna acheive stardom on the internet. Episode 12 is about to be released, you can download it on the site or see it's silverscreen premier in Toronto.

Highlights:
-Doug's (Jeremy's friend) comment about RL (real life): "It's basically like FPS but better graphics"
-Jeremy - You can train a n00b, but he'll just be a trained n00b...

Bayblab podcast episode 1

You can download or stream the first episode of bayblab podcast here until i setup a proper rss feed for you ipod lovers...

Distractions

Thought the other members of the bayblab would appreciate this.
Found on Boingboing.

Bayblab #1 at predicting the IgNobels

We have a surge of traffic to the bayblab website today thanks to our successfull prediction of "Termination of Intractable Hiccups with Digital Rectal Massage" as a IgNobel 2006 laureate in medecine. We are currently the #6 hit on google for those particular search terms. It never felt so good to be experts in the science of assology. This is a testament to the superiority of bayblab to sites like thompson scientific. Our team of experts recognised back in June the potential of this reaserch based on the limited scope of this new field of assology and the lack of any references and citation to the work. Other winners include :
Maths: How many photos must be taken to almost ensure no-one in a group shot has their eyes closed, by Nic Svenson and Piers Barnes
Ornithology: Why woodpeckers do not get headaches, by Ivan Schwab and the late Philip RA May
Nutrition: Why dung beetles are fussy eaters, by Wasmia al-Houty and Faten al-Mussalam
Acoustics: Why the sound of fingernails scraping on blackboards is so annoying, by D Lynn Halpern, Randolph Blake and James Hillenbrand

Methuselah

Some info on the 'Methuselah' tree. Apparently it's the longest living thing alive. However I was wrong when I stated earlier that it is a species. Methuselah is the name of a specific bristlecone pine tree that is 4725 years old. There is also a somewhat interesting NOVA doco on Methuselah. Someone needs to update the wikipedia entry on Methuselah, because the biblical Methuselah doesn't hold a candle to this tree, he lived and died during the course of this trees life.
Lo-res pic included.

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.