Thursday, April 27, 2006

scientific illiteracy...

PLOS has this great/apalling article on scientific illiteracy that I think is quite topical these days... It asks scientists to become more involved politically, and to stop tolerating ignorance. "they would be asked to define DNA in their own words. “I got things like the ‘Dow Jones News Association,’” Miller says, laughing. “If you don't know what DNA is, you can't follow the stem-cell debate.”


Hot paper - pyknons

This red hot paper from PNAS talks about short patterns found in non-coding DNA, arranged into mosaics spaced at every 22 nucleotides in intergenic and intronic sequences called pyknons. Almost 130 000 of these elements were found in the human genome. When present in UTRs, they are thought to form secondary structures. Within intergenic sequences they may participate in in other regulatory processes. Maybe they can explain co-regulation over large areas ...


Interferons and jehova's witnesses

We have all heard that JW believe that blood has a sacred meaning and refuse blood transfusions. I was suprised to learn that the list of things not allowed is actually more precise than just crude blood transfusions, it also involves thigs that can be found in trace quantity in the blood such as albumin, cytokines etc, depending on how orthodox you are...


Chromatin maps

For the other chromatin freaks out there, Abcam published some new detailed chromatin maps for your personal enjoyment and home decoration projects...


Wednesday, April 26, 2006

Testing therapies one cell at a time

It seems the good old fashioned way to test therapeutics on a plate of cells is getting obsolete. now the new thing is to test it in individual cells. You can certainly save on the cost of reagents. All you need is a freekin laser, a bunch of fluoresent markers and dyes and 13 million dollars. And so is born the National Technology Center for Networks and Pathways from Carnegie Mellon University and the University of Pittsburgh.


Friday, April 21, 2006

Scientists send a letter to Harper...

60 prominent canadian scientists have sent a letter to prime minister Harper asking him to back down with the Kyoto protocol. The letter was published not surprisingly in the National Post and at the same time as Harper started making cuts with the liberal's program to comply to Kyoto. There has been an increase recently with political personalities and even scientists expressing doubts about global warming. The increased global temperature in the upper strata of the atmosphere and accumulated latent heat in the ocean is supported by a mountain of evidence, and so it is suprising to me that there is so much skepticism even with scientists about global warming ... It seems that people are still working on proving the hypothesis that human-produced greenhouse gases are the cause, or that stoping further increase of those gases will stop or revese this warming trend. But not believing in a warming seems like an extreme position. The earth has always had temperature fluctuations. The last mini ice-age was only 1000 years ago. So are they suggesting that now the temperature does not change anymore, even in the face of all the evidence to the contrary? I have also seen some scientist talking about being alienated because they did not believe and were publicly against global warming. I think one must be careful not to hear only a few dissenting voices over the buzz of the thousands that agree. I personally doubt that there is a conspiracy depriving researchers of grants for research disproving global warming. Or that these researchers are muzzled. Sometimes paranoia is a reflection of big egos, and self victimization. If this is confusing to scientist imagine to the public, who are more prone to taking the opinion of a few people rather then critically assess the available data. It reminds me of the letter by scientist that did not believe in evolution, even scientists make mistakes, we're human... Perhaps it is time that the thousands of other climate scientists send a letter to Harper. Do we need to scrutinize the latest data or the people that signed this letter?


A Brief History of Cancer Research

Nature Milestones is now running a cancer feature. A must-read for anyone in cancer research and a great reminder of the big ideas behind the research we usually pursue with such intense focus on a day-to-day basis.


Wednesday, April 19, 2006

Phycisist send a letter to Bush...

13 Phycisists, including 5 Nobel laureates, have sent a letter to president Bush asking him to back down with the nuclear threats to Iran. The phycists also reportedly tried to teach him how to pronounce nuclear [ˈn(j)uː.kli.ə(ɹ)] without much sucess...


Speaking of which...

Some of you may know that I've been involved in testing of therapeutics with a company called IBEX. Well my results cought the attention of some journalists at the AACR and a PR was issued. Basically I showed that expression of Kallikreins may modify disease progression in an ovarian cancer model in ways that hadn't been anticipated.


Sunday, April 16, 2006

Cambridge Science Goes Corporate

In a sad sign of the times, the University of Cambridge has changed it's tech-transfer regulations so that scientists no longer have any control over the licensing of their inventions/patents. Instead, the university will now license their work to whichever corporate entity they please. This policy change, touted as a huge advance in this Nature News propaganda article, puts Cambridge on par with such academic powerhouses as the OHRI/University of Ottawa. If you believe the article, this is exactly what Cambridge biological scientists have been needing. Yeah, I'm sure it's exactly what the world's leading academics want. Remember how Einstein was always crying about Princeton's crappy tech-transfer initiative and how it cost him the patent on the atomic bomb? Imagine the royalties they could have made off of the Cold War! What a missed opportunity for science. Or how about Cambridge scientist Stephen Hawking? Hopefully the poor guy will get a bit of cash when tech transfer commercializes the black hole as the ultimate garbage dump. Expect an increase in corporate interference and a concomitant decline in the quality of science at Cambridge in coming years.
On the topic of rants about the general state of science, don't you hate it when labs put out hokey, corporate-style "job" ads for post-docs?

Thursday, April 13, 2006

Oh Canaduh!

Further proof of americanization of Canada: Dr. Brian Alters, director of the McGill Evolution Education Research center, who was the only Canadian expert witness at the american Dover trial his getting flack at home. He submitted a grant application to SSHRC to study how the intelligent design movement in America affects how Canadians view evolution. Ironically his funding was denied because according to the reviewers, he failed to prove evolution theory had any merit! I'm scared, ignorance is gaining ground here too.


A New Kind of Science

Theoretical physicist Stephen Wolfram spent 15 years in seclusion developing what he says is a whole new apporoach to science independent of traditional mathematics. He also claims that the field he has opened up will solve most of the currently unresolved problems of sociology, physics, biology and pretty much everthing else. I'd say it's about 50/50 that he's either right or a complete lunatic. Either way, I was intrigued and nearly broke my back lugging home his 1280 page book from the library. Then, Rob found it for free on the web. So check it out, without the weight limitation, there's really no reason not to.


Wednesday, April 12, 2006


Apparently being a college proffessor in the US is the second best job possible. I don't know about their research however I don't see bikini inspector in the top ten jobs.
Also interesting is that included in the worst jobs for your investment is the academic research scientist.


Tuesday, April 11, 2006

The Universe - A Ball of Strings?

The NOVA series called The Elegant Universe reviews the physics of the universe and presents one of the latest attempts at a Theory of Everything, String Theory and M-Theory, and is freely available on the web. I say we organize a bayblab-sponsored group viewing.


Get Yourself an MIT Education Without the Hassle

Lately I've been thinking a lot about the potential merits of having a multi-disciplinary background as a biologist. For example the way things are going, mastery in fields like math and/or computer science could a lot of fun when combined with a background in biology. Unfortunately, becoming a recognized expert in another field means for most people going back to undergrad and going through the formal education process all over again. This idea is nauseating for many reasons, ie: a) You have to pay a university tuition, b) You have to live without a stipend or salary c) More exams d) You have to show up to classes e) You have to spend time on campus and risk getting beat up by the football team f) You would have to listen to dorky TAs who think they know more than you, beacuse they actually do.

With MIT's OPENCOURSEWARE you can get a lot of the benefits of a top-of-the-line university degree without wasting your time on any of the above. The site contains class notes, directives to TAs, assignments exams and textbook/web resource citations from real MIT courses, allowing you to do a self-directed course of study in any of a variety of different fields. Of course you don't get an actual undergrad degree, but hey neither did Matt Damon and he seemed to know a lot in that one movie. Of course you might argue that there's value in hearing real lectures by real professors, but the web has more podcast lectures than you could ever listen to in a lifetime...


Quantum Computers

For quantum idiots like myself there is a reasonably good science friday podcast on quantum computing by some dude from MIT who wrote a book.
Basically he suggests that the universe is just a quantum computer. And an interesting discussion on the monkeys on typewriters trying to write Hamlet sillyness.


North Wing gangsign

I have come to the realization that the northwing gangsign that I decided was cool is just never going to really hit the northwing mainstream.
So I guess that the bayblab posters are going to have to have their own gangsign.
Flash this bad boy next time you aren't carrying tissue culture:


Parasites in sushi

Because I'm a sushi fanatic people always ask me wether it's dangerous. Well there was one disease outbreak in Singapore that was related to salmonella coming from sushi. But we get those from chicken in North America all the time, and people still eat chicken. Some people have suggested parasites could be present in the sushi. Well according to my research tuna don't live in an environment conducive to parasites and so are not a concern. Salmon on the other hand does contain nematodes sometimes. Those do not survive well in the freezer and will be cleared by a week at -20C. If one does somehow make it to your stomach, we do not represent a natural host and it will just go through. On rare occasions it may illicit Anisakiasis, which is basically vomiting and diahrea 12h after ingesting the fish. The parasites howerver cannot go trhough their life cycle in humans and will die within a week. There is however one reported case of fish-to-bird tapeworm parasite implanting in human which made for some interresting fishing vacation stories about the size of the worm. Thankfully those are easy to clear with drugs or the milk-cookie-hammer technique. Pollution can also be a concern with red tides, heavy metals (mercury etc..). On a bright note, it seems sushis can protect from cancer!


You are sick!

Are you tired in the morning, does your stomach hurt when you are hungry, is your leg restless at the movies? It's no secret that people overmedicate, and that pharmas have a vested interrest in caracterising new chronic conditions. Well captain obvious investigates disease-mongering.


Monday, April 10, 2006

SETI is going broke!

SETI needs our help. When Arthur C. Clark speaks, geeks listen. Over the years, 5.4 M volunteers have given over 2.4 M years of computing power. With my own pentium 100 and a dialup connection I gave a whopping 0.007 computing years. SETI now called BOINK (Berkeley Open Infrastructure for Network Computing), no doubt in tribute to Calvin and Hobbes (scientific progress goes boink). They have just released a new software that raises sensitivity 2 fold and the region of space observed 30 fold. They need to raise 750 000$ to continue doing this work and need donation since the .com collapse has left them pennyless.


Saturday, April 08, 2006

Systems Biology

This month's Nature Reviews Molecular Cell Biology is dedicated to "Systems" Biology. This is a redundant term but the distinction is necessary today since most of biology operates under a reductionist paradigm rather than focusing on systems. It's time to start doing so because the key to understanding and manipulating the phenotypes of cells, organisms and populations (the only worthwhile reason for studying for biology in the first place) is essentially an exercise in modeling complex systems. So read it. Also, is a great resource, with links to hot new papers, conferences etc. The First Conference on Systems Biology of Mammalian Cells...interesting.


Thursday, April 06, 2006

I Always Knew miRNA Was A Hoax

The miRNA field is so hot these days, the Nature/Cell papers are being put out by the truckload. If you believe everything you read, they apparently play a critical role in regulating every critical cellular process. No doubt a lot of the data is true, but its hard to know what's real and what's fake these days. The problem with the rush to publish on such hot topics is that it makes it easier for fakers. A Japanese researcher in the RNA field is being accused of fabricating his results by someone in his lab, sounds like his supervisor. The accuser is calling for the retraction of several key papers, including two from Nature, on miRNAs in neuronal differentiation and in regulating DNA methylation and silencing.


Wednesday, April 05, 2006


  • The Human Genome Project is the world's largest collaborative science project. Everyone and their monkey has published a map of the yeast interactome. Who will speak for the poor old Human Interactome? At least one scientist, Marc Vidal, is calling for a collaborative Human Interactome project.
  • Michael Stebbins, a former senior editor at Nature Genetics, congressional advisor, and Cold Spring Harbor-resident researcher just put out an interesting-looking book, Sex, Drugs and DNA, on controversy and politics in current biological research. He's running a website and blog as part of a self-declared "campaign to get rid of elected officials that have done something egregious in health or science policy". The website also has a hitlist of American politicians to be "eliminated". Ha. Lots of ID proponents on the list as you might imagine.


Useless facts

1) Today at exactly two minutes and three seconds after 1 AM, the time and date will be 01:02:03 04/05/06. That will never happen again.

2) The world record for masturbation is 36 times in 24h. ouch.

3) The answer to overpopulation is apparently ebola... weirdo.


Tuesday, April 04, 2006

If Ants Could Fly...Origins of Insect Flight?

A very cool article - these wingless South American ants can achieve a primitive form of flight through orchestrated movement of their limbs. Like skydivers without the parachutes. I've been extensively studying the diagrams and video footage in preparation for my own inaugral flight off of the ORCC roof. Stay tuned for details...


Nucleotide Sequence is So Passe

Forget the human GEnome, it's all about the Human Epigenome Project. A much more difficult undertaking in some ways, but my money's on way more useful in the long run.


Don't Believe the Hype

Medical journals are an extension of the marketing arm of pharmaceutical companies.


Latest Mod/Hack for Your Urinary Tract

A few too many St. Patty's day beers left you with a leaky bladder? No worries, biotech has you covered: convenient, autologous bladder replacements can now be grown in a dish.


Saturday, April 01, 2006

April Fools

After having quite a few drinks last night, Rob finally admitted to wearing these, when engaging in role playing games.