Science Top 10 of 2006

I took a quick look for top stories of 2006 and of course nature news has the best and most comprehensive top 10 lists of 2006 science. Unfortunately a ridiculously expensive subscription to Nature is required.
Top 10 readers choice
Top 10 editors choice
Top 10 news features
Top 10 most commented on
Science magazine also has a rundown of top 2006 science and named the solving of the proof of the Poincare Conjecture as #1. The runners up are also briefly described. Obviously lots of overlap with the nature top 10s.
For those without a university subscription to Nature or Science, Discover magazine has a readers choice of top10 science news stories of 2006.
Also the Science Friday podcast (direct XML link) has a typically mediocre review of 2006 science.

Faster Buzz via CO2 (s) & alcohol

Found on Digg.com videos , something that I'm sure that we will simply have to try soon. I'm thinking new years. Check out this great video of alcohol inhaling using dry ice. Update: as mentioned in the comments the bayblab carried some tests in the lab and came to the conclusion that this is a cruel hoax...

The Rabbit & the Fox & urine & poop

Cool stuff. I got a fox face for christmas. The fox face is basically just the hide of the face with eye mouth and ear holes. No other taxidermy specialness.
Anyways I introduced to my pet rabbit (which my wife insists is very cute) and it totally freaked. I tried it a couple of more times and tried to make it's environment otherwise comforting, however, it still FREAKED, sprinting back to it's cage.
Interesting since this rabbit has never even been outside. I would take this to mean that the scent of a fox INSTINCTUALLY freaks out rabbits. The fox is a rabbits number 1 predator, in some habitats, and it's urine scent is actually sold as a rabbit repellent. Is it possible that this repellent works on rabbits even if they have never smelled a fox previously? Perhaps it similar to the instinct that I have that poop stinks. Not that poop is my predator but that it is associated with disease.

Geek's guide to the holidays

The holidays are upon us, and with them comes the feasts ad libitum, the presents and all that time consuming inter-personal mingling with people sharing a recent common ancestor with you. Lab geeks are really a breed of their own, they will actually come to work on christmas because those mice wont inject themselves, those cells need passaging, that 96h time point happens to fall that day. If you are in that situation here are a few things that may help you out find last minute presents in the lab, and prepare some last minute cooking.

Top five things found in the lab suitable as stocking stuffers:

1. Rack of 50ml Falcons, you can pass those as a customizable "spice racks".
2. A seringe/needle set, for your diabetic cousin.
3. A roll of pH paper, for your rich uncle who owns a pool.
4. A roll of autoclave tape, always usefull.
5. A box of medical gloves, practical for cleaning.

Top five lab dishes:

1. Eggnog: ddH2O, 5% skim milk powder, 10-40% EtOH (molecular grade, denatured may contain methanol).
2. Ice cream: 50 creamers from the coffee club, 30g Glucose, add liquid N2 slowly while swirling.
   
3. Munchies: irradiated rodent food pellets, NaCl.
   
4. Seafood platter: If your model organism is an Echinodermata, you're in luck as they are good raw with some lemon (Other mammalian model organisms may be roasted in the autoclave if need be).
   
5. Marmite: use the LB recipe but dilute less. You may substitute NaCl for glucose and add agar for a jello-type desert.

Hope this helps... Happy holiday suckers!

IA updates

I gotta get everyone to go to IA once again. The updates are top notch including some science stories missed by even the bayblab. Unfortunately dark matter is accidentally referred to as, "Hawkin's missing universal mass". I'll have to check in on Stephen next podcast to see how he feels about that particular inaccuracy. There's even a link to a groups page who's mission it is to safeguard humanity from the creation of a blackhole in particle accelerators.
" Our goal is to prevent, and also make plans on surviving when possible, particle accelerator mishaps including quantum vacuum collapse, mining the quantum vacuum, formation of a stable stranglet, and the creation of artificial mini-black holes."

The origin of geranyl geranyl

Just thought I'd share this. Geranyl geranyl is a post-translation moiety that is added to proteins like Rho and Ras to make them stick to membranes. It is a byproduct of the cholesterol-mevalonate pathway. Have you ever wondered what geranyl stood for and if it had anything to do with the geranium plant? Well it turns out geranyl related compounds are terpenoids found in the essential oil of the geranium and also from other plants such as roses. Geranyl diphosphate, pyrophosphate, acetate and geraniol (with an alcohol group) are all fragrant compounds. They are used in flavoring, perfumes, as insect repellent, insecticides, and apparently in cosmetics. The cigarette manufacturers are all too happy to add them to their cancer sticks, so next time someone complains about the smoke smell, you can tell them it smells like a rosebush.

The evolution of robustness

Genomic robustness is just one of those things that seems almost counter-intuitive. For evolution to take place, one needs to have imperfect replication of the genetic material to generate diversity. At the same time mutations are a danger to fitness as the chance that they will be beneficial is slim. And so most organisms have mechanisms to protect against deleterious mutations such as proofreading enzymes, DNA repair enzymes, apoptosis, and redundant genes. And so there is a fine balance in the evolvability rate, where a less stable genome permits higher diversity and presumably a better chance to evolve fast enough to cope with changing environments, versus robustness to make sure the species doesn't go the way of the dodo. A nice article in PLOS asks this question: "And if robustness has evolved to maintain performance, what prevents systems from becoming ever more robust?"

The articles then goes into more details, one of which might interest you virus people:
"Populations evolving at high mutation rates may settle in regions of genotypic space where mutations are less deleterious, on average, than those regions that attract populations that experience low mutation rates. The idea is that evolution at low mutation rates favors populations that achieve high fitness peaks, even if they are surrounded by steep cliffs, because mutations that push progeny off those cliffs are rare. By contrast, at high mutation rates, most offspring carry mutations, and selection favors populations that find lower fitness peaks surrounded by less precipitous mutational chasms. Experiments with digital organisms (self-replicating computer programs) provide direct support for “survival of the flattest” at high mutation rates [8]. RNA viruses also have very high mutation rates, and a recent experiment implicated the importance of mutational robustness for them, in this case, by showing the loss of robustness in viruses that evolved at high multiplicities of infection, where co-infecting particles guaranteed redundancy and allowed their native robustness to decay [9]."

Very interresting stuff. Darwin would be proud. He was rich bitch.

Creationists are Less Susceptible to HIV

That's right, true-believers. Two trials have demonstrated that circumcision dramatically reduces the risk of HIV infection in heterosexual, African men. In a study of 8000 men in Uganda and Kenya those who were circumcised showed a 50% reduction in new HIV infections. This supports a previous South African study that showed similar (60%) reduction in circumcised males. In fact, the results were so dramatic that the NIH ended the study early claiming it was unethical to not offer circumcision to the control group. The reason for protection is unknown, but it has been speculated to be due to either an increased susceptibility of foreskin cells to HIV infection or that the circumcised penis is less sensitive and less likely to bleed. Dr. Kevin de Cock (*snicker*) of the World Health Organization warns that this is by no means a magic bullet, but is a complementary approach to other HIV prevention methods currently in use in sub-Saharan Africa (such as encouragement of condom use) where AIDS is a devastating problem.

What does this all have to do with creationists? Well, God-fearing folk are more likely to already be circumcised, and therefore already at a lower risk. And while the results of these studies are dramatic, I don't think Richard Dawkins will be marching willy to the guillotine any time soon.

Chemical Origins of Life

The citric acid (or Krebs) cycle is a core metabolic pathway conserved amongst all aerobic cells. How this pathway came to be in the absence of complex macromolecules (enzymes) in the primordial soup is a key question to the origins of life. Several of the steps of the citric acid cycle involve decarboxylation or oxidation and their reverse reactions provide an interesting platform for creating useful organic molecules from carbon dioxide. A recent paper published in the Journal of the American Chemical Society has driven the reverse reactions of several steps of the TCA cycle using photoreactions and a simple mineral catalyst, ZnS (full text, may require subscription). In total, 3 of the 5 reductive reactions of the reverse Krebs cycle were succesfully driven in this manner, demonstrating the plausibility of the idea that useful biomolecules can be generated in a prebiotic system.

Bayblab podcast episode4 part II

In the second half of episode4: Hawking eats babies, a canadian celebrity impregnates american cows, Rob wants to burn the amazon and Jack Bauer is on drugs. PLEASE VOTE FOR US ON DIGG!

Supernumerary limbs

So a couple weeks ago, japanese researchers found a dolphin with an extra pair of fins near his tail. Obviously all sea mammals had land dwelling ancestors, which explains why cetaceans still have vestigial hind limb bones, even though the limbs never get to poke out. Now most of the patterning and limb development relies on, you guessed it, Hox expression. Therefore this is likely another example of the power of Hox which presumably was desilenced in the protolimb. Is this some sick joke by Darwin, or a test from God? I mean this looks awfully similar to the darwin fish. Lets see what the "Answer in Genesis" has to say about that:

"Biblical creationists have been so successful in disseminating information that counteracts evolution/millions of years, that as soon as anything arises that remotely looks like it could in some way support evolutionists/millions of years, it almost immediately becomes headline news." Yes obviously creationists are crumbling under their mountains of evidence, we're just happy to get a dolphin once in a while.

"Because of their obvious evolutionary bias, they have already jumped to a conclusion in interpreting these fins as back legs—before they have x-rayed the fins and carried out detailed research. " Hmm, yes scientists are so biased by facts.

"Homologous structures are seen throughout the vertebrate phyla—but as creationists have pointed out so many times, the homology argument does not support evolution, but rather a common designer. There are many problems with the homology argument as used by evolutionists. For example, the rudimentary male mammary gland and nipple are clearly homologous to those of the female, but they are not taken as evidence that males once nursed their young." Well maybe they should read the bayblab, they could learn a thing or two about that.


I find that last "argument" particularly absurd. Lets take the example of the banana. Creationist call it the atheist nightmare (video included on how to convince atheists about it). I mean what better proof of intelligent design than the banana. It fits perfectly in your mouth (or any orifice really), it tells you when its ripe, it tastes good, it has no seed and it comes pre-wrapped for your convenience! And if you really think about it, doesn't the banana look a lot like a dolphin. It's practically the same shape, but a different colour and it's in the sea and doesn't really fit in your orifices. Obviously they have the same designer. That argument is fool proof. In fact, it's true bananas where intelligently designed, I agree, except it was designed by humans, by very carefull selective cloning. In fact all the bananas out there are sterile clones! In fact this type of clone monoculture is the reason the much better "gros michel" banana was wiped out by disease, forcing us now to rely on the "cavendish". Now for more animals with extra limbs check out this seven-legged transgendered deer... enough said.

A Trojan Horse Vehicle for Shameless Self-Promotion

A current featured article at nature.com...you gueseed it - "Trojan Horse Delivery of an Oncolytic Virus Circumvents Anti-Viral Immunity". We actually changed the "trojan horse" part of the title to "cell-based" on the last revision at the editor's request, but somehow the good old trojan horse got mysteriously smuggled into the website...

Male Lactation

This post is Anonymous Cowards fault. He mentioned that it existed in the podcast and therefore I HAD to look it up. There is a Wikipedia entry on male lactation, however to me much of it sounds pretty sketchy. While maybe it's possible while men are on hormone treatment or something I'm sure that it is not possible in most men. Articles like this on male lactation add to my skepticism because the author suggests that the male started to lactate using the power of his mind. The power of my mind tells me it's pretty gross and there will be some serious psychological damage to a baby who is forced to feed from a hairy man boob. This link, about halfway down, has another account of male breast feeding, from the Talmud, where it is suggested it was a miracle. I wonder if the infant would agree that it was a miracle.

Senile mutant ninja turtles

If you have listened to the podcast yet, you'll know that we discuss the subject of aging research to great lenghts during which i bring up the point that perhaps some of the clues of old age could be gained from organisms that do not age or are very long lived. Recently, examples have come up quite close from here, in Quebec. The arctic shark, or greenland shark is found in the St-Lawrence or living under the ice in the North Atlantic. This 6m long beast weighing up to 2 tons may be the longest living vertebrate, presumably because of its slow metabolism and because sharks are long lived in general (and cancer free). Another example is the turtle, which some biologist think might not experience aging at all. Could this be related to their ability to breathe through their ass? The article gives quite a bit of interresting facts on turtles... This one was particularly interresting: "Geneticists have proposed that the turtle shell may have appeared quite suddenly in the distant past, rather than emerging slowly through modest, mincing modifications of pre-existing structures. They suggest that the dramatic innovation could have arisen from just a few key mutations in master genes like the so-called homeobox genes, which help specify an animal’s basic body plan. If the shell did burst on the reptilian stage more or less fully formed, they said, that would explain the lack of “intermediary” fossils or prototurtles in the paleontological record. "

Phage Therapy

Dr. Ken Garson, lab guru and suspected former KGB agent, once told me that in Russia they used to use bacteriophage in operating rooms to prevent infection. Cool.
So I finally checked it out and it was all mainstream science news in 2002. Even making it into Wired magazine article about the promise of bacteriophages as antibiotic resistance increases in prevalence, the article also mentions a company Novolytics that is trying to develop this as a new bacteriophage technology. Also the authoritative Nature News had a nice article that has a bit more background on the previous Soviet technology. Apparently phage creams and such were commonly available there. For the truly interested there have been some sophisticated studies of the effectiveness of these phages, even going as far as to use the Trojan Horse concept.

bayblab podcast: Episode 4 part-I

Finally the latest podcast is born, rejoice. Now with 50% less Rob laughing into the mic. In the first part of episode 4: A fight to the death of Dawkins versus Collins who will win? What to do if your tool gets stuck in the zipper? Can you cook an egg with your cellphone? Why engineers are intelligent designers but biologists suck at fixing radios? Which bayblab crew-member has extra nipples and how to make them lactate and finally how bubble tea may give you more orgasms than you can handle....

Cellular Polarity

Apparently not only are cell divisions asymmetric in terms of distribution of old and new DNA between daughter cells but it looks like even aggresomes, those nasty aggregates of misfolded proteins such as those found in both Huntingtons and Parkinsons disease, also segregate asymmetrically between daughter cells. Thus loss of cell division polarity, that has been shown to occur in cancer, may have other disease consequences.

Conflicts of Interest

Related to the 'Pfizer is in Trouble' post on the bayblab, is a story from the BBC that Professor Sir Richard Doll, the scientist who is credited with linking smoking with lung cancer, took some money inappropriately from some chemical companies. Sounds like he got away with it because discloser was not an issue back in the day. Pretty disappointing that someone who is kind of a hero of science, knighted by the queen and all, may have contributed to public distrust of science.

Patents and Science

Coming from a lab where patents are part of the game I often think about their influence on research. Patents, I think, have encouraged our lab to focus research on subjects that will lead to products that could actually improve the health of patients. A very good thing. However patents can also be an extreme hindrance to moving research to patients, because it moves the focus away from helping people to making money. A recent science friday episode talks with Lori Andrews, a co-author of a opinion piece in Science, about patents and science. [Link to the opinion piece in Science Mag (probably requiring a subscription).] Not really much new information about the debate on the show, however, some examples of disgusting abuses of patent law (not in the opinion article) will convince anyone that the system (at least the one in the States) needs change.

IA updates

Check out Informationaddiction for your dose of politically slanted tech news. Some interesting Biology and Genetics links up this time for your enjoyment. One of the links talks about the molecules that are probably responsible for migratory birds ability to navigate using the earths magnetic field. The link is terrible but here is a link to an article from PNAS that is much better. (and older). Apparently birds likely 'see' the magnetic field of the earth as these molecules are found in their retinas.

ViTa database

This is pretty much most interesting to me, but since the previous post mentioned a new database I thought I would mention ViTa. This is a new database that catalogues predicted (an separately experimentally confirmed) microRNA target sites on viruses. I give it a thumbs up on the interface, however I noticed that none of the DNA viruses I looked at (adenovirus, herpes and vaccinia viruses) had NO predicted targets while the RNA viruses I looked at (vesicular stomatits virus, poliovirus and HIV) had LOTS. I assume this means the database is still incomplete.

Pathway Interaction Database

From the cool resources department: the Nature website now features a pathway interaction database. Less flashy than Biocarta (another good pathway resource), the PID features almost 300 pathways and over 4000 interactions (from both Biocarta and an NCI-Nature collaboration) showing regulators, interactions and up- and down-stream effectors, all clickable for even more detailed information. Great for when your PI just needs to see a picture. The default display is SVG, which didn't seem to work on my laptop, but GIF, XML and other formats are available.

Pfizer is in trouble

Pfizer has been in the news a lot recently because they halted development of their next cholesterol drug Torcetrapib, which increases HDL levels while lowering LDL, which was supposed to replace Lipitor, the $12B blockbuster that is soon coming off patent. Until then, Pfizer has gotten a ruling in canadian courts to block the development of generic versions of Lipitor. However here at bayblab, we know this whole cholesterol thing is bullshit. Consider a similar scenario: high PSA levels are indicative of prostate cancer. Does lowering PSA levels prevent prostate cancer. Hell no. In fact the popular hairloss drug Propecia, which does just that, sometimes impairs the diagnosis of prostate cancer, putting you at risk to have unreported disease. That is because a diagnostic marker is not necessarily a therapeutic target. Often they are a consequence of the disease not a cause. In fact numerous studies have pointed out that cholesterol lowering drugs do not improve health of reduce mortality: "In the 22 controlled cholesterol lowering trials studied total and coronary heart disease mortality was not changed significantly either overall or in any subgroup. A statistically significant 0.32% reduction in non-fatal coronary heart disease seemed to be due to bias as event frequencies were unrelated to trial length and to mean net reduction in cholesterol value; individual changes in cholesterol values were unsystematically or not related to outcome; and after correction for a small but significant increase in non-medical deaths in the intervention groups total mortality remained unchanged (odds ratio 1.02)." Yet these drugs get approved by the FDA (and Health Canada). Is it a case of corporate meddling with regulatory approval? Well it wouldn't be suprising considering Pfizer has been caught in the act today: "A government researcher pleaded guilty Friday to misdemeanor conflict of interest for taking $285,000 in consulting fees from pharmaceutical giant Pfizer Inc. for work that improperly overlapped his official duties.".

Human Epigenome Progect

Now that the genome is done it's time for HEP. Epigenome I guess refers to the epigenetic information in the genome, which has been shown to differ between different tissues ect, usually this refers to DNA methylation. A paper recently reports the high-resolution methylation profile of a few human chromosomes. I personally didn't get much out of the paper but I really enjoyed the news and views on the paper. Also interesting in the same issue of Nature Genetics there is a paper that demonstrates a relationship between aberrant transciption suppression via histone methylation (another epigenetic expression control mechanism), and bladder cancer.

Atheists for Jesus

The always entertaining, always provacative Richard Dawkins did this great Q&A with the general public via email. The questions just about cover it all and cut right to the point, for example:

Are people who advocate intelligent design stupid, and do you think natural selection will operate to remove them from future generations?

Not surprinsingly, the reponses are intelligent and often extremely funny. I recommend. 10e692 bayblab points.

Water on Mars?

Water on Mars? Hey maybe there is bacteria there too.: what is the most abundent protein on Mars?

What is the most abundant protein in humans? ...on earth?

Today at lunch we had a heated discussion on what is the most abundent protein in humans (by mass?). We speculated that it would be a member of the cytoskeleton (actin, keratin), or part of blood (albumin, hemoglobin), an extracellular matrix/bone component (collagen), a mithochondrial enzyme (GAPDH), a very small abundant protein (ubiquitin), or a component of chromatin (histones). We each picked one and made a bet to what google would tell us. Well after a bit of searching here is what I find. From google answers: "I have found definite statements that collagen is the most abundant, followed by actin. I have found claims that osteocalcin takes the 7th place, and SOD the 5th. Albumin, myosin, keratin and the globulins are also strong contenders for places in the top 10."
There is of course differences when you compare moles and mass, as proteins like collagen are massive (>1000AA) compared to something like ubiquitin (<100AA). But looking at mass we can guess something like this...

1. Collagen (25% of proteins)
2. Actin (20% of dry muscle mass)
3. Myosin? (second most abundent in muscle) or keratin (most abundent in epithelium/hair)?
   
4. Albumin? (60% of serum protein,and only 40% of all albumin is present in serum)
5. Superoxyde dismutase (most abundent in mitochondria)
   
6. Hemoglobin? (95% of RBC dry mass)
   
7. Osteocalcin (second most abundent in bones after collagen)

But which protein is most abundant on earth? Well it turns out it could be rubisco, the photosynthesis enzyme (30-50% of soluable chloroplast protein), found in plants, algea and plancton...
However, I have not given up on the idea that it should be a bacterial protein considering they have so much biomass, all to way to 2km down the crust and at the bottom of oceans. I would quote Stephen J Gould for this matter : "When one considers how deeply entrenched has been the dogma that most earthly biomass lies in the wood of our trees, this potentially greater weight of underground bacteria represents a major revision of conventional biology and quite a boost for the modal bacter. Not only does the Earth contain more bacterial organisms than all others combined (scarcely surprising, given their minimal size and mass); not only do bacteria live in more places and work in a greater variety of metabolic ways; not only did bacteria alone constitute the first half of life's history, with no slackening in diversity thereafter; but also, and most surprisingly, total bacterial biomass (even at such minimal weight per cell) may exceed all the rest of life combined, even forest trees, once we include the subterranean populations as well."

The Beginning of Direct Online Results Publishing?

The David Ron lab website is the first I've seen to publish data (albeit negative data), helpful hints, and positions on contentious issues directly to the web. Nice job. 10e37 bayblab points. Of course the idea was first proposed by us bayblabbers, who talk a lot of smack but never do anything about it.... Interestingly, the one piece of data posted so far was a mini-paper in support of the notion that nuclear translation is bullshit. Still, this is extremely cool and demonstrates the potential power of direct online results publishing.

Gene therapy in your jeans

Forget cialis and viagra, ED treatment is now turning to gene therapy. The first human trial in which a naked DNA plasmid of the gene slowpoke is injected directly in the corpus cavernosum: "Eleven patients with moderate to severe erectile dysfunction (ED) were given a single-dose corpus cavernosum injection of hMaxi-K, a "naked" DNA plasmid carrying the human cDNA encoding hSlo (for human slowpoke), the gene for the alpha, or pore-forming, subunit of the human smooth muscle Maxi-K channel.". This is from the same research team that brought you this quality research (for you triathlete females out there) : "Bicycling is associated with neurological impairment and impotence in men. Similar deficits have not been confirmed in women. Aim. To evaluate the effects of bicycling on genital sensation and sexual function in women. Methods. Healthy, premenopausal, competitive women bicyclists and runners (controls) were compared. Conclusion. There is an association between bicycling and decreased genital sensation in competitive women bicyclists. "

When liquid N2 goes wrong

Lets face it liquid N2 is fun. From freezing biological matter, to making smoke, having droplet races, or making ice cream, liquid N2 is pretty versatile. It appears you can also make rockets, as this Texan lab was surprised to find out (oh these Texans, always blowing shit up): "The cylinder had been standing at one end of a ~20' x 40' laboratory on the second floor of the chemistry building. It was on a tile covered 4-6" thick concrete floor, directly over a reinforced concrete beam. The explosion blew all of the tile off of the floor for a 5' radius around the tank turning the tile into quarter sized pieces of shrapnel that embedded themselves in the walls and doors of the lab. The blast cracked the floor but due to the presence of the supporting beam, which shattered, the floor held. Since the floor held the force of the explosion was directed upward and propelled the cylinder, sans bottom, through the concrete ceiling of the lab into the mechanical room above. It struck two 3 inch water mains and drove them and the electrical wiring above them into the concrete roof of the building, cracking it. The cylinder came to rest on the third floor leaving a neat 20" diameter hole in its wake. The entrance door and wall of the lab were blown out into the hallway, all of the remaining walls of the lab were blown 4-8" off of their foundations. All of the windows, save one that was open, were blown out into the courtyard." Also, in the same vein, here is why a 230kg liquid N2 tank should not be brought UP the stairs by a summer student. no kidding!

Praying-induced oromandibular dystonia

Or praying disease, not to be confused with prion disease. One turkish man was reported to be afflicted with involuntary movements of the jaw while he recited islamic paryers. No kidding check the videos. Repetitive movements can sometimes lead to dystonia, in assembly line workers for example. It is related to the fairly common twitchy eye syndrome known as blepharospasm. I wonder if grad student ever get pipetting diseases. The fact that Marc Abrahams wrote a piece about this in the Guardian makes me suspect this could be a potential IgNobel...

Cancer and Evolution

For those of us way behind the curve, too filled with molecular biology to understand Dr. Scott Findlay's presentation a couple of weeks ago that related ecological concepts to cancer therapeutics, there is a recent paper in Nature Cancer Reviews that nicely summarizes the ideas behind thinking about cancer in terms of ecology and evolution. I ganked the picture from the paper, but since I've been trying to download it again my browser keeps crashing. Coincidence?

Don't sit up straight!

While at WIP today, Bayman suggested it was better for your back to slouch when you are at lectures, since the 135º angle produces the least stress. This piece of research certainly agrees with his assertions: "Alterations of Lumbosacral Curvature and Intervertebral Disc Morphology in Normal Subjects in Variable Sitting Positions Using Whole-body Positional MRI". Time to petition for an imax seminar room with fully reclining chairs. I will never miss an afternoon seminar again. Now we need to find something about ipods leading to better research, since it his now officially banned AND enforced. No words yet if the labs are also banned to the hearing impaired.

Improper use of lab equipment

What could a biologist studying hummingbirds do with a bottle of chlorophorm, and 55 gallons of hydrochloric acid? If you guessed kill his boss' husband and get rid of the evidence, than we should probably start locking the acid cabinet...

Cool Sci visuals

If you're patient enough to wait for the video to load, check out this crazy look at the inside of a cell set to classical music-it was made at the Harvard medical school and so is at least conceptually accurate-my personal favorite part is the myosin "walking" along the actin-some of the protein-protein interactions are pretty touching too! On a different note, the national geographic special "animals in the womb", which first airs dec 10 on the national geographic channel (and will likely be up to download soon thereafter!) features some pretty amazing pictures of embryonic development in different vertebrates-its hard to believe how similiar we start off!-maybe the fact that such a huge portion of the genome in mammals (and sea urchins!) is transcribed during early embryonic development suggests that only a small number/arrangement of genes is actually responsible for the diverse phenotypes we see by the time an individual is born-think about that-you might be only a few gene products away from having a trunk!

Stem Cell Lies and Misinformation

I randomly came across a site called "LifeSite" by a group lobbying the public and the Canadian government to place a moratorium on human stem cell research. I was horrified to read their "scientific" arguments as to why this should be done, all basically just wrong:

• Embryonic stem cells appear to be subject to random and uncontrollable growth. On the other hand, adult stem cells seem to be more predictable in responding to the growth factors and hormones that function to re-direct their development.

The Facts: ES cell growth is not "random". For example, mouse ES cells when injected into a host blastocyst in a surrogate mother, are able to give rise to embryonic tissue and undergo the tightly regulated developmental process to form a perfectly normal adult animal. One of the main reasons it's so important to do ES cell research is to learn how to manipulate them in the dish to form whatever tissue one might need, and scientists can do this pretty well already.

• Embryonic stem cells have been known to grow into the wrong type of cells, in some cases such as hair and teeth growing in the brain of treated patients.

The Facts: ES cells haven't even been used in human therapy yet so of course there has never been any evidence of hair and teeth growing because no patients have been treated. Again the point of researching human ES cells in the lab is to learn how to control their differentiation (what type of cell they become) so that this sort of thing would never happen when they are actually used for therapy, just like drugs are tested on animals to minimize the risk of side effects when used in people.

• Perhaps the greatest clinical problem with implanted embryonic stem cells is that the body flags them as foreign material. Consequently, they are subject to rejection by the patient's immune system.

The Facts: Any cell, embryonic or not, can be rejected by the immune system if its genes do not match the recipient patient. Therefore it is important to use autologous cells (from the same patient) for regenerative therapy, but whether the cells are adult or embryonic is of no consequence as far immune rejection goes. In fact, customized autologous ES cells generated by nuclear transfer or harvested pre-natally are probably the most promising potential source of cells for future therapies. There is a huge need for autologous cells, since they are often difficult to obtain once a patient already has a deadly diseases like leukemia, multiple sclerosis or muscular dystrophy.

The fools running this site push research into the therapeutic potential of adult stem cells, claiming they are just as useful or even more useful than embryonic stem cells. Also untrue. This goes way beyond simple ignorance to deliberately twisting scientific knowledge to misinform people and it's pretty sad. All the more reason for real scientists to get on the ball in educating the public.

Everything You Need to Know About RNA in Four Pie Charts and a Venn Diargram

Looking through Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution, I came across this great little figure that just says it all. Maybe pie charts and Venn diagrams are useless individually, but together...they may just be an unstoppable combination.

A brief history of life

From the uncyclopedia, the encyclopedia written by bears to piss Colbert off:

13,775,000,000 B.C. - After a night of sex known as the Big Bang, God creates the universe.
4,550,000,000 B.C. - The Earth is created
3,850,000,000 B.C. - The God of Evolution creates the First Organism
3,000,000,000 B.C. - Evolution becomes the main religion of earth's earliest residents known as the Prokaryotes
2,100,000,000 B.C. - Some of the Prokaryotes break away from the mainstream and start their own sect of Darwinism known as Eukaryia.
1,200,000,000 B.C. - The Eukaryotes permit some of their members to have more than one cell. The Prokaryote sect still forbids this practise.
670,000,000 B.C. - The Plant and Animal branches of the Eukaryote sect arise.
543,000,000 B.C. - Plants and Animals split into numerous denominations.
495,000,000 B.C. - The Vertebrate denomination, to which most practising evolutionists belong to is formed from the Animalian Eukaryote sect. Up to this point all life lives in the ocean, it is considered blasphemy to step onto land.
425,000,000 B.C. - Plants are granted land permits
410,000,000 B.C. - The God of Evolution gives vertebrates and other animals a land permit after years of protests and civil disobedience.
300,000,000 B.C. - The Reptilan branch of the Verebrates is formed.
251,000,000 B.C. - A group of animals reject the teachings of Darwinism and are promptly send to hell in the Permian Mass Extinction. The small sect of Mammalia branches off from Reptila, they remain a minority until after the Asteroid of Judgement.
245,000,000 B.C. - Dinosaurs are selected by God to become the rulers of the Earth.
200,000,000 B.C. - The real Jurassic Park starts filming. Directed by Steven Stegasaurus.
144,000,000 B.C. - Jurassic Park comes out on video.
65,000,000 B.C. - After a long reign, dinosaurs have become more arrogant, greedy, and cruel. Many reject the teachings of Darwinism. God punishes them by delivering the Asteroid of Judgement. A small group of dinosaurs, the Avians are loyal to the teachings and are spared. After this, God assigns Mammals to become the dominant sect of Life.
60,000,000 B.C. - Primates the sect that includes the degenerate Homo sapiens is formed.
50,000,000 B.C. - The early Equine sect of Mammalia which later forms an alliance with Homo sapiens is formed.
48,000,000 B.C. - Whales lose their limbs because of landmines, forced to live in the ocean.
35,000,000 B.C. - The Monkees, a popular group of Primates start their own sect.
20,000,000 B.C. - A group of Monkees, lose their tails and become known as apes.
8,000,000 B.C. - A group of Apes known as Hominids form their own sect.
5,555,555 B.C. - The last known mating between chimps and humans takes place.
4,444,444 B.C. - The prophet Lucy is born. She leads a sect known as Australpithecuses.
2,500,000 B.C. - An Australpithecus gives birth to the world's first, Homo.
2,499,999 B.C. - All Homos are banned from Australpithecus society, forced to start their own sect.
1,800,000 B.C. - Filming of the Ice Age Movie, Pleistocene begins, Homo gets his first erectus
1,000,000 B.C. - Clothes are invented.
750,000 B.C. - Fire is invented
200,000 B.C. - A group of well educated gay people known as sapiens form their own sect and begin to massacre other sects of Homo
50,000 B.C. - Homo sapiens enter into a pact with Canis lupus
40,000 B.C. - The Neanderthal massacre is perpetrated by Homo sapiens.
10,000 B.C. - Under what they believe is the instruction of God, woolly mammoths are massacred. The movie Pleistocene is finally done filming
9,999 B.C. - The movie Pleistocene is released on video. Agriculture is invented. Production of Holocene a sequel to Pleistocene begins.
7,000 B.C. - The wheel is invented.
4,004 B.C. - The false religion of creationism is started by a radical group of Homo sapiens.
3,000 B.C. - Homo sapiens enter into alliances with both the Felis and Equus sects.
2,000 B.C - Most Homo sapiens forced to adopt creationist beliefs by the prophet Moses. Dissidents are slaughtered summarily.
44 B.C. - Julius Caesar is murdered for his Darwinist beliefs'.
0 A.D. - Jesus Christ, the prophet of Creationism is born.
666 A.D. - Mohammed, another creationist prophet is born.
1,809 A.D. - The great evolutionary prophet Charles Darwin is born.
1,835 A.D. - Darwin has a religious revelation while vacationing on the cruise ship Beagle
1,859 A.D. - The Bible of Evolution, The Origin of Species, is published
1,882 A.D. - The Prophet Charles Darwin passes away at home.
1,925 A.D. - High School Science Teacher John Scopes is sentenced to death for having Darwinist beliefs.
1,987 A.D. - Darwinism is tolerated but the majority of Homo sapiens still support Creationism.
1,999 A.D. - Kingdom of Kansas forbids teaching of Darwinist beliefs
2,005 A.D. - Judge Jones upholds Religious Freedom and allows Darwinism to be taught.

bayblab podcast: Episode 3 part-II

Finally part 2 of the bayblab podcast episode3 has arrived. Guest speaker Stephen Hawking and the bayblab crew discuss life on mars, how plants move when you're not watching, why male contraception makes us squirm, why old poeple are breeding grounds to cancer, Trogdor the bruminator, and giving wine to mice to extend their lifes... Enjoy!

The Journal of Visualized Experiments

It's been mentioned before on the bayblab that more cool science pictures, and especially science videos are needed. Wait no longer! You can now find all sorts of videos detailing methods in the Journal of Visualized Experiments. The journal is strictly online, open access and free to publish to. Think of it as YouTube for scientists.

Kentucky: More Than Just the Home of Creationism

Intrigued to know more about the state that so loves creationism, I immediately consulted Wikiality to get the facts. Looking up Kentucky, I discovered that this state is also the birthplace of the great Abraham Lincoln, founding father of the Bear Hunters of America. Here's an excerpt:

"Abraham Lincoln was born in a one room log cabin in Kentucky in the year 1809. Which when you really think about it, isn't that much of a surprise ... it WAS 1809 Kentucky! 1809 Kentucky was not the inbred, butt raping, banjo playing kind of place full of Democrats depicted in the film Deliverance. But, was actually a haven for gutless and godless bears. The young Lincoln would spend a good portion of his early childhood wrestling with these beasts, until his family moved to Illinois; little did Lincoln know that his hatred of bears would ultimately lead to his demise."

Jack Bauer's Insomnia

I can just imagine the testimonials for the next generation of stimulant drugs.
"When I'm fighting terrorism for 24hrs, I am always on modafinil." Jack Bower.
The always sensationalizing newscientist has an article suggesting that taking drugs, specifically modafinil, instead of sleeping is going to and is becoming more common. Apparently modafinil is safe and has not that many side effects for those extra long covert operations, according to a Canadian militart report from 1995.
I simply have to get me some of that. from some sketchy online pharmacy.
This interested me because I have heard that you can die from lack of sleep or insomnia. In fact there is a condition called Fatal Familial Insomnia that indeed is fatal. There was a recent Science Friday interview with the author of a book about Fatal Familial Insomnia and the history behind it. It is a really good listen, the science is crappy but the history of the disease is interesting.
Amazingly, apparently mentioned by the bayblabs own Kamel in a journal club presentation, this disease is caused by a prion which doesn't start to cause affects until middle age. So those who carry this mutant protein have symptoms that accelerate rapidly resulting in loss of sleep, dementia and death.
So that means I'm going to have to go off the modafinil periodically, just to make sure I can still sleep.

Creationist museum in Kentucky

Earlier this summer I was visiting Washington state, and admiring the canyons of the Columbia river. To my suprise the brass panels explaining the geology of the canyons at a lookout site had been vandalized to remove the age of the formation. The X-million years had been scratched out, probably with great effort. And I thought that state was progressive! Things weren't better in New-York, where I finally got to visit the museum of natural history and its impressive dinosaur collection. I was shocked to learn that some groups where given a "cleaned up" version of the tour that distorts the fact to make them agree with genesis. At least it wasn't sanctioned by the museum... But now Kentucky gets the Dawkins award, for opening a museum specifically devoted to spreading that bullshit. The $25M museum will display the 6000 year history of the earth complete with humans riding on the backs of dinosaurs. The moto: "prepare to believe"...

Good environmental news

Man, I wish there was more good environmental news, but it just seems as though society is designed to exploit their surroundings to excess. This ultimately has lead to the demise of many societies, as in the main thesis of A Brief History of Progress by Ronald Wright.
When I hear good environmental news it actually gives me pause to think that this modern world with unprecedented population density can actually dig itself out of these problems one at a time through science and technology, and sound policy. The most memorable good environmental news for me includes the saving of Clayquot Sound in BC, and the Montreal Protocol banning CFCs.
So when I heard that "tree stock has increased in 22 of the world’s 50 most densely forested countries" I was pretty impressed. I don't know much about how these things are analyzed, however, if by any method this is true, I'm still impressed. The analysis showing a slightly optimistic view of the state of the forest was published in PNAS.
Don't get too excited, of course, forests are still dwindling on a global scale. Interestingly in the article, Canada is not doing that well compared to countries with similar GDP. But surprisingly has a zero net forest loss, and apparently this statistic accounts for size of trees ect. As a primary resource country that is somewhat impressive.
PS I'm still going to enforce recycling in the bay like a fanatic.

Cloned Meat is Just as Good as the Real Thing

George W. Bush may not be interested in stem cell research that advances our knowledge and treatments of to human diseases, but his buddies down in Texas sure know that cloned animals are good for a nice juicy steak. This is cutting edge research from the journal Theriogenology.

Good Times at the OHRI Stem Cell Symposium

Yesterday's field trip of the official bayblab.blogspot.com press corps to the OHRI stem cell symposium was definitely awesome. The Sprott Stem Cell Centre features a sweet A/V set-up with a big-ass projector screen, an HD-ready LCD TV, and a fully wired sound system. (Would be a great set-up for a movie night or maybe a hockey game)...Anways, it's also great for science talks. High marks also awarded for copious amounts of delicious sweets, coffee, lunch and the wine and cheese. Definitely the highlight of the day for me was the talk from Rudolf Jaenisch of the Whitehead Institute. The first to make a transgenic mouse in the 70s, Jaenisch now works on somatic cell nuclear transfer. He strongly argues that somatic cell nuclear transfer is absolutely necessary if stem cell therapy is ever to become a reality, since it is the only way to get a truly pluripotent, autologous, embryonic stem cell that would be immunologically matched to each patient. Although non-embryonic adult stem cells could also provide a source of autologous cells, he seems quite unconvinced that they have any real regenerative value. On the other hand, he feels that the other application of nuclear transfer, cloning organisms, is pretty useless because it doesn't work. He cites that nuclear transfer never has nor will give rise to a normal, healthy animal as they invariably suffer from severe epigeneitc defects. Therefore his lab is now mostly focused on developing methods to use nuclear transfer to generate blastocysts from which it is possible to derive ES cells for therapeutic use, but that cannot implant in the uterus and therefore could never possibly give rise to an embryo. This would sidestep any concern that the derivation of human ES cells is killing potential embryonic life or fetuses etc. and open the door to nuclear transfer research using human materials to derive ES cells. So far, they have succeeded in using donor nuclei expressing a cdx2 shRNA to yield a recipient blastocyst incapable of implantation.

Overall bayblab rating: 10e45/10. Cutting-edge biology approached from a big-picture/philosophical point of view. Very political with cutting anti-Bush cartoons (+10 bayblab points), criticizing him for protecting the rights of ES cells while caring less about killing thousands of humans in Iraq, and suggesting that ES cell research would advance unimpeded if scientists simply found a way to derive oil or biofuels from them. Good usage of high- complexity Venn diagrams. Penalty of -1 bayblab point for spreading the idea that "male imprints cause cancer".

ES Cells: Conundrums and Cures

Embryonic stem (ES) cells (self-renewing, pluripotent cells derived from embryos) are often hailed for their potential in regenerative medicine and just as often at the centre of controversy. The minefield of ES cell research has become something of a celebrity deathmatch with heavyweights weighing in both praising (e.g. Michael J. Fox, Christopher Reeve) and condemning (e.g. George W. Bush, Pope Benedict XVI) the field. One possible solution is the use of adult stem cells - pluripotent cells from adult tissues. However these cells are more rare, less robust and more difficult to culture than their embryonic counterparts (for a good primer on ES cells, adult stem cells and the differences visit the NIH resource page particularly the section on stem cell basics).

While conscientious researchers and philosophers argue ethics, some researchers are trying to sidestep the debate by developing techniques and creating 'ethical stem cell' lines. One example is the the 'de-differentiation' of fibroblast cells into ES-like cells by expression of defined factors (Cell 126:663-676). These cells could differentiate into multiple cell types and when injected into a blastocyst, contributed to embryo development. This method has the advantages of not involving an embryo at all -- a patient's own somatic cells could be used, which would also skirt problems of rejection when transplanted. However, one of the factors used in de-differentiation is the oncogene, c-myc, which may limit clinical application and the advantages over naturally occuring adult stem cells.

Another approach is the creation of stem cells of embryonic origin that don't involve desctruction of the embryo. In a recent letter to Nature, ES cells were derived from single blastomeres using a technique similar to that used in preimplantation genetic diagnosis (PGD) where single cells are extracted for genetic analysis at an early (8-10 cell) developmental stage. In this case, the cells were cultured to develop new ES cell lines. This paper has been the centre of some controversy since it's publication and is unlikely to offer a complete solution to the ethical dilemmas. In this study, all the embryos used were still destroyed (the authors claim this was so they wouldn't be wasted) and the success rate for establishing lines was low. (More recently, a group has show that using older embryos makes the process more efficient in mice) Additionally, while the technique used for PGD gives rise to healthy babies, subtle long-term effects of removing cells at such an early developmental stage hasn't been determined.

But once those kind of issues are resolved, where do we go from there? Are stem cells the cure-all they're made out to be? In one case, sight was restored in blind mice through retinal cell transplants. Because human ES cells can be coaxed into the same cell type, this offers some promise for future regenerative therapy using autologous transplantation. In another situation, a vaccine made from stem cells protected mice from lung cancer under various conditions. The vaccine exploits similarities between ES and tumour cells, protecting 20 of 25 mice from tumours in a xenograft model and 8 of 9 mice in a simulated smoking chemical carcinogenesis model, both with no obvious side effects. Safety issues aside, this again demonstrates the potential for stem cells if applied to a human disease.

Parkinson disease (PD) is one of the conditions most often held up as the disease most likely to benefit from stem cell therapies. Indeed, if all the promise holds true, most neurodegenerative and many other illnesses stand to gain from stem cell research. It's not all so rosy, though. Recent studies have demonstrated substantial recovery in a rat model of Parkinson disease. In this paper, human ES-cells were differentiated into dopaminergic neurons (using new techniques to enrich this cell population, which is lost in Parkinson disease) which were then transplanted into PD model rats. These rats showed significant recovery of motor function. The downside? Incompletely differentiated cells in the transplant showed persistant proliferation after engraftment. Among other problems described in the paper, these proliferating undifferentiated cells could potentially lead to the unfortunate side-effect of tumour formation.

So where are we on stem cell research? Limitless possibilities? Highway to Hell? As Steve Goldman, senior author on the Parkinson study, puts it, "Neither gene therapy nor stem cells are ready for primetime." But I wouldn't change the channel just yet.

Strange diseases of the woman

I recently came across two bizarre diseases that affect woman. The first one involves woman who believe they are transforming into a man, against their will. The rare disorder of reverse delusional misidentification syndrome may be encountered in schizophrenic patients. "Evaluation revealed complaints that the patient's ovaries were testes that produced sperm and her clitoris was a penis capable of erection and ejaculation. Gynecological examination revealed only atrophic vaginitis.". The other one, might be even stranger if that's possible. Woman who have persistent sexual arousal syndrome, and are constantly hit by orgasm for doing pretty much anything, despite having no sexual desire. In Japan this disorder is called "iku iku byo" or cum cum disease. It has been associated with anything from withdrawal from SSRI medication, to soy intake, menaupose and traumatic event and apprently makes sleeping difficult.

Aubrey de Grey

Wise like Gandalf the Grey is Aubrey de Grey. Maybe not. Make up your own mind as you check out his talk at TEDtalks. I haven't checked it out yet, lemme know if he's under the influence of Sauron. Found on www.boingboing.net.

Genomic Imprinting Evolution

Genomic Imprinting is an epigenetic phenomenon that limits expression of a particular gene to either the paternal or materal allele specifically through silencing one allele. (I believe it is through DNA methylation.?)
A new study indicates (according to the synopsis) that not only is genomic imprinting is still evolving in viviparous mammals, it also appears that evolution occurs in a coadaptive evolutionary mechanism. This is somewhat contrary to theories that I had heard before that include that the mechanism allowed males to pass on genetic fitness specifically to male offspring and females to female offspring. I have also heard that the mechanism reflects a competition of interest in males in their offspring and females in their offspring. A male wants large offspring because the male is unconcerned about the maternal investment in raising a more energetically expensive large offspring and the female is opposite.
I am still not sure if I understood the synopsis ( that is written for a general audience) so if anyone has insight.. have at it.
I included the picture because of all the nipples.

Polythelia and polymastia

Recently, a fellow bayblabber claimed to have a supernumerary or accessory nipple. While not quite as impressive as polymastia (an accessory breast), he's in good company: Mark Wahlberg and Anne Boleyn, as well as fictional characters Krusty the Clown, Goldmember and Chandler from Friends all had extra nipples. While I don't recommend a google image search for pics (at least with SafeSearch off) there are some pics and histology here.

Most of the literature on polythelia is quite old. Extra nipples are more common in women than men, but even then are only 'diagnosed' in about 2% of the female population. The extra nipples can vary in appearance from a patch of hair to full blown polymastia. Early studies suggest a dominant inheritance pattern, and Alexander Graham Bell was successful in raising sheep with multiple extra nipples through selective breeding.

So is it a third nipple? It seems to be on the milk-line which runs from the armpit, through the real nipple and down to the groin, which supports his case, but I think we may need to check his parents.

Canada & Kyoto

I have to say that I actually am happy with the conservative government on the specific issue of staying in the Kyoto agreement. It sounds like Canada is being a total ass at the talks in Nairobi, however at least we are staying with it and acknowledging we can't make our targets. We suck basically. And I think we should have to pay. It's not like we aren't affluent enough and if it actually hits us in the pockets we might have some motivation to actually achieve something. Because apparently so far we haven't. As soon as the conservative government has to acknowledge that it's books aren't as good as they could have been because of carbon dioxide production perhaps they will invest in this countries future as a technology leader and not just a big oil sand.
Perhaps I'm preaching to the choir on the bayblab but maybe I'll provoke a response from some redneck in Alberta.
Disclaimer: "Redneck" was added for provocation purposes only. Rednecks are great people too (and we need them to do the actual hard work.)

Healthmap

Check out how disease outbreaks are mapped on Google maps. Healthmap. This thing totally rocks and will be great for the next flu pandemic.

Can a biologist fix a radio?

Bayman was recently discussing in the bay systems biology and modelling of seemingly simple pathways. How for example we've really only just started getting accurate mathematical modelling of the Lac operon and how it confirms what we previously knew but in a quantitative manner. It begs the question, are we efficiently investigating the "black box" that is the cell? Is the biological approach the right one, or is it better to have an engineering approach. Yuri lazebnick explains the "David paradox" in an old issue of cancer cell, on how a biologist would solve the problem of a defective radio and how this relates with our approach at investigating mollecules such as p53... "[...]any engineer trained in electronics would unambiguously understand a diagram describing the radio or any other electronic device. As a consequence, engineers can discuss the radio using terms that are understood unambiguously by the parties involved. Moreover, the commonality of the language allows engineers to identify familiar patterns or modules (a trigger, an amplifier, etc.) in a diagram of an unfamiliar device. Because the language is quantitative (a description of the radio includes the key parameters of each component, such as the capacity of a capacitor, and not necessarily its color, shape, or size), it is suitable for a quantitative analysis, including modeling."

Cellphones and Brain Cancer

I watched Thank you for not Smoking last night, and thought it had some pretty funny parts. The humour was refreshingly satirical. SPOILER: Interestingly the main character ends up being the spin doctor for cell phone companies and the association with brain tumours. I wondered if there was a parrallel between smoking / lung cancer and cellphones / brain cancer. Nowadays would science have enough power to publish links of cellphones to brain cancer? I guess the question is then; Is there a link between the two? A pubmed search of "mobile phone cancer" gives 131 hits and not many that I could find suggested a link between the two. However alot of studies received funding from the telecommunications industry and a competing interest statement resides at the end of some papers. I also found a paper that I had heard about that suggested that while your incidence of cancer is not increased with cellphone usage, if you get a brain tumour it is significantly more likely to be on the side of your brain that you use your cellphone. That sounds really sketchy, however, the researchers chalk it up to recall bias. Here is an old article that summerizes some data that I have not found as well as the abstract of a paper that seems the most authoritative on making a link between cancer and cell phone use.

Yo' Momma's Ancestor was a Sea Urchin!

Having just come out over the weekend, i've lucked out in getting to post about the recent sequencing of the sea urchin genome. The genome of the male California purple sea urchin (Strongylocentrotus purpuratus) has been sequenced and the depth of analysis to be discussed in the next few months (look for 40 articles in the December issue of Developmental Biology) seems incredible. A team of 240 scientists, including groups from Toronto and BC, have collaborated to determine the GENETIC CODE AND TRANSCRIPTOME (using NASA computers to do microarrays-how cool is that?!) of this highly studied model organism. The sea urchin has been used for over a century as a model for many biological processes and is best known for advances made in developmental biology due to their clear embryos which facilate the study of evolutionarily conserved developmental processes common to deuterostomes. The sea urchin genome which codes for 23 300 genes displays a surprising level of sophistication and suggests a global view of the genes necessary for human evolution-further touting the strength of this species as a model organism. Some of the most interesting findings include the identification of genes coding for human analogues involved in vision and chemosensation (sea urchins were not thought to possess organs to sense light and odour), a very complex innate immune system(including a rhobust defensome), and orthologs of many human disease-associated genes.

Bayman's Book Club

There's nothing I like better than a piece of classic science literature. And in the true tradition of wine-snobs and gold-digging socialites, older is invariably better. Inspired by Discover magazine's compilation of their 25 greatest science books of all time (check out the Dec. issue), I thought I'd throw out a few of my faves to at least fuel some discussion at the next podcast. The list is of course incomplete, as is my reading progress through most of these works.

The Origin of Species, Charles Darwin (1859).
The famous evolutionary theory contained within the hundreds of pages of this biological epic can be described in only a paragraph. While the theory was revolutionary to say the least, reading through the pages of CD's own words offers a great look into a truly rigorous and critical scientific mind. Darwin's ability to influence thinkning and open minds to new ideas was likely in large part to the beautiful exploration of the arguments AGAINST his theory which he systematically deconstructs and ultimately uses to strengthen his position.

What is Life? Erwin Schrodinger (1944).
Leave it to a physicist to shake the foundations of science with three words and a question mark. I originally wanted to see what this book was all about because James Watson cited it as his inspiration to seek the structure of the gene. Unfortunately I don't totally know what it's all about yet because the first few paragraphs got me thinking about genetics so much that I set off on a tangent of reading basic genetics (see next title) and haven't yet found my way back to poor old Erwin.

Experiments in Plant Hybridization, Gregor Mendel (1865).
Reading this paper one is struck by the stark contrast between the massive significance of this work (ie the founding of modern genetics) and its sheer humility. A monk counting pea plants in his garden. It doesn't get any humbler than that. He also puts forward in these pages a great example of how to write a real scientific paper. Of course, no mention in the discussion predicting how his discoveries would cure the diseases of humankind, extend lifespan or save civilization...(nor are there any trojan horse analogies for that matter)

Signs of Life: How Complexity Pervades Biology, Richrd Sole and Brian Goodwin (2000). Before anyone was talking about "Systems Biology", this book attracted my attention for its elegant use of nonlinear and "chaos" mathematics to describe the weird and fascinating behaviour of biological systems ranging from viral quasispecies to ant civilizations to the human brain. By no means a fully-developed classic, but I though it was pretty cool at the time.

Viruses and the Nature of Life, Wendell Stanley, Evans Valens and others (1961). Fundamental virology by the people who discovered it. Written back in the day when there was no microarray or RNAi and viruses were still the sexiest and coolest thing out there, it's hard to read this little book even today and not come away thinking that viruses are the answer to everything. Even the black-and-white illustrations are great. If I ever taught a introductory course to virology I'd base it on this book. Also full of great general biological prophecy, for example, in cancer: "Huebner discovered that adenoviruses would destory the abnormal cells of cervical cancer in women...However, the virus could not destroy all the cancer cells before antibodies to the virus developed...Work of this general nature is only in its infancy...by selective cultivation of mutant virus strains, it should be possible to develop viruses which ignore normal cells but will have a special predeliction for the destruction of cancer cells." Hmmm...sounds kind of like an oncolytic virus...

bayblab podcast: Episode 3 part-1

Finally the latest installment has arrived. This week we have Stephen Hawking as a special guest and he gets piss drunk as we discuss milking the one eyed snake, the size of testes in nerds, and compare coke, clamato&beer and fermented horse urine. Due to the size of the podcast it will be released in 2 parts. So tune in next week for part 2.

Nuclear Translation

I really have no opinion on the existence of nuclear translation because I know nothing about it, however it is an interesting debate. Here is a pro-nuclear translation article and an anti-nuclear translation article. I don't really understand why nuclear translation would be necessary to explain nonsense mediated decay but it's nice to know that someone is challenging the dogma.

Improbable research

You know that bit in "there's something about Mary" when the guy gets his tool stuck in the zipper and the firemen (no pun intended) are called in? Well chances are that they are not using the jaws of life, but rather a pair of plyer and following the instruction of this 1990 paper in the journal of emergency medecine: Acute management of the zipper-entrapped penis.
"A zipper-entrapped penis is a painful predicament that can be made worse by overzealous intervention. Described is a simple, basic approach to release, that is the least traumatic to both patient and provider."
In fact I can find close to a hundred articles on this subject in pubmed, some would say it's a growing field...
Check out more improbable research here.

RNAa

A recent paper from PNAS shows that short 22bp dsRNAs can be used to INDUCE gene expression when the sequence is in non-CpG islands in the promoter of the gene. The effect is dependant on Ago2, sensitive to DNA methylation and works like microRNA in that some mismatch is tolerated. They coin the term RNAa or RNA activation and it looks pretty convincing. This just adds another complication to the RNAi mechanism that just leaves me scratching my head. It also suggests even more potential for off target effects when using the nobel prize winning RNAi as a tool.

IA updates

IA updates . Apparently the UK is leading the world to '1984'. They have some loudspeakers hooked up to video surveillance and have started fingerprinting people who drink in pubs. Also some good info on video software. Basically I have to try Adobe Premier Pro. It's time to get the video podcast going on.
Check out the informationaddiction.com

Richard Dawkins vs. Francis Collins: The Crusading Atheist and the God-Faring Scientist Go Head to Head on God

I picked up the current issue of Time magazine to see if I could find any entertaining quotes in a write-up of a Francis Collins (leader of the NIH human genome project/christian) versus Richard Dawkins (Oxford evolutionary biologist/author/hard-core atheist) debate on religion and science. Although there's lots of photo-ops showing the two of them looking like they're thinking really hard about the mysteries of the universe, it's mostly pretty diplomatic but still pretty decent. Although both men showed themselves to be strong debaters, no punches were thrown or blood drawn. Perhaps the most interesting aspect was that Collins represents the religious camp much better than the yahoos that Dawkins kind of bullies around in his doco "The Root of Evil" (which curiously I can no longer find on Google video).
Some selected quotes:

Dawkins: "What Francis was just saying about Genesis was, of course, a little private quarrel between him and his Fundamentalist colleagues...he'd save himself an awful lot of trouble if he just simply ceased to give them the time of day. Why bother with these clowns?"

Collins: "Atheists sometimes come across as a bit arrogant...characterizing faith as something only an idiot would attach themselves to is not likely to help your case"

Collins: "I don't see that Professor Dawkins' basic account of evolution is incompatible with God's having designed it."

Dawkins: "I think that's a tremendous cop-out. If God wanted to create life and create humans, it would be slightly odd that he should choose the extraordinary roundabout way of waiting for 10 billion years before life got started and then waiting for another 4 billion years until you got human beings capable of worshipping and sinning and all the other things religious people are interested in".

Collins: "My God is not improbable to me."

One-Click Referencing As You Surf

From the Nature people, Connotea is web-based reference management. Basically they keep track of your references in a web-accessible, user friendly database for you. Puts a little button on your web browswer and you just hit it whenever you have an abstract or paper loaded in your web browser. The program then automatically puts all the relevent info into your database. You can easily download the library into a reference manager file, and share databases with your science buddies via the web. I've been testing it out, and so far it seems pretty damn cool. Think of it as the cure for "How did I find that abstract on PubMed that one time???