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...