Monday, April 30, 2007

Banana man thinks he can prove the existence of god

Remember Kirk Cameron, who demonstrated that bananas are the atheist's nightmare? Well he's challenging atheist in a debate, where he is going to prove the existence of god without using the bible. I wish he had invited Dawkins, if only for the comedic value. Here is what he has to say : "Evolution is unscientific. In reality, it is a blind faith that's preached with religious zeal as the gospel truth. I'm embarrassed to admit that I was once a naïve believer in the theory,” said the former television star in a statement. “Atheism has become very popular in universities – where it's taught that we evolved from animals and that there are no moral absolutes. So we shouldn't be surprised when there are school shootings."


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Sunday, April 29, 2007

Vitamin D Supplementation the Answer for Cancer?

This weekend the Globe and Mail published a piece on what promise to be the blockbuster findings of a study done by researchers in Nebraska:

"A four-year clinical trial involving 1,200 women found those taking the vitamin had about a 60-per-cent reduction in cancer incidence, compared with those who didn't take it, a drop so large -- twice the impact on cancer attributed to smoking -- it almost looks like a typographical error."

The women were apparently given 1,100 IU of vitamin D3 per day over the four years.

These claims are exciting but given their grandeur must also be greeted with skepticism. I am therefore anxious to examine the data myself. Unfortunately the article failed to mention when, or in which peer-reviewed (I assume) journal these results will be published. However the article did cite one of the authors as Robert Heaney, MD, of Creighton University, who "has worked for over 45 years in the study of osteoporosis and calcium physiology, and has published more than 300 original papers, chapters, monographs, and reviews in scientific and educational fields".

Check back for updates here on the bayblab as more information becomes available.

Also, see the slashdot post for interesting discussion, including why vitamin D has nothing to do with the evolution of human skin colour.

Update: A representative from the Creighton University Medical Center has informed me that the principal author of the study is in fact Joan Lappe, PhD in Nursing and Associate Professor and Creighton.

Update 2: I have also been informed that the article will appear in the June edition of The Journal of Clinical Nutrition. However, upon my request (wherein I identified myself as a member of the cancer research community), the authors informed me that no further information will be made available until the study is published. Which leaves me scratching my head as to how the Globe and Mail got a hold of the results and chose to jump on the story when the results haven't even yet been made available to members of the scientific community for discussion and scrutiny. Interestingly, no other media outlet accessible to Google news has reported on the study to date.

Update 3: Interesting paper that Jim Wint pointed out is in fact real and recently appeared in Cell - see "
Central Role of p53 in the Suntan Response and Pathologic Hyperpigmentation". Good to see even tanning bed proprietors are up on the scientific literature. I love it! (Haven't read the paper yet though, so can't say at this point whether I think it supports his claims.)

Update 4: I just bought 120, 000 IU of vitamin D3 at Shopper's Drug Mart for $6.99. Figured it couldn't hurt. Based on my previous experience with supplements, I'll take it faithfully for a couple of days then forget the whole thing.


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Williams syndrome

My fascination with Williams-Beuren syndrome started a few months ago when I saw a documentary on that subject on the french CBC show Découverte. On the show, they interviewed people who had the disease, and talked about their unusual musical abilities. It turns out that they are really good at memorising music or singing, and that when they listen to music, their whole cortex lights up with activity, compared to very small limited regions in normal people. This is particularly surprising considering they have limited abilities to write or do maths because of their learning and memory problems. Yet they can sing a song after hearing it once, and use very advanced vocabulary when they speak. They also have difficulties with visuo-spatial perception, and motor skills and are hyper-social, meaning they have no social anxiety. Additionally they have characteristic elfin-like facial features, like pointy ears, prominent cheeks and upturned nose and a short stature which have lead to the theory that they might be the origin of the folk tales about pixies.

When you think about it, some of these features are quite unique, and they are all linked to a relatively small deletion affecting 20 or so genes on chromosome 7. The fact that gene dosing could be responsible to these striking changes in musical abilities, speech and social behaviour, things that are so characteristically human, is an incredible window into how genes dictate cognition. Additionally, while the syndrome was initially included in the autism spectrum disorder, the hypersocial aspect and the "islands" of cognitive strength are in stark contrast to what is observed in autism. Maybe we could we learn about social behaviour, empathy, and how the brain makes us social animals by comparing both diseases.
And so I started examining the genes which were hemizigous as a result of the disease. While a few genes are thought to contribute to the cognitive aspects of the disease, two really stand out: LIMK1 and ELN. They are part of the minimally deleted region that can give rise to the syndrome (since the size of the deletion varies from patient to patient). Elastin (eln) is a structural protein and its deficiency is linked to the cardio-vascular problems and to the facial features of the disease. LIMK1 is a kinase that is expressed in the brain and which regulates actin threadmilling (via cofilin) to allow synaptic plasticity and remodelling.

So I thought, maybe LIMK1 can tell us what is the neural substrate for cognitive processes that are affected by the disease such as social behaviour, musical abilities, visuo-spatial cognition etc... Using the Allen brain project data, which we've spoke about on the blog in the past, I looked at where the gene is expressed in the brain. To my surprise it wasn't expressed in the cortex or the limbic system, the structures which are thought to regulate higher cognition and behaviour. Instead it was very limited to the brainstem (see my figure above). Yet all the studies done so far have focused on the hippocampus, the amygdala and the cortex, because that is where everyone expected the defects occurred. People with lesions in those areas have memory problems, social behaviour problems, so it was only natural to assume, that it was the neural substrate of the disease. After reading quite a bit about brain areas and behaviour I came across a few very rare papers dealing with the brainstem in cognition and behaviour. The authors suggested that maybe higher brain function is dependent on integration of incoming sensory signals (or outgoing motor signals) from the brainstem. If the brainstem doesn't do its job at pre-processing that information, the higher brain structures don't know how to deal with the signals, and how to relay it to the specialized areas like say the Broca area for speech for example. This in turn may explain why Williams patients have difficulties with motor skills, visuo-spatial integration. And so is behaviour also dependent on the brainstem? While I don't have the resources to prove it, I certainly think it's a possibility. After-all many primitive animals that have complex behaviour have a mostly brain-stem centric brain and underdeveloped cortex. The brain stem is responsible for the basic stuff like breathing, eating, vomiting so why not also of basic behaviour like anxiety...

Which leads me to my final point, if you restore the synaptic plasticity in the brainstem, can the brain adapt and the symptoms associated with Williams syndrome disappear? A recent paper in science (Guy et al, 2007) demonstrated that restoration of MeCP2 expression post-nataly in mouse models of Rett syndrome, can correct the neurological defects. This suggests that mental retardation syndromes which are not neuro-degenerative can be corrected and reversed. So I am very optimistic that one day, there will be therapies available to these people, or maybe even, that we might harness that knowledge to enhance our own brains. Have you ever wanted to have a musical brain?


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Friday, April 27, 2007

New Canadian Carbon Legislation Pays off for Oil Tycoons

Talk about jumping on a business opportunity. Only days after the federal government announced its latest plan for climate change, which stipulates 18% reductions in industrial CO2 production by 2010 and the payment of carbon taxes, Norway's Statoil today bought itself $2.2 billion worth of the Canadian oil sands. Interestingly, Statoil leads the world in carbon sequestration technology, and has previous experience in dealing on carbon markets through the EU emission trading scheme. The Norewegian state-owned oil company is one of the fastest growing in the world. Calgary oil tycoon and world's 382nd richest man, Clayton Riddell, (pictured above) and his company Paramount Resources Ltd. will make nearly $1 billion off this deal. Now that's what I call timing the market.


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Candiru



If you watched Grey's Anatomy last night you've probably seen the penis fish. You're also probably a girl. What they left out of the explanation, is that the Vandellia cirrhosa is in fact just as happy to swim up a vagina, or in fact any opening/orifice. It is a type of parasitic catfish that usually lodges itself in the gills of other fish and feeds on their blood. There is no reported case in pubmed, other than it is a gift to urology (?), but natives living on the amazon fear it (understandably so). However, reports of the fish swimming in the urine stream into the penis outside of the water are an urban legend. But if you are submerged , then beware. I'm scared of channel catfish myself...


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Hawking in space

As soon as he comes down, we'll have him for an interview on the podcast...


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Thursday, April 26, 2007

Update: Chimp denied legal guardian

A quick update on this bayblab story from earlier this month. In a blow to 'ape rights', the chimp in question has been denied a legal guardian by the courts. As expected, the ruling is being appealed.


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Sexual education

I've had an interesting debate recently about gun control. My opponent suggested that people who own guns and are familiar with them and have "gun education" are more likely to use them safely and respect how dangerous they are. This reminded me of the debate on how early kids should receive sex education. Are they more likely to experiment earlier if they are exposed to it, or are they safer if they do, or both. To address this question I used data from the Durex survey. More specifically I looked at the age of first exposure to sex ed and age of loss of virginity in 41 countries. First a few facts:
  • the average age of sex education is 13.2
  • Asian students receive education last, with Vietnam trailing at 16
  • Nordic European countries are the earliest, with Germany leading at 11.3
  • The average age to lose virginity is 17.3
  • The same trend is observed with the loss of virginity, with India at 19.8 and Iceland at 15.6

At first glance there is a strong correlation (R^2=0.7) with sex ed and loss of virginity. But I would argue that it is not causal, because if you look into the details all countries wait 4.20 years between theory and practise with a very small standard deviation of 0.59 . This to me suggests that countries are pretty good at introducing the subject well in advance, and do so according to the local cultures rather than a universal standard age...


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Fair use in science blogging

A recent post on slashdot directed me to this science blog which was threatened by a journal publisher because it reproduced some of the figures of a recent paper on alcohol and anti-oxidants. (On a side note, the article is quite interesting but flawed, suggesting that alcohol makes fruits healthier, even though the paper does not). Fair use does allow the reproduction of copyrighted material for the purpose of criticism if it is fully cited and contains only a portion of the material (ie not the entire paper). considering we routinely add figures from published material here on the Bayblab, I was happy to see it ended well, with apologies from the journal. But this exemplifies why it is good to know your rights, whether it is to criticize a paper or, as we've learned ourselves, a science quack.


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Inside the Anthill

Plaster casts of the part of the anthill you can't see:




Awesome! Lots more cool details and pics in Walter R. Tschinkel's original paper.


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Wednesday, April 25, 2007

Bio-censorship

This excellent article in Wired explains how fears of bio-terrorism might lead to restrictions in research and censorship. Just as physics research was censored during the cold war, or defense engineering research is overviewed by the government right now, scientists working on pathogens may be the next ones on the list. Already scientists cannot work on the pox virus, or any virus with over 85% homology (or sequence identity to be exact), which includes the vaccine itself! How long before you need an iris scan to get into level 2.5 labs, or you need to send your latest VSV paper to the censors? Thankfully I doubt terrorists have the level of sophistication needed to engineer dangerous viruses, and why bother, when any scoop of soil can provide you with anthrax, and a turd could make an excellent E coli "dirty bomb". In any case we're already feeling the effects of 9/11 in science, as it's getting increasingly difficult to ship samples over the border. And I'm not even talking about fears of pandemics. There are no more swans in the Rideau river here in Ottawa because officials are worried about the avian flu! Damn bird terrorists...


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New AIDS drug approved

Maraviroc, Pfizer's new drug for HIV has the backing of the FDA. It will be the first new drug against HIV in over a decade. It works by antagonizing the CCR5 receptor, and blocking virus entry. This is good news, and another success of targeted small mollecule therapy, and it was developed in a record 10 years!


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Tuesday, April 24, 2007

WTF?



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Adam's (or Anne's) Apple

The laryngeal prominence is actually the region where the two lamina of the thyroid cartilage meet at 90º. It creates a visible Adam's apple. While most people consider it a sexually dimorphic trait, both sexes actually have one, and many man have a small Adam's apple, while many woman have a prominent one, including the one above. There is a surgery available for these woman, and it is also often used during sex changes. The role of that extra cartilage is unclear, and the differences between the sexes seem to stem from the angle at which the plates connect, since it is 120º in the females. It does not contribute to the pitch of the voice and its function appears to be mostly protective, especially from karate chops.


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Shrinking Penis

Koro ("head of turtle" in Malay) is a type of mass hysteria (which is greek for uterus) , particularly prevalent in Asia and Africa, where men panic about their genitals retracting into their abdomen and subsequent death. Often people will be accused of witchcraft and the afflicted individual may attempt desperate measures to stop the shrinkage, by tying rocks of heavy objects on the pecker. This is a surprisingly well-studied phenomenon with over 130 publications on the subject on pubmed. There has even been documented "epidemics" of Koro. In the west, koro is rarely observed, but can be induced as a consequence of marijuana intoxication. However these drugs may also cause you to grow giant balls and rescue drowning people. I'm just saying. While there are no "cures" for koro, psychological treatment is very effective. Hypnosis might also be worth a try, since it can cure woman of sperm phobia...


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Monday, April 23, 2007

Colony Collapse Disorder

There has been a lot in the news lately about massive disappearances of honeybees in the US and around the world. This is of particular importance, as bees are major pollinators responsible for pollination of approximately one-third of the food consumed in the United States. The phenomenon is called colony collapse disorder but the cause for it is unknown. Some possibilities being investigated are:
  • habitat loss
  • climate change (drought)
  • pathogens carried by mites
  • pesticides
  • electromagnetic radiation from cellphones or power lines (2006 study shows that such radiation can affect bee behaviour and ability to return to the hive [pdf])


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Science consultant for TV

I always thought it would be fun to be a consultant for movies & TV, which are desperately needed, judging by the amount of cringe-inducing moments in Hollywood. Even "24" has science advisers:
"The show was interested in this scenario: Terrorists release a biological agent in a hotel air conditioning system, making people sick in a matter of minutes and killing roughly 2,000 people within a few hours. They concocted a genetically engineered "Cordella virus" to do it, and wanted government officials to be able to wave an electronic device that could instantly detect the virus in the air. They consulted CDC officials, who said there are no such devices. The CDC also suggested that health officials might try to deal with such a situation by isolating the ill from the well, perhaps reducing the contagion's impact, said Dr. Mitchell Cohen, director of CDC's Coordinating Center for Infectious Diseases. The writers took the tip, and the final death toll fell to under 800. "We saved 1,200 virtual people," said Cohen, who consulted with the "24" writers and did an on-camera interview for the DVD boxed set of the series. "


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Bayblab Book Club

I occasionally get reading recommendations from an online book retailer. Their state-of-the-art matching algorithm sometimes turns me on to books and authors I might not otherwise read. Their supercomputers must have had a glitch this weekend, when they actually sent me the following suggestion, likely from Rob's reading list:

"Camp Princess 2: Unicorns? Get Real!
When rumors of wild unicorns come to Camp Princess, there's a frenzy of excitement as the royal maidens prepare for the Unicorn Round-Up. But Princess Gundersnap has more important things to worry about. Her war-inclined mother has taken her beloved pony, Menschmik, into battle, and Gundersnap fears for his life. Besides, Gundersnap is much too practical to believe in unicorns.

Or is she? Both the magical tapestry in the tower and her favorite local witch, Berwynna, seem to be trying to tell Gundersnap something. Could the Unicorn Round-Up be more than just a bunch of royal hooey?"
The book is set to go on sale tomorrow, so I'd better finish off Camp Princess 1 before my preorder arrives.


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Caspase 8 indel protects against cancer

A recent publication in nature genetics demonstrated that a small 6bp indel which reduces the inducibility of the caspase 8 promoter protected against various forms of cancer in a large population (10 000) of Chinese. This of course is surprising, since apoptosis is mostly viewed as protective, but the effect is apparently mediated by protection of T-cells upon stimulation with cancer cell antigens. The variant showed up in 25% of people who where cancer free but only in 20% of those with cancer. Now the difference is not huge, but this is probably the type of variation that humans will accumulate as reproductive age goes up in the evolution of our species...


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Friday, April 20, 2007

It's not easy being green

A proposed City of Ottawa bylaw prohibiting excessive idling of vehicles is about to be sent to committee for review. If the law is adopted, anybody who leaves thier car idling for longer than 3 minutes (with certain exceptions) could face heavy fines beginning in September. Current city anti-idling law falls under noise bylaws. Opponents of the proposal argue money is better spent on planting trees and other green initiatives than a difficult to enforce law. The new bylaw hopes to curb emissions, but for the average person there's more than just the environment to think about, but also your pocketbook as the cost of fuel wasted while stopped at the curbside can easily exceed $100 annually (not much, but enough to cover at least one ticket under the new bylaw). Of course if you drive a hybrid car, you don't have much to worry, unless you live in Georgia.

Prius owners in Georgia are discovering that their cars aren't road worthy, at least by letter of the law. Part of the emissions test used collects exhaust samples from an idling vehicle, since the combustion engine in a hybrid shuts off when idling, the Prius registers an aborted test and fails. Owners still have to pay the $25 testing fee. This strikes me as another case of the law (or in this case the test) failing to keep up with new, green tech.

The sting for hybrid car adopters doesn't end there. As mentioned at the recent recording of Bayblab Podcast Episode 8 (in press), governments are offering financial incentives to 'go green' in the form of tax rebates. Prospective buyers shouldn't get too excited about that just yet. The credit is on the taxes paid, so trade-ins and leases can expect to see far less than the advertised rebate amount. It's a similar scenario in the US where a non-refundable tax credit is offered, meaning that if your tax liability is less than the advertised rebate after applying all other credits, that's all you get (discussion forum).

Finally, it should be noted that not all hybrid vehicles are created equal. There are a number of hybrid technologies out there. Some, like Toyota's Hybrid Synergy Drive, are full hybrid drivetrains can run on just the combustion engine, just the batteries or both. Other cars advertised as hybrid may be so-called 'mild hybrids', which can't drive in a full electric mode but rather just shut off the engine when stopping or coasting resulting in a 10-20% improvement in fuel efficiency. These are otherwise essentially conventional vehicles, but still bear the hybrid mark.


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Thursday, April 19, 2007

Harmful marijuana

Today at lunch we were discussing the ironic front page story of a recent "Metro" newspaper cover. In it patients complained about the 1500% markup (150$ an ounce) health Canada is supposedly making on the sell of medical marijuana. It seems health Canada probably wants to sell the therapeutic herb at market value so that patients are not tempted to resell at a profit. In any case, compared to other types of medication it is still cheap, and Canada is being pretty progressive in this matter compared to its southern neighbour. We were also discussing the possible adverse effects of marijuana, considering the recent re-classification that was done in the UK, which while putting marijuana as safer than nutmeg, cigarettes and alcohol, still scored more harmful than ecstasy or LSD. Most of the adverse effect come from the smoke inhalation, which could be avoided by using other delivery methods without combustion. However, propaganda still rages in the States and some of the adverse effects attributed to smoking marijuana (picture above) are definitely not based on sound science, with statements such as: clogged synapses, brain damage, cancer and "destroy" number of chromosomes!!!


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Tom Cruise: Quack of the Week

If you thought cheating terminal cancer patients was evil, wait until you hear this one. This week's bayblab quack award goes to Tom Cruise and L. Ron Hubbard's scientology cult for their "New York Rescue Workers Detoxification Project". This pseudoscience scam is aimed at capitalizing on the health problems of surviving 9-11 rescue workers. The brilliant program apparently encourages people to stop using inhalers or taking anti-depressants because they're evil. Instead, subscribers are encouraged to take vitamins and hang out in saunas to "de-toxify". Shame on you Tom Cruise. I hereby banish you from left-handedness forever.


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Super Scientists


Peter Parker, Bruce Wayne and Bruce Banner are just a few famous comic book scientists, but what about the science behind the heroes? The Ontario Science Centre recently put together a Superhero Science Exhibit, which has since ended its run a the Toronto museum, but is currently on tour (no word on whether it's coming to Ottawa any time soon). There are plenty of books out there determined to analyze the plausibility of comic book physics, and this light BBC piece on the science of superheroes. For the real scoop on what gives all heroes their powers, check out this guy's theory. But if you're more interested in what your favourite hero believes than what he can do, or are just curious whether he or she is more likely a creationist check out this comprehensive list of superhero religious beliefs, some with very detailed evidence. Holy Batman, batman!


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Gilson pipetting biopunks


I listened to the newest installment of the bayblab podcast and in addition to finding out that I care deeply about gilson pipettors, I went on about an old article in Nature. It is in the 'futures' section that is probably not around anymore. It's an inspiring read of sci-fi about biopunk and thought that it was relevant to the podcast discussion. (Picture was ganked from that article.)
Also here is a link to the kids home DNA kit that was mentioned on the podcast. (WIRED mag)


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Wednesday, April 18, 2007

Will Bill Gates Fix Science?

  • "Four reasons why academic research is broken", a great little article by Jason over at Unsought Input. He raises some great points regarding the current sad state of access to scientific information and how its hurts society. I think the article's right on the money. I especially like the thing about citations - the way journals cite literature is just like so 1940s.
  • On a more optimistic note, the Gates Foundation, now backed by the fortunes of the world's richest two men (Bill Gates and Warren Buffet) is changing the landscape of drug development with its mission of prioritizing humanitarian project funding. Even the big pharmas are starting to shake in their boots and will probably have to fall into line and also start developing AIDS drugs and vaccines for underprivileged majority who need them. Serves them right for being so damn greedy in the first place. One cool project that the Gates Foundation is helping to make happen is Jay Keasling's engineering of bacteria to synthesize cheap anti-malarials. Throwing $43 million at project such as this one, which will eventually make a curative dose of Artemisinin available for a quarter, you can see why big pharmas are sleeping with one eye open.


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Tuesday, April 17, 2007

Holy multiplexing batman!


CDKN2A which inactivates both RB and P53 is aparently the most common chromosomal deletion in cancer. It is therefore of interest to use this as a diagnostic marker. But how do you detect a rare mutated DNA in a very large pool of normal DNA? Well you multiplex your PCR! These guys who just published in PLOS ONE have a new multiplex method "Primer Approximation Multiplex PCR (PAMP), for enriching breakpoint sequences followed by genomic tiling array hybridization to locate the breakpoints" . When they say multiplex they don't joke... It's has no less than 7 primer pairs!


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Neutrophil Extracellular Traps (NETs)


Neutrophil Extracellular Traps (NETs) were brought to my attention by a Neighbour Of the Bay (NOB) today. They are essentially extracellular strands of DNA and proteases produced by neutrophils and function to trap foreign bacteria. They were discovered way back in 2004 and they definitely remind me of Spiderman.


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Monday, April 16, 2007

Hygiene hypothesis


I just did some quick poking about pubmed about the hygiene hypothesis. The hypothesis is that the increase in some diseases especially atopic diseases in some countries is a direct result of high quality hygiene. The diseases are type 1 diabetes, multiple sclerosis, Crohn's disease and allergic diseases (atopic diseases such as asthma). All have increased incidence in countries with high quality sanitation and an overactive immune system plays a role. The idea is that a developing immune system that is not exposed to enough innocuous antigens does not have sufficiently repressed TH1 and TH2 reactions to allergens and self-antigen. It sounds quite reasonable, however, it seems as though it is far from established. I found this decent review of the evidence for the hygiene hypothesis. Correlations such as the early use of antibiotics and incidence of asthma have to make you wonder if there is something to this hypothesis.


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Depleted Uranium and Cancer: What Does The Science Say?

After reading this news story mentioned on a Digg post (Digg my comment) which suggested that an American Gulf War veteran's cancer had been caused by exposure to depleted Uranium, I was interested to see what the science had to say. The use of high-density depleted Uranium in armor-piercing ammuntition and armor by American, British and NATO forces has been the subject of much controversy. Critics cite it as a cause of cancer in troops exposed on the battlefied, and a hazardous environmental pollutant for local residents. Actually, quite a few studies have been done to investigate this matter, most of them by various European countries falling outside the influence of the so-called American "military industrial complex". Here's what they say:

  • A Danish study published September 2006 examined cancer incidence in 14,000 of that countries veterans who had been deployed in the Balkans as part of the UN force. Contrary to previous speculations, no increased incidence of leukemia or testicular cancer was found amongst veterans in comparison to the overall Danish population.
  • A UK study comparing cancer incidences of 50,000 British veterans of the 1991 gulf-war to 50,000 control servicemen who had not been deployed showed no increased risk.
What's the bottom line? Studies have been done and so far there seems to be no evidence linking depleted Uranium use to cancer. Of course, cancer is a slow-developing disease and continued follow-up studies will be necessary to determine if incidences are affected decades from now. So while human beings firing armor-piercing ammo at each other while littering the environment with heavy metals and explosives (ie war) should probably be considered as something that is bad for human health, it doesn't seem to make a difference whether you're firing lead or depleted Uranium. Can't we all just settle our differences over a little LAN party?


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Sunday, April 15, 2007

Test for diabetes predisposition launched

Since we spoke about Iceland in our new podcast, I wanted to mention what Iceland's deCODE genetics has been up too. The company takes advantage of the relative inbreeding in Iceland and their good health system and nation-wide DNA banking to mine for disease-related SNPs. Their first test, for a mere 500$, will tell you wether or not you have a particular SNP which raises your type 2 diabetes risk by 100%. This SNP is carried by roughly 10% of the population. In the next year they will launch 10 new test for other diseases such as breast and prostate cancer. The idea is that you could make some lifestyle changes early, if you were at risk. I wonder if that could backfire, perhaps if you weren't carrying the diabetes SNP you would indulge more in sweets thinking that you were safe...
In any case this is good news for the icelanders who will now get these tests for free as payment. Keep an eye on those vikings you never know when they might take over the world again. THIS IS ICELANNNNDDD!!!


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Friday, April 13, 2007

Single nucleotide evolution


A cool summary of a research article in PLoS Biology discusses the finding that a single point nucleotide difference in a bacterial symbiont of an aphid leads to a differential reproductive fitness in hot or cold climates. I think that I'm going to get all my bacterial symbionts sequences and make sure that they aren't responsible for my bad reaction to the tartar sauce I had with lunch.


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Backboner

A couple of years ago, I went to the meeting of the Society for the Study of Reproduction (SSR) where J. Tilly presented his paper on the repopulation of germ cells in the ovary by a circulating stem cell in the blood. It was the first time that I saw both a standing ovation and grumbling from skeptics at a scientific talk. It went against everything we knew about female germ cells, and raised the possibility that woman with bone marrow tranplants or blood transfusion may not be the biological mothers of their own child. I am still not 100% convinced, but the idea that the niche can dictate what a stem cell will become is becoming more and more supported by evidence. This recent report that bone marrow cells injected in the testes can give rise to sperm further substantiates that claim. So maybe females can become, biological fathers? And it is good news for my friend who's spontaneously grown ovaries after watching too much dancing with the stars...


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Thursday, April 12, 2007

Quack of the week

This quack seems to think he can bend the laws of physics to make free energy: "Orbo produces free, clean and constant energy - that is our claim. By free we mean that the energy produced is done so without recourse to external source. By clean we mean that during operation the technology produces no emissions. By constant we mean that with the exception of mechanical failure the technology will continue to operate indefinitely."
Unfortunately there are no details yet on what the technology is, but it seems based on magnetism (forum), which according to the inventor (wikipedia), is being tested by over 500 scientists. Somehow I find that hard to believe. Check out this interview (video) with the man...


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Tuesday, April 10, 2007

Chocolate-Funded Researchers Fudging the Data?

Unfortunately, corporations seem to have perfected the art of corrupting academic research to help up their street cred and push their products. It's fairly simple to do if you have a decent sized budget and can be accomplished in three easy steps:
  1. Throw lots of soft money into funding research chairs, grants, conferences, lectures, consultancies, etc. for cash-strapped scientists at public institutions to investigate your product. Remember, "industry-funded research is 4 to 8 times more likely than independently funded research to result in findings favorable to the sponsor".
  2. See what they produce and reward those who put out positive results with continued funding, while cutting support when you get results that don't help you sell products. It's survival of the fittest - but don't worry, the theory of evolution is public domain and can be freely exploited without necessitating royalty payments to the descendants of Charles Darwin.
  3. After a few cycles of this "directed evolution of truth" the data should more or less be saying what you want. Polish things off by having your scientific pawns publish drastically over-hyped and over-stated interpretations of their data in a peer-reviewed journal, the higher the impact factor the better. Boisterously announce the publication of these findings with an even more over-hyped press release to major media outlets. Don't forget to to reward your peons with an all-expenses paid trip or at least a nice dinner party. Or maybe a chocolate bar.
I think the big pharmas were probably one of the first to use this method to beef up the street cred of their drugs, and more recently other industries like the winemakers have been getting into the action. Sure...a glass of red wine a day is the key to longevity because it contains flavonoids. Then again, if you're really after health, you could always skip out on the toxic alcohol content and just eat a grape or drink some juice.

Anyway, now it's chocolate-funded research, and things are just getting so ridiculous it's funny. This great article by blogger Mark Klempner describes how the Mars bar company is manipulating academia to demonstrate the supposed benefits of the "flavanols" in their products, while of course ignoring the massive negative effects of the sugars and fats they contain. I mean come on, we're talking about JUNK FOOD here. I would be embarrassed to be associated with a would-be serious academic institution such as the University of California at Davis, who support a Mars bar endowed chair in nutrition and have allowed their researchers to recieve at total of $10 million in research funding from the chocolate bar maker. Maybe they should be calling themselves something like "Department of Junk Food and Obesity Promotion, University of Mars Bar at Davis" instead. These guys even have a paper in PNAS that is commonly cited on chocolate industry propaganda websites. On these sites you can find quotes from people at the center of this conflict of interest, like Harold Schmitz, Mars Chief Scientific Officer and UC Davis visiting professor in nutrition: "Traditional cocoa processing often destroys the flavanols, but Mars technology helps to retain these naturally occurring nutrients from cocoa. This new research emphasizes the importance of understanding the potential public health applications of emerging cocoa science, which is a challenge we take very seriously at Mars." Priceless.

The saddest part is that it's usually not obvious, when you read a paper like this, see a poster or hear a talk, that the research has been funded for corporate gain. Instead you're just left wondering why you've wasted your time listening to a bunch of meaningless, over-stated, irrelevent and massaged data disguised to look like science.

Great piece though, and I think he's bang on. The Brave New World reference is interesting although disconcerting. (Naturally, Klempner manages to tie global waming into his article as well).


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Grant proposal

I've been working all weekend on a grant on Williams syndrome for a class. Over the course of that weekend I read over the internets twice, and I found this great scientific proposal which we should replicate in the bay: Breeding M&M candies.

"Whenever I get a package of plain M&Ms, I make it my duty to continue the strength and robustness of the candy as a species. To this end, I hold M&M duels. Taking two candies between my thumb and forefinger, I apply pressure, squeezing them together until one of them cracks and splinters. That is the"loser," and I eat the inferior one immediately. The winner gets to go another round.
I have found that, in general, the brown and red M&Ms are tougher, and the newer blue ones are genetically inferior...
Occasionally I will get a mutation, a candy that is misshapen...

When I reach the end of the pack, I am left with one M&M, the strongest of the herd. Since it would make no sense to eat this one as well, I pack it neatly in an envelope and send it to:

M&M Mars, A Division of Mars, Inc.
Hackettstown, NJ
17840-1503 U.S.A.

along with a 3x5 card reading, "Please use this M&M for breeding purposes."

This week they wrote back to thank me, and sent me a coupon for a free 1/2 pound bag of plain M&Ms.
I consider this "grant money." I have set aside the weekend for a grand tournament. From a field of hundreds, we will discover the True Champion. There can be only one."


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Monday, April 09, 2007

Engineering the Brain into a Solar-Powered Calculator and Will Biology Ever Be a "Real" Science?

  • As a biologist I'm always jealous of physicists, what with the Feynmanian mathematical certainty and Einsteinian grandeur that they wield in their quest to explain the universe. We biologists are are less self-confident bunch, tempered (and tortured) by lives predominated by experimental failures within the lab. Will biology ever join chemistry and physics as a so-called "capital-S Science", with a set of its own all-powerful, generalized and quantitative Laws? (Not to be confused with The Ten Commandments...) MIT biological historian Evelyn Fox Keller argues that biology may never see its Moses descend from the mountain. Instead, she suggests in this Nature essay, that biology is special, and the exceptions more important than the rule. Enquist and Stark, in this response, are more optimistic about the prospects for a quantitative Biology with all-encompassing Laws. Maybe there's hope for biology after all, and there will come a day when we can make predictions that even a VC investor would take to the bank.


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Sunday, April 08, 2007

Starlings in School


I've heard that fish are able to swim in tight schools in part due to their lateral line. Basically this anatomical feature can sense small vibrations and therefore can aid in schooling. While sight aids in schooling, apparently a blind fish is capable of schooling with only its lateral line intact.
Starlings do some pretty crazy things, and often it looks like schooling. How do they do this without an analogous feature like a lateral line? I have no idea. Check out these crazy starlings mobbing a tree (video) in schooling form.
If you are going to only check out one link in this post it's this one of starlings. (video) Turn up the tunes or something and watch the whole thing. awesome. [I think I've seen this posted somewhere else before. Hope it wasn't bayblab.] The excuse for schooling in fish as described in the first link, namely predator evasion, simply does not apply to the nuttiness of these crazy formations.


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Guerilla fundraising


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Saturday, April 07, 2007

You are what you eat


I was at the National Zoo in DC yesterday. I haven't been to a zoo in probably 15 years, but it's nice to know that 2.5 science degrees later, I can still learn a thing or two from such an outing. In this instance, I discovered that the beautiful but deadly 'poison dart frogs' are not naturally toxic. Raised in captivity, these amphibians are harmless. The reason for their toxicity is the accumulation of alkaloid compounds from ants and other arthropods that they consume. This is true of frogs from Madagascar as well as those from Australia or South America. Geographically isolated, the ants that are the source of the toxin for frogs from these regions are not closely related, making this a cool example of convergent co-evolution of arthropod and frog species.


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Rise of the hybrid?

I've been spending my Easter weekend in the United States, a land where car is king. I'm in the Washington DC area, and as one might expect gas guzzling SUVs, minivans and pickup trucks dominate the roadways. One thing that's surprised me, however, is the number of hybrid vehicles on the road as well. Now I know that Prius sales have been consistently rising, and I haven't done a proper count, but it seems like they're the single most dominant make of car out here (I've also seen 2 Honda hybrids and a Highlander hybrid as well, but the Prius is everywhere.) I'm not sure what it's like in other parts of the country (Ben?), whether there's a real environmental concern or it's that the hybrid premium price elevates them to status symbol, but this seems like a promising trend. Personally, I'm holding out for an electric car.


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Friday, April 06, 2007

Math nerds can rap

Move over spaghetti nerds..."What You Know About Math"


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The butterfly effect and global warming

Forget about pirates, the real culprit in global warming could be ... butterflies. You may be familiar with the butterfly effect: "The phrase refers to the idea that a butterfly's wings might create tiny changes in the atmosphere that ultimately cause a tornado to appear (or, for that matter, prevent a tornado from appearing). The flapping wing represents a small change in the initial condition of the system, which causes a chain of events leading to large-scale phenomena. Had the butterfly not flapped its wings, the trajectory of the system might have been vastly different." Now just think of the maths. Consider monarchs, there are between 200-500 million of them that migrate between Canada, USA and mexico. Now each butterfly flaps its wings 5-12 times per second. So if one flap of the wing can cause a tornado, it's not inconceivable that the trillions of flapping from monarchs could cause global warming. In all seriousness, there is actually a link, and it's sad. According to the royal society: "Species with northern and/or montane distributions have disappeared from low elevation sites and colonized sites at higher elevations during the twentieth century, consistent with a climate explanation.". In Canada, the range of the monarch also appears to be changing. And parasites are more common: "The spread of certain viral, protozoan, and nematode parasites in temperate insects may be favored by warmer climates that increase the host's breeding season. Prevalence of the protozoan parasite Ophryocystis elektroscirrha is higher in monarch butterfly populations that breed year-round in warm regions than in more seasonal climates where monarchs migrate long distances between breeding intervals."


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Spagetti Bridges


One of the coolest things I did in grade school was the spagetti bridge building contest. I was thinking about it recently and so googled it and was shocked to find that it isn't as widespread as I had assumed. I was under the impression it was a national competition. Personally I think that the bay needs a good science contest to determine who is the biggest bayb in the lab.


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Inside Cancer



Found this website that has a great overview of cancer, without being too oversimplistic. Pretty interesting for any bayblab reader who doesn't study or know much about cancer, since cancer is bayblabs #1 tag. It has a nice interface and lots of animations and video. Funded by NIH.


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Thursday, April 05, 2007

Vegetarian Cancer rates


I overheard that some bay members were off to eat some vegetables for dinner this evening, and I found this interesting article on cancer rates and diet. Check out some of the correlations between meat intake and occurrence of different type of cancer in various countries. I think more attention to this type of data could be very important as finding preventative therapies. Note that most of the data is over ten years old.


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Wednesday, April 04, 2007

Left-Handedness is the Pinnacle of Evolution

Enough with the molecular reductionism. We all know it's fun to theorize and hand-wave about the molecular basis of life, but of course real biologists ignore molecules and go right to the in vivo models. And what have we learned about the evolution of left-handedness from these more relevant human studies?

  • Left-handed men are worth more to society than right-handers, as evidenced by the fact that their salaries are 26% higher.
  • Left-handers get their own special scissors, because they are better at arts and crafts.
  • The QWERTY keyboard was designed specifically for lefties, with all the important letters on the left, becuase left-handers are the only ones who have thoughts worth typing.
  • Bike helmet straps designed for right-handers, because lefties more co-ordinated and don't need to wear helmets.
  • The leaders of the most successful empires of human history were left-handed - most of the British Royal family, Alexender the Great, Charlemagne, Julius Caesar and Napoleon were lefties. This obviously contributed to their success and TOTAL WORLD DOMINATION. For example Napoleon taught all his soldiers to be kick-ass left-handed swordsmen and based his military strategy around this special ability...the rest is history.
  • George Bush Sr. (the smart one) is left handed. George Bush Jr. (the illiterate one who invaded Iraq) is not.
  • In music, Jimi Hendrix was left-handed and the greatest guitar player to ever live.
  • The most intelligent two humans ever born were left-handed. Albert Einstein and Leonardo DaVinci.
You might ask, why then, if left-handedness is superior and therefore under positive selection, are there currently much fewer lefties than right-handers around? Actually this has nothing to do with evolution. The true reason for this discrepancy is that God is jealous of left-handers because they are better than him in all ways, which he did not intend when he first began to direct the evolution of humans. He therefore banded with the right-handers, convincing them to form a right-handedness conspiracy in an effort to wipe out the lefties. It is well known that the church persecuted left-handed children as "devil-spawn", and school-masters tried, with significant success, to beat the left-handedness out of young children. The church also refused to marry left-handed "agents of satan", directly leading to diminished reproductive success.

Fortunately, enlightened lefties like Joan of Arc, Leonardo da Vinci, Pablo Picasso, Jack the Ripper, Benjamin Franklin, Fidel Castro, Gandhi, Buzz Aldrin, Ted Koppel, Bart Simpson, Ross Perot, Tom Cruise (in Mission Impossible), Rocky Balboa (especially in part III), Rambo (the original) and Bob Dylan refused to cave to oppression and fought to overthrow the church's dominance of society, establish human rights and develop more just societies. As a result, human evolution has been freed from the reign of the right-handed conspiracy, and the frequency of lefties has been on the rise for the past sixty years (see fig below). Obviously, left-handedness is superior and that is why life evolves to be left-handed, not just at the molecular level, but the important ones too (although there is an outside chance that it may be caused by global warming).





Digg this story NOW.


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Stereo is Homer

Over lunch we were discussing why life had chosen left-handed amino-acids versus right-handed ones. Was there any advantage for that initial choice? Rob suggested that comets actually carry more left handed amino-acids so they may have been more abundant on earth. Turns out he was right: "Amino acids found in meteorites from space, which must have formed abiotically, also show significantly more of the left-handed variety, perhaps from circularly polarized UV light in the early solar system (Engel and Macko 1997; Cronin and Pizzarello 1999)"
Other reasons that may have contributed for that preference, is that left-handed AA may be required for catalytic production of other left-handed organic molecules (sugar, lipids). Although this is kind of a chicken and egg thing. More surprisingly, some bacteria actually use right handed amino-acids: "From the ratios of right- to left-handed amino acids in seawater, McCarthy and his colleagues conclude that a substantial fraction of the dissolved organic matter comes from bacteria. This challenges the traditional view that algae produce most of the ocean's soluble biological material. Bada notes that bacteria coat themselves with right-handed amino acids because the unusual structures provide a tough exterior that resists other organisms. This is what helps bacteria evade digestive enzymes in human stomachs, he says."
Interestingly, a new hypothesis suggests that while reactions may produce equal amounts of L and D, the L AA dissolve better in water..."Donna Blackmond at Imperial College London and colleagues dissolved a mixture of solid L and D versions of the amino acid serine in water. They found that a small difference in the initial proportion of one version gets amplified in the resulting solution. So a 100:1 mixture of L- and D-serine produces a solution made up almost entirely of L-serine, but so does a 100:99 mixture (Nature, vol 441, p 621)."
So should we expect life on Mars to also be left-handed if it exists?


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Should chimps have human rights?

I found this on slashdot... Apparently the justification for giving human rights to chimps is this: "He recognises himself in the mirror, plays hide-and-seek and breaks into fits of giggles when tickled. He is also our closest evolutionary cousin.". There is even talks of including chimps in the Habeas Corpus. Obviously these people have their hearts at the right place, but I think they are wrong. Firstly chimps are not human, no matter what their behaviour is like. In fact Bonobos are much closer to us when it comes to behaviour. What will happen when a chimp kills a human? Can it plead insanity because its IQ is lower? Should it get equal opportunity rights? Obviously it doesn't work that way. And why single out the chimp. Do we love ourselves so much that we'll only save animals that look like us? For me I'd rather have all the animals protected under the law to some degree. If we have to give them personal rights, we better design a new system from scratch. Are different species at birth unequal under the law?


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Tuesday, April 03, 2007

Plasma Gasification

According to the excellent news source for celebrity gossip, the metro (ottawa edition), Ottawa (the capital city of Canada), is considering a waste-to-energy technology to deal with the MHW (municiple household waste). The technology sounds too good to be true, basically incinerate MHW, (emitting no pollutants into the atmosphere) use the energy produced to make some electricity to run the plant and sell some back to the grid. Check out this article that explains how theoretically this should work and how it's going to save us all. I have yet to find any one in operation in the world and many examples of seriously problematic similar schemes. Some websites point to westinghouse as a leader in this as they have some pretty serious plasma torches already in successful operation in industry, however their website says only "it is widely hoped plasma gasification can be practically applied." Here is a company selling a plasma gasification system that lays out the issue pretty well, and at the end starts talking about 'what ifs' such as "Lets say, however, that the gasification plant doesn't work at all." That doesn't sound like a proven technology that should be employed on a large scale to solve a large problem.
I would love to hear something from someone who knows more about this than me but where does the garbage go then? Assuming conversation of matter, if there are no emissions into the atmosphere and this system gets rid of the mass that used to be garbage where does it go? Don't get me wrong I have high hopes for tech to solve some environmental problems, I just hope that city council has an independent review of this whole idea.


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Mitochondrial Madness

Our often-neglected bacterial endosymbionts the mitochondria seem to have their fingers in all aspects of eukaryotic cell functioning. Not only do they make us ATP and tell our cells when to die, they even have their own genome, which they can replicate, transcribe and translate all on their own. But mitochondria don't just use proteins encoded in their own genomes; they've also got some out on loan from the nucleus. And this is where the madness begins. Somehow this excellent Molecular Cell review on mitochondrial transcription found its way onto my lab bench, so I read it. Here are a few of the mind-blowing facts you can discover therein:


Also, check out this wicked album of artistic renditions of cells by Gary Carlson which I ganked the above photo from. Nice job Gary!


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Who needs eyes when you have a tongue?

I remember reading about "hacking" your senses a little while back, and an engineer fan of the bayblab sent us this wicked article in Wired illustrating where the field has progressed since. The idea is that the brain is so plastic that it can adapt to process information, no matter where the signal is originating. Basically the brain is very good at processing signals. At first people experimented by implanting strong magnets under their skin and being able to "feel" magnetic lines to determine their orientation. Then someone had the clever idea of using the tongue for sensory input since it has dense nerve inputs to provide a "tactile display". By placing an electrical array on the tongue and relaying signals about your orientation it permitted its wearer to "see" in situations where visual cues are poor such as flying an airplane or diving. Interestingly it has found its way into medical use and is entering clinical trials : "The researchers started testing the device on people with damaged inner ears. Not only did it restore their balance (presumably by giving them a data feed that was cleaner than the one coming from their semi circular canals) but the effects lasted even after they'd removed the mouthpiece — sometimes for hours or days."
Obviously this would be great for blind people too. And I can only speculate about the pleasures of added tactile senses when combined with regular vision. You can read more about this sort of stuff on the author's blog...Also check out this guy who wants to hack your memory!!!


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Synthetic Genetic Elements take over

A recent article in Science demonstrates propagation of a synthetic genetic element that replaces the endogenous genotype in drosophila in under 10 generations (subscription required). A freely available synopsis is here at The Scientist. The idea is that if, for example, a mosquito that is genetically programmed not to carry the malaria parasite were set off into the wild to replace disease carrying mosquitos it would not be successful because there is no reproductive advantage. Associating the genotype closely with this synthetic genetic element would make this genotype dominate. The system works by encoding two microRNAs (the 'toxin') that are expressed in the germline of the female. These microRNAs repress the expression of an gene essential for embyogenesis, so the system also encodes for a microRNA resistant form of that gene (the 'antidote'). Therefore a female carrying this genetic element can only produce viable offspring who carry the genetic element. In any case apparently if introduced at a minimal threshold level of 25% this element rapidly replaces the other genotypes. I'm still not sure exactly how this happens as you would think that a female that has less viable offspring than one that doesn't carry this element would make it less reproductively fit.


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