Monday, March 31, 2008

A history of 'beardism' and the science that backs it

Great men throughout history have worn beards - Darwin, Jesus, Lincoln, Zeus to name a few - but this symbol of dignity, wisdom and knowledge has also brought persecution throughout history (no doubt from those lacking the aforementioned traits). Alexander the great insisted that his armies be clean shaven, for fear that they could be used by his enemies in combat (think hair pulling), and to this day some militaries still insist on bald-faced soldiers - but for more practical reasons. In this age of biological and chemical warfare, an unkempt beard could prevent a good seal on a gas mask and cause an untimely demise. In the 1500s, Henry VIII instituted a special tax on bearded men which was repealed after his death. The tax was revisited by Elizabeth I. More famously, in the late 1600s, Tsar Peter I (Peter the Great) enacted a beard tax, charging men who wanted to grow beards and personally shaving his nobles. Not only were bearded men taxed, but they were also required to wear a medal (pictured) that some say translates as "Beards are a ridiculous ornament", adding insult to financial injury. Brigham Young University insists students be clean shaven with few exceptions. These are just a few examples of bald-facers keeping the bearded man down! (Though it should be noted that Henry VIII hypocritically wore a beard himself)

In addition to taxation, forced shaving also has a history as punishment. During the 60s, peace-activists (aka hippies) were sometimes forcibly shaven. Other alleged anti-beard actions include a plot by the CIA to use chemicals to make Castro's beard fall out and a delay in the knighthood of Sean Connery because of his beard (a more likely explanation was his support of Scottish independence). Beardism is so rampant that in 1995, the Beard Liberation Front was formed to support those of us who choose a distinguished beard over a baby-faced shave. And anti-beard sentiment runs deep - surveys suggest that bearded politicians receive up to 5% fewer votes than their non-bearded counterparts. This is counter intuitive to me: the 10 minutes saved shaving is 10 more minutes that the politician is working for the people (or that the scientist spends in the lab, etc.). We bearded folk need to stand together against this oppression! When a non-whiskered friend, spouse (bearded people do attract women, despite what the smoothies want you to think) or co-worker suggests you go hairless, remind them of the words of Mussolini: "I am anti-whiskers. Fascism is anti-whiskers. Whiskers are a sign of decadence."

However, there is a downside to beard growth - and perhaps the underlying factors of facial-hair phobia, and it would be unfair of me to call on my brothers to drop their razors without full disclosure. The fitting of a gas mask has already been mentioned, and that argument extends to scuba masks (though I've never had a problem) and respirators and facemasks. An entertaining piece in Inkling Magazine highlights these and other problems:
"But anti-beard arguments also ran rife in pre-Victorian times: Beards trapped food and the stuff you spewed out when you sneezed. At a stretch, they could even go as far as to catch fire and trap vermin, some argued. This all came to a head in 1907, with a rather remarkable experiment. A French scientist took one bearded and one clean shaven man from the streets of Paris and asked each of them to kiss a woman, whose lips were previously swabbed with antiseptic. After each smooth, her lips were swabbed and the the cultures were smeared on agar. The hairy kiss, it turned out, was by far the more microbial-ly diverse."
This has been backed up by more recent studies that showed that beards retained microbes, even after washing with soap (someone should have told Pasteur). This, of course, makes some sense. Why call it a flavour saver (an expression that has much more vulgar origins than I naively thought) if it doesn't retain anything? Maybe beards are chock full of bacteria because they prevent them from entering the body - sort of like a crude air filter - but at an increased risk of those around you. And this says nothing of the inherent risks of shaving - cuts, ingrown hair, and microabrasions that can lead to infections.

For those who work in a lab, this bacteria retained in the beard and the excess bacterial shedding associated with it may affect your experiments. Who knows what bacteria might be introduced to cell cultures, bacterial preps and other experiments? And don't forget the possibility of beards as vectors for crystals or other replicating structures that can spread to other labs causing isomeric conversion of drugs or other disappearing polymorphs.

All the studies of beards as bacterial breeding grounds means they get a lot of bad press, so it's no wonder so many people frown upon them. But the most compelling anti-beard argument I'm aware of is a 2000 study that showed a full beard costs a drinker 23GBP ($46 CAD) a year in lost beer, or a combined loss of over 160 000 pints in the UK alone. Still, if bearded drinker Ernest Hemingway could live with that kind of loss, so can I.

(HT Pure Pedantry, Pharyngula)
(Photos: World Beard Championships)


Friday, March 28, 2008

Earth Hour and Solar Cooking

On March 29th, between 8 and 9pm, people are being asked to turn off their lights to participate in Earth Hour (traffic lights, street lights, etc. will still be operating as necessary). The event, run by the World Wildlife Fund, began last year in Sydney, Australia but has been expanded to a global effort. The goal is to highlight the problem of climate change, encourage energy conservation and demonstrate how easy it is to take a small individual action (with the notion that millions of small individual actions add up to a large effect). Individuals and businesses can sign up on the Earth Hour website, but it isn't required to participate. Even McDonalds has pledged to turn off golden arches across Canada (where, incidentally, more people have signed on than our southern neighbours). For those who are local, Ottawa Hydro will be reporting on how much energy was actually saved after the event.

If you want to get more active in energy conservation, you may want to look into solar cooking. Reflecting sunlight to cook food is nothing new, going back as far as the late 1700s, but cooker designs have progressed beyond the basic tin-foil reflector (though not by much, they all work on the same principle of concentrating sunlight). Of course, how useful they are depends on time of day, year, amount of sun, etc. That hasn't deterred the Indians though: the world's largest solar cooker that can cook almost 40000 meals a day has just been build in Taleti. This is no 4th-grade science project - the system can generate temperatures of 650 degrees to produce 3-4 tonnes of steam for use in cooking. Time for lunch!


Aubrey de White

We have discussed the ideas of Aubrey de Grey quite a bit on the bayblab previously. Basically he is a former artificial intelligence researcher turned theoretical biologist who believes that aging itself can be slowed down or stopped using near future technology. In fact he has suggested that we may be in the presence of people who will be immortal, ie people for whom this kind of technology will be available to them before they die.
It is easy to dismiss Aubrey due to his lack of experimental biology experience and his likeness to Gandalf the Grey. His ascendancy to Aubrey de White seems unlikely, however, I was fairly impressed with an actual in depth interview with Aubrey on "Futures in Biotech". He has a more broad understanding that I initially gave him credit for. I think I will read his book "Ending Aging".
Some of the research that the Methuselah Foundation is funding he speaks of.
An example is trying to make proteins that are coded for in mitochondrial DNA function but be less hydrophobic. Proteins that are encoded in mitochondria are apparently more hydrophobic. The mitochondria has maintained these proteins in it's small genome because they can not be translated and transported to the mitochondria, like many other mitochondrial proteins. These proteins are too hydrophobic to be unwound and then placed into the mitochondria so the mitochondria encodes for them itself. By engineering these proteins to be less hydrophobic they could be encoded in the nuclear DNA and transported to the mitochondria. This would protect these genes from the high mutation rates found in mitochondrial DNA. Great stuff. I can't imagine how they would actually get this to work but Aubrey is ambitious.
Anyways if you aren't going to read the book at least listen to the podcast interview with Aubrey. The interviewer is not quite as good as the newest bayblab podcast where we interview a dentistry student, and it's over an hour long, but overall I though it was quite good.


Wednesday, March 26, 2008

All Hail Venter, Emperor of Planet Earth!

Caesar Craig Venter tells us how DNA can solve all the world's problems, real or perceived: infectious disease, hunger, poverty, natural disasters, fuel shortage, global warming, etc, etc. in this lecture. It's not as bad as I expected - he certainly does a great job selling biology to the wider audience. The world could probably use an all-powerful benevolent dictator at the helm right now; Venter would probably be a good choice.

A lot of the ideas are grandiose but doable, although I'd like to hear more about how he thinks synthetic organisms can possibly replace fossil fuels to support the energy demands of industrialized civilization. I don't buy it. I'd love to see the world's oil-based economy converted to a bio-economy, but as long as there's black gold spewing out of the ground I don't see it happening. And when the oil does run out, I don't see how any biological energy production system can support civilization as we currently know it. Remember the Roman Empire? That was probably the last serious bio-economy of human history. How much better can we do?

Anyway have a watch and see if you can come up with better ideas for saving civilization.

(HTs: Palazzo, Hsien-Hsien)


Creationist Museum Tours

This video clip has been making the rounds, so apologies if you've seen it already. Still, I think it's important and highlights a need for sound science policy and science education - particularly critical thinking skills. (On the plus side, a major news outlet featuring a story like this is definitely a good move)

Found via Sandwalk


Tuesday, March 25, 2008

Progesterone may impair your drinking

Since we've been discussing questionable papers about weak correlations between drinking and strange variables, a tipster sent me this original piece of research linking sex hormones and ethanol elimination rates. My first shock was that kilo for kilo (of lean body mass), woman eliminate ethanol faster than man, which means that in theory they should "hold their alcohol" better. The reason for this remarkable feat is that woman have larger livers than man as a percentage of lean body mass. In fact the average liver size is not statistically different between women and men, despite the body size difference. but don't cheer too quickly, woman are more susceptible to alcoholic liver disease...

Now on to the paper in question. The study is from a German group, no surprise there. They got healthy volunteers:

"Forty-seven healthy men (average age 25 ± 6.1 years) and 61 healthy women (average age 24 ± 2.4 years) received 0.79–0.95 g of ethanol/kg body weight in the form of an alcohol beverage of their choice."

And then they measured sex hormones and followed blood ethanol kinetics:

"The mean hourly elimination rate (ß60) was 0.1677 ± 0.0311 g/kg/h in men. In women, the mean hourly elimination rate was 0.2044 ± 0.0414 g/kg/h in the high progesterone group and 0.1850 ± 0.0276 g/kg/h in the low progesterone group "

Now I'm not sure how the author went from this data to the conclusion that gender differences in kinetics are partially explained by progesterone, but I wouldn't mind being a study subject... So that I can brag about my high progesterone levels...


Cancer research carnival

The next edition of the cancer Carnival (#8) is coming up on Friday, April 4th. Make sure you submit your posts here by April 3rd. This edition will be hosted by the Skeptical Alchemist a great blog that doesn't shy away from discussing peer reviewed science.


Lin-28 is Master of Let-7 miRNA Processing

In yet another report from the incredibly boring and slow-paced field of microRNA research, Viswanathan et al. report on the biochemical purification of a factor that controls the processing of the let7 miRNA. For those of you who have wisely been ignoring recent developments in this mundane field, the Let7s are a group of pretty much useless miRNA genes. All they seem to do is control the fate of stem cells, which intelligent people know are mythical entities invented by people from Canada. Oh, and they're underexpressed in cancer and **may** act as tumor suppressors. Whatever.

Anyway these guys pulled out an interesting protein called Lin-28 in a screen for regulators of Let-7 processing in embryonic stem cells. In stem cells, and presumably cancer cells as well, the idea is that Lin28 binds to the primary Let-7 transcript and prevents processing to the active form. Genes that would otherwise be regulated by Let-7 can therefore be expressed and pluripotency/proliferation carries on. In differentiated cells, Lin-28 is down-regulated, freeing Let-7 to go about it's business repressing it's targets. Or so the story goes.

We already knew that Lin-28 was an RNA-binding protein of developmental significance, so this new finding makes a lot of sense. Palazzo has been drooling all over this paper, and he's particularly worked up about the fact the Lin-28 was also recently identified as one of the magic factors that can reprogram adult somatic cells into pluripotent, embryonic-like stem cells. Read what he has to say for more on this. I find it interesting to note that Lin-28 can be found in P-bodies, cytoplasmic sites of RNA processing that seem to be part of the whole miRNA game (see also here for recent developments in the miRNA-P-body connection).

Anyway, that's enough blathering for now on the clearly trivial research that is being done over at the Harvard Medical School.


Sunday, March 23, 2008

The Identicality of Identical Twins

OK... Monozygotic twins - identical twins to the majority of us.
Most know how they are made, but for those who don't it's pretty simple. Daddy meets Mummy, and they love each other very much. Something involving a stork happens, and you get a single celled embryo called a zygote. If that zygote somehow splits into two embryos, you get two twins.
Conventional wisdom would have it that, since Daddy DNA and Mummy DNA had already gotten together by the time the embryo split, the two twins look so similar because they have the same mixture of DNA. It sounds reasonable. Even Wikipedia claims it to be true.

It's wrong.

A recent article in the American Journal of Human Genetics (which appears to be open source - I can read it without being at work) looked at the Copy Number Variation of 19 pairs of monozygotic twins - those who should have identical DNA. Now epigenetic effects of monozygotic twins have been studied, and it is well known that there can be some startling differences between identical twins. However this is the first study which really looked at the actual information coded in the DNA of those twins.

What the paper presents is a curious bit of epigenetics (or possibly 'proper' genetics): monozygotic twins, who started off with exactly the same base DNA sequences and chromosomes, have different Copy Numbers.

Apart from the sheer interest value, this immediately places doubt on some of the very good work which has been previously done, on the basis that monozygotic twins have the same DNA, while dizygotic twins (or fraternal twins) have differing DNA (and thus any differences in genetic disease must have come about from those differences). Some of the CNV differences were in genes which are known to be connected to very serious diseases, like Parkinson’s disease and Lewy body dementia.

It all points to just how little we actually know about the pre-implantation phase of human development, and just how big an impact it can have on the future of health.


Thursday, March 20, 2008

Get Rid of Your Old Textbooks

Back in October I put out a call for charities that take used textbooks and distribute them to universities and schools where they can be put to use. I have thousands of dollars (and pounds) of textbooks that I'm sick of moving that could be useful elsewhere.

One of our readers came through and pointed me to this book collection going on at the University of Ottawa. For the month of April, the Faculty of Medicine will be accepting books to send to developing nations.

If you live in the Ottawa area and are sitting on a mountain of textbooks, get them to the people at the link above and they'll get them to where they're needed.


Stem Cell Tourism in China

I've written before about StemEnhance, a piece of pseudomedicine that purports to improve "wellness" by stimulating stem cell release from the bone marrow. In that post I questioned whether the supplement a)did what they claimed and b)whether, if it worked as advertised, the mobilization of stem cells would have a positive, negative or no effect.

Well now, instead of $60 a bottle for algae extract, you can drop a grand on a flight to China and another $20000 to be injected with umbilical cord cells - guaranteeing an at least temporary boost of stem cells in the body. (Nevermind that these cells are foreign and will be attacked by the immune system) Of course the same questions remain: Will this kind of treatment have positive, negative or no effect? Dr. Hu, the chairman of the company selling this treatment claims that 70% of the 3000 patients who have had these injections for a variety of conditions have seen an improvement. On the other hand, the NPR article (linked above) points out:
No rigorous, controlled clinical trials were carried out before the treatment was offered to patients. No research has yet been published in established peer-review journals overseas. And no one knows for sure what the possible risks might be.
So once again, we have an untested, unproven therapy. Let's look at the possible scenarios:

1) The injections work. People's varying conditions are being improved. Great! Test it. Prove it. Show it's safe. Yes trials are expensive, but why wouldn't you want to do it to silence skeptics, better understand what's going on and potentially improve this kind of treatment. However, the likelihood of this therapy working as advertised is small.
Bruce Dobkin is director of the neurologic rehabilitation and research program at the University of California, Los Angles. In response to questions from NPR, he writes in an e-mail that "it is extreme nonsense to think that cells can be incorporated into the complex nervous system and do so much, when we cannot even get cells in mice and rats to do very much.
There's also no evidence that umbilical cord stem cells can become the kind of neurons these doctors are claiming, nor evidence that they'll even get to the desired site to begin with.

2) The injections have negative effects. Regardless of whether these injections are a useful treatment, there's the very real posibility that there could be serious consequences that haven't been discovered (no testing means no awareness of effects good or bad). Immune response. Cancer. Take your pick.

3) The injections have no effect at all. Thanks for your 20 grand! Goodbye.

This kind of treatment may hold some future promise, but once again someone is putting the cart before the horse when it comes to stem cell treatments. Do the research, then treat. And don't ask desperate families to plonk down crazy amounts of money for what is generously described as experimental treatment. Sadly, this makes StemEnhance look good by comparison.

More blog reaction here and here.


Wednesday, March 19, 2008

Alcohol may impair your science

If you're a graduate student, chances are you came into the lab yesterday hungover from St Patrick's day and that your productivity was impaired. So how does drinking beer impact your science? The February issue of Oikos, an ecology journal, features a paper by Tomas Grim from the Czech Republic entitled "A possible role of social activity to explain differences in publication output among ecologists".

We at the bayblab take beer drinking and science very seriously, and these new findings are cause for concern. The study is mostly a correlation between beer consumption and citation counts. As per the abstract:

"One of the most frequent social activities in the world is drinking alcohol. In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance. Using a survey from the Czech Republic, that has the highest per capita beer consumption rate in the world, I show that increasing per capita beer consumption is associated with lower numbers of papers, total citations, and citations per paper (a surrogate measure of paper quality)."

Unfortunately I do not have access to the paper in question to peruse the figures but here are some great quotes about the results from the NY Times:

It’s rather devastating to be told we should drink less beer in order to increase our scientific performance,” Dr. Symonds said."

"Though the public may tend to think of scientists as exceedingly sober, scientific schmoozing is often beer-tinged, famous for producing spectacular breakthroughs and productive collaborations, countless papers having begun as scrawls on cocktail napkins."

"Yet the new study shows no indication that some level of moderate social beer drinking increases scientific productivity. "

"More important, as Dr. Grim pointed out, the study documents a correlation between beer drinking and scientific performance without explaining any correlation. That leaves open the possibility that it is not beer drinking that causes poor scientific performance, but just the opposite"

I think this needs to be investigated to find the optimal number of beers to produce good science. We'll get into this matter as soon as we've figured out the optimal number of beers for bowling... So what is your citation count and beer consumption?


Monday, March 17, 2008

Size matters for non-coding RNAs

You may already be familiar with the Tsix/Xist non-coding RNA system which is responsible for the inactivation of the second X chromosome in females. The system is quite elegant, and uses long non coding RNA with complementary sequence to "coat" the X chromosome which starts a chain of rearrangements leading to condensation and Lyonisation. This way the female genome can compensate its transcriptional output to match that of the male.

Well it turns out that there are 940 other long (>100bp) non-coding RNAs in humans. What is their function? Are they also involved in modulating chromosome architecture? This study (subscription required) looked at a set of abundantly expressed, evolutionarily conserved long non coding RNA (l-ncRNA). The authors decided to look at their expression in normal versus cancer tissues, and found differences in levels and the presence of mutations. They conclude:

"The function of these NCTs is currently unknown. Their abundance, tremendous sequence conservation and aberrant expression in many ovarian and breast cancers suggest that they not only play an important role in normal cellular growth and immune response, but also in the development of cancer. Consistent potential mutations at specific nucleotides within some of these NCTs also suggest that these alterations are not random, but have an important functional role in cancer development."
  • Perez et al. Hum. Mol. Genet..2008; 17: 642-655
    PMID: 18006640


How much Science in the News?

It's been discussed before on the Bayblab (in the comments here, for example) about the state of public understanding of science, and how more mainstream attention to science news and issues could help that problem. It's a bit of a chicken and egg dilemma: The media (for the most part) reports on what people want to hear, but how do people get interested if they never hear about science? Matt Nisbet at Framing Science highlights the issue, pointing out a study that shows for 5 hours of cable news, only 1 minute of that will be science covereage. Looking at the numbers Nisbet quotes, I might be more generous and say it's 6 minutes (lumping in 'the environment' and 'health and health care' with science), but that's still a miniscule fraction of reporting. I've said before that if a newspaper can devote a full weekly section to "wheels" or "food" then surely it can spare the pages for a science section. What needs to change? Does the media need to be more active in reporting science? Does education need to change so people are more aware of science issues? Or is 10 minutes of celebrity news to 1 minute of science a ratio that everybody is happy with?


Rock Salt Pollutes my pants

Here in Ottawa we are having a near record snowfall winter. We are well over 4m of snow so far. With so much snow comes road and highway maintenance that I'm sure is costing the city a fortune. Also they are dumping record amounts of salt on the road. I'm sure that we are all aware that salt is put on the road in order to decrease the freezing point of water, thereby melting snow and ice on the road. Of course, the effectiveness of salt is only good down to -18C at which point salty water still freezes, so sand and gravel are also used.
If you have ever seen the amount of salt on the road in the winter in Ottawa it is incredible. Canada uses about 10 million metric tonnes of rock salt for deicing purposes. It stains my shoes and pants. But probably of more concern it catalyzes rust formation, not only on cars but on infrastructure like bridges and drainage systems. I don't think these concerns are considered in the evaluation of the true costs of rock salt. I wear some pretty fancy pants.
It is a necessary evil, of course, because road safety is really not an option. Too many people still get killed and seriously injured due to winter road conditions in this country despite heavy salt usage.
However the environmental impact of salt usage is a concern. Ontario has done some work trying to minimize salt usage by more efficient storage and more sophisticated methods of application to the road surface. Environment Canada recognizes that chlorides have detrimental effects on our environment, but road salt gets a exemption from regulation. Chlorides are poisonous to plants and aquatic environments if present at high concentrations. And there are alternatives to sodium chloride, but they are more expensive (good article). Calcium Acetate seems to me to be one of the best. Here is a huge report that contains some great data on environmental impacts of salt and deicing alternatives. The punchline is that sodium chloride is, by many criteria, the worst for the environment.
Interestingly just because there is more ice and snow this year doesn't necessarily mean more negative environmental consequences of the increased salt usage since it will be diluted in that much more water when it all melts.
I emailed Environment Canada specifically at an address that is responsible for road salts (roadsalts(at) asking if there is any consideration of evaluating alternatives to rock salt and they only pointed me to the large (american) report. Lame.


St. Patrick's Day

No new St. Patrick-themed post this morning, so here are a couple from years past: The first is about green beer of the environmental sort, using alternative energy to power breweries. The other is about the annual greening of the Chicago River with fluorescein (or is it vegetable dye?)


Thursday, March 13, 2008

More on the Warburg Effect

We've blogged (and podcasted) before about the Warburg Effect: The observation that cancer cells rely primarily on glycolysis for energy production.

Two papers in Nature this week have identified a key player in this process (subscription required, summary here). The protein is the M2 isoform of pyruvate kinase (PKM2), which is the fetal form of this protein. PKM2 is also expressed in tumour cells, while normal adult tissue expressed the M1 form exclusively. These papers show that PKM2 is inhibited by phosphotyrosine affecting cellular metabolism. One of the papers suggests:
"this mechanism evolved to ensure that fetal tissues only use glucose for growth when they are activated by appropriate growth factor receptor protein-tyrosine kinases. Cancer cells, by re-expressing PKM2, acquire the ability to use glucose for anabolic processes."

In other words, re-activation of PKM2 allows the rapid growth associated with cancer. This was shown a variety of ways, by measuring glycolysis rate, cell proliferation and glucose incorporation into lipids after PKM2 knockdown/re-introduction or phosphatase inhibition (increasing the available phospho-tyrosine for PKM2 inhibition).

To further implicated PKM2 in cancer biology, the second paper showed that introduction of the M1 form into cancer cell lines increased their oxygen consumption and decreased lactate production (consistant with increased oxidative phosphorylation). Additionally, mice injected with cancer cells expressing the M1 isoform had slower tumour development, fewer tumours when they did develop and smaller tumours compared to M2 cell injections.

Both of these papers identify a key player in the Warburg effect, PKM2, and show it contributes significantly to tumorigenesis. Because PKM2 was found in all the tumour cells the authors analyzed, this unique biology could be exploited as a broad therapeutic target.
  • Heather R. Christofk, Matthew G. Vander Heiden, Ning Wu, John M. Asara & Lewis C. Cantley. Nature 452, 181-186(13 March 2008) doi:10.1038/nature06667

  • Heather R. Christofk, Matthew G. Vander Heiden, Marian H. Harris, Arvind Ramanathan, Robert E. Gerszten, Ru Wei, Mark D. Fleming, Stuart L. Schreiber & Lewis C. Cantley Nature 452, 230-233(13 March 2008) doi:10.1038/nature06734


Wednesday, March 12, 2008

There's Bacteriophage in my Bologna

Listeria is a bacterial contaminant of food and while infection is rare, it has a higher mortality rate than Salmonella. Infection may be rare, but the bacteria itself isn't and it can grow at low temperatures, meaning even when refrigerated Listeria can multiply on contaminated food. Of particular concern are foods that aren't cooked or reheated before eating - like the bologna or deli-sliced ham on your sandwich at lunch. Two recent scares at New Zealand hospitals have lead to quarantine of certain ready-to-eat foods after positive Listeria tests as a precautionary measure.

But if Listeria is everywhere and it persists under normal food storage conditions, why aren't infections more common? Well, for one thing, companies do their utmost to eliminate bacterial growth niches in their processing plants - especially after a "kill" step (eg. cooking) - by sanitary design (eliminating nooks and crannies that are difficult to clean) and proper cleaning, followed by other quality control testing. In 2006 (old news, I know), the FDA approved another tool for use in an anti-Listeria arsenal: bacteriophage.

Bacteriophage are bacteriolytic viruses and have a history of use as an antibiotic in the Soviet Union and Eastern Europe. Bacteriophage is the bane of some food making (and other) processes - those based on bacterial fermentation, such as yogurt production. For Listeria management it was approved and recognized as a safe food additive by the FDA in August, 2006. The phage used is a mix of 6 different forms used to target different Listeria strains and to minimize development of resistance. The phages themselves are grown in Listeria and purified before being applied just prior to packaging. The FDA has a FAQ about the bacteriophage additive. (Unfortunately I couldn't find any information about phage use in Canadian food manufacturing, or if there was an uproar in the US when the decision was made) This decision opened the door for other phage uses in the food industry, such as controlling E. coli or Salmonella in a similar way. The designation as 'safe' may also help resurrect the idea of using bacteriophages as antibiotics, particularly to combat emerging superbugs (MRSA).

So there you have it - that turkey sandwich you had for lunch may be a turkey and phage sandwich, so keep it away from your probiotic yogurt.


Loon Battles

About 10 years ago or so, I was flyfishing on Pennask Lake in BC, when I saw something I will never forget. I am only letting bayblab readers know about Pennask cause I'm such a nice guy. It is probably the best fishing spot I have ever been to. The rainbow trout are small but plentiful and they jump half a meter out of the water on such a regular basis it can sound like it's raining.
In any case, a friend and I were sitting in our bellyboats as the sun was going down on a perfectly still lake. We were waiting our friends with the motor boat to pick us up to head back to camp. We had drank many beers, of course since that's part of fishing, when 2 meters in front of us two loons broke the surface of the water and did some crazy aggressive posing thing. It was bizzare. Both birds streched out their wings and pecked at each other but never actually hit each other. It also looked somewhat synchronized. One then went underwater and the other followed, then they would pop up not too long afterwards, again fairly close and repeated their display.
We had come to the conclusion that we had witnessed some sort of courting ritual. That is until I heard this past Saturday's Quirks and Quarks. Apparently loons will fight to the death over territory and Pennask is some good territory. This is a recent discovery that affirms the fact that I was pretty lucky to witness it. Especially so close.
Check out the video of two loons battling. The ones that I saw, as I said, weren't nearly as aggressive, no pecks actually landed, and I thought what I saw was a bit synchronized, but generally this is what I saw.
Here is a link to the paper on loon fighting. Apparently they often drown during battles.
Pretty cool behavior for the animal on the Canadian dollar coin.
Here is a link to the Quirks and Quarks episode that talked to Dr. Piper. There is an mp3 file there of an interview.


Monday, March 10, 2008

Cancer Carnival #7 is here!

Pop on over to Highlight Health to check out the latest edition of the Cancer Research Blog Carnival. It's chock full of good stuff. Submit entries for the next edition here and drop us a line if you'd like to host a future edition. Watch for the next carnival Friday, April 4th.


Friday, March 07, 2008

Quack of the Week: John McCain

To be fair, both Democratic presidential hopefuls seem to be unaware of the science surrounding the issue* but John McCain is being singled out for the following statement which he made last week:
"It's indisputable that (autism) is on the rise amongst children, the question is what's causing it. And we go back and forth and there's strong evidence that indicates that it's got to do with a preservative in vaccines."
Probably the same kind of 'strong evidence' that there were WMDs in Iraq. But this isn't really about McCain per se - there is no shortage of people who share this stance - it's about the idea that mercury-based preservatives (thimerosal) in vaccines are responsible for a rise in autism.

First of all, is it even true that autism and autism spectrum disorders (ASD) are on the rise? It's possible that what we're seeing is an increase in diagnosis of ASD rather than an increase in the disorders themselves - either due to improved diagnostic tests or changes in the way these disorders are classified. This paper from the journal Pediatrics puts some numbers to that idea and shows that autism diagnoses took an upswing at the same time that diagnoses of mental retardation and learning disability declined suggesting that changes in diagnostics may explain the apparant autism epidemic. Orac at Respectful Insolence blogs about this paper in greater depth.

Regardless of whether autism is actually on the rise or not, it's still important to find out the underlying cause. Are mercury-containing vaccines the culprit? The science says no. A link between thimerosal-containing vaccines is not supported by science. Several studies have been done that show no causal link between mercury in vaccines and autism.

"But still," some will say, "we avoid eating certain fish because of mercury levels, so having it in vaccines makes no sense." First of all, the mercury build-up in fish (methyl-mercury) is different from the form in thimerosal (ethyl-mercury). Ethyl-mercury has a much shorter half life and does not build up in the body the same way. And that's beside the point: in the US thimerosal hasn't been used as a preservative in recommended childhood vaccines since 2001. Yet in the US and other countries that no longer use thimerosal, autism diagnoses continue to rise. This tells us that it's not the mercury, but more likely - as mentioned above - changes in the way autism spectrum disorders are identified.

For those who refuse getting vaccinated "to be on the safe side": Don't. Vaccines are responsible for the eradication of smallpox, near-eradication of polio and a host of other diseases (presumably, this is why anti-vaxers feel they can get away with it - because there's little fear of smallpox, polio and the like). Not receiving these routine childhood vaccinations has real public health implications. It's irresponsible to not have your children vaccinated.

As for John McCain, it's irresponsible for HIM to make such strong claims about a connection between mercury in vaccines and an autism epidemic. He needs to surround himself with better science advisors than that.

*Clinton says: "I am committed to make investments to find the causes of autism, including possible environmental causes like vaccines. [...] I will ensure that all vaccines are as safe as possible for our children by working to ensure that Thimerosal and mercury are removed from vaccines."

Obama says: "An Obama administration will go where the science and the facts lead us, whether it is about climate change or toxic heavy metals in our environment. [...] I support the removal of thimerosal from all vaccines and work to ensure that Americans have access to vaccines that are mercury free."

(source: Age of Autism)

Some people argue that these viewpoints are worse than the stronger McCain statement.


Thursday, March 06, 2008

Autophagy and Radiation Resistance

Autophagy is a cellular process that involves the lysosomal degradation of macromolecules or organelles within the cell. It plays a role in cellular homeostasis, response to infection and potentially as a cell death mechanism. Autophagy has also been shown to be activated in tumour cells after cancer treatment, but whether autophagy is playing a role in survival or death in this context is unclear.

A recent paper in Cancer Research explores the role of autophagy in cancer. They find that irradiation of cancer cells induced autophagy-related genes and accumulation of autophagosomes and that downregulation of some of these genes sensitized resistant cell lines to radiation. This suggests a survival role for autophagy in radiation-resistant cell lines, though the authors note that "the inhibition of autophagy in cancer cells may vary dependent on the type of cancer, individual characteristics of cancer cells, microenvironments, and therapeutic treatment." However other studies have shown that suppression of autophagy enhances tumorigenesis. In spite of this, inhibition of autophagy combined with radiation may be a viable treatment strategy provided the proper cancer-types and conditions can be determined, as well as the proper target (SirT1?).


Blogging on Pseudo-scientific Douchebags

In a similar vein as the Blogging on Peer Reviewed Research aggregator is Blogging on Pseudo-scientific Douchebags. From the website:
"Because Intelligent Design provides us with a never ending cycle of asshattery, because there are so many variants of woo available on the internet and because there are those of us who love vivisecting all forms of pseudoscience, it had to be done."
Simply tag your posts about quacks, creationists, pseudoscience and other woo with the BPSD icon and link back to their site. I may have to go back and tag some of our quack of the week posts.



The Band Nerds of Science organization "bayblab" does not claim responsibility for the recent attacks on the scienborg (TM) oppressors. While this is clearly a copycat attack, we suspect it was an inside job, like 9/11. It's probably Physioprof, he blogs anonymously like a terrorist, and personally insulted Barack Obama. While we do not condone or condemn the allegations that all but 3 of the sciencebloggers are white, and that there is a strong underrepresentation of woman on scienceborgs, we suggest you take these matters very seriously and join us in calling the perpetrators juvenile. We are band nerds, we are anonymous, we will prevail.

Oh and if anyone wants to share some ideas on cancer research, today is your last day to submit a post to the Cancer Carnival...


Monday, March 03, 2008

Mendel's Garden #24 - March 2008

March has roared in like a lion; the freezing rain here may not be great for venturing outdoors, but it's perfect for a virtual walk through Mendel's Garden, your monthly carnival of genetics. Welcome to the 24th edition.

Greg Laden starts us off with some true garden fodder: the potato. There, he tries to get to the bottom of the potato origins debate: Did the European potato come from the Andes or from Chile? The answer is important. As Greg informs us:
"[G]etting the history right is very relevant to developing potato varieties that are both, well, good at being potatoes, and resistant to blight."
As if knowing where your fries are from wasn't enough, Greg also delves into the origins of your 20-piece bucket. In his piece "The Origin of the Chicken", he explains new genetic evidence that the domestic chicken is actually a hybrid of (at least) two South-east Asian jungle fowl.

Now that we know where the chicken comes from, GrrlScientist lets us know how old they are in another bird-related post. In her piece "Rocks vs Clocks: When Did Modern Birds Really Appear? ", she discusses a recent paper challenging the notion that modern birds first appeared 60-65 MYA, as the fossils previously suggested. When molecular clock corrections are applied to the phylogenetic tree to date the branching of the bird lineage, the last common ancestor with dinosaurs appears to be much older, around 100MYA.

If you're a paleontologist, and you now find yourself between a rock and a hard place, but yet still cheering the discovery, perhaps you should look out for signs of bipolar disorders. Grrlscientist comes to the rescue, describing a recent controversial report of a blood test for bipolar disorder. She Laments that the discovery:

"presents great opportunities for research combined with terrible opportunities for abuse."

Finally we wrap this up with a homegrown post on another neurological disorder, autism, whose genetic basis is finally getting unraveled. Recent findings point to a location on chromosome 16 and copy number variation as the culprits in a subset of afflicted individuals. You can find the list of genes at that locus, and bet on your favorite candidates.

That concludes this edition. Submit your blog article to the next edition of
mendel's garden using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page.


How Quackery "Works" Part 6: Confirmation Bias

Most quackery and pseudoscience depends on testimonial evidence rather than scientific evidence. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study.

So far, this series has tried to explain reasons for false positives - how people can think something is working when it isn't. The next couple of posts will focus on why those false positives seem to be all that's reported. It's a common refrain in the face of skepticism that "there are none who have anything negative to say about the product." In the comments of the last post on recall bias, AC pointed out that you're more likely to recall the one time a treatment 'works' than the hundreds of times that it doesn't. Confirmation bias is searching for or interpreting facts in a way that supports or confirms existing beliefs (or, conversely, ignoring evidence that contradicts existing belief). The Skeptic's Dictionary offers the following example:
" if you believe that during a full moon there is an increase in admissions to the emergency room where you work, you will take notice of admissions during a full moon, but be inattentive to the moon when admissions occur during other nights of the month."
(More on that particular fiction here) Confirmation bias is an underlying element of all the reasons for positive testimony previously discussed in this series. The placebo effect causes temporary relief - this is confirmatory. Fluctuating symptoms give the appearance of a working treatment - this is confirmatory. When AC (quoted above) says you're more likely to recall the one time when something works than the times when it doesn't it isn't just about remembering, it's about a natural cognitive bias to confirm our hypotheses.

Deliberate or no, this leads to an accumulation of testimony asserting a treatment works. And this effect is self-amplifying: someone who purchases the next miracle pill searches out confirming testimony. This confirming data convinces the purchaser that the product *does* work, leading to yet another piece of positive testimony. Scientists are not immune to this, and similarly publication bias is the tendency for positive results to be treated differently from negative ones. To combat confirmation bias, one must consider all evidence - whether it confirms or not - and, rely on solid experimental evidence. Furthermore, the peer-review process helps minimize false results due to confirmation bias, unless the reviewers hold the same bias themselves.


Where do Chickens Come From?

Southeast Asia apparently. Genetically speaking? Turns out our feathered friends descend from one bad-ass mother of a bird, the jungle fowl. Head over to Greg Laden's blablablog for discussion of new genetic evidence showing that the modern day chicken is actually a hybrid of at least two different wild species of the jungle fowl, one with grey skin and one with yellow skin. Some commenter also points out on his website that these birds may have been initially domesticated for cock-fighting rather than food. Check it out if you want to read more about cock-fighting.

Continuing along with his fetish of birds/southeast Asia/hybridization, Laden also discusses a new paper on the evolution of the flu virus. The authors present evidence showing that some particularly nasty flu epidemics of the 20th century arose as a result of segmental reassortment between the genomes of different strains. This reminds me that it's been a while since we've had a good old-fashioned bird flu scare. Good to know people are still studying this.

For some reason I'm now imagining being pecked apart by a Jungle Fowl carrying a lethal strain of H1N1. Ouch. Bad way to go...