Thursday, January 31, 2008

What is it with men and vacuum cleaners?

Men have a love-hate relationship with vacuum cleaners. On one hand it seem to symbolize their domestication, while on the other it is a fetish of robotic love. Is it a coincidence that the first robot to have invaded our homes is the roomba?

Take this man for example, giving a review on amazon:
"Listen, maybe because I am a man, and in our society men have been stereotyped as helpless boobs who couldn't make a bowl of cereal without the help of a wife/mom/fairy godmother, I should be not the person to review this product. But since my wife likes this vacuum, and because as such I cannot smash into a million pieces with a fungo bat, I have to write this review to get even the Electrolux Oxygen Ultra, an object that is now my sworn enemy, from now until the end of eternity. I hate this vacuum. Every moment I use it is a chance to ruminate on how much I hate it. Seriously. I vacuum around the house saying to myself, "I hate this vacuum. You know what? This is a really terrible vacuum. I don't think I like this vacuum. [...] This is clearly what I get for being dumb enough to buy a $600 vacuum. I'm sure the Electrolux has the sucking power of 1,000 Kevin Federlines, and can filter out all the potential carcinogens and death spores I've been told pollute our air."

And contrast it to this man:
"A 51-year-old man decided to satisfy his fantasy of robotic love by seeking sexual gratification with his vacuum cleaner. Most men would think twice before poking a valuable organ into a vacuum, but this optimistic fellow had no qualms about the safety of his intended course of action. [...] His search for pleasure was cut short seconds after he stuck his penis into the vacuum and the blade lopped off part of his penis."

You may (or may not) be surprised to learn that this type of injury is quite common. According to this report in the European Urology Journal, out of 48 masturbation related injury, 12 were from inserting objects into the urethra while a whopping 36 were from vacuum cleaners.

According to this abstract, it is a dangerous occupation: "Erotic stimulation by the use of vacuum cleaners or electric brooms appears to be a common form of masturbation. Unfortunately, and contrary to apparent public appreciation, injury due to this form of autostimulation may not be unusual. Five cases of significant penile trauma resulting from this form of masturbation are presented, with a spectrum of severe injuries, including loss of the glans penis."

But the best part is the "explanation" that is given to the physician...


Biblical genetics

Before Mendel came along, there were various explanations about inheritance of traits by sexual reproduction. Here is how the hide pattern in goats is inherited in Genesis 30:37-39

30:37 And Jacob took him rods of green poplar, and of the hazel and chesnut tree; and pilled white strakes in them, and made the white appear which was in the rods.
30:38 And he set the rods which he had pilled before the flocks in the gutters in the watering troughs when the flocks came to drink, that they should conceive when they came to drink.
30:39 And the flocks conceived before the rods, and brought forth cattle ringstraked, speckled, and spotted.

So you're warned: simply looking at striped patterns during sex gives your offspring with stripes.


Wednesday, January 30, 2008

Coral Reef Sunscreen Followup

Previously on the Bayblab:
I was informed that sunscreen was bad for coral reefs. However no explanation was given.
Very recently a lucky group of researchers in Italy who presumably get sunburned and get to snorkel around coral reefs have figured out at least part of the story.
It appears that exposure to common active ingredients in sunscreen activate latent lytic viruses within the symbiotic algae of coral reefs inducing the observed coral bleaching.
Heres the open access paper.
Embarrassingly I ran across this on Not surprisingly the comments suck there, as usual. The best being, " Why does science hate us?"


Nurture vs. Nature

Twin studies can be an invaluable tool for scientists who are interested in studying whether aspects of human behavior are influenced by genes or environment (ie learned). Generally, this means tracking down adult identical twins who happen to have been separated at birth, getting their consent, and enrolling them in a study. Psychiatrist Peter Neubauer took things to a new level when he initiated a program that split up adopted twins at birth and then followed the differences and similarities that emerged during their lifetimes. Apparently the results of the study will be sealed in a library at Yale until 2066, however one pair of these twins has since found out about the study and they speak about the experience in the video below. Neubauer discussed the general topic of genetics and behavior in a 1996 book, Nature's Thumbprint: The New Genetics of Personality, which I haven't read but you can find here.


Tuesday, January 29, 2008

"Alternative" Approaches

We chirp from time to time about alternative medicine and other quackery. Have you ever wondered what would happen if we applied the alternative approach to other fields? Behold alternative cleaning and alternative engineering.

Found via Respectful Insolence


Monday, January 28, 2008

Can mammals renew their eggs?

I've talked about this subject in the past, and we briefly mention it in the upcoming podcast, but where are we with the question of whether a germline stem cell exists in female mammals? PLOS as a great article which summarizes the ongoing debate on whether a woman is born with a limited pool of eggs that will last for her reproductive life or whether that pool is continuously renewed... Obviously the presence of a hematopoietic stem cell which has the ability to form eggs, as Jonathan Tilly believes, would radically change the way we view conditions such as infertility, menopause and bone marrow transplants. As mentioned in this article, it's still too early to call, considering so little of the work has been replicated. Additionally, while bone marrow transplants in irradiated females is sufficient to reestablish fertility, none of the ovulated eggs match the donor, despite such eggs being supposedly present in the ovary.

In addition to this story being interesting, it highlights how reproducibility is so seldom tested in the current constrained funding environment. In fact it seems that this situation is particularly true of the whole field of stem cell biology...

What anyone publishes is not really the corpus of scientific knowledge unless it can be verified,” says Gosden. “You don't get a paradigm change until you have a consensus of expert opinion,” he says, and that is certainly not the case here. This follows physicist and science historian Thomas Kuhn's view of scientific revolutions—that many inconsistencies must build up in a field of science before a paradigm shift can occur.

The Kuhn model of paradigm shifts describes how most central ideas in science get revised or overturned, but there is another model that some would argue is equally valid, if rarer: the “lone voice in the wilderness” of a single scientist pushing a revolutionary idea forward. There are notable examples of lone voices who both succeeded and failed in overturning an idea. Stanley Prusiner's hypothesis that aberrant protein structures called prions could cause infection initially lost him his bid for tenure at the University of California at San Francisco and significant funding from the Howard Hughes Medical Institute, but eventually won him a Nobel prize in physiology or medicine in 1997. The cold fusion work of the late 1980s, which was never replicated to the satisfaction of the nuclear physics community, eventually resulted in Martin Fleischmann and Stanley Pons dropping out of academia.

“There's a fine line between being a maverick and a genius prescient person,” says Durant. Currently, Tilly is gingerly straddling that line, which can mean the difference between receiving the highest scientific honors or the scorn of your peers."


The origins of the biohazard sign

An article in the New York times reveals the modest origins of the biohazard sign. I've always wondered what it was supposed to represent. It bears an uncanny resemblance to the radiation sign, but with claws, which I find suggestive of some insect. But it turns out to be completely abstract, according to the engineer from Dow Chemical who designed it:

"We tested the sample symbols across the country -- the marketing department had survey groups to test different labels for Dow products. There were half a dozen of our original symbols in this survey of 24 different symbols. The rest were recognizable, like the peanut man for Planter's peanuts, the Texaco star, the Shell Oil symbol, the Red Cross and the swastika. They were asked to look at them and then asked to guess at what each one meant. The biohazard symbol got the fewest guesses. Then we went back one week later to the same set of people and the same set of symbols, plus 36 more common ones, and asked them which of these did they remember the best. And they picked out the biohazard symbol."


Sunday, January 27, 2008

A Step Backwards

The CBC is reporting that the government position of science advisor is being phased out. The post was created less than 4 years ago under the Paul Martin Liberals and will disappear once the current science advisor, Arthur Carty, retires at the end of March. Needless to say, not everybody is happy with this decision.

Especially at a time when science matters such as global warming, cloning and other genetic technologies, and science education (particularly evolution and particularly south of the border) are highly visible issues, shouldn't we have more science voices guiding our Prime Minister, not fewer?

More reaction at the CBC Quirks and Quarks blog here.


Friday, January 25, 2008

It pays to be lazy

As a grad student, chances are you're going to work/school by bus. The bus which goes to our hospital is notoriously unreliable. Have you ever been in the situation where you're debating waiting at the bus stop or walking in the right direction hoping the bus won't pass by you? Are you as obsessed as I am to make the most efficient decision? Well some mathematicians have worked it out for us, and the answer is pretty intuitive, you'd better wait in the cold, unless the bus goes by less often than once per hour and the distance to the next stop is under 1km...

"Justine Chen of the California Institute of Technology, and Scott Kominers and Robert Sinnot, both of Harvard University, have drawn up a formula to calculate whether waiting or walking is the best option for those facing a sporadic bus service. Their equation has these variables: n, for the number of bus stops spaced along the bus route; d, for the distance along the bus route; Vb, being the bus speed; Vw, the walking speed; and p(t), being the probability in time that a bus will show up."


Real Bioluminescence, Chameleon Octupus and Ant Networking

If you've been spending too many hours in the lab pounding out luciferase assays, these couple of TED talks are a quick reminder of how cool real biology is. The first video starts with some amazing bioluminescence patterns being generated in the deep sea, but even cooler is the last clip of an octopus changing color. The second is a more science-oriented talk by Deborah Gordon on her amazing research on the self-organizing behavior of ant colonies. Makes you wonder whether similar principles underlie the workings of other complex biological system like cells and the brain. Here's a link to a brief essay by Gordon if you're interested in reading more. 2007 Gordon, D. M. Control without hierarchy. Nature 4468:143. Enjoy!


Thursday, January 24, 2008

"Natural" Cancer Therapy

The last edition of the Cancer Research Blog Carnival saw a submission with a link to an anti-chemotherapy site urging patients to seek out 'natural' alternatives to chemotherapeutics (no mention of what these natural alternatives might be). My first thought was 'what about taxol?' - a compound derived from the bark of the yew tree commonly used to treat a variety of cancers. A lot of the push for 'alternative medicine' is based on a fear of traditional medicine - that is, man-made chemical treatment. Personally, I think these fears are largely unfounded and ignore the history of many pharmaceuticals in use. Here are some natural products currently in use in the cancer clinic. Someone preaching natural cures over tested medicine probably doesn't know what they're talking about.

Taxanes - Taxanes are plant alkaloids that interfere with spindle fibres during mitosis. As already mentioned paclitaxel (taxol, pictured) is a chemotherapy agent derived from the Pacific yew tree (Taxus brevifolia). The drug is approved for use in treating many cancers including ovarian, breast and lung. Originally discovered in 1960s as part of a plant screening operation, the Pacific yew was virtually the only source of taxol until 1993 when alternative sources were sought for ecological reasons - in 1969 it took over a metric tonne of bark to produce 10g of paclitaxel. Now the drug is produced by a plant cell fermentation method.

Vinca alkaloids - In a different class of plant alkaloids from taxanes are the vinca alkaloids, with vincristine (pictured) being a typical example. These compounds are used as intravenous chemotherapeutics primarily in the treatment of lymphoma and, similar to taxanes, are mitotic inhibitors. Vincristine is derived from the leaves of the Madagascar periwinkle, Catharanthus roseus (also the source of the chemo drug vinblastine), and was approved as a cancer drug in 1963. However, the leaves of this plant had been used for ages as a folk remedy which is how the initial discovery was made and is a fine example of how 'alternative medicine', once tested, ceases to be alternative and becomes mainstream medicine. (This is not to say that all folk remedies have some underlying efficacy).

Topoisomerase Inhibitors - One method of killing rapidly dividing cancer cells is inhibiting topoisomerase. Topoisomerase I inhibitors include camptothecins (pictured) which are plant compounds derived from Camptotheca acuminata (Happy Tree), discovered in a systematic plant screen. Topoisomerase II inhibitors include etoposide, which is derived from the American Mayapple. Both are used as part of a chemotherapeutic strategy.

Anthracyclines - Anthracyclines are a class of drug that include epirubicin, daunorubicin and doxorubicin (pictured) which act as DNA damaging agents, inducing strand breaks by inhibiting topoisomerase II or causing oxygen free radical damage. They can also intercalate with DNA and prevents DNA and RNA synthesis. These drugs are commonly used in chemotherapy and find their origins in soil microbes. Daunorubicin and the related doxorubicin (and some related compounds) date back to to the 50s when they were isolated from the bacteria Streptomyces peucetius and shown to be effective against mouse tumours. Incidentally, the bacterial genus Streptomyces also produces a large number of clinically useful antibiotics (such as puromycin, chloramphenicol and streptomycin) and the anti-metastatic migrastatin.

Antitumour antibiotics - One of the antibiotics produced by Streptomyces is bleomycin (pictured) which gained FDA approval as a chemotherapeutic in 1973. This bacterially produced glycopeptide is used to treat testicular cancer and Hodgkin's lymphoma, among others, and works similarly to anthracyclines, generating oxidative damage and DNA strand breaks.

Of course, this is not a comprehensive list - there are other molecules found in nature that are used in cancer treatment. Some are based on natural compounds, but modified to be more effective. Others rely on modern synthesis rather than extraction from the source organism. One thing in common between the naturally derived drugs above and 'unnatural' modes of therapy is that all of them have been tested and shown to have some efficacy. Don't accept less from your treatment.


Carnival time!

The 6th edition of the Cancer Research Blog Carnival is coming up. If you have an interesting cancer story or hot research you want to discuss leave us a link. The carnival will be up Friday, Feb 1 here at the Bayblab.

If you have a story regarding cancer research, including (but not limited to) therapeutics, diagnostics, standard care, survivor stories or basic science you can submit a link either in the comments here or the carnival submission form on this site.


Rethinking transplants

The NEJM has a series of articles on transplantation without the maintenance of immunosupression.The idea is that along with the transplanted organ, say a kidney, you give some of the donor's hematopoietic stem cells. If the stem cell graft is successful it will result in a chimeric immune system which tolerates the transplanted organ despite being HLA mismatched. However, one wonders why the stem cell itself isn't rejected, since immunosupressive drugs are only given for a short period of time, so that the graft takes :

"Five patients with end-stage renal disease received combined bone marrow and kidney transplants from HLA single-haplotype mismatched living related donors, with the use of a nonmyeloablative preparative regimen. Transient chimerism and reversible capillary leak syndrome developed in all recipients. Irreversible humoral rejection occurred in one patient. In the other four recipients, it was possible to discontinue all immunosuppressive therapy 9 to 14 months after the transplantation, and renal function has remained stable for 2.0 to 5.3 years since transplantation. The T cells from these four recipients, tested in vitro, showed donor-specific unresponsiveness and in specimens from allograft biopsies, obtained after withdrawal of immunosuppressive therapy, there were high levels of P3 (FOXP3) messenger RNA (mRNA) but not granzyme B mRNA."

The cool thing is that this can spontaneously occur, such as this case of a young girl who received a liver transplant. Somehow either a liver stem cell or a resident cd34+ cell was a ble to colonise her bone marrow and turned her into a partial chimera, thus removing the need for lifelong immunosupression:

"Complete hematopoietic chimerism and tolerance of a liver allograft from a deceased male donor developed in a 9-year-old girl, with no evidence of graft-versus-host disease 17 months after transplantation. The tolerance was preceded by a period of severe hemolysis, reflecting partial chimerism that was refractory to standard therapies. The hemolysis resolved after the gradual withdrawal of all immunosuppressive therapy."


Wednesday, January 23, 2008

Evolution is a blind watchmaker

Simply brilliant.


Tuesday, January 22, 2008

You know you're a biologist when...

Inspired by the chemistry blog...(a few borrowed)

You know you're a lab rat when:

You open the toothpaste with one hand.
You wash your hands before and after using to the washroom.
When you hear tween, you think of the surfactant not the age group.
For you, media is something which increases your culture.
You can identify organs on roadkills.
You have a callus on your thumb.
You use the word "aliquot" in regular sentences.
Sometimes you momentarily vanish from social activities because of a timepoint.
You've never worn a clean lab coat.
You don't fear rodents, rodents fear you.
You say "orders of magnitude" in regular sentences.
You flinch when you hear the word "significant".
Showing up at 10AM and having a coffee is a productive day.
You can't stand god-like physicians, while secretly wishing you had their job.
You're very good at diluting things.
You're also very good at transferring small amounts of liquid between containers.
You are fed up of people saying alcohol, when they mean ethanol.
You hear the word ‘Molar’ and teeth are the last thing on your mind.
You say “conjugation” instead of “sex”, and "pili" sounds dirty.
SOB is not an insult, it's what you grow your bugs in.
You say "mills" and "megs".
No-one in your family has any idea what you do.
You can make a short film in power point.
You consider a green laser pointer to be science bling.
A falcon is not a bird....
And you have 5 of them with different types of water.
When your fruits go bad and you get fruit flies, you can't help but check their eye colour
You own invitrogen t-shirts and actually wear them.
You think that drosophila geneticists have a good sense of humour.
You refer to your children as the F1.
You've suffered carpal tunnel from the pipetman.
You've used kimwipes as kleenex.
A timer clipped to the hip is not only practical, but dead sexy.
You've played Battleship using tip boxes.
The front pages of Science is your light reading.
You think the following is a quality insult: "I've seen cells
more competent than you!".
The scent of latex reminds you of work, not play.
You're looking for a cooking book by maniatis.
You've used, "I'd like to get into your genes" as a pickup line.
You've made dry ice grenades.
You've lost many friends to ice grenades...


Sunday, January 20, 2008

Clonal Discrimination

Today the lay public is very concerned that they are eating the meat of cloned animals. When I first learned this I had trouble understanding why, as this seems like such a non-issue (for numerous reasons). Naturally, I figured the media was somehow to blame for the confusion, and a quick surf over at google news confirmed my suspicions. Turns out the FDA has, not surprisingly, approved cloned animals for human consumption. Basically a non-story. Until you enter the doomsday prophecies and start playing on people's fears of unknown new words and technologies. As I said, I think this is a non-issue, but I'm interesting in knowing why people think they should be worried about cloned meat. Here's what Reuters asks readers on their website:

"Would you consider serving cloned meat at your dinner table?"

And here are some responses that echo similar things I have heard from people in real life:

"No, we already do too many experimental things like rBGH and antibiotics."
That's right. I don't care if you've got gangrene or whatever, just stay away from those untested "experimental" antibiotics. Who knows what they might do.

"I’d never eat Cloned Meats, or genetically engineered fruits and vegetable. It’s not a natural creation. Seems to me that mankind has not totally destroyed all of nature yet for us to result to eating scientifically generated food."

Yeah I'm sure you only eat the products of "natural creation". Like coca cola, refined sugar or enriched flour? Or "scientifically generated" fermentation products like yogurt and beer? Unless you're living in the garden of Eden, there's no chance your living off "natural creations" dude. And what makes something so "unnatural" just because human knowledge is involved? Is knowledge "unnatural" too?

And on and on. Basically a lot of people think they should be scared of cloned meat, but it's pretty obvious from the commentary that none actually know what a cloned animal is. What exactly are they afraid to ingest? The cattle's aberrant histone modification patterns? At any rate, the question is irrelevant. It's just a programmed instinct to fear the unknown. The compulsion seems particularly strong when it comes to food. And hey, maybe that's a good thing - you wouldn't want people walking around randomly sampling concrete or poisonous mushrooms. And although I can't seem to think of any real reason cloned meat would be dangerous, maybe the infinitesimal risk is not merited if it doesn't offer any benefits. So the bottom line for me on cloned meat is this: no clear risk, no clear benefit. And so, for the time being, a total non-issue. Does anyone think I've missed out on something worth worrying about here?

Maybe it would be beneficial for us all if the media helped to spread some education while they are on the topic instead of promoting ignorance and knee-jerk fears?

UPDATE - Here's the marginally more informative article CBC ran.


Thursday, January 17, 2008

Best application ever

For you lucky ones with a macbook in the lab, you should check out "papers" which won the apple design award for best scientific application. It's like an itune for science. from the website:
"Search for articles using the built in search engines, retrieve and archive PDFs, and read and study them all from within Papers, your personal library of Science."


How does one calculate gauge?

Over diner last night I had a conversation with a friend in which the subject turned to gauge. The question was this: the gauge is a measure of which properties of the gun? Is it a measurement of the bullets or a measurement of the barrel? I knew that in needles, gauge is inversely proportional to the diameter of the hole, so I assumed it must be some kind of ratio over either diameter, circumference or cross-section area.

But before I give out the formula, one needs to understand the history of canons. See when canons were first used they were handcrafted and thus each canon was unique. The problem with having varying size of barrels, is that you needed to custom-make the canon balls. Now the easiest way to know if the ball was right, other than actually trying it, was to weight it. For example a 5lb ball of lead will always have the same diameter, assuming it is spherical enough. So the canon would be a "five pounder". Now when applying this to shotguns you obviously have to use fractions of a pound: (from wikipedia) "The gauge or bore of the inside diameter of a barrel corresponds with the number of identical solid spheres that can be made from a pound of lead.". So the smaller the barrel, to smaller you have to make the spheres, and so the more you can make with a pound of lead, hence a high gauge. Now as a scale it can be problematic because I assume that since volume varies proportionally to the power of three in respect to the diameter, the relationship is not linear.

here is the formula

(diameter of barrel in mm)= [(6*1lb converted to grams)/(density of lead*gauge*Pi)]^1/3

Now lets get back to needles. (from wikipedia):
"The diameter of the needle is indicated by the needle gauge. Various needle lengths are available for any given gauge. There are a number of systems for gauging needles, including the Stubs Needle Gauge, and the French Catheter Scale. Needles in common medical use range from 7 gauge (the largest) to 33 (the smallest) on the Stubs scale."

"The Stubs system was the first wire gauge recognized as a standard by any country when Great Britain adopted it in 1884. Each gauge increment roughly correlates to multiples of .01 inches, but the system is not truly linear"

now if you're interested in how needles are made, I recommend checking out the Straight Dope:

"The key to syringe making is forming the hollow tube, or cannula. Processes to make small tubes and hollow needles are quite old, and almost always begin by forming a large tube. This large tube is formed by either rolling a sheet of metal into a tube and welding the seam, or by taking a solid billet of metal and boring a hole through the center while the metal is heated (creating "seamless tubing").

This large tube is softened by heating it (called annealing), then drawn through a tool called a die--which in this application of the word is essentially a hardened piece of metal with a small hole. As the tube is drawn through the die it both stretches, increasing the tube length, and shrinks, decreasing the tube diameter. The tube is passed through smaller and smaller dies, continuing to stretch in length and shrink in diameter, until the desired size is reached. The last drawing through the die is often done without heat, therefore cold-working the tube to increase its strength and hardness. Sometimes a stiff piece of wire or a mandrel is placed inside the tube to prevent the walls from collapsing while it is being drawn, but often the process relies on incredibly consistent steel quality and high-tolerance equipment to manufacture cannulae that meet the specifications."


Nature Futures

A feature that I thought was canceled, Nature Futures, is for short science fiction stories. Indeed the achieves have a gap and the intro mentions that this is the return of Futures. I just really like the idea that research scientists who read Nature are often also sci-fi fans.
Nature is also selling a stand alone collection of Futures. Sweet. (found on Boingboing)


Wednesday, January 16, 2008

SHARP: Where Politicians Stand on Science

Here in Ontario, we recently went to the polls to elect our members of provincial parliament and vote on electoral reform. Given Canada's current minority goverment, we could face a federal election call anytime. In the meantime, political junkies will have to be content to sit on the sidelines and watch as our neighbours to the south decide on the next 'leader of the free world'. Will the next POTUS be a staunch creationist? Support stem cell research? Where will s/he stand on global warming? What about other science issues?

Scientists and Engineers for America has launched the SHARP Network (Science, Health and Related Policies Network), an online resource to see where candidates stand on science related issues. The site doesn't limit itself to presidential candidates - congressmen and senators can be found as well. The site is wiki-style, meaning users can login and edit candidate information so they can remain updated throughout the campaign. Does anybody know of a similar resource for us Canadians?


Hamiltonians are Mutants

A new study published in PNAS (open access) takes a look at the health implications of exposure to particulate air pollution. In this particular study, mice were caged near 2 steel mills and a major highway in the Hamilton, Ontario area and exposed either to ambient air, or the same air passed through a HEPA filter to remove particulate pollution.

When exposed to Hamilton air (but not HEPA filtered air) for 10 weeks (followed by 6-weeks recovery in the lab), the mice had a 1.6-fold increase in sperm mutation frequency and an increase in global methylation of germline DNA. From the article:
"We have demonstrated that exposure of inbred mice to particulate air pollution near two integrated steel mills and a major highway caused tandem repeat DNA mutation and hypermethylation in spermatogonial stem cells. [...] The overall implications of these findings for the health of humans are unclear. Heritable mutation, germ-line DNA damage and epigenetic modifications have the potential to affect disease incidence in the descendents of exposed individuals. In addition to its potential importance in the maintenance of genome stability, appropriate methylation of DNA is critical for imprinting, regulation of gene expression, mammalian development, and disease."

No word yet on whether any of these mutations conferred super-powers.


Tuesday, January 15, 2008

Judah folkman passed away

The famous cancer researcher was the first one to popularize the idea that tumour growth is dependent on blood vessel growth and that anti-angiogenic therapy could someday transform cancer into a manageable chronic disease like diabetes. He passed away at age 74, from a heart attack. He'll never get to see if this type of therapy will be successful, or have a chance to get a well-deserved (in my opinion) Nobel.


Monday, January 14, 2008

Michael Crichton on Gene Patent Lunacy and Global Warming Myths

In this great conversation with the mind that brought you Jurassic Park, Crichton discusses why genetic patents need to be eliminated, why the global warming "consensus" and its mouthpiece Al Gore are wrong, and why real science has nothing to do with consensus anyway. Watch the video and if you think Crichton's got it wrong, I'd be interested in knowing why.


Top 100 stupid christian quotes

Not sure if I should laugh or cry. These quotes were taken from forum posts. Obviously I don't want to disparage Christians, there are stupid people in every faith (or non-faith). But most of them relate to science, such as this one:

"Everyone knows scientists insist on using complex terminology to make it harder for True Christians to refute their claims.

Deoxyribonucleic Acid, for example... sounds impressive, right? But have you ever seen what happens if you put something in acid? It dissolves! If we had all this acid in our cells, we'd all dissolve! So much for the Theory of Evolution, Check MATE!"


Friday, January 11, 2008

Five things I learned from teaching

While it's a very rare occurrence for a grad student to teach an undergrad biology class, at least in my university, I had the chance last semester to teach a reproductive anatomy and physiology class. While it is still fresh in my mind I'd like to share some of the insights I gained from this experience.

1- If you really want to teach, go to the interviews, even if you have no chance of getting the job. The fact is, the post-docs are probably better qualified than you, and so is junior faculty, but at least you get your name out there. You never know when someone suddenly can't teach, and there is no-one to replace them. They'll remember you.

2- This is not a seminar or a scientific talk. You need to forget about everything you've learned about presentation so far. You need lots of text on screen and to go slowly. If you talk without text, the students freak out: they write down everything. I swear some of them even wrote down my jokes. Giving handouts helps, but you don't want to give away too much or they won't come to class. I found 25 slides was a good size for a 1:20 lecture. I know it sounds crazy, since as a talk that would last me no more than 30 min, but it forces you to take the time to explain. I found that repeating myself each time with a slightly different figure, and highlighting different aspects worked well to get the point across. And it's better to finish early than to cram too much into one lecture.

3- Include anecdotes and factoids into your lecture but only if it is directly relevant. I found the students really related to them but it's also a slippery slope. For example I contrasted a certain aspect of physiology which differs between humans and most other mammals, only to have many students give it as an example of human physiology in the exam. It's clear that it's best not to confuse the student with superfluous facts or give exceptions to rules.

4- Don't ask questions directly to the class. I tried it once or twice just to see, and no one bit. But I know from having been a student, that the question is either too easy, in which case you don't want to sound stupid by answering it, or it's too hard and then you look like you're trying to show off. Rhetorical questions are fine. In any case, if the material is interesting the students will come up with questions by themselves. Giving them examples of questions that they could find on the exam is also a good preparation.

5- Exam questions are surprisingly hard to write. For multiple choices I abhor the questions which include combinatorial answers such as a) ... b)... c)... d) a+b, e) a+c. I always thought it was laziness on the part of the professor, so I made them as clear as possible. No point in tricking the students. The long answer questions are much more sensitive. I found that the language used must lend itself only to one interpretation. For example there is a slight difference in asking which hormones are important for implantation (of the embryo), versus which hormones are important during implantation.


MIT scientists test the effectivness of aluminium foil helmets

Clearly MIT is also copying the bayblab, with original research published straight to the web. The results are quite surprising, the helmets are not only useless at shielding radio waves, but they actually amplify certain frequencies:

" The helmets amplify frequency bands that coincide with those allocated to the US government between 1.2 Ghz and 1.4 Ghz. According to the FCC, These bands are supposedly reserved for ''radio location'' (ie, GPS), and other communications with satellites (see, for example, [3]). The 2.6 Ghz band coincides with mobile phone technology. Though not affiliated by government, these bands are at the hands of multinational corporations.

It requires no stretch of the imagination to conclude that the current helmet craze is likely to have been propagated by the Government, possibly with the involvement of the FCC. We hope this report will encourage the paranoid community to develop improved helmet designs to avoid falling prey to these shortcomings."

Speaking of fringe community and paranoids publishing research, it seems Answers in Genesis is doing a call for abstracts for their new journal ARJ:

"Papers can be in any relevant field of science, theology, history, or social science, but they must be from a young-earth and young-universe perspective. Rather than merely pointing out flaws in evolutionary theory, papers should aim to assist the development of the Creation and Flood model of origins."

I am sooo tempted...


Thursday, January 10, 2008

Cephalopod friday

Watch out pharyngula ;) ...taken from the three king festival in Madrid, Jan6 2007.


Quack of the Week: Toby Alexander and DNA Activation

According to
"What exactly is DNA Activation?
Most people know that DNA is the 'blueprint of life' and is located in every cell of the body. In addition to each chromosome's 2 strand double helix of DNA, there are an additional 10 etheric strands of DNA available to each human, which have been dormant since the beginning of recorded history. Each additional strand possesses attributes that permit the individual to perform greater human accomplishments. Scientists acknowledge that we currently only use 3% of our current 2 strand DNA. Thus we live in a society where people are sick, unhappy, stressed out, create wars, have difficulty experiencing love, and are totally disconnected with the universe. Most people have to meditate for many years just to have a so-called 'mystical' experience, that's how disconnected we are now. Imagine activating 100% of your 2 strand DNA, PLUS 10 additional strands! You will go from using 10% of your brain to becoming a multi-dimensional being with psychic, telepathic, and manifestation abilities beyond anything you've ever dreamed of. Plus, you will stop the aging process and actually start to rejuvenate to look and feel YOUNGER. This is the Original Divine Blueprint, what man USED to be. It has been written that Jesus had 12 strands of DNA activated. There have been children born throughout the history of humanity to raise the frequency of the planet that have more than 2 strands of DNA active - they are known as Indigo children. These are the incredibly intelligent, loving, and amazing children that are being mistakenly diagnosed as having A.D.D. because they are too smart to pay attention in class. Your DNA is your blueprint of life and is what controls every single function inside each of your cells. If you change your DNA, you really will change your life."

This has got be one of the most blatant corruptions of molecular biology I have ever seen I my entire life. Check out the rest of the site at for some more laughs. The material is endless - I can't even begin to cover it all here. These guys are TOTAL lunatics.


Dawkins et al. Seek to Emulate the Bayblab Podcast

Richard Dawkins, Dan Dennett, Sam Harris and Christopher Hitchens sit down for drinks to discuss whether they are arrogant atheist assholes. A very entertaining conversation on the psychology behind irrational beliefs, and why people get so upset when these beliefs are questioned or criticized. In other words, why isn't it cool think freely about religon in a "free-thinking" civilization?

While these discussions clearly had a more substantial budget than the bayblab podcast (notice the martini glasses, fireplace, bookshelves and full-length video footage), we are clearly a better-looking bunch. Pretty entertaining, even if you're getting tired of all the creationist vs. evolutionist fuss like me.

(HT: Sandwalk)


Training in photocopiers?

They are constantly bugging us with all the biosafety training, but now they've gone too far, I got this by email:


I am setting up training on the photocopier, by Dr. J* B*'s office. I think everyone has a grasp on "basic" photocopying, but we are looking to get training on the more advanced features like scanning. If you or one of your students/trainees would like to attend this training session, please let me know. If there are too many people who need/want training, I can add on another training session ie, 2:30-3:30 (or another day). We can only have 5-6 people training at one time."

I think we also need a retreat to discuss what body parts are appropriate or not to photocopy.


Buffalo Soldiers

Wow! This EPIC battle deserves its own Led Zepplin song. I wasn't too surprised that the cats could stage an ambush, but I always thought the Romans Greeks invented the phalanx. Take home message: don't mess with baby buffalo and watch out for the crocodile as well. Crickey!


16p11.2 linked to autism

We've discussed in the past how copy number variation in the genome may be the smoking gun behind autism. Well a new paper in the NEJM attributes 1% of all autism cases to a CNV on chromosome 16 at 16p11.2. Hopefully this discovery will shed some light on physiological basis of autism. There are some indications that autism may be reversible if only we knew what was wrong. In fact it seems that even a fever can temporarily improve behavior of autistic patients... The paper fails to really get into the details, but find bellow a list of genes in that region, and what little information I could find on them. Notice that there is an enrichment in brain transcripts, implying a multigenic basis of the disease. Place your bets now on which gene will the next big breakthrough:

BOLA2: cell proliferation & cell cycle
GIYD1/2: sulfotransferase family
SULT1A3/4: sulfotransferase family
spn: important for lymphocyte funstion, is also defective in WAS, an x-linked mental retardation
QPRT: Elevation of qprt in the brain may be involved in the pathogenesis of neurodegenerative disorders
c16orf54: hypothetical protein
kif22: kinesin-like protein family
maz: MYC-associated zinc finger protein
prrt2: glucan 1,4-alpha-glucosidase activity
c16orf53: hypothetical protein
mvp: resistance to lung infection
cdipt: phosphatidylinositols biosynthetic pathway
sez6l2: homologous to a seizure related genes
asphd1: A transcript abundant in the brain, catalyses oxidative reactions in a range of metabolic processes
KCTD13: binding partner to PCNA at replication foci
loc124446: hypotethical protein
toak2: ?
hirp3: ?
ccdc95:coiled-coil domain containing 95, function unknown
doc2a: implicated in neurotransmitter release
fam57b: transmembrane protein of the cerebellum
aldoa: aldolase
pp4c: Serine/threonine-protein phosphatase
tbx6: required for choice between mesodermal and a neuronal differentiation pathway during gastrulation
ypel3: cell division,mitotic spindle
gdpd3: glycerol metabolism
mapk3: erk signalling and growth. erk1 knockout mice have behavioral problems

Blogging on Peer-Reviewed Research
ref: January 9, 2008 (DOI: 10.1056/NEJMoa075974), in print February 14, 2008


More fun stuff - Blogging is bad for your health

Found this over at the TED talks (via A Blog Around the Clock). Help fight local warming.

(link to video on TED page here)


Scientists for Better PCR

Here's a dose of science silliness for you - a friend sent me this video advertisement for a new line of PCR machines. It's a "Band Aid"-esque music video about the polymerase chain reaction. Canadians may find it reminiscent of the 'Got Milk' milk rap advertisements.

"PCR when you need to know 'who's your daddy'"

Check it out here.


Tuesday, January 08, 2008

Happy Birthday Alfred Russel Wallace!

The real ARW, that is, not our pseudonymed contributor. I found this over at, more specifically The Questionable Authority. Go forth and read, and learn a bit of science history.


Monday, January 07, 2008

Ask Sydney Brenner: Should We Fund More Scientists?

"I think the profession of science will change markedly over the next 25 years, because I don't think it can last in its present structure. The present structure is assumed on infinite growth. In other words, every student expects to be a post-doc, every post-doc expects to be an assistant professor with five students, every assistant professor expects to be an associate professor with eight post-docs and five students, and so on and so forth. And that can't last. And I think the "industrial" structure will have to change. And what I think will happen in the future is that, I think, people will do research for only part of their lives. Research with very few exceptions is really the job for young people. Largely because, as I've said, they contain the required ignorance that is necessary for this. And I think it would be perfectly reasonable for people to do research for five years or eight years of their lives, and then go on to do other things like be doctors or be farmers, or something else in society.

But I think the profession of the professional scientist with a career structure will change. Because I think it may well be that doing biology will become like the old days of doing natural history, but with molecular tools. And I think we have to have some solution of that if we are to simply maintain the advance, because all of history shows that notwithstanding the great growth and professionalization of science, the number of important scientists has remained constant, roughly speaking, since the 17th century. So, the point is, as long as those people gravitate to the subject, that'll be fine."

- Sydney Brenner, Peoples Archive


Quote of the Day

"Evolution is to allegory as statues are to birdshit. It is a convenient platform upon which to deposit badly digested ideas."

- Steve Jones


Sunday, January 06, 2008

Blogging on Peer Reviewed Research Icon

Just so you all are aware that, starting now at least, the bayblab should include the "blogging on peer reviewed research" icon. It's actually a great idea, that I first ran across at sandwalk. The site where this idea is based out of Check it out for the concept and guidelines for its intented use. Basically this can aggregate blog posts about original research articles. The aggregation system isn't quite up yet as I understand it. However you can use technorati to check out the newest blog posts that use the icon here(I will be checking out this link regularly). To me this is a great idea and I hope it gets implemented by good science blogs, so that means us. Here's hoping that some spamming moron doesn't abuse it somehow.


Friday, January 04, 2008

Cancer Research Blog Carnival #5

Welcome once again to the Cancer Research Blog Carnival! There were a lot of submissions - seems like people had some spare time over the holidays - of varying quality, and a real mixed bag in terms of content (read my postscript. If anybody is interested in hosting future editions contact us here at the Bayblab. Off we go!

Cancer Biology

Ramunas from offers us a one-two punch of articles on cancer genetics. First off, he offers a round-up of diagnostic and prognostic genetic markers for cancer. He writes:

"2007 will be known in history as a breakthrough in understanding of our genome variation and enormous success in genome wide association studies (GWAS) for complex disorders) cancer included.

2008 will be definitely an exciting journey through a highway (yet in a desert) of personalized genomics."
It's a nice summary of commercially available tests, as well as a hint of what's to come.

He follows this up with an even more recent list of new tumour markers and targets. Hot off the presses for 2008, these are molecules that we may see in future diagnostic tests or as therapeutic drug targets.

Our very own Rob here at the Bayblab informs us about p53 and microRNAs: an unholy alliance between one of the hottest topics in biology and everybody's favourite tumour suppressor.
"So the question was if p53 has all these important cellular functions how much of that can be attributed to the microRNAs transcribed by activated p53? As it turns out quite a bit."

The small RNA involved is miR-34 whose expression is decreased in a variety of cancers. Check the link for more details.

Ryan DuBois at The Daily Dub gives us a brief overview of HeLa cervical cancer cells and their 1991 designation as their own species, Helacyton gartleri. He uses this as a recent, obvservable example of evolution in action.

Standard Care

Jose DeJesus from Physician Entrepreneur tells us about the use of stem cells in breast reconstruction.

"Current treatments for breast cancer include lumpectomy and radiation treatment, which are more conservative than mastectomy and reconstruction with an implant, but these more conservative approaches may result in deformity that is harder to reconstruct, because the use of mini-implants to replace tissue removed in lumpectomies are not a normal procedure."
As discussed in a previous carnival drastic changes in appearance are one of the emotional issues faced by survivors post-treatment. This new technique using stem cell enhanced grafts may lead to more natural breast reconstructions post-surgery, as well as other reconstructive surgeries.


Kate and gregre write to inform us of a resource for people interested in mesothelioma - an aggressive cancer caused primarily by the inhalation of asbestos fibres. In particular, they highlight how to find a good mesothelioma specialist, disease prognosis once diagnosed, and asbestosis.

Steve Pavlina writes to us with his personal experience switching to a vegan diet: how he did it, and what the effects have been.

" I read that vegetarians supposedly live longer, need less sleep, and have lower risks of many major illnesses like cancer and heart disease. That sounded attractive..."
The article doesn't discuss the relationship between diet and cancer any further than that, but it does chronicle a change from omnivore to vegetarian to vegan for any who are interested in making a similar lifestyle choice.

In a similar vein, Roger Haeske's infomercial blog gives us not one, but two advertisements submissions encouraging and supporting a switch to a raw diet. As he writes:

"If you feel excited and motivated to go raw, it will be easy. If you feel it's going to be difficult and painful then you will likely fail in your attempts to go raw and stay raw. Maybe reading these points below will help to motivate you to go raw with a little bit of help from your friend Roger."


Mitch McDonald writes to us about natural alternatives to chemotherapy further linking to a site called ''.

"Your first instinct is to listen to everything your doctor says. But you need to seek a second opinion if he says chemotherapy."
And you need a third opinion if you're being directed to untested, unproven natural products. In typical fashion, there's a lot of fear-mongering, no real alternatives presented and a complete failure to recognize that some chemotherapeutics (taxol) ARE natural compounds. Chemotherapeutic treatment isn't something anybody looks forward to, but as this site demonstrates 'natural alternatives' are lacking.

Postscript: As I mentioned before, the nature of submissions was quite varied. I decided, for better or worse, to include them all regardless of quality or relevance (with a certain degree of editorializing in the descriptions). However, since this is a cancer blog carnival, if I'm writing up future editions I'll be more selective of stories relating to cancer and cancer research and exclude those that are unrelated, obviously marketing a product or of other dubious merit.


Wednesday, January 02, 2008

Breakthrough of the year on DVD

If you haven't heard the latest Science Magazine podcast (direct link to the RSS feed no subscription) or haven't checked out the Science magazine website recently they have given recognition to the breakthrough of the year (subscription req'd). There is also a video presentation but the link is SO SLOW that I would not bother. Apparently the breakthrough is the sequencing of an individuals genome. I don't see this so much of a breakthrough as an inevitability, however, it certainly has some very important implications. Not only for personalized medicine but also for privacy concerns (subscription req'd). I guess the T-shirt in the picture above from the website is supposed to be covered in annotated genome representing a personal genome? Don't you think it would at least be long sleeved?
Found this tidbit interesting re: privacy concerns:

Baylor and 454 settled on a "data release pathway," McGuire and Egholm say. The company will put the completed genome on a DVD and hand it over to Watson--perhaps, Egholm says, with a small ceremony. Watson will accept responsibility for discussing the risks of its release with his family, decide what should be blocked, and determine how and when to make the sequence public. Watson declines to say more until the company is ready to publish an article--by July, he expects.

Is that in fasta format? What do you think Watson is going to do with that information? Is he going to spend the rest of his life checking it out? Looking for informative SNPs?
What I actually found more interesting was the 'runners-up' for breakthrough of the year (subscription req'd). It's a nice snapshot of some interesting fields of science that I don't regularly keep up with.
The link between memory and imagination I found pretty thought provoking.
I can't even imagine having a good memory.


p53 & microRNA

My extreme originality for a post specifically for the cancer research blog carnival resulted in me checking out the top 20 downloaded articles from one of the top cancer research journals, Cancer Cell. Number 15 at the time of posting was "p53 enters the microRNA world" (short free abstract). This one is near and dear to me.
p53, "the guardian of the genome" is a particularly intensely studied tumour suppressor protein because it has been found mutated in almost all cancer types. It is a transcription factor that regulates/coordinates important and diverse cell fate programs such as cell cycle, apoptosis (programmed cell death), DNA repair and senescence. What is new about p53 in this cell paper (review subscription required) is that another transcriptional target has been identified as the microRNA family miR-34.
MicroRNAs are small RNAs that repress translation of target mRNAs. Target mRNAs contain partially complementary sequence in their 3'untranslated regions (3'UTR). New functions, activities and mRNA targets of microRNAs are being discovered at a rapid pace as researchers try to catch up on this important mechanism of gene regulation that has been a large oversight until their relatively recent discovery.
An connection between microRNAs and p53 is that in addition to specific transcription activation of genes, p53 has also been found to inhibit expression of some genes, for instance those involved in cell cycle. Since this is the function of microRNAs perhaps this was a mechanism by which p53 can mediate some of its effects. Also it is becoming obvious that aberrant expression of microRNAs accompanies cancer phenotypes.
A barrage of papers in late 2007 showed that the miR-34 family are direct transcriptional targets of p53. So the question was if p53 has all these important cellular function how much of that can be attributed to the microRNAs transcribed by activated p53? As it turns out quite a bit. Expression of miR-34 microRNAs results in cell cycle arrest, inhibited colony formation, senescence, tumour cell senescence, and apoptosis in various studies. And based on inhibition of miR-34, it is possible to say that miR-34 may be sufficient and required for tumour suppression by p53. Also important miR-34 mRNA targets were identified as crucial genes involved in cell cycle and apoptosis.
Interestingly miR-34 loss is observed in neuroblasoma, its expression is low or undetectable in 11 of 15 pancreatic cancer cell lines, and its expression is decreased by more than 90% in 6 out of 14 lung cancers.
So in summary, perhaps the tumour suppressing function of p53 is mediated through small RNAs! Obviously p53 itself is required in the cell but these studies point to novel therapies involving restoration or ectopic expression of miR-34.


Tuesday, January 01, 2008

Fact or Fiction: Tryptophan Turkey Sleep

By now everybody should be emerging from their food-induced Christmas comas (and recovering from New Year binge drinking), and the annoying relative who passes out on the couch while the rest of the family does the dishes is cleverly blaming it on tryptophan in the turkey.

I never really understood that claim. Until recently I wasn't aware of how a humble amino acid could have such an effect, and even then I wasn't sure why turkey should be so much more rich in tryptophan than, say, chicken or duck or pork (all of which were in the turducken we shared for our Christmas meal). After all, I seem to feel just as drowsy after a meal replacing the turkey with roast beef. But it's such common knowledge that it must be true. Or is it?

The Facts: Tryptophan is a precursor to both serotonin and melatonin - regulators of the sleep cycle (among other functions) - and high levels could cause drowsiness. L-tryptophan was sold as a nutritional supplement and sleep aid, but a link to eosinophilia-myalgia syndrome prompted an FDA ban in 1991. Sale of tryptophan supplements has since resumed.

The Fiction: Turkey contains no more tryptophan than other meats. According to the USDA National Nutrient Database, 100 grams of roast turkey (light meat) contains 0.340g of tryptophan. The same amount of roast chicken (white meat) contains 0.361g, and roast beef (eye of round, prime grade) contains 0.325g/100g.

The post-meal drowsiness? Well, it could be the alcohol or it may be the other components of the meal. A typical turkey dinner is accompanied by potatoes, bread, stuffing - plenty of carbohydrates. It's been shown in rats and humans that high carb meals have an effect on plasma tryptophan concentrations and serotonin synthesis. The insulin release after eating carbohydrate rich foods stimulates amino acid uptake into muscle, in particular large neutral-branched amino acids. This increases the plasma concentration of tryptophan relative to other amino acids where it can then outcompete for amino acid transporters into the CNS for conversion to serotonin/melatonin leading to the familiar post-feast forty winks.

So the long and short of it is that the turkey sleep isn't imagined, but it has more to do with the rest of the meal than the turkey itself.