Thursday, October 22, 2009

Fashion Accessories From the Lab

Before some nut job sends me death threats again, I'm joking, and I think this is gross, but in a very entertaining kind of way... More pictures if you follow the link and have a strong stomach...


Monday, October 19, 2009

How Physicists Always Get it Wrong

A few months ago, Nature Physics published an article about an eventual overthrow of evolutionary theory. It's seen often enough - and in different fields. Sometimes there is legitimate grounds for strong skepticism, sometimes it's contrarianism masquerading as skepticism and often, as in the aforementioned publication, it's a case of experts speaking outside their expertise (something we do at the Bayblab quite often). In a humourous paper entitled "A Simple Model of the Evolution of Simple Models of Evolution" [free pdf] the authors explain how it can happen, using an explosion of evolutionary models made by physicists as an example:

The question presents itself: why are we being deluged with such models? In the spirit of the field, we present a simple evolutionary model of this process.

  1. A physicist runs across or concocts from whole cloth a mathematical model which is simple, neat, and contains a great many variables of the same sort.

  2. The physicists has heard of Darwin (1859), and may even have read Dawkins (1985) or some essays by Gould, but wouldn’t know Fisher (1958), Haldane (1932) and Wright (1986) from the Three Magi, and doesn’t dream that such a subject as mathematical evolutionary biology exists.

  3. The physicist is aware that lots of other physicists are interested in annexing biology as a province of statistical physics.

  4. The physicist interprets his multitude of variables as species or (if slightly more sophisticated) as genotypes, and proclaims that he has found “Darwin’s Equations” (cf. Bak et al. (1994)), or, more modestly, has made an important step towards eventually finding those equations.

  5. His paper is submitted for review to other physicists, who are just as ignorant of biology as he, but see that it’s about equivalent to the other papers on evolution by physicists. They publish it.

  6. The paper is read by other physicists, because at least it’s not another derivation of specific heats on some convoluted lattice under a Hamiltonian named for some Central European worthy now otherwise totally forgotten. Said physicists think this is cutting-edge evolutionary theory.

  7. Some of those physicists will know or discover simple, neat models with lots of variables of the same type.

They continue:
[O]ur model predicts that simple statistical-physical models of evolution will continue to proliferate until either (a) all the available models are exhausted, or (b) they become as common and as boring as any other subject in the statistical physics literature, or (c) physicists learn some actual biology. We are not entirely confident that the third limiting factor will become operational before the others.
So there you have it: this will continue to be a problem until everybody learns more biology.

Of course, as much as we would like to think so, this isn't limited to physicists, even if they aren't as humble as us bio-types. And it's really just an extension of what we often lament in science writing (and other journalism) - poor understanding of the subject and headline grabbing, like the title of this post.


Wednesday, October 07, 2009

What's The Most Boring Molecule in the Cell?

The knee-jerk for many of us raised on the Western blot loading control is actin, but biologically speaking, it's far from it...

But surely not everything in the cell is such a barrel of monkeys?????

What's your pick for the cell's most boring molecule?

(Video is from Michael Way's lab. Even boring molecules do cool things when viruses are in the house!)


How Fast is Your Internet?

A couple of weeks ago, Larry at Sandwalk posted the results of an internet speed test on his blog. If he was living in South Korea, Japan or Sweden his results would probably be quite different - these countries are the top three in terms of average internet speed. (The USA ranks 28th, no word on Canada) Likewise, if he lived in South Africa, we may still be waiting for that post to appear.

Earlier this month, a carrier pigeon was used to transfer data faster than South Africa's leading internet provider, Telkom. The bird successfully flew a data card 80km to it's destination in 1 hour, 8 minutes. Transferring the 'conventional' way, including download, took 2 hours, 6 minutes and 57 seconds - a time which apparently only accounted for 4% of the data.

Strangely, CPIP (carrier pigeon internet protocol) data transfer isn't a new idea. It started as an April Fool's joke almost 20 years ago, and the first actual implementation happened in 2001.

No word on how to adapt avian carriers for bittorrent distribution. If only those massive flocks of passenger pigeons hadn't gone extinct.


Another Nobel for Non-Coding RNA

By now you have heard that Blackburn, Greider and Szostak have won the Nobel for their work leading to the discovery of telomeres and telomerase - the eukaryotic solution to the end-replication problem. Other than gawking over "THE SECRET OF AGEING" and all the other shit journalists are copying and pasting into each other's newspapers, now would be a good time to take a moment and remember what a badass enzyme telomerase is. A cellular encoded reverse transcriptase, with structural homology to viral RTs, viral RNA polymerases and phage DNA polymerases. That is also composed of an ncRNA component which functions as a sort of a primer.

The molecular secret of ageing could have been something boring like actin. Is it just a coincidence that it's also cool?


Tuesday, October 06, 2009

Avalanche Testing

Here's a quick video on how to test the snowpack for the presence of avalanche conditions. And here's another quick video on some of the basic science behind avalanches hosted by Bob McDonald of the CBC (warning: this footage is OLD.)
Another video with some avalanche information including your chance of survival should you get caught in an avalanche.
Here is an AMAZING video from a skier wearing a helmet camera getting caught in an avalanche. He is buried alive. If you watch this whole video without fast forwarding it will disturb you, but it is definitely worth it.
This video makes me think that this snowboard season I should take up skootching (aka cross-country snowboarding) to avoid the mountains and the associated avalanche dangers.


2009 IgNobel Awards

This is usually AC's department but since he's MIA - working on some improbable research of his own, no doubt - I'll cover for him.

On October 1, the 2009 IgNobel awards were handed out at Harvard University. The winners:
VETERINARY MEDICINE PRIZE: Catherine Douglas and Peter Rowlinson of Newcastle University, Newcastle-Upon-Tyne, UK, for showing that cows who have names give more milk than cows that are nameless.

PEACE PRIZE: Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining — by experiment — whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.

ECONOMICS PRIZE: The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa — and for demonstrating that similar things can be done to an entire national economy.

CHEMISTRY PRIZE: Javier Morales, Miguel Apátiga, and Victor M. Castaño of Universidad Nacional Autónoma de México, for creating diamonds from liquid — specifically from tequila.

MEDICINE PRIZE: Donald L. Unger, of Thousand Oaks, California, USA, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand — but never cracking the knuckles of his right hand — every day for more than sixty (60) years.

PHYSICS PRIZE: Katherine K. Whitcome of the University of Cincinnati, USA, Daniel E. Lieberman of Harvard University, USA, and Liza J. Shapiro of the University of Texas, USA, for analytically determining why pregnant women don't tip over.

LITERATURE PRIZE: Ireland's police service (An Garda Siochana), for writing and presenting more than fifty traffic tickets to the most frequent driving offender in the country — Prawo Jazdy — whose name in Polish means "Driving License".

PUBLIC HEALTH PRIZE: Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, Illinois, USA, for inventing a brassiere that, in an emergency, can be quickly converted into a pair of protective face masks, one for the brassiere wearer and one to be given to some needy bystander.

MATHEMATICS PRIZE: Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers — from very small to very big — by having his bank print bank notes with denominations ranging from one cent ($.01) to one hundred trillion dollars ($100,000,000,000,000).

BIOLOGY PRIZE: Fumiaki Taguchi, Song Guofu, and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.
An interesting and entertaining crop as always. Links to papers and other information can be found here.


Monday, October 05, 2009

Epidemiology of Gun Violence in the City of Brotherly Love

A recent paper from the American Journal of Public Health takes a look at gun possession and gun assault in Philadelphia. From the abstract:
Objectives. We investigated the possible relationship between being shot in an assault and possession of a gun at the time.

Methods. We enrolled 677 case participants that had been shot in an assault and 684 population-based control participants within Philadelphia, PA, from 2003 to 2006. We adjusted odds ratios for confounding variables.

Results. After adjustment, individuals in possession of a gun were 4.46 (P<.05) times more likely to be shot in an assault than those not in possession. Among gun assaults where the victim had at least some chance to resist, this adjusted odds ratio increased to 5.45 (P<.05).
The paper also had some stats on gun violence that were surprising, though I admit I don't know much about gun statistics. During the study period (2003-2006) there were 3485 shootings in Philly (Population 1.4M, metro 5.8M) or an average of 4.77 shootings per day and an average of 9 shooting free days per year. I wonder how that compares to a city like Toronto (Population 2.5M, metro 5.5M).

The study was done by taking a case-control approach. Case participants were enrolled via the police department and excluded accidental, unintentional, self-inflicted and police-related shootings - the study interest was assault with a firearm. Control participants were matched according to age, race (black or white only), gender, and time of shooting. In other words, the researchers took people who were shot, matched with people who were not then looked at whether each was in possession of a gun or not. After their analysis they conclude:
On average, guns did not protect those who possessed them from being shot in an assault. Although successful defensive gun uses occur each year, the probability of success may be low for civilian gun users in urban areas. Such users should reconsider their possession of guns or, at least, understand that regular possession necessitates careful safety countermeasures.
However, there were some flaws in the study. For example, the authors "assumed that the resident population of Philadelphia risked being shot in an assault at any location and at any time of day or night", nor do they look at the legality of the guns in question. As such, matching wasn't based on location and thus excludes, for example, the possibility of 'bad neighbourhoods', it also excludes the possibility that people with illegal firearms may be involved in other illegal activities that increase the risk of a shooting. This despite their finding that people being shot were more likely to be in areas with lower income and more illicit drug trafficking.

This, of course, doesn't invalidate any results, but it does make it harder to suggest causation as strongly as the authors do in their discussion. From these results it's difficult to say that carrying a firearm increases your risk of assault vs. being in a high-risk group (eg. living in a certain area) increasing the chances of carrying a gun.

Still, the fact remains that gun possession is an indicator of assault risk (even if not necessarily the cause) and offers no guarantee of protection from being shot in an assault.


Saturday, October 03, 2009

Don't mess with the kakapo

We have previously posted about the strange nocturnal ground-burrowing kakapo parrot of New Zealand. Just because it sounds like an evolutionary disaster doesn't mean the kakapo won't rape your head if you try to get too close.


Friday, October 02, 2009

Cancer Carnival #26

Here we are again with the Cancer Research Blog Carnival #26 - your monthly roundup of posts from the cancer blogosphere.

The first post comes from the blog Asbestos Lung Cancer which, as you might guess, focuses on asbestos-related disease. This post discusses asbestosis symptoms and detections.
A history of asbestos exposure may provide the first clue to the diagnosis of asbestos diseases such as asbestosis and asbestos pleural disease. It often takes decades involving the patient’s asbestos exposure and the appearance of early symptoms such as shortness of breath and chest pain.
Francisco Barriga, who blogs at MolBio Research Highlights (who will be hosting the next edition, so start writing those posts!) follows up on a previous post on cancer stem cells (featured in Cancer Carnival #23) with some research blogging: Targeting cancer stem cells: chemical style.
In a previous post I tried to summarize the major points underlying the Cancer Stem Cell Hypothesis, which states that tumors are hierarchically structured and that a particular subpopulation of cells, cancer stem cells (CSCs), are capable of initiating and sustaining the growth of the tumor. This has obvious clinical implications since eliminating these cells would lead to the definitive disappearance of the tumor.
He takes a look at a recent Cell paper that takes a high-throughput approach to targetting cancer stem cells and finding that conventional chemotherapeutics aren't effective against this population.

Here at Bayblab, and staying on the cancer stem cell theme, AC takes a look at a new paper from Cancer Research that finds that a widely prescribed diabetes drug might be effective against breast cancer stem cells.
A friend of the bayblab sent me a link to a paper that just came out in Cancer Research showing promising results of Metformin against breast cancer. Not only does the drug seem to selectively kill CD44 positive breast cancer stem cells, but it seems to inhibit mammosphere formation.
Like the Cell paper above, one conclusion seems to be that future effective drug treatments will require targetting both tumour 'bulk' cells and cancer stem cells.

At HighlightHEALTH, the results are in and Allison Bland reports on lifestyle changes that prevent breast cancer. A recent update to the 2007 report by the American Institute for Cancer Research/World Cancer Research Fund (AICR/WCRF) that describes certain measures that can be taken to reduce breast cancer deaths
The study is an update to the breast cancer chapter of Food, Nutrition, Physical Activity and the Prevention of Cancer: a Global Perspective. Earlier conclusions were based on data from 873 studies evaluating the relationship between diet, physical activity, obesity and cancer. The 2009 update includes evidence from an additional 81 studies.

The report estimates that over 70,000 breast cancer cases in the U.S. — 40% of cases every year– could be avoided every year by simple lifestyle changes.
The post provides more details on the report, and outlines some of the preventative measurest that can be taken.

Elsewhere in the blogosphere, Orac lays the smack down on Bill Maher for some wacky views on medicine and cancer
Maher responds that he "doesn't know whether Laetrile works," but that he knows that "the shit we've tried for the last 50 years doesn't. I know they've made no progress as far as cancer in this country. So, yes, there are people who actually go out of this country when they get cancer. Some of them come back alive after a death sentence. But in this country you can't talk about that. I might get arrested right now."
Follow the link to find out the many ways Maher has it wrong.

Finally, September marked the passing of Patrick Swayze who succumbed to pancreatic cancer. More here and here. One alt-med 'treatment' for pancreatic cancer is called the Gonzalez protocol. The Journal of Clinical Oncology recently published a study showing that this regimen is substantially worse than standard care. You can read more at Science-based Medicine and Neurologica.

That's it for this month's Cancer Research Blog Carnival. For older editions, visit the Carnival Homepage. Don't forget, the CRBC has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.

November's issue will be posted at MolBio Research Highlights. If you'd like to host a future edition, email


Thursday, October 01, 2009

Diabetes drug kills cancer stem cells?

A friend of the bayblab sent me a link to a paper that just came out in Cancer Research showing promising results of Metformin against breast cancer. Not only does the drug seem to selectively kill CD44 positive breast cancer stem cells, but it seems to inhibit mammosphere formation. The puzzling part is that it seems to improve survival in nudes, but only when in combination with doxorubicin. Does this mean that killing the cancer stem cell is not sufficient to stop cancer growth? If this treatment works in humans, it might actually have a shot in combination with chemotherapy. In fact it's not the first time a link between metformin and cancer epidemiology in diabetic patients has been noticed. Hopefully the drug doesn't kill other "good" adult stem cells in the body since it is the most prescribed drug in the US (40M!). The paper also doesn't address the mechanism, but it may have something to do with MAPK, AMPK or PKC (then again what doesn't)...

Here is the abstract:
The cancer stem cell hypothesis suggests that, unlike most cancer cells within a tumor, cancer stem cells resist chemotherapeutic drugs and can regenerate the various cell types in the tumor, thereby causing relapse of the disease. Thus, drugs that selectively target cancer stem cells offer great promise for cancer treatment, particularly in combination with chemotherapy. Here, we show that low doses of metformin, a standard drug for diabetes, inhibits cellular transformation and selectively kills cancer stem cells in four genetically different types of breast cancer. The combination of metformin and a well-defined chemotherapeutic agent, doxorubicin, kills both cancer stem cells and non–stem cancer cells in culture. Furthermore, this combinatorial therapy reduces tumor mass and prevents relapse much more effectively than either drug alone in a xenograft mouse model. Mice seem to remain tumor-free for at least 2 months after combinatorial therapy with metformin and doxorubicin is ended. These results provide further evidence supporting the cancer stem cell hypothesis, and they provide a rationale and experimental basis for using the combination of metformin and chemotherapeutic drugs to improve treatment of patients with breast (and possibly other) cancers. [Cancer Res 2009;69(19):7507–11]


The Anatomy of...

Have you ever wondered what's inside a Lego man?

A balloon animal?

What about Godzilla?

Lego man, balloon animal (and more!) can be found at Moist Production

Godzilla (and other Japanese monster classics) via Pink Tentacle