Friday, November 28, 2008

The Rise and Fall of Phrenology

Recently, my sister sent me a paper she wrote on phrenology to proofread. Being the wonderful older brother that I am, I obliged, after all it's not a subject I'm overly familiar with and it was definitely more up my alley than the women's studies papers I often receive to read the morning they're due.

For those who didn't grow up in Victorian Europe and are otherwise unaware of this particular "science", phrenology is the determination of a person's personality and mental capacity according to the shape of the skull. Phrenology earned a fair bit of popularity in the early 1800s, but is now (rightly) shunned by the psych and neuroscience communities.

The idea behind phrenology stems from the notion that mental functions are localized to discrete areas of the brain. German physiologist Franz Joseph Gall's interest in the area was piqued at an early age when he noticed that among his classmates, those with prominent eyes also excelled at verbal memory tasks. He deduced that the frontal lobes were the centre for verbal memory and suggested that the size of a brain region is directly connected to its functional strength. From there it followed that stronger (and therefore larger) areas would create bulges in the skull to match the corresponding bulges in the underlying brain tissue. Using a map of brain function and scalp massage to determine cranial topology, an individual's personality could be assessed. And thus was born phrenology (then called craniology).

It was Gall's student, Johann Spurzheim, who really helped the spread of phrenology. He popularized it in the English speaking world and, notably, America, where one of the first Phrenological Societies was established. Spurzheim switched the focus from the anatomical to the social and political applications, appealing to those looking for guidance, and offering people a way to change through mental exercise.

Interest in the technique picked up, largely due to the innate human desire to understand - and predict - oneself. We can still see this today with the inordinate interest in things like fortune cookies, psychic readings, palmistry and astrology. The trend then, as now, was for man to try to rationally explain his own behaviours. Gall's craniology provided a tool understand, predict and maybe even control human behaviour and its popularity began to snowball.

In the US, popularity was booming. Journals such as the American Phrenological Journal granted legitimacy to the practice, earning praise from the likes of Thomas Edison and Alfred Russell Wallage, and the businesses popping up popularized it through talented salesmanship. The Fowler brothers turned phrenology into big business in the tradition of the great snake-oil men, with an entertaining and riveting show advising individuals on all aspects of their lives, from love lives to employment prospects, and ending each show with a practical demonstration. Phrenology had established itself both as a science and in the public mind as a legitimate industry.

Obviously, the shine of phrenology didn't last forever - it certainly isn't an acceptable specialty at any medical school I'm aware of. It was a combination of things that contributed to its downfall. While phrenology was enjoying popularity in North America, it was coming under attack across the pond. One of the primary figures challenging the science was Peter Mark Roget, the English physician famous for his contributions to Encycolopedia Britannica and the eponymous Roget's Thesaurus. Roget, and others, disputed phrenology on both methodological and physiological grounds.

The first objection raised was against the very underpinnings of the phrenological movement. While the field was predicated on skull topology being directly related to brain topology, there was no evidence of a connection between the two. In fact, whether 'high energy' (i.e. more developed) parts of the brain were quantitatively larger was the object of dispute, nor could the hypothetical sub-organs being proposed by phrenologists to explain their science be observed on dissection. On top of physiological arguments, phrenology fell prey to the classic fallacy of equating correlation with causation.

Phrenology was also under assualt from outside the scientific community, with religious leaders taking aim. Central to the phrenological 'science' was materialism, which is in contrast to the church's position of mind-body dualism. That is, the idea that personality and behaviour is strictly a consequence of the physical attributes of the brain is contrary to teachings of a soul. As a result, phrenology was condemned as implicit atheism. This, coupled with growing rejection in the scientific community and waning novelty of the practice led to the disappearance of phrenolgy and its being discarded as a credible science.

Now, there are other pseudosciences that have a similar history to phrenology, yet they endure. Astrology, for example, was widely accepted as reality. It was (and continues to be) opposed by religious leaders and has been rejected as a real science. However, astrology columns can still be found in any newspaper. Likewise, you can still get a tarot card reading, have your palm read or visit a psychic very easily. How is it that they persist but phrenology did not? There are a couple of reasons that might be.

First is its short history. Compared to the other pseudoscience mentioned above, phrenology was a flash in the pan. It may not have had time to establish itself in the public consciousness in the same way that astrology was able to. Furthermore, despite the poor methodology and basis in reality, phrenology was a scientific endeavor. Being such, results couldn't be rationalized with occult-based explanations. If predictions were wrong, the theory was invalidated. Phrenology was pushed out in favour of other ideas of self, such as the psychoanalysis of Freud or Jung. More importantly, some aspects of phrenology were absorbed into the body of scientific thought, making it easier to discard the invalid ideas. Modern neuroscience obviously still holds a material view of the mind, but the idea of localized functions and specialty areas - the basis of phrenology - have also survived. Every fMRI lighting up the music centre of the brain, for example, owes itself in part to phrenology - the brain science of its day. (Some have even suggested that functionl imaging is the phrenology of the 21st century) Despite having gone the way of the dodo, the study of phrenology remains an interesting piece of science history whose influence can still be seen.


Thursday, November 27, 2008

Call for Submissions!

It's that time of the month again - dig up your best posts about cancer, or hit the keyboard and write something new for the Cancer Research Blog Carnival. You have a week to get your submissions in here. And if you have a blog and want to host a future edition, be sure to contact us!


Wednesday, November 26, 2008

How to make a sandwich

McDonald's tries to patent the greatest thing since sliced bread. Click picture to enlarge.

(h/t: Greg Laden)


Drunk Red Asians

Recently went drinking with a FOB (friend of the bayblab) and, as usual with him, he turned pretty red in the face. Apparently approximately half of people of Asian decent have this reaction to the consumption of alcohol, which has been nicknamed the "Asian glow".This glow shows up really well in this particular FOB, because he is half Caucasian, providing a pale, pastey canvas for his inebriated glow.
I had heard that the Asian glow was the result of a variant or deficit of the acetaldehyde dehydrogenase (ALDH2) enzyme. This enzyme is responsible for the conversion of acetaldehyde into acetic acid. Acetaldehyde is the first breakdown product of ethanol produced by alcohol dehydrogenase and it is this nasty compound that causes all of the "Asain glow" symptoms which also include: nausea, headaches, light-headedness, an increased pulse, occasional extreme drowsiness, and occasional skin swelling and itchiness. It is also responsible for the scurge of mankind; the hangover.
Worse still for the previously mentioned FOB is that the east asian drunken red face variant of ALDH2 is associated with increased risk of alcoholism related cancer. This is likely because acetaldehyde is carcinogenic and would be in increased concentrations if you posses a less active ALDH2 enzyme.
If you're smart and paying attention you'd remember that the FOB is of both Asian and Caucasian decent. So what about his Caucasian allele? How could an enzyme deficiency be domninant? Well, the origonal paper on the subject explain demonstrates that ALDH2 exists as a homotetramer and that the Asian allele has a markedly reduced half-life and in a cell expressing both versions of the subunit passes on it's reduced stability to the resulting heterotetrameric complex. So presumably the increased acetaldehyde is not due to decreased specific activity of ALDH2 in some Asians but due to lower stability of the active enzyme complex. Therefore this allele is dominant.


Shinerama dumps Cystic Fibrosis

This is one of those rare occasions where Carleton University and Ottawa make the news, but unfortunately it's for all the wrong reasons. If you haven't heard already, the frosh week shoe shining activity "shinerama" where funds are collected for cystic fibrosis research by Carleton U (and Ottawa U) students, has ditched Cystic Fibrosis as the recipient. Now I'm not necessarily opposed to raising money for other diseases but the students' association decision was based on the fact that cystic fibrosis isn't "inclusive" enough, apparently it only affects the "white man". What a twisted idea. Apparently we need our diseases to hit all sexes, ethnicities and socio-economic status equally. Of course that's ludicrous because pretty much every major disease be it diabetes, cancer, heart disease, etc has some bias. And to top it all, the council's decision was full of inaccuracies since CF affects males and females equally, and caucasian does not mean "white" in the strictest sense, not that it really matters. It makes me wonder: Are the rare spontaneous genetic disorder the only disease to hit everyone equally? I mean even pathogens, think of those that cause AIDS or dysentery, do not infect equally across those arbitrary lines.... Does anyone know any "PC" disease?


Friday, November 21, 2008

'Tis the Season

Christmas season is almost upon us - and if you're to believe the mall displays, it has been since mid October. With it comes office parties, rum-laced egg nog (marrow rum?) and gift exchanges. And with family gift exchanges, often come Santa 'wish lists'.

The Christmas list remains something of a puzzle to me. Sure it removes much of the stress of gift giving (What should I buy? Will they like it? etc.) but it seems to fly in the face of the conventional "It's the thought that counts" wisdom, since they're meant to take thought out of the equation.

But conventional wisdom is often wrong and a more fitting aphorism would be "It's the act that counts". And in fact, the act may be as (or more?) important for the giver as the receiver. Families that cut back on gift giving by doing a "Secret Santa" type exchange may be doing themselves a disservice, the New York Times reports:
But while it’s reasonable to cut back on spending during the holidays, psychologists say that banning the gift exchange with loved ones is not the best solution. People who refuse to accept or exchange gifts during the holidays, these experts say, may be missing out on an important connection with family and friends.
Of course retailers are probably thrilled with that idea. Gift giving is a social interaction and by not participating either by not giving or declining gifts you miss out on social cues and opportunities to strengthen bonds
“[Not participating in gift exchange] doesn’t do a service to the relationship,” said Ellen J. Langer, a Harvard psychology professor. “If I don’t let you give me a gift, then I’m not encouraging you to think about me and think about things I like. I am preventing you from experiencing the joy of engaging in all those activities. You do people a disservice by not giving them the gift of giving.”
Psychology Today explains further. Giving a gift forces the giver to reflect on the relationship (at least subconsciously). It focuses the giver on who their important relationships are, and the nature of those connections (the nature of the gift, the effort willing to be made, etc.) and answering these questions is satisfying. And gift giving reinforces itself through these feelings in a sort of feedback loop:
We usually think that the more we care about someone, the more we want to give to them. This is probably true. But what is even more interesting is that the more we give, the more we come to care about the person to whom we are giving. We feel alive in the activity. And it is the receiver who has provided the opportunity for us to feel this good, so we feel loving in return. Moreover, as social psychologist Daryl Bern, Ph.D., has taught us, we deduce our attitudes from our behavior. "I must really care or else why would I have given such a meaningful gift?"
A recent paper in Science supports the idea that giving is good for the giver. The authors show, through both survey and field study, that spending money on others is predictive of happiness. While one might think that happier people are more prone to giving (which may be true), the authors also showed that people randomly assigned to give to others reported more happiness compared to those told to spend on themselves.

So on that count the old wives may have got it right: It is better to give than to receive.


Dancing your PhD

The AAAS had its annual science dance contest, and the results are in! The idea is to use body movement and art to communicate the findings of your first-author publication, so that you may perform in February at the AAAS meeting. Clearly they are taking cues from the evermore popular IgNobel. This will appeal to the subset of people who like both "So You Think You Can Dance" AND are members of the AAAS (judging by my lab, it may be greater than you'd think). Of course they are not the first to create this overlap, it's been done before, but never in a competitive setting. .

Here is the winner for the graduate Student category: "The role of vitamin D in beta cell function"


Wednesday, November 19, 2008

Nobel Prize: Look to the Stars

If you have your eyes on the Nobel Prize, you may want to think again if you were born in the midsummer months. A study published in the Canadian Medical Association Journal (CMAJ) compared the birthdates of 171 Nobel laureates with 375 scientists who had not won the prize and shows that people born under the star sign Leo are the least likely to win the prestigious prize for Medicine or Physiology, while Geminis have the best odds. This is just common sense for any astrologer
Selective retrieval from the multitudinous traits attributed to particular astrological signs showed that "Gemini produces persons of greater intellect and more powerful invention and genius than any other sign of the zodiac" and that Gemini are "thirsty for knowledge and eager to study."
But don't worry Leos, you still have the "natural creativeness and magnetism" that attracts others to you.


Friday, November 14, 2008

Elementary science experiment

A total FOB (friend of the bayblab), who's all talk no post, recently sent me this email about an interesting science story she heard on CBC.
Pretty impressive for an elementary student.

thought this is a cool story... dad (geologist) studies paleoclimatology
on south american glacier... comes across what may be a birds nest up
there on the ice. Brings back some pictures... his son - in ELEMENTARY
SCHOOL at the time - picks up where dad left off.... they recently
published this paper. they found the only other bird known to date that
lays eggs on ice (besides penguins)!! Crazy!

Hardy, D. and S. Hardy 2008. White-winged Diuca Finch (Diuca speculifera)
nesting on Quelccaya ice cap, Peru. Wilson Journal of Ornithology 120:


Thursday, November 13, 2008

It's the plastic, stupid!

One of the original baybz alerted us of this paper in science which discusses contaminants found in plastic that can inhibit enzymes. We use disposable plastics a lot in the lab, from tips to eppies , without thinking too much about it. There are a few people who religiously believe that you should not change any of your plastic supplies (tips/tubes) when repeating an experiment. Well these people maybe on to something as this Canadian team from Alberta has shown as much as 40% inhibition of hMOA-B from coumpounds such as DiHEMDA and oleamide which leak into water or DMSO from tubes, tip, and TCware. And that's not even all. Apparently microbicides are added by manufacturers to the plastic along with other chemicals to prevent water from "sticking' to the sides:

" Related slip agents such as erucamide and stearamide are endogenous molecules used routinely in plastic manufacturing (3), whereas quaternary ammonium compounds are included as biocides or antistatic agents. Many such biocides bind substantially to proteins and DNA and have recently been linked with fertility problems in mice (6). Our findings that processing agents leach from laboratory plasticware into biological media and solvents, particularly when liquids are stored in plastic vessels, identify a likely source of error in many assay systems."


Wednesday, November 12, 2008

How do you like them apples?

As I'm typing this I'm snacking on a granny smith apple, one of my favourite varieties. Even though you'll typically find only a half dozen or so different varieties at the grocery store, there are over 7500 different cultivars (though not all are eating apples). The apple is a member of the rose family, and as one might expect they have a long history. They originated in Asia, and Alexander the Great is credited with bring dwarf apples back to Greece in 300 BC. The first apple orchard in North America is said to have been planted in the 1600s in Massecheusetts.

AC wrote before about modern hybrid fruit. It should come as no surprise that having been around for centuries and being an important food crop, the apple has gone through several rounds of its own breeding to produce popular varieties we eat today. It can take 15-20 years to develop a new variety and promising cultivars are selected on the basis of appearance and flavour as well as ease of shipping, longevity in storage, and even length of stem to allow pesticides access to the top of fruit.

The granny smith apple I mentioned above is originally an Australian fruit, but Canada is famous for apple varieties of its own. Every McIntosh apple can trace its lineage to a tree discovered in 1811 in Dundas County, Ontario. One of its offspring, the Spartan (another one of my favourites) was developed in BC in 1936 as part of Agri-food Canada's apple breeding program. It's widely described as a cross between McIntosh and Newton Pippin but recent DNA tests have put the Newton parentage in question.

Over the past few weeks, I've been sampling several different apple types from the common Granny Smith (still my favourite) and McIntosh (which I find too soft) to less 'brandname' varieties such as Honeycrisp (which was almost unnaturally crisp and a bit too sweet) and Braeburn.

Extensive lists of apples, their origins and descriptions can be found here and here.

What's your favourite apple?


Monday, November 10, 2008

Recycling Myths Debunked

Ran across this quick read about the realities of recycling on Bottom line is that recycling makes more sense than ever. Although I have read that the 'economic crisis' has recently caused a drastic reduction in demand for recyclable waste.


Friday, November 07, 2008

Cancer Carnival #15

The 15th edition of the Cancer Research Blog Carnival is now up on the carnival home page. Go check it out here and thanks to everybody for their submissions.


Thursday, November 06, 2008

'Coons Get the 'Fluenza...Who Knew?

The globe and mail reports on the TOTALLY GROUNDBREAKING discovery that wild raccoons get infected with influenza. Thanks guys. Now I know not to eat my garbage after the coons have been into it. As if the fear of rabies wasn't already enough.

It's always interesting to see which science stories newspapers choose to report on. There's a lots of fascinating questions in virology. This is not one of them. Is it really surprising to learn that raccoons, who will pretty much stick their noses into anything, get infected by a virus that will stick its genome into pretty much any available cell? As the author of the study says, "More diseases have been found in raccoons than pretty much any other wild animals,...You name it, raccoons get it. But they're tough as nails." Ok, this is getting a bit more interesting. Apparently infected coons can shed and transmit the flu, but they don't get sick.

Maybe someone needs to establish a coon model for immunology. What's so gosh-darn special about the raccoon immune system? That would be interesting. Warm fuzzy mammals for press releases AND some novelty...


Patents and Graduate Students

I'm about to sign over the rights to a patent application to the institution where I am doing my graduate studies. Does anyone have experience with this? Advice?
I'm pretty sure Bayman has experience with this. (?)
I fully understand that the institution will be the full and exclusive rights holder and financial beneficiary, however, I would still like my name on the patent as the inventor so that I may refer to it in the future in job applications. Is that the default? The paper work I have in front of me seems pretty vague about such details.


Junk DNA and Transposon Driven Evolution

A press release out of the Genome Institute of Singapore is claiming a function for junk DNA. The researchers show that a number of transcription factors bind repeats found in transposable elements.
More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution. [...] The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.
Now I could be wrong, but I thought we already knew that portions of these transposable elements acted as transcription factor binding sites (for example see here) so I don't think Larry over at Sandwalk is going to have to revise his estimates of junk DNA percentage yet. But what about the "deflated ego problem"? Is this an answer to Larry's excuse #5: that humans are more complex than other organisms in spite of similar gene numbers because of more complex regulatory mechanisms? Unfortunately I don't have access to the paper, but the press release and abstract seem to think so.
Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.
The argument here isn't for more complex gene regulation in humans, but rather different regulation depending on where these elements landed in early evolutionary history.


Wednesday, November 05, 2008

Research Funding: Low Hanging Fruit

A few weeks ago, Bayman posted a story from the Globe and Mail about unrealistic expectations for a cure for cancer and in the comments AC wrote
I think the expectation comes from the fact that we've basically cured many diseases that were low-hanging fruits [...] And it might or might not be worth the money; perhaps we could cure 100 smaller diseases for that price.
It turns out that focus on low-hanging fruit is also an issue within the cancer research community. The Independent reports that in spite of record levels of funding for cancer research in the UK many "unfashionable" cancers are being neglected:
Some of the deadliest cancers, such as those affecting the lung and pancreas, get the least amount of public money, while five cancers with some of the best survival rates, including breast and leukaemia, receive nearly two-thirds of the money.
This seems counterintuitive. One would think that cancers such as lung cancer - which remains the leading cause of cancer death for both men and women - would receive a higher percentage of funding dollars. But that isn't the case. This is attributed to the fact that current research focuses on areas where major discoveries are more likely or the disease is easier to study, and this is partly due to the fact that future grants can depend on past success so reaching for those higher fruits can be risky career-wise. Is this a problem? Should focus shift from areas with diminishing returns to those where there's still a lot of ground to be covered? Or should we finish off the 'low hanging fruit' before climbing the ladder? And if the former, how do we accomplish it?


Tuesday, November 04, 2008

Coffee and cancer

I recently had an armchair expert tell me that french press style coffee vs a filtered coffee preparation method increases your risk of cancer. [Don't confuse french press coffee for the biological apparatus]. This person was foggy on the details but indeed got rid of their Bodum(tm). Personally I find coffee from a french press tastes superior, but then again, I'd drink it off a dog some mornings. Some googling revealled one source of the idea that unfiltered coffee increases your risk of cancer the source they cite is an article that shows increased homocysteine levels in drinkers of unfiltered coffee vs NO COFFEE. (no coffee?!?!) Homocysteine itself is not directly derived from your diet, however, high levels in the blood are indicators for high risk of heart attack and stroke, and possibly cancer. The thought was that filtering coffee removed what the authors assumed was causing the rise in homocysteine levels. Turns out filtering coffee doesn't change the fact that drinking coffee raises homocysteine levels.
To me this is a good example of something I see often, that is, cancer research NOT serving the public who funds it. If this is the crappy way that the public is informed about cancer research I'm surprised it still is funded. Someone gets rid of their french press because their concerns for their health based on the mainstream medias reporting of an incorrect assumption in the literature. What is also strange is that the damage is done. I think I would have a hard time convincing this person that their french press coffee is no worse for them.
Also I think there is a leap of logic here that I have heard is similar to the leap in logic made for the statin class of drugs. That is that since higher homocysteine levels correlate with higher risk of cancer (let's assume the one article I found linking the two is correct), then homocysteine is a cause of cancer. An indicator is not necessarily the cause but is merely associated with increased risk.
Also it may be that coffee raises cancer causing homocysteine levels by an appriciable amount, however, other factors associated with coffee drinking may result in an overall reduction in cancer incidence. So again even if homocysteine causes cancer, coffee may not.
Of course, perhaps coffee has so taken over control of my thought processes that I am in denial.


Last Call for Cancer Posts!

The 15th edition of the Cancer Research Blog Carnival will be up on Friday at the carnival home page. For all you procrastinators/last second folks it's time to write or dig up something and submit it to the carnival.