Friday, December 28, 2007
Monday, December 24, 2007
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.
Friday, December 21, 2007
Bad news for those of us who think that oncolytic viruses show great potential as cancer therapeutics is coming out of Hollywood. I haven't seen it but apparently the plot of 'I am Legend' starring The Fresh Prince revolves around an cancer curing virus mutating and killing almost everyone except his Freshness.
From wikipedia (I am Legend):
A genetically reengineered measles virus called Krippen Virus or KV, created as a cancer cure by Dr. Alice Krippen (Emma Thompson), rapidly spreads and wipes out the population of the world by the end of 2009, leaving military virologist Robert Neville (Will Smith) the last human survivor in New York City and possibly the world.
The virus killed 90% of the people on the planet; fewer than one percent are immune. The remaining survivors were infected, initially exhibiting the early symptoms of rabies, but then degenerated into an animal state driven by hunger and blind rage. Neville is watched by these "Infected" people, who react painfully to UV radiation. They therefore avoid sunlight and hide in the dark underground, and in buildings (in groups called "hives" by Neville), swarming out at night. Dogs and rats are also susceptible to the virus. By 2012, Neville has not seen another normal human being since the virus' release three years earlier, and suspects that the Infected have succeeded in killing the remainder of the immune survivors. Neville is outnumbered by the infected and running out of time as he seeks a cure.Some pretty bad press for a treatment that's just getting out of the gates, and this might be the first time many people hear about the potential of treating cancer with replicating viruses.
Thursday, December 20, 2007
Discussion over beers turned to rodeo, specifically bull riding. I thought I had heard that bulls were electrocuted on their testicles just as the gate is opened. This is apparently a mixture of partial truths. The bulls do have a flank strap which some people have thought causes pain to the bull's testicles, however here's the info on the flank strap:
The flank strap is often misunderstood. Its purpose is to entice the bull to kick more. Without it, most bulls would have greater tendency to run or fall. The flank strap serves to regulate their bucking somewhat and cuts down the risk of injury to a bull. If you are familiar with a dog's ticklish spot, then you have an understanding of how a flank strap works. Bulls and horses are notoriously ticklish around the flank area.
There is also an electric shock involved in getting the animals fired up, illegal however in most places. Almost all the information I can find on the internet is about animal rights abuse. Apparently the 'hot shot' delivers 5000volts. It is applied to the rear end of the animal just before the gate is opened. video.
Not quite as bad as getting it straight to the genitals but it sounds uncomfortable. I'm not going to weigh in on the moral issue but I find watching the bull riding entertaining( video -NSFW because of soundtrack = footloose). I think I cheer for the bull though....
Posted by Rob at 5:41 PM
Monday, December 17, 2007
One of the baybs from the Bay sent us this juicy tidbit: The Kangen Water Maker. Behind this slick website is another 'miracle' water treatment that can solve your problems of indigestion, diabetes, obesity, osteoporosis and constipation (among other things). It's good for non-health applications too: artists and painters can expect more vibrant hues and smoother strokes when their paints are mixed with alkaline water! Apparantly Kangen means 'return to original' in Japanese (according to one seller) which is ironic because pure, unadulterated water should have a pH of 7 not the pH 8-9.5 that these guys suggest you drink.
How does it work? The Kangen water maker is basically an electrolysis machine that uses dissolved minerals to acidify or alkalize water. This alkaline water, they claim, contains water molecules that cluster in groups of 5-7 instead of 10-14 like 'normal' water. The theory is that the smaller molecular grouping allows the water to travel to places regular water can't, making it better for hydration and delivery of nutrients. Additionally, they claim that Kangen water alters body pH, which prevents acid build up, an associated leaching of calcium from bone and increase in fatty acid deposits.
Why doesn't it work? Even if you can maintain alkaline water for more than a transient period of time (this is accomplished by adding minerals to the water, which can alter the taste - just think about drinking 'hard' water which is also alkaline) as soon as it hits the strong acids of the stomach any alkalinity will be neutralized. Not to mention there seems to be no scientific evidence that this clustering effect is real or that it would be anything more than fleetingly transient. Most studies support the idea of a dynamically changing, disordered water structure. Not to mention that there are water quacks out there who pitch acidic water or water with LARGER clusters as the true 'healing' water.
Of course this has all the standard hallmarks of quackery to go with the pseudoscience: untested medical claims and large disclaimers about lack of FDA review. Some sellers are part of multi-level marketing schemes, and one goes so far as to combine his selling of water ionizers with marine phytoplankton for 'the best whole food nutrition available' and our pet favourite StemEnhance.
For a more in-depth analysis of the pseudoscience of alkaline water, this chemist from SFU does a pretty thorough debunking.
Sunday, December 16, 2007
Friday, December 14, 2007
Here is the explanation. First you have to accept the fact that genes do not control life. That's a lie. We just repeated it for so long that that we have come to believe it is true. But apparently it was never tested scientifically. If you don't believe me, watch this video. The quack behind this video is Dr. Bruce Lipton, who apparently was teaching medicine at the University of Wisconsin. He also wrote a book called the "Biology of Belief", which is a deceptive title since it's actually about changing your own biology with your mind. The irony of which seems to be lost on the author. Apparently he's also pretty much discovered epigenetics, which if you were not aware explains how energy from the mind alters protein expression.
While lots of nutjobs seem to love the book, there are few amusing reviews on amazon such as this one by a Columbia University researcher:
"Furthermore, Dr. Lipton claims that illness can be cured by mere belief. This isn't only nonsense; it is incredibly unprofessional and irresponsible. This is the equivalent of a TV Evangelist banging his palm against the foreheads of cancer patients, pushing them back down in their seats and proclaiming them cured, only to then say later to an investigating reporter who mentions that the patients later died that the Lord's magic stopped working because doubt entered into the hearts of the disbelieving patients. What an incredibly cruel sentiment. "
Which brings me back to water. Dr Lipton's ideas have inspired the creators of "Healing Water Online" because apparently your mind can also alter water and vice-versa. Now I'm sure a cold shower can elicit some spiritual experiences in some people (I highly recommend that link). In fact I often praise the lord when somebody flushes while I'm in the shower. But this is different. Somehow, this has to do with the energy you can produce with your mind, and the unique properties of water. For example did you know that:
"Water's reputation as a powerful solvent derives from its ability to absorb energy vibrations and its particular electromagnetic and chemical qualities, being able to break down substances into their constituent parts. Naturally flowing water creates complex structures: micro clusters of vibrating energy centres, constantly receiving and transmuting energy from every contact the water body makes; and laminar structures which generate energy from the interaction of the planes against each other."
So how can I harness this power you ask? Well it's easy, you just need to buy a $144 jug that has a propeller inside. Why? Well isn't obvious by now:
"The compact motor housed in the lid of the 2-litre jug drives a left-turning silver propeller wich forms a beautiful vortex throughout the depth of the plain tap water for 3½ minutes; this re-enlivens, restructures, reoxygenates and purifies the water by the spiral movement alone.
The energy wave field of normal tap water is 35 cm; Living Water Vortex Jug's is 2,4 metres! A healthy person has an energy wavelength of about 1,9 metres, and as a person consists of 75% water, s/he will be regenerated by the greater energy of restructured water."
Wow what a deal. That's almost a 26% increase of your wavelenght, or only 88 cents per centimeter! And they also suggest you combine your healing water with long distance healing. That's right, for only $44 they will channel energy to you, sorta like what kamel's power to make people dumb at a distance. Actually it's exactly like that.
Thursday, December 13, 2007
Posted by Rob at 3:54 PM
Wednesday, December 12, 2007
Any other nominations for favourite cell lines?
I sent an email to ATCC asking for a "Top Ten most popular cell lines" and they replied with a LAME response:
I am writing from Cedarlane Laboratories, which is now the exclusive
distributor of ATCC products within Canada. Your query regarding top ten
cell lines from the ATCC has been forwarded to us.
ATCC cannot provide the information that you have requested because it
Posted by Rob at 11:03 AM
Tuesday, December 11, 2007
While it remains to be seen whether iPS can give rise to autonomous souls, Jaenisch's groups has now shown that iPS can be applied therapeutically. They derived iPS from the tail fibroblasts of sickle cell anemia mice, fixed their genetic deficiency ex vivo, differentiated them into hematopoietic progeintor cells and transplanted them back into the affected mice to restore a functional pool of red blood cells. Pretty damn cool.
Monday, December 10, 2007
Just when I thought that social isolation was a cheap and easy alternative to cigarettes.
Personally, I don't care what people believe or do with their spare time, but for a publication of the BMI Grad Student Association to spin and legitimize tarot card reading and the supernatural as science is embarrassing for me as a member of the department. The following is our response sent to the editors of the publication:
RE: "Specializing in the Natural and Supernatural Sciences"
Science is the investigation of physical and natural phenomena through observation and experimentation. The supernatural, by definition, is unexplainable by natural law and falls squarely oustide the scientific realm.
I understand the desire to profile members of the department and, as an author of the science blog "The Bayblab", I understand that it can be difficult to come up with ideas for stories. However, a profile of the *scientific* acheivements of the student, or even a critical analysis of research articles (the references of which were omitted) mentioned in the interview, would be more appropriate. (Incidentally, we at the Bayblab devote a considerable amount of energy to promoting critical thinking and distinguishing between science and pseudoscience or quackery.)
To include an article in the departmental bulletin about the supernatural and classify it as science is a disservice to your readers and a disservice to the reputation of the department as a scientific body.
Friday, December 07, 2007
I think every field needs a solid critic like Marilyn Kozak. We are talking about THE Kozak of the "Kozak consensus sequence fame". She has published a few papers on criticizing the field of internal ribosome entry sites (IRESs). Her lastest is still critical of the existence of viral internal ribosome entry sites which have not only studied for quite some time now but are used as molecular tools for expressing multiple genes from one mRNA. She is persistant. Here is an older response from some scientists in the field to some of her critisisms. Despite being perhaps frustrating to those in the field it is probably good to have such a dedicated (and famous) critic to point out shortcomings in the published data. I wish there was one in my field, at least just for entertainment purposes.
Thursday, December 06, 2007
What does this have to do with cancer? The paper discusses the therapeutic potential of the drug in terms of cystic fibrosis and muscular dystrophy - two diseases with pathology known to be caused (at least in some cases) by nonsense mutations in specific genes; CTFR for cystic fibrosis and dystrophin for muscular dystrophy. An obvious target for cancer therapeutics is p53. The p53 gene is mutated in over 50% of human tumours and of those mutants, almost 8% are nonsense mutations (source:IARC p53 mutation database). Research has shown that reactivation of p53 has therapeutic potential in mouse models of cancer, leading to growth arrest and regression of tumours. One need not limit this idea to p53. Nonsense mutations in many other genes, such as BRCA or Rb, have been associated with cancer and bypass of nonsense-mediated decay represents an interesting area to explore when dealing with cancer, and other, therapeutics.
Tuesday, December 04, 2007
"Students are at a stage of their lives where these choices are most urgent and compelling, and when they also enjoy unusual, if not unique, freedom and opportunity to explore the choices available, to evaluate them, and to pursue them. [...] Well, there are really some moral truisms. One of them is that opportunity confers responsibility. If you have very limited opportunities, then you have limited responsibility for what you do. If you have substantial opportunity you have greater responsibility for what you do. I mean, that's kind of elementary, I don't know how it can be discussed. And the people who we call 'intellectuals' are just those who happen to have substantial opportunity. They have privilege, they have resources, they have training. In our society, they have a high degree of freedom-not a hundred percent, but quite a lot-and that gives them a range of choices that they can pursue with a fair degree of freedom, and that hence simply confers responsibility for the predictable consequences of the choices they make. "
Monday, December 03, 2007
Greg Laden presents The Nematode Vulva and the Nature of Evolution. Greg explains how the vulva can be used as a model in comparative genetics to determine whether evolution is primarily governed by selection and/or selection-independent constraints, not stochastic processes such as drift in unconstrained phenotypic space. He concludes that evolution is more deterministic than stochastic.
96well presents Where do you express your transgene? posted at reportergene.com. This post does a good job of explaining one of the biggest problems with transgenics, namely how poorly we understand integration. The transgene can integrate in any place in the genome and be subject to tissue-specific chromatin remodeling which may render results uninterpretable. One way around this is to target insertion near the beta-actin gene as the author explains: "Recently, the lab of Bernd Kinzel (Novartis), published a technology report in Genesis (vol.45), in which the locus of beta-actin was identified as a good dock for gene expression. Beta-actin is a cytoskeletal building-block expressed in almost every mammalian cell, and it is necessary for life, so only heterozygous transgenic can be developed."
FitBuff presents What Is Healthy? posted at FitBuff.com's Total Mind and Body Fitness Blog. FitBuff is asking the question "What is healthy"? At first, this may seem like an easy question to answer. However, when you actually stop and think about it, it's not easy at all... here is what he thinks: "In my opinion, healthy is following a positive lifestyle; one that is manageable, as stress-free as possible, involves the eating of several small meals throughout the day (including lean protein, complex carbohydrates, and healthy fats), incorporates a workout program that is realistic and consistent, and always ends with a good night's sleep."Techniques
"I had an interesting (mostly one-sided… sorry Laura) conversation yesterday, which has led me to write a little opinion-piece.
I obtained my first research experiences working in a basic biology department at a small university. I was lucky enough to find a phenomenal mentor and get some experience in molecular biology in a department with a faculty that focused mostly on ecology, fish biology, teaching, and (for many tenured profs) reading the paper while waiting-out the years until retirement. The graduate students that I worked with were paid primarily by the department; however, they had to earn their living wages (which amounted to about $12,000 a year). They worked as TAs for 2-3 afternoons a week and marked lab reports for at least 10-15 hours every week. They did this to have the opportunity to do research. Similarly, graduate students in basic science programs throughout Canada are paid very little; they also need to TA and to mark reports to earn it. Therefore, they do their research in what amounts to spare time. Although it makes doing their research difficult, it gives them independence. They are not employees of a prof, they are students; they learn in their chosen lab, work on projects that are within the scope of the research interests of their PI, but tailored to their own interests and goals. This should sound familiar: it’s called being a grad student.
In Ottawa, particularly at the OHRI, we are paid comparatively well, and asked only to do our thesis research in return. However, our salaries (unless externally-provided) are paid by our PIs, through their grants. I found the research environment very different when I arrived in Ottawa. People here refer to their PIs as “boss”. They call their research “work”. I have always rejected the term boss for my PI. He is my mentor; I’ll even go as far as to call him my “thesis supervisor”, but never my boss. I don’t go to work. I go to the lab. This matter of semantics has been my private rejection of a system that I have never been able to understand.
To me, a PI has a specific role. They obtain funds to work on projects that they find interesting. They recruit like-minded people to help them work towards their research goals. The PI obtains funds, and thus has responsibilities to both the providers of funding - to ensure that the money is well spent - and to the people that work in their lab, to ensure that they are able to pursue their research in a good environment. This is where the formal authority of the PI ends for me.
Graduate school is a learning experience, not a job. Any PI that tries impose hierarchical ruling on a graduate student (outside of the realm of authority that I described above), is not only exercising unwarranted power, but is also harming the potential of the project and the student. Creativity and invention are what makes good research great research. When creativity is stifled, mediocrity is inevitable. Whenever such unnecessary imposition of force is encountered, it should be rejected and fought. However, it is so pervasive in Ottawa that all incoming graduate students undergo a form of indoctrination that keeps them from questioning the role of their mentor in directing their day-to-day activities.
I will finish with an excerpt from a biography of James Watson (maybe not the greatest role model for potential PIs, but a man who often makes some great points and who obviously achieved great things in his mentoring and administrative careers):
“(Watson’s students and post docs) knew that they were working “primarily to advance their own careers.” Though terrified of Watson, they weren’t working for anyone but themselves. “I never worked for anybody,” Watson recalled on his 60th birthday. “I could never work under others. You only get somewhere with people if they feel they are working for themselves”."
Sunday, December 02, 2007
"Twenty positions were tested by computer simulation to obtain the best 10, he says. "Two guinea pigs then tested them in real zero-gravity conditions. The results were videotaped but are considered so sensitive that even Nasa was only given a censored version."
Only four positions were found possible without "mechanical assistance". The other six needed a special elastic belt and inflatable tunnel, like an open-ended sleeping bag.
Mr Kohler says: "One of the principal findings was that the classic so-called missionary position, which is so easy on earth when gravity pushes one downwards, is simply not possible.""Too bad it's a hoax. When is NASA going to concentrate on some real priorities that people actually care about ;)
Wednesday, November 28, 2007
Monday, November 26, 2007
The data to data do indeed suggest that if you have rotavirus induced diarrea probiotics may definitely be helpful. And collegenous colitis, which is difficult to treat, may be slightly relieved with probiotics. And a big one, irritable bowel syndrome (IBS) may be treatable using B. infantis (that is the bacteria that are largely found in the intestines of human infants)
Unfortunately since bacteria are pretty easy to make, and they are already in your food like yogurt and other fermented milk, anyone can make something and call it probiotic. And of course it is suggested that we all need it and that it is a general 'cure all'. For instance this manufacturer states that:
• Chlorinated drinking water
• Stress, aging and disease
• Born by caesarean section
• Alcohol consumption
• Bacterial infections
• Traveler's bugs
• Antibiotics in food production or prescription medications
So maybe probiotics are great for some conditions and maybe we should all be eating more yogurt but I don't know if eating a bunch of lyophilized bacteria is going to make me 'feel better.'
Wednesday, November 21, 2007
Nature, 302, 21 (April 1983): 652.
Tuesday, November 20, 2007
"Because of their avid adaptation to growth in tissue culture plates, HeLa cells are sometimes difficult to control. For example, they have proven to be a persistent laboratory "weed" and they can contaminate other cell cultures in the same laboratory, interfering with biological research. The degree of HeLa cell contamination among other cell types is unknown, because few researchers test the identity or purity of already-established cell lines. It has been demonstrated that a substantial fraction of in vitro cell lines - approximately 10%, maybe 20%, are actually HeLa cells, due to the fact that the original cells in the cell culture have been overwhelmed by a rapidly growing population derived from HeLa contaminant cells. Stanley Gartler in 1967 and Walter Nelson-Rees in 1975 were the first to publish on the contamination of various cell lines by HeLa."
And recently the TE-7 which have been used for over 20 years as an esophageal cancer model, were found to be a completely different cancer. This has led to the proposal that all cell lines be continuously tested:
"He said the best way to get scientists to comply would be to withhold research grants and publication in scientific journals unless their research used authenticated cell-lines. This verification can be achieved using a technique of DNA profiling which compares the cell-line with a list of known contaminants and can cost as little as £180 per sample. "
Paranoid or justified?
Monday, November 19, 2007
More interestingly, we recently had a great journal club about the evolution of paralogous histone-modifying enzymes in yeast. The paper examined the evolutionary balance between redundancy and diversity of function in duplicate gene pairs, and showed that functionally distinct (non-redundant) paralogues can compensate for their partner when, and only when, the other is deleted. Presumably then, a similar evolutionary dynamic could be at play in the evolution of ribosomes and the regulation of translation in general.
Speaking of histones, if there's no such thing as histone code, maybe it's more of a universe. The complexity of chromatin structure is unbelievable. What's even cooler is that it's dynamic. So not only is chromatin complex, it's ALIVE. At least that was the impression I took away from a recent talk by Ottawa chromatin mapper Marjorie Brand. Check out her lab's latest paper on how spreading of chromatin-associated MLL protein mediates communication between a distal upstream activator element and the B-globin promoter during differentiation.
Another random factoid that was mentioned in the first paper, and news to me: the yeast (S. cerevisiae) arose from a massive whole-genome duplication, but eventually all but 10% of duplicated genes were lost. Weird. Was the initial duplication event selection-neutral for the original yeast cell it occurred in? Hard to imagine, since I would think two genomes take longer to replicate than one, not to mention the structural instability associated with having all that homologous DNA around. So what's the advantage? Not much, if most duplications were eventually lost. Doesn't this say there was indeed a fitness cost to having extra copies of all those genes if they were ultimately weeded out by selection? The only thing that makes sense to me is if the cost/benefit of duplicate genes has varied over yeast evolutionary time. So it was advantagenous to have backup gene copies back sometime in ancient history, but then became unnecessary or cumbersome more recently. Maybe the environment or the yeast's response to it changed. For example, maybe at one point gene inactivation via radiation-induced DNA damage was a big problem for yeast, so it was often useful to have a backup genome copy around. Then, either environmental radiation diminished or yeast evolved a system for preventing or repairing DNA damage, and they no longer needed to keep the backup genes around. I suppose another possibility is that it has something to do with the role of sexual reproduction..........
Alas, I rant like a raving lunatic. Someone set me straight.
(Above figure is from Volkin and Astrachan, Virology, v2 pg. 149 (1956).
The culmination of this series are the 10 rules to do your best research:
- Drop modesty (strive for excellence)
- Prepare your mind (luck favors the prepared minds)
- Age is important (research strategies should be different depending on your age, although I'm not sure I agree with that one)
- Brains are not enough, you also need courage (I assume this means taking risks)
- Make the best of your working condition (don't let your environment limit you, but exploit the advantages you have)
- Work hard and effectively (all the successful scientists I know are workaholics)
- Believe and doubt your hypothesis at the same time (so be skeptical and accept data for what it is, but don't give up on ideas before you test them)
- Work on the important problems in your field (work on something interesting and relevant, no matter what the current trends are)
- Be committed to your problem (because it might take a looong time to solve it)
- Leave your door open (interact as much as you can with other people, you never know where the insights might come from)
Friday, November 16, 2007
"Delays and setbacks are built into the scientific process no matter where it occurs, but researchers in Iran face an additional burden imposed, largely, by politics. Cell biologists lack even the machines that sort cells by surface-protein markers because the necessary US-made equipment cannot be imported. They cannot perform many experiments that we consider routine, but rely on collaborators who have the necessary equipment. Even when equipment has been procured, Iranian researchers face logistics that prevent them from getting on with their experiments.
It seems to me that these restrictions are not in anyone's interest. Scientists themselves exacerbate the situation, fuelled by misinformation that they put themselves at personal risk by travelling to Iran. Of course, people who would not be able to refrain from political discussion or dress as expected would be wise not to go. But the vast majority of scientists would find themselves surrounded, as I was, by courteous, hospitable, well-informed men and women who relish interaction with other scientists. Unfounded apprehensions about the risks of travelling to Iran effectively add a scientific embargo to the politcal one.
I think it's commendable that Jaenisch has the guts to take positions that powerful people in his country might disagree with, rather than bury his head in the sand alongside many of his colleagues.
I love it. There is a bit of conjunctivitis (aka pink eye) making it's way through the lab in which the bay is a part of. It may be that it is from microscope eyepieces, so I wanted to see what I could find on other experiences with this, but I couldn't really.
I did find one person on a forum who said they have encountered pink eye contaminated eyepieces, not once but twice.
I also found out that breast milk cures pink eye. I'm skeptical.
I think one of the reasons I think it's funny is because it's such a childhood thing and one of the funny scenes from "Knocked Up" indicates it can be caused from farting on someone's pillow.
I'm sure I'll think it's funny until it infects someone in the bay.
Wednesday, November 14, 2007
In the fine tradition of marrow rum and in keeping with the season, a pumpkin was chosen as the fermentation vessel of choice. On Hallowe'en night, a small hole was bored into the top of the pumpkin and it was inoculated with a package of baker's yeast, some sugar and a healthy dose of spookiness. The pumpkin was then filled with water and left to ferment at room temperature.
One week later, on the notably less spooky 7th of November, the pumpkin brew was deemed, by arbitrary measure and impatience, ready for tasting.
Tapping the keg: AC makes the first cut
The usually clean Rob, splattered with a mix of pumpkin and baby vomit
Once the pumpkin was cracked open, the yeasty aroma of our brew and the foul stench of evil filled the air. What does evil smell like? As one bystander put it: "It smells like cheese beer." Spectators were simultaneously turned away in disgust and drawn to the spectacle.
Pumpkin ale, or portal to hell?
The resulting liquid
Filtering out the filth
The liquid inside the pumpkin was deemed too 'chunky' to swig fresh from the fruit, so it was put through a coffee filter before tasting. While AC and Rob argued over safety (and who would drink first), I took a sip of the filtered brew. It passed the first test: I didn't keel over. Despite the stink, it was drinkable. It was what I imagine watered down dough put through a blender would taste like. Slight pumpkin overtones. It didn't taste good enough to drink enough to get a buzz given the low alcohol content. This was more bread than beer.
Rob and an uncowardly Coward contemplate the pumpkin ale
Anonymous Coward reacts as Rob takes a healthy swig, while a bystander looks on in disgust
Rob was unsatisfied with the weakness of the drink, so he braved drinking the unfiltered swill. My recommendation for Pumpkin Project 2.0: skip the water, let the natural pumpkin liquids provide the base and let it ferment longer. Of course we still wanted to see what the inside of the pumpkin looked like, so we cracked it right open and let its full bouquet permeate the Bay.
The pumpkin innards and remaining brew
A handful of the resulting goo
Most of the pumpkin innards had pulled away from the shell of the fruit and partially liquefied. Have we stumbled upon a quick and easy way to clean a pumpkin for carving? the inner surface of the pumpkin had softened and was covered with yeasty growth. All drinkers survived the experience, but adjustments need to be made for a successful recipe.
**The Bayblab encourages attempting this experiment at home and posting the results here but takes no responsibility for any injury or illness - physical or mental - that may occur.
"Imagine, if you will, a load of horseshit. And we’re not talking just your average load of horseshit; no, we’re talking colossal load of horsehit. An epic load of horseshit. The kind of load of horseshit that has accreted over decades and has developed its own sort of ecosystem, from the flyblown chunks at the perimeter, down into the heated and decomposing center, generating explosive levels of methane as bacteria feast merrily on vintage, liquified crap. This is a Herculean load of horseshit, friends, the likes of which has not been seen since the days of Augeas."
Tuesday, November 13, 2007
This man has some kind of mutation which rendered his immune system unable to control the warts growing as a result of an HPV infection. Another reason to get the HPV vaccine! The doctors have proposed to use high doses of vitamin A to stop the warts, and remove the rest by surgery.
This 7ft tall 12 year old, had all his teeth by 4 months and was already has big as a 12 year old by the time he got to kindergarden. This is not a case of gigantism, which occurs because of pituitary tumours excreting too much growth hormone, rather this seems to be a new kind of mutation. Joining the 50 or so different genetic syndromes which cause excessive growth such as:
"Extra sex chromosomes (beyond the normal two) with therefore extra copies of the SHOX gene (beyond the normal two) usually results in enhancement of height growth. The most common of these karyotypes are 47,XXY (Klinefelter syndrome), 47,XYY, and 47,XXX. The added height increment is usually modest.
A very rare but more extreme version of "eunuochoid" tallness occurs when a mutation of the estrogen receptor reduces the response of the bones to estradiol. Estradiol is a byproduct of testosterone in both males and females, and is the most potent accelerator of bone maturation and closure known. If a person fails to respond to estrogen, growth can continue until late-20s or longer, and the affected person can reach 8 feet or more in height. Estrogen resistance is the only other endocrine condition that can rival growth hormone excess in producing gigantism. In contrast, the tallness associated with the more common androgen insensitivity syndrome averages only a few inches, as estradiol is not produced directly but rather through conversion from androgens by aromatase.
Marfan syndrome is an uncommon genetic disease due to an inherited defect of connective tissue. In addition to moderate tallness, persons with this condition usually have a slender body build with unusually long fingers (arachnodactyly). Many can also develop a dislocaton of the lens of the eye or, more seriously, a progressive deterioration of the walls of the aorta which can result in sudden death in adulthood. It is usually inherited as an autosomal dominant trait.
Sotos syndrome resembles acromegaly in its mild distortion of facial growth. In addition to tallness, the chief characteristics are large head size, slow development, and autosomal-dominant inheritance."
Monday, November 12, 2007
Next up will be Science Friction: Where the Known Meets the Unknown, by Skeptic editor Michael Shermer. This one also promises to be a doozy, kicking it off with the following gem of an opener:
"It is in the vacuum of such will-nilly whencing and withering that we humans are so prone to grasp for transcendent interconnectedness. As pattern-seeking primates we scan the random points of light in the night sky of our lives and connect the dots to form constellations of meaning. Sometimes the patterns are real, sometimes, not. Who can tell?"
So many ideas, so little time. I'll go so far as to recommend both before even reading them. Or, check back at the bayblab for periodic updates and (what I think) are the coolest memes therein.
One last bonus - since I find myself reviewing the arts - I have to recommend Feist for great music to write or read to. Funky enough to stave off depression and keep you alert, soft enough not to be distracting. I've been checking out "Let it Die" and "The Reminder", and there's not a non-kick-ass track to be found on either. Big up to Amherst, Nova Scotia. Maybe she'll sit in with the spineless Kevin-Z one of these days. Hey, I could see it...
Saturday, November 10, 2007
Thursday, November 08, 2007
"I don't think we're for anything, we're just products of evolution. You can say 'Gee, your life must be pretty bleak if you don't think there's a purpose' but I'm anticipating a good lunch."
- from a BBC interview with Richard Dawkins
Posted by Bayman at 5:21 PM
Wednesday, November 07, 2007
The method is simple: cut the stalk off a fresh marrow (a marrow is a squash, similar to a large zucchini) and scoop out the seeds leaving as much flesh behind as possible. Pack the resulting opening with sugar (most recipes use Demerara - or raw cane - sugar). Replace the top, puncture the bottom and suspend over a bowl or some other receptacle. Most recipes I've seen depend on natural yeasts entering the marrow and fermenting the fruit, but I suspect adding yeast may be required. Some call for the addition of chopped ginger or raisins to add flavour. Fermentation time seems to range from a week up to several months, depending on the recipe!
A sample recipe:
Whether the ensuing brew is a tasty potable, or instead something worthy of its British cooking heritage is unclear but it seems like a good candidate for the next bayblab project. Perhaps other fruit would make good candidates for recipe adaptations.
Pair ladies' nylon stockings
Slice the top off the marrow and scoop out the seeds, but leave as much of the flesh as possible, and don't puncture the skin. The seeds are attached to the inside of the marrow with little strings: one way to detach obstinate seeds is to fill the marrow with water and shake well. Fit a stocking onto the marrow, and pack the marrow tightly with Demerara sugar. Stand upright in a large vase or similar and leave for a day. Osmosis will draw fluid from the marrow into the sugar, dissolving some and leaving a gap below the end of the marrow. Add a teaspoon of ginger (finely chopped fresh ginger root if available, otherwise dried ginger) and pack more sugar on top. Replace the marrow upright in the pot, and cover to ensure nothing can fall into the pot or the end of the marrow. Pulling the second stocking down over the top of the marrow and pot is a good way to do this. Leave in a cool dark place for at least two weeks, and if possible, four. Inspect at intervals.
The idea is that the sugar ferments, generating an alcoholic liquor which gradually eats its way through the bottom of the marrow and collects in the pot. It takes three or four weeks to reach full strength, during which time the marrow becomes very floppy. The stocking filters the liquor and also provides much-needed surgical support. I have tried this recipe three times, twice with marrows and once with a Turk's Head Turban gourd, also from Elder Stubbs. One week's fermentation gives a liquor which has a pleasant taste but is not very strong - after three weeks, it has a noticeable punch. The ginger adds pungency to counteract the blandness of the marrow, giving the rum a pleasant warmth.
Tuesday, November 06, 2007
When thinking about it a little more it didn't surprise me that reproductive organs would contain the ligand, since they are known to express the receptors:
"With respect to reproductive organs, cannabinoid receptors and/or endocannabinoids have been detected in the pituitary gland, testis, Leydig cells, epididymis, prostate, sperm cells, ovary, uterus, oviduct, preimplantation embryo, placenta, embryo, fetus and neonates"
It is thought that in sperm, the anandamide prevents the acrosome reaction, therefore preventing the sperm from activating before it reaches the female tract and also preventing polyspermy during fertilization. The question is, how much anadamide (AEA) is there in reproductive biological fluids?
"We detected AEA, OEA, and PEA in human seminal plasma, mid-cycle oviductal fluid, and follicular fluid analyzed by HPLC/MS"
And the sequela, how much of that stuff do you need to feel a buzz?
"Oral administration of AEA and 2-AG to mice can produce psychotropic effects, suggesting that these endocannabinoids reach the brain ( Di Marzo et al., 1998)."
A quick survey of the literature suggest that 5.8mg/kg is the ED50 of AEA to impair working memory performance (i.e. get a mouse high). So a rough approximation of the dose of milk for an infant to feel the effects is 20,209 L of milk, or for a woman to get high of seminal fluid she would need to chug a good 62,142 L. Notice that calculating the converse would be morally reprehensible.
I suppose the fact that it's so dilute is a good thing for the baby since: "Newborn humans, that had been exposed to marijuana prenatally, exhibit increased tremors, exaggerated responses to stimulation, and spend less time sleeping quietly ( Fried and Smith, 2001).".... but it fails to explain why babies have such munchies...
Sunday, November 04, 2007
"If everyone is thinking alike, someone isn't thinking",
is apparently a classic Patton line.
While I'm not sure to what extent independent thinking is valued in the army, it certainly is useful in science. Here are a few more Patton gems that might be useful advice for the scientist:
- "It is only by doing things others have not that one can advance."
- "Never tell people how to do things. Tell them what to do and they will surprise you with their ingenuity."
- "Pressure makes diamonds."
- "Success is how high you bounce when you hit bottom."
- "Few men are killed by the bayonet, many are scared by it. Bayonets should be fixed when the fire fight starts."
Pretty smart for an army grunt, even if he was
Clearly NK cells are well-trained Christian soldiers.
"Onward Christian soldiers marching as to war
With the cross of Jesus going on before.
Christ, the royal master leads against the foe
Forward into battle, see His banners go"
Sounds like inspiration for a new tune from our friend Kevin-Z. I'm hearing a Led-Zepplinesque epic about God's NK and CTL armies battling Satan's tumor cells and their pro-inflammatory macrophage minions. What say you KZ? Do you have the backbone for holy immunology?
Friday, November 02, 2007
cancer biologyWenchypoo presents Meet “Epi”—the Ghost in Your Genes posted at Wisdom From Wenchypoo's Mental Wastebasket, saying, "How everything we experience, eat, drink, and take affects our family tree for three generations.". Epigenetics holds a special place in my heart since I've been secretly trying to figure out the histone code while pretending to work on reproduction. I'm especially interested in transgenerational effects such as those explained by Wenchypoo in this post. Indeed you may not be only getting bad genes from your parents, but also transcriptional memory that was imprinted during their lifetime.
CAD presents VWXYNot?: On the Origin of Tumours by Means of Natural Selection posted at VWXYNot?, saying, "The gradual evolution from normal to malignant cells illustrates a very simple natural law. If an individual produces a number of offspring via an imperfect copying mechanism, the result will be a mixed population of individuals with slightly different characteristics. If one of the variants is able to produce offspring faster than its peers, then those offspring will be over-represented in subsequent generations. ". Is transformation then a kind of speciation event?
prevention & managementAlvaro Fernandez presents 10 Highlights from the 2007 Aspen Health Forum posted at SharpBrains, saying, "Check out this overview of the Health and Science trends discussed in this recent policy event.". While cancer was on the agenda, it's interesting to see how it fits in the global health perspective. Many topics are touched, including how successful patient advocacy groups have been in raising money for cancer research, and the importance of lifestyle and prevention for a healthy population.
Colon update: the red bit is cancer… posted at Dodgeblogium. Andrew shares with us the impact of his diagnosis along with a picture of his colon! It just shows how simple diagnostic methods, such as colonoscopies have drastically changed cancer prevention and diagnosis.
psychologyKamel presents Depression in cancer survivors and their partners posted at Bayblab. Kamel highlights the emotional aspects of coping with a cancer diagnosis and death. Sometimes depression doesn't come from the contemplation of your mortality but rather the loneliness.
Tiffany Washko presents Crazy Sexy Cancer posted at Natural Family Living Blog. This book comes from a recommendation from Oprah, so you know it must be good. Mostly personal tips for people with the disease.
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