How to solve problems in your PhD

I hate self help books with a passion. I find they are written to create a dependence on "self help", which has obvious financial benefits for their authors. If you've already recognized you need help, and you are willing to tackle it alone, than why bother with a book. The insights in these books are usually shallow and meaningless when you actually think about it. This one is unique in that it is directed at PhD candidates. Obviously they are preying on the weak now. It is based on the 6 thinking hat method:

• "The White Hat: The white hat is concerned with facts and figures. With the white hat you focus on the available information. Look at the information you have and see what you can learn from it. While wearing this hat, try to obtain a good picture of the knowledge available to you.

• The Red Hat: Red-hat thinking is all about emotion. While wearing the red hat, you look at problems using intuition, gut reaction, and emotion (For example: ‘I hate that idea’ or ‘I would love to try this’).

• The Black Hat: Black-hat thinking is cautious, faultfinding, and defensive. This type of thinking is important because it highlights the weak points in a plan so that you can eliminate them, modify them, or prepare a Plan B.

• Yellow Hat: The yellow hat is like sunshine: it helps you think positively. Yellow-hat thinking allows you to see all the benefits of a decision and the value in it. Furthermore, yellow-hat thinking can help you keep going when the going gets tough.

• Green Hat: The green hat represents creativity. This is the type of thinking at work during a successful brainstorming session. Green-hat thinking helps you develop creative solutions to a problem. Green-hat thinking is freewheeling; anything goes, no matter how outlandish, when you’re wearing the green hat.

• Blue Hat: The blue hat represents process control. Think of an airtraffic controller or a traffic cop. In a meeting, the blue hat is worn by the chairperson. The wearer of the blue hat must direct the thinking when ideas start to run dry. That’s when it’s time to switch to green-hat thinking. Or perhaps the chairperson will need to remind the others that it's time to put on the black hats and look for weaknesses in the plan."

Splicing out integrated HIV

Those of us doing mouse work are probably already familiar with the CRE-lox system, which uses a recombinase called CRE to excise fragments of DNA in the genome that are flanked by loxP sites (floxed in the lingo). This technique is mostly used for conditional transgenic to gain tissue-specific Ko for example, which is the bane of my existence.

Well some clever folks in Germany decided to evolve the CRE enzyme in vitro to recognise the viral LTR flanking sites of HIV instead of loxP. The results are quite encouraging:

"HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses."

Panspermia

No, I'm not talking about bukkake videos, but rather the idea that life on Earth originated from some extra-terrestrial seed. A typical view is that this seed was some sort of spore or bacteria that arrived on earth via meteorite but more extreme views hold that directed panspermia occurred, with advanced civilizations elsewhere in the universe intentionally seeding life.

The notion of panspermia doesn't add to the creation/evolution debate in terms of origin of life, but only tries to explain the origins of life ON EARTH and requires that life arose elswhere in the universe, survived an interplanetary journey, found Earth, and our planet was hospitable. Despite this series of potentially improbable events, panspermia does have some high profile proponents, including Craig Ventner and Francis Crick.

Francis Crick, in fact, supports the directed panspermia view, though he thinks rather than specifically selecting Earth to seed, a more likely (and cost effective) scenario is that "seeds" were launched in all directions in hopes of eventually finding a compatible planet. Colonization of the universe is an interesting exercise in narcissitic altruism (at least in the sense of planetary catastrophes and ensuring the future of the human race). Given our current lifespans and foreseeable technologies, nobody who were to begin such a project would ever see any fruits from their labours and would simply have to be satisfied that thier DNA was out there somewhere and the species might live on. For an interesting essay on why space colonization can't happen, check out this blog.

Hmmmm you smell like whale vomit

Ambergris is sperm whale vomit used in perfumes. It is found washed up on beaches and can be quite a windfall as it can be worth more than 10$/gram. Here is a good story about a woman with a hunk of the smelly vomit. There is also a story of a couple from Australia that found a large hunk worth $500 000 but they are having legal trouble selling it. I also found a great collection of anecdotes from a museum curator about ambergris. It has been worth a lot of money since "time immemorial" and perhaps justifiably so. It so happens that it causes increased sexual behavior in male rats. Does it work it humans? Just thinking about the scent hunk of vomit, that originated in the small intestine of a sperm whale, and subsequently matured floating in the sea for perhaps years doesn't make me personally excited. Perhaps I'm emetophobic.

Career Choice: Science or Acting?

Have you been discouraged by the worst jobs in science? On Monday, I spent a day as an extra on a TV movie filming in Ottawa (keep your eyes open for "Custody of the Heart") and it struck me that there were a number of similarities to grad school, mostly the long hours and lack of respect but here's a head-to-head comparison:

1) Hours - We all know that working in the lab can often mean strange hours, weekend work and late nights. This was no different. After coming in to take care of some work before my 10:30am call time, I spent over 15 hours on set, never being allowed to stray too far in case we were needed.

Advantage: Grad school. We may work long hours, but we have more say in the matter, and can spend down time as we wish.

2) Food - A large part of the grad student lifestyle scavenging for free food, whether it's leftovers from a meeting or some kind soul leaving cookies in the lunch room. Free food was moderately abundant on set, but the good stuff wasn't for us. A salad at noon, a box lunch at 4pm, gyros when it was clear we going to be working late and chicken wings towards the end of the shoot. Of course, with the exception of the box lunch, most of this food was only available once cast and crew had been fed, but we did get the leftovers of their hot lunch to supplement the sandwich and apple we were given.

Advantage: Film Extra. While we get free food fairly often at the lab, it's unpredictable and the variety and reliability was better on set.

3) Hierarchy - There was a definite order to things at the shoot. Cast and crew were the big shots, obviously - the PIs and techs of the set. Better food, better pay, more perks. Union extras are next in line. Like postdocs, they get to sit at the big table, eat the hot lunch and hobnob with the big shots. Better pay, but no authority, just trying to impart what little wisdom they've gained to the little people. Which brings us to the grad students of the set - non-union extras. In the background, doing what you're told, when you're told, looking to everyone else for guidance and just hoping that your work makes the final cut for the manuscript scene

Advantage: None. Either way you're scraping the bottom of the barrel.

4) Monotony - Repetition, repetition, repetition. Whether it's an experiment or a film shot, both jobs require double, triple even quadruple takes to get a usable end result and timing and precision to get you there. The film set is a bit more forgiving but grad school is far more intellectually stimulating.

Advantage: Grad School. Sure there are a lot of 'do-overs', but figuring out what went wrong is half the fun. And there's no feeling in the world better than reproduceable results.

5) Pay - For an extra not in the union: $10/hour. For a graduate student without outside funding: $17,500/year. As an extra, you get paid for every minute you're on set, but the con is that the number of minutes can vary. On the flipside is that no matter how many hours you put in as a grad student - 8 or 18 - at the end of the day you're still only getting $50.

Advantage: Film Extra. A studentship is more steady, and there are opportunities for bonus funding, but the $150 I made for one day's work is almost a quarter of what you would make in 2 weeks in the lab. Of course we're not in it for the money.

6) Wardrobe - Bring your own clothes, but no whites, blacks, reds or anything with a logo. At least three sets of casual and three of more formal wear. And be ready to hear why your jeans and "University of Ottawa" t-shirt don't look 'student' enough. (I didn't know about the 3 sets of clothing rule, but luckily the clothes I brought met approval). Everything has to be nicely ironed and look presentable. And be ready to have to wear a sweater over a button-up shirt on the hottest day of June since the scene is really taking place in the fall. In grad school, you're out of place if your (free) shirt DOESN'T have the logo of a lab supplier, formalwear is never required but safety standards must be met.

Advantage: Grad School. It's all unstylish lab coats, gloves and closed-toed shoes, but who really enforces those rules anyway?

7) Fun factor - Where else can I mime a conversation while sharing a fake cup of coffee with a real professional model? (and yes, it was captured on film so I can prove it). Plenty of waiting meant plenty of goofing with the other extras, and the crew was pretty cool too. On the other hand, weekend parties, volleyball teams and miscellaneous other fun with the lab is nothing to complain about.

Advantage: Grad School. OK, this was a close one but the amount of sitting around waiting for cameras and lights to be set up is what killed it for the acting job. That and a real conversation beats a pretend one any day.

Overall: Grad school. My day on set was a pretty good experience, I met a lot of cool people, and it was interesting to see what goes into a film production first hand. I'd definitely do it again, but until I'm cast as a real star I'm going to stay the course. Plus I've sunk too much time and money into this to run off for Hollywood now.

Find a caption for these pictures...

Stories can be found here and here....

The dangers of bikini waxing

The evolution of hairlessness is one of the most popular bayblab post judging by the amount of traffic we get. Well rejoice:

"A 20-year-old Australian woman with poorly controlled type 1 diabetes presented with life-threatening Streptococcus pyogenes and Herpes simplex infection of her external genitalia following a routine perineal "Brazilian" bikini wax. Extensive pubic hair removal is now common among young adults in Australia and elsewhere. However, the infectious risks of these practices, particularly among immunosuppressed individuals, are often underappreciated."

The paper covers in great detail how bad the infection got, the pictures are too gross even for the bayblab:

"During the subsequent 4 days, worsening vulval swelling, redness, and pain were noted, as well as a copious vaginal discharge. On the day of presentation, the patient reported excruciating perivulval pain, severe dysuria, fever, and a diffuse erythematous rash."

The worst is that after going through all that, the woman tried to shave again and got a second infection. I would mostly agree PZ myers over at pharyngula:

"I've never quite gotten the appeal of this practice. Is it to appeal to men with pedophilic tendencies? Or is it more of a desire to look like you've got a mollusc in your crotch? Everybody has their own little kink, so if hairless pubes appeal to two people, I'm not going to worry about it…but it seems to me it ought to be OK for a woman to want to look like a female mammal, and that individuals ought not to feel obligated to follow a very weird and highly artificial standard of beauty to the point where they suffer severe illnesses."

Plus, I hear they have a special at the laser hair removal for the ballz-&-all...

Worst Science Jobs

Just to make grad students feels better, Popular Science magazine has compiled a top ten of BAD science jobs. Science Friday interviews one of the authors of the article and get some interesting phone ins about more really bad science jobs. It's a tough job, but someone has to wash semen.

I'll take a side order of science with that policy please

In an opinion piece of the Ottawa Citizen that came out yesterday, there is a rant about the lack of scientific method in the decision making process of politicians. The piece was written by our own Dr. Findlay, two-fingered typist extraordinaire, as he proposes a four step plan:

"What is the solution? First, those responsible for administrative decision-making need to be far better schooled in the scientific method. Think of it as analysis, a means by which we can unite our non-scientific egos and scientific ids. Many public institutions invest considerable sums in language training for senior decision-makers: Is it too much to ask that some resources be allocated to scientific method training?

Second, we need to reinvest in government science capacity. The past several decades have witnessed a dramatic loss of science capacity at all levels of government. This erosion cannot be mitigated by planting more scientific groundcover on the shoreline of academia. Government science must address itself largely to the quest for solutions to current or anticipated problems, or the documentation of such problems in the first instance, whereas academia is -- as it should be -- the wellspring of curiosity-driven research.

Third, we need to vaccinate science against political pathogens. Jacob Bronowski observed that no science is totally immune from political infection, and this holds doubly true for government science: If it cannot be immunized, it must quarantined through appropriate governance structures.

Fourth, we need to enhance the dialogue between the scientific and policy processes. The loss of science capacity means that much of the science required for sound public policy and administrative decision-making is external."

Religion in science

After doing a quick search for jesus on pubmed I came across a lot more abstract than I anticipated. To my surprise I even found some christian medical journals such as JCN. My favorite abstract about jesus has to be this one:

"PURPOSE: We study the controversies manifested in religious writings, art, sculpture and music as well as the theological disputes surrounding the circumcision of Jesus Christ. MATERIALS AND METHODS: Data are derived from relevant historical and theological articles. RESULTS: Jesus Christ was circumcised as a Jew on the 8th day after his birth. Until 1960 the Catholic church celebrated the day as Circumcision Day. In medieval times the holy foreskin was worshipped in many European churches. CONCLUSIONS: Christianity never condoned the ritual of circumcision and established the sacrament of baptism in its place."

Also interresting is the number of abstract about mormons, mostly because of their special medical needs. I was surprised to learn for example, that mormons have lower incidences of heart and lung diseases as well as MS. Perhaps as a side effect of polygamy .

But more interrestingly I discovered that when swarms of mormon crickets start to run out of food, there is a salt and protein deficiency treshold that sets off cannibalistic behavior. The perfect plot for 28 years later...

Quack of the week: Simon Brodie

I was reading an old copy of new scientist while having coffee the other day and I read about Allerca, a company which had promised hypoallergenic cats back in 2004 for about $3500 a piece, not including a 250 non refundable deposit. I was aware of the offering, since it was widely reported in the media, even winning Time magazine's invention of the year. In fact even nature reported on it. But what I didn't know was that it is a complete scam. While the allergic protein has been identified, Fel d1, no KO cats have been engineered. The company claims to have a naturally occurring mutant, however it is unclear what the mutation is, and whether it is sufficient to dampen the allergy. Furthermore, no trials or peer reviewed science has been conducted. If that wasn't worrying enough the individual behind the company, Simon Brodie, has had a shady past, sometimes using pseudonyms to conduct business, often fake biotech companies. One of his other project was to make a GFP-deer, so that the wouldn't get hit by cars at night. wow. Not surprisingly a hypoallergenic cat as yet to be seen after over 3 years. I feel bad for all the people who put a deposit. Actually I don't, anyone stupid enough to pay $4000 for a cat, when animal shelters are full, is asking for it...

Introducing: bayblab definitions

schmer·oid (smîr'oid', směr'-) n. : Aggregate of cells, that vaguely ressembles a sphere, resulting from mistreating your tissue culture. They are thought to have mystical powers to differentiate into anything, including brain, kidney, ipod or a rock, provided you pray to the right gods. But mostly, they are just balls of cells. If you count them, sometimes you can be rewarded with a cell paper or a microscope-induced headache.

functional definition:
-ability for self-denial
-ability to solve differential equations

see also: transit-pimping cells, commited prudo-genitals and terminally disoriented cells.

IA updates

new IA links. cool as usual.

She's dirtier than you think

Consider this questionnaire, do you agree or disagree with the following statements:

…In category 1, “sex as personally and physically pleasurable,” statements included:

• I should get drunk to enhance my sexual experience.
• If I want to be close to someone, I should have sex.
• I should have sex with my partner so he/she will not leave me.
• I should have sex with as many people as possible.

In category 2, “sex as beneficial in creating positive feelings about oneself,” statements included:

• Sex makes my partner love me.
• I feel attractive after sex.
• I trust my partner more after sex.

In category 3, “sex as personally costly in terms of having negative emotional, psychological or physical consequences,” statements included:

• Sex makes me feel guilty for violating my morals.
• God will punish me for having sex.
• Having a one-night stand makes me feel cheap.
• I will get an STD by having sex.

In category 4, “sex as a violation of social injunctions," statements included:

• I should engage in premarital sex.
• I should be with my partner a long time before I have sex.
• I should not have sex because I’m too attached to someone I’m having sex with.

Well if you are female you are more likely to agree with the emotional aspects and if you are male with the physical aspects. Nothing new here. however if you are in a stable relationship, the differences tend to disappear. This is supposedly a counter-intuitive finding. But is it really? If you take an evolutionary perspective, males want to reproduce with as many females as they can while investing the smaller amount of resources in the offspring as possible, whereas females while more choosy, once they decide on a suitable mate will also want to want to reproduce as much as possible. It's in the initial choosing where the differences occur, after that it's all gravy. It's definitely in the female's best interest to reproduce frequently once she has secured a quality mate, so you'd expect sex to be on the mind of males more at the beginning of encounters while in females to be more during the long term.

For the male it is important to figure out which females are receptive, and thus worth investing resources in courtship. Unfortunately, in humans we lack the fire-red bottom indicator of other apes, and thus it is difficult to detect intentions especially from afar (or in smoke-filled dark nightclubs). This may explain why, when looking at pictures of naked woman, man spend more time looking at the faces than females looking at pictures of naked man. Man need to empathize and recognize facial traits that indicate willingness while females need to look at the quality of the genes by inferring from the whole body. Willingness I assume, is much less of a factor.

This balance of quantity/quality is what makes sexual reproduction so great. Mixing the genes is just an added bonus. It is like the offer and demand paradigm, which makes capitalism so effective at maximizing profits. This explains why for example in a mite species which as reproduced asexually for millions of years, and quite successfully, sexual reproduction re-evolves independently. I'm inclined to think it is a universal imperative for any life form complex enough. On whatever planet we find life, we'll find evolution and we'll find sex, if the lifeforms are advanced enough. Perhaps there is even causation here.

Zeedonks, Beefalos, & Wolphins

The title of this post is the names of some lesser known intra-specific hybrid animals (check the link for more), namely a cross between a Zebra and donkey (aka zonkey), a cattle/bison cross, and a rare cross of a False Killer Whale and a Bottlenose Dolphin. Of course, the most common and well known hybrid is the mule, a cross between a horse and a donkey. Most intra-specific hybrid animals are sterile as a result that they can not produce viable gametes through meiosis because of a lack of homologous chromosomes. Since a hybrid has one set from one animal and one set from another they don't pair up properly during metaphase, they most often also have a different number of chromosomes to begin with. Some animal hybrids are fertile however such as the female tigon.
From Napoleon Dynamite:

Deb: What are you drawing?

Napoleon: A liger.

Deb: What's a liger?

Napoleon: It's pretty much my favorite animal. It's like a lion and a tiger mixed. Bred for its skills in magic.

Napoleon dynamite was a bit of a dweeb (magic is an innate or learned ability and not a skill) but a liger is pretty awesome. Check out this video that will make you respect the liger.

I guess I was thinking about this since someone mentioned that they had heard of a cat/rabbit cross. They are mythical and probably don't exist although there are lots of breeds of rabbits that have cat like appearance. They don't exist but that's not from lack of trying.

Virtual visit of the creationist museum

Check out the pictures here, I love the thought of tofu-eating T-rex, and human-mounted triceratops. Creationist have an awesome sense of humour.

Venter's Microbesoft and Synthetic Biology

Word on the street, from the highly speculative New Scientist, is that SyntheticGenomics will soon unveil the first synthetic bacterium. (speculation is the very last sentence of the artcle). SyntheticGenomics is a company started by Dr. Craig Venter of the private human genome project fame and has the goal of creating a synthetic cell based on a minimal genome as an industrial bioproduction tool (the science behind this is on their website). I don't really understand the huge advantage over just using the old fashioned biotech workhorse, E.coli, however it has sparked some protest, notably by a technology watchdog, ETC group, based here in Ottawa, Canada. Their concerns don't include many specifics except for the lack of public consultation and the implications of a broad patent held by SyntheticGenomics. There are comparisons made that SyntheticGenomics could become the Microsoft of synthetic biology hence the term Microbesoft. The Science Magazine article about the controversy includes a statement that the patent could likely be easily sidestepped. Nevertheless the ETC group must have some good lawyers as you can see by their recent success against Monsanto's broad soybean patent.

Ride at your own risk

I've never been a big fan of rides, especially after some bad experiences in the gravitron, but I'd like to try the roller coasters. After all they should be pretty safe right? Well maybe not, because they do not have regulations like motor vehicles, some bad stuff can happen like this little girl who had a partial hepatic amputation (i.e. her liver ripped apart), by a roller coaster crash.

How often do accidents like that occur? According to this study of 1994-2004 , more often than you think: "Forty people, ranging in age from 7 to 77 years, were killed in 39 separate incidents. Twenty nine (73%) deaths occurred among roller coaster patrons. Eleven fatalities resulted from external causes related to injuries from falls or collisions. Eighteen people died from medical conditions that might have been caused or exacerbated by riding a roller coaster; 15 were the result of intracranial hemorrhages or cardiac problems. Eleven (28%) deaths involved employees; all were caused by injuries."

The TC wars of 2007

Every summer it's the same thing, tissue culture becomes hectic, with increases in contamination, messy hoods, overflowing garbage, poorly trained summer students and fights to even get into a hood. I was thinking of sharing a few TC tips with you, to help you survive the war, being a veteran culturer myself. You could even say I was born in the hood.

First you'll need your own media bottles. Commercial stuff is good, because you don't have to worry about contamination. I always add antibiotics, this will provide you with safety in case an enemy spits into your bottle while you have you back turned. I write my name on it, and a caption saying "touch this and die". I'm not even joking. Otherwise, if you discontinue TC for more than a couple of weeks, you'll find that your bottles have vanished and someone taken your spot in the fridge.

Then you'll need a hood. I recommend getting used to work with your left hand, as the left spot in the TC hoods are usually less in demand. Also if you need additional space in the hood, it helps if you're working with viruses or mycoplasma, or cancer-causing agents ... nobody will want to be your TC neighbour.

Then you need to secure an incubator. This can be tricky. I usually plan a massive experiment that take a full shelf with no room to spare. Now move all the stuff from that shelf into other spots. This is where you need to assert dominance. Once you have taken possession of the shelf, remove anything that is put on there, and take control of it. And soon it becomes yours. If you need the whole incubator you can spread rumours of mycoplasma or fungus from that hood.

Use an ipod, it doesn't even need to be turned on. Like that no-one will creep up to you and start talking about their summer vacation or worse, their wedding/baby showers. The ethanol spray is also very effective in discouraging intruders.

Secure the coulter counter area. That area has strategic military importance, keep control of it, and make sure you sit there with a lot of samples. It's like Poland or Kamtchatka.

If you do get contamination, keep aliquots somewhere in safety, where WMD inspectors can't find them.

Finally if you can't beat them, join them. Be part of the TC gestapo and enforce order in TC. Bossing around summer students can be quite entertaining. Look out for offenses such as not cleaning and disinfecting after use, not respecting your authority and free speech.

Also watch out for bats in the hood ventilator...

Coprophagia & the human microbiome

I found this interesting article on the evolution of symbiotic bacteria in the human gut in PLoS. A good summary article accompanies it. Some interesting implications of the work are that considerations for the evolution of 'our' bacterial genomes should be considered when looking at human evolution. In fact a hot topic in the blogosphere is the possibility of a human microbiome project. (check out this link for sure.) Without these bacterial communities we would not be able to acquire much of the energy from cellulose that we get when we eat plant material. I would assume then, and it is mentioned in the summary, that perhaps the makeup of the bacteria in the human gut would be influenced by the hosts diet. Would a vegatarian then have more bacteria able to break down cellulose for example thus making the host a more efficient user of plant energy? Since we humans lack the complex digestive system of the ruminant, as we are evolved to be omnivorous, perhaps vegetarians should consider eating their own feces to more efficiently extract energy from plant matter.
Coprophagia, or eating your own poop, is a term first brought to my attention by fellow bayblabite, Alfred Russel Wallace. My pet bunny practices this behavior, however, I have, thankfully, rarely noticed it doing this. One of the best sites I have seen on the subject of bunny poop eating is a must see and informative. For example, the site points out, if you overfeed your bunny you might inhibit coprophagia and malnurish your pet. The disgustingly cute animated gifs add to the atmosphere of this site.

Quack of the week: A wolfberry in sheep's clothing

The goji or wolfberry (Lycium barbarum) are rich in vitamin and nutritional content and have been the subject of numerous medical claims. One of the most vocal supporters of this 'miracle berry' is Earl Mindell, a nutritionist and author of several nutrition books. Mindell is also involved with a company, FreeLife International, pushing 'Himalayan Goji Juice' as a 'powerful anti-aging food.' Bottles of the juice can run up to $50 for 1 litre, but when tested in the lab by CBC Marketplace, contained few of the nutrients found in the berry itself (in fact the label of the bottle avoids making vitamin claims). Instead the product relies on 4 'master molecules' - polysaccharides in the juice - having a unique 'spectral signature' not found in other goji products.

One of the several health claims made my "Dr." Mindell (Mindell holds a Ph.D from Pacific Western, an uaccredited unversity) is the cancer-fighting properties of goji juice. He claims that a study out of Memorial Sloan-Kettering Cancer Centre shows that goji berry extract inhibits growth of hormone-responsive breast cancer cells - a claim that Sloan-Kettering has distanced itself from. The berry extract has show this property in vitro, but safety and efficacy hasn't been tested in humans. Even the author of the study being used to promote the product says his research does not show that goji juice has anti-cancer properties. If goji extract is able to inhibit cancer growth, it certainly hasn't been demonstrated beyond a tissue culture dish or using Mindell's vitamin-depleted version.

On top of the dubious health claims made about Himalayan Goji Juice, the whole company reeks of a pyramid scheme. New customers must be referred by a 'Freelife Marketing Executive' for the privilege of shelling out $500 a month on goji. You can become a 'marketing executive' for just a small fee ($40 US) and earn money for recruiting new customers to the goji craze. In addition, you get a small percentage for each successive level of recruitment in their multi-level marketing system.

So lets review:
1) stands to make a large amount of money from sick/desperate people
2) exaggerated medical claims
3) claims based on single, non-comprehensive, in vitro studies
4) reliance on testimonials, rather than scientific evidence to back claims
5) pyramid-scheme like marketing system

How does the saying go? If it walks like a duck, and talks like a duck.... quack, quack, quack.

Watch the CBC Marketplace report on Mindell and Himalayan Goji Juice here.

Teaching tricks to spiders

During a recent discussion of spiders during the recording of episode 10 with Dr. B a few misconception about daddy longlegs (who are not spiders) came up: "There is an urban legend claiming that the harvestman is the most venomous spider in the world, only its fangs are too small to bite a human, and is thus not actually dangerous. This is untrue on several counts (see also cellar spider). Phalangids are not spiders, and none of the known species have venom glands or fangs, but rather chelicerae. The size of the jaws varies by species, but even those with relatively large jaws virtually never bite humans (or other large creatures), even in self-defense. The few known cases of actual bites did not involve envenomation, and had no lasting effects."

I have been looking recently into keeping a house spider as a pet, maybe a wolf spider, since they do not build nets. Part of the reason I want a spider was to see if I could teach it tricks. I'm a bit jaleous of kamel and his rat circus, so I was hoping to condition the spider using a laser pointer, to tell it where and when a meal was coming. We've all heard of Pavlov's experiment with dogs but few of us know about his work with slugs which was recently replicated to look at memory.

Interrestingly, a new paper in PLOS shows that it is indeed possible to condition insects: "this study, we investigated the effects of conditioning trials on the level of salivation. Untrained cockroaches exhibited salivary responses to sucrose solution applied to the mouth but not to peppermint or vanilla odor applied to an antenna. After differential conditioning trials in which an odor was paired with sucrose solution and another odor was presented without pairing with sucrose solution, sucrose-associated odor induced an increase in the level of salivation, but the odor presented alone did not. The conditioning effect lasted for one day after conditioning trials. This study demonstrates, for the first time, classical conditioning of salivation in species other than dogs and humans"

However I was disapointed to find out that in flea circus, they do not teach the tricks via conditioning, but rely on cheap tactics: "Chemicals such as camphor that repel fleas are placed on lightweight balls and the fleas kick them away, this makes the fleas look like they are juggling or playing football. A recent example of this is the Munich beer festival Floh Zirkus. Training fleas in this way simply shows off their natural talents and in no way harms the fleas. However there are historical reports of fleas glued to the base of the flea circus enclosure, instruments were then glued to the flea performers and the enclosure was heated. The fleas fought to escape giving the impression of fleas playing musical instruments"

So I'll keep you posted on that experiment...

Bayblab podcast Episode9

Finally available in all its glory..an epic two part series.

Part1: Steven Hawking presents... glycolysis and the Warburg effect in cancer and heart attacks, and road density in the United States.

part2: Pharming drugs and the production of interferon in transgenic tobacco plants and opportunities from advances in sequencing technology such as mapping the beer genome...

Also if you want to subscribe to this podcast, simply search for bayblab at the iTunes store...

The Most Common Phobias

I have a friend who has a vomit phobia. Recently, a link was posted on the bayblab to the International Emetophobia Society a group that claims that emetophobia (the fear of vomit and vomiting) is the 5th most common phobia, which seems strangely high. So I did some poking around on the web for a list of the most common phobias. I couldn't find a definitive list, or numbers to back up any of the claims, but after a perusal of several 'unofficial' lists I pieced together the following rankings. A few seemingly common phobias such as achluophobia (fear of the dark) and mysophobia (germophobe) make occasional appearances on these lists, but not as frequently. While this is a rough order, all of these are almost unanimously listed:

1. Arachnophobia (spiders, a clear #1)
2. Social Phobia (this would include public speaking)
3. Aerophobia (flying)
4. Agoraphobia (open spaces)
5. Claustrophobia (closed spaces)
6. Acrophobia (heights)
7. Emetophobia (vomit)
8. Carcinophobia (cancer)
9. Brontophobia (thunderstorms)
10. Necrophobia (Death/dead things, a unanimous #10)

The top 5 or 6 are what might be expected, but I'm still surprised that vomiting (and thunderstorms for that matter) rank so highly. If you have your own phobia, and want to know what it's called, you can try checking this site. They'll tell you that the fear of peanut butter sticking to the roof of your mouth is called arachibutyrophobia

Random friday afternoon science

"Scientific Psychic® abides by the methodology of science. Therefore, the word "psychic" refers to adjective definition number 1 ( of or relating to the psyche or the mind); any other meaning would constitute an oxymoron. Predictions are based on the scientific method. Here is a prediction: On March 9, 2016 there will be a total solar eclipse in Sumatra and Borneo."

Yet on the site they talk about paranormal stuff I'm not sure wether it's a subtle joke or it's for real... But the tests are funny.

Since it's friday, here's a really geeky joke for you found on bash :

"A trichinosis larva and a botfly maggot walk into a bar. The botfly maggot turns to the trichinosis larva and says "hey buddy, I heard you like pork." The trichonosis larva looks the the botfly maggot right in the spiracles and says "indeed, I encyst upon it."
Hahah. You get it? It's a homonymn.
fuck you all."

Finally check out this PhD project, where a student defended her thesis in underwear with someone playing pong by fondling her. I can't make up stuff like that!

Blue people with chocolate blood

No I'm not talking about smurfs, but actual people with a blue coloration. Methemoglobinemia, or Met-Hb, is an anemic condition where there is an overabundance of methemoglobin. The excess of methemglobin is due to a deficiency in the NADH Met-Hb reductase which usually prevents the spontaneous formation of Met-Hb. The blood of patients afflicted with that condition is hypoxic and dark brown. The treatment is to supply pure O2 and inject a 1% solution of methylene blue which restores the iron in the hemoglobin to its reduced state.

The condition has given rise to different blue people mythology in Kentucky, just read this story:
"Dark blue lips and fingernails are the only traces of Martin Fugate's legacy left in the boy; that, and the recessive gene that has shaded many of the Fugates and their kin blue for the past 162 years. They're known simply as the "blue people" in the hills and hollows around Troublesome and Ball Creeks. Most lived to their 80s and 90s without serious illness associated with the skin discoloration. "

The blue coloration can also be induced by ingestion of nitrites barbyturates and other chmicals, or by explosions. So be careful on Canada Day with the fireworks you've smuggled from the states...

Popularity in science

According to google trends, Richard Dawkins has just surpassed Stephen Hawking on the media whore popularity contest. We might just have to dump Stephen for Richard on the bayblab podcast...

Can plants sense kins?

Ok I admit that story has already been all over the media. When I first read about it, I just didn't think it was that interesting so I didn't post it. However now that I've actually read the paper I have a few comments. Firstly its 4 pages long and has 2 figures, wow it's a big conclusion for such a simple experiment. Second I want to explain Hamilton's kin selection idea since it is the basis of that paper. It essentially boils down to this: "if individuals have the capacity to recognize kin (kin recognition) and to adjust their behavior on the basis of kinship (kin discrimination), then the average relatedness of the recipients of altruism could be high enough for this to be favored."
Now because I have a huge man-crush on Dawkins, and I would carry his half-ape half retarded fish babies, I have to mention Dawkin's views of kin selection. In writings on Kin Selection there are often references to Richard Dawkins’s article ‘12 Misunderstandings of Kin Selection’, in Zeitschrift für Tierpsychologie, 51 (1979), 184-200. Basically Dawkins doesn't think that kin selection is a special type of natural selection. He opposes the view that natural selection can be exerted on a group, since only the individual survives and reproduces and not a group. There is more to his arguments, but It's worth actually reading it.

So how does this relate to plants. Well kin selection is a complex process usually associated to social animals. Plants on the other hand, can't see, smell or move, or at least are limited in their ways to sense kinship. And if you can't recognize a kin, how can you have altruistic behavior? Now it's well known that when plants are in close proximity, they will exhibit more aggressive competitive behaviors, in order to secure resources. Rather than using its energy to grow or flower, it will allocate more to roots to cover larger areas. Now this group asked a simple question, will the plant be as competitive with its root system if the other plant in the pot is from the same species. Surprisingly it wasn't as agressive, suggesting it knows about the plants in its environment, but how? Anyways, I like this experiment because it would make for an awesome science-fair type experiment, or a good way to teach kids about evolution, kin selection
and natural selection.

Does Dawkins exist?

Footwear in the lab

I received an interesting email this week, I even had to temporarily pause my mouth-pipetting of sulfuric acid because it made me laugh and I snorted some of it. The safety officer sent us a nice reminder to keep our feet properly covered in the lab, and not to start wearing flip-flops. I'm personally not a fan of the flip flop, it is a medical menace according to the British medical journal (just read past the bottle in the rectum portion). Now the funny part is that attached to the email were pictures of acceptable and unacceptable footwear. lets just say even an unfashionable grandma wouldn't get caught dead wearing some of them. And I don't understand why we want to protect toes but not ankles! Effective immediately I propose we all wear hip waders in the lab.

Anger Managment

We often hear the advice not to act when angry to avoid making a rash decision. This may seem reasonable, but in reality is not good advice. Researchers at the Univeristy of California, Santa Barbara conducted a study conducted a study on how anger affects decision making and found that anger helped people make more rational decisions. While this may seem counter-intuitive, it actually makes sense. Armed with heightened skepticism, people when angered will tend to ignore pleas to emotion, irrelevant statements and other hallmarks of a weak argument. Unencumbered by these distractions, they can hone in on the stronger arguments and make better, more analytical decisions.

why trial by jury sucks

Who doesn't like democracy right? Well sometimes, a group of people is worse at taking decisions than multiple independent individuals. At least that's Dawkin's very convincing opinion which starts like this: "Trial by jury must be one of the most conspicuously bad good ideas anyone ever had. Its devisers can hardly be blamed. They lived before the principles of statistical sampling and experimental design had been worked out. They weren’t scientists. Let me explain using an analogy. And if, at the end, somebody objects to my argument on the grounds that humans aren’t herring gulls, I’ll have failed to get my point across.".

All of this to introduce this story, about a federal hearing of a court case against the US government presented on behalf of a family of a girl afflicted with severe autism. You may have heard of it, there has been a long suspicion that childhood vaccines such as the Measles-Mumps-Rubella (MMR), the vaccine additive thimerosal, or the mercury preservative in vaccines may be the cause of autism. Yet time and time again studies have shown the absence of causation, and that the correlation between the age of onset of autism and childhood vaccines is just that, a correlation. Even the correlated rise of autism cases and vaccination in the past decades can be explained simply by better records and diagnosis of autism, there probably hasn't been a major increase in actual cases. So lets hope that this particular jury is not a loose canon and can appreciate the subtleties of causation and correlation, and that there is a good expert witness at that trial, since there are 5000 other similar cases for which it might set a costly precedent.

New stem cell journal from "Cell"

It was bound to happen, cell, the top tier journal when it comes to cell biology spun off a new journal dedicated to stem cells last week. It took a few days for the university to get access, but I was finally able to peruse it today. I had a little bit of a double take actually regarding the landmark paper published in this first edition. You may have heard that Myc, sox2, oct4 and klf4 are sufficient to reprogram fibroblasts into stem cells. In fact you may have heard of it a full year ago, as this experiment was done by a Japanese group (Takahashi K, Yamanaka S.) and published in Cell. This new paper seems to be almost the same experiments except it takes 12 American scientists to do the work of 2 Japanese :). And if that wasn't confusing enough, another team from the Whitehead Institute also published similar findings last week in nature. This latter group is a proponent of the bivalent histone code regulation of key stem-cell factor. The idea is that both repressive and active histone modifications mark the promoters of these factors making them easily inducible but also primed for repression may the cell wish to differentiate. As talked about previously on the bayblab, these bivalent promoters may be suceptible to dysregulation by epigenetic factors (trithorax/polycomb) over time and may be one of the mechanisms to transformation...
While we have talked about sox2, klf4, c-myc and oct4 when the first paper came around there are a few things worth highlighting this time around... While the ectopic expression of these transcription factors is required for the reprogramming it is not really sufficient. There was a large lag period between the expression and the reprogramming, suggesting there is an additional stochastic event that needs to occur. Also, c-myc is the odd one of these transcription factor as it tends to regulate very large areas of chromatin rather than just specific genes. Perhaps the lag is due to chance remodelling event over large areas. For example the authors show that the inactive X chromosome is re-activated by these factors. So this begs the question: what happens to the chromatin, how is the histone code changed, what is the lag for, would expression of members of the trithorax/polycomb make the process more efficient?

More on that later....

Joel's Science Hero #2

Today's science hero is Robert Tjian (pronounced Tee-Jin). Dr. Tjian is an investigator of Howard Hughes Medical Institute at the University of California Berkeley and co-founder of Tularik inc. (recently aquired by Amgen). I should stress now that, although I greatly admire what Dr. Tjian has accomplished during the span of his career, I do not see him as a role model per se. To be honest, the man scares the hell out of me. A former PhD student in his lab told me (and I am paraphrasing) that "Bob just can't see eye to eye with people who aren't as enthusiastic about science as him, and he can't work with these people. But, if you do see eye to eye with Bob, he'll make sure that nothing stands in your way, and he makes sure that you have everything availble to do anything you need to do." To give an example of what seeing eye to eye with Tjian involves, a local PI told me that he knew a man who post-doc'd with Dr. Tjian. According to this PI, the post-doc in question received a phone call one morning at about 3 AM. The caller was Dr. Tjian, and he said (once again, I am paraphrasing): "I just loaded your gel, you'd better be here to take a picture before it runs off".

I don't say these things to in any way diminish Dr. Tjian's character. If anything, I wish I could approach science with his enthusiasm and work-ethic. Dr. Tjian began his education at UC Berkeley. As an undergraduate, he worked Dr. Daniel Koshland (after whom the building in which Tjian now works is named, and winner of the 1998 Lasker Award for Special Achievment in Medical Science). Koshland was so impressed with Tjian that he brought him to Oxford to assist in his sabbatical research. After his stint at Oxfor, Tjian went to Harvard for his PhD (which he finished in less that 3 years). He then pursued post-doctoral research with Nobel Prize winner James Watson at Cold Spring Harbor Laboratories, where he isolated with first eukaryotic transcription factor (SV40 large T antigen). Throughout all of these periods, he displayed phenomenal techinal prowess, great ingenuity, and an incredible work ethic, leading most who met him to assume that he would accomplish great things as an independent investigator.

They weren't wrong. Tjian went to Berkeley as an assistant professor in 1979, where he began his monumental career examining the mechanistic basis of eukaryotic transcription. His first major discovery was indentifying the first human transcription factor, Sp1. From there, Tjian never looked-back, and continued to achieve accomplishments, that grad students like myself can only stare at in slack-jawed awe. I recommend searching pubmed with - Tjian R 1989 - to see an example of what he accomplished in one slightly better than average Tijan year.

To me, the one great mark of Tjian's success is looking at the places where his one-time trainees have gone. Tjian may have expected a lot from his students and post-docs, but, as mentioned above, Tjian would open every door they could possibly reach for. The same former student mentioned above said that Tjian had his pick of the best newly-minted PhDs of the day, and they accomlished incredible things in his laboratory. He, in turn, helped them to move-on to incredibly productive independent careers. Some of his former trainees include: James Kadonaga (UCSD), Kathy Jones (Salk), Steve Smale (HHMI/UCLA), Stephen Bell (HHMI/MIT), Stephen Jackson (Cambridge; interesting side-note: Dr. Jackson was supposedly the youngest professor to be granted tenure at Cambridge since Isaac Newton), Bryan Dynlacht (NYU), Anders Naar (Harvard), Mark Biggin (Lawrence Berkeley National Laboratories), Laura Attardi (Stanford), Naoko Tanese (NYU), Benjamin Pugh (Penn State), Richard Myers (Stanford), Donald Rio (Berkeley), amonst many, many more.

That's why Bob Tjian is my science hero.

PS, I don't link to other webpages, because (A) I'm lazy and (B) I assume that, if you really care, you can google it. Sorry Dave.

Wireless Power: More than Just Another Useless Idea from the Bay

Once again, a great idea that originated in the Bay (that's our laboratory bay and the Bay in Bayblab) has been ripped off and put into practice by brilliant engineers at MIT. This one was the topic of a random conversation about how awesomely liberating wireless data transfer technology is, except that the true portability of your laptops, PDAs, iPHONES, etc is still severely limited by short battery life. Enter wireless power was our idea, and then you would have ultimate electronic freedom and connectivity available anytime, anywhere. Good thing the geeks at MIT were listening in on our conversation with their Whisper2000s, because now they have demonstrated the feasibility of the idea by beaming power wirelessly to a 60W lightbulb over a distance of 7 feet. The power transfer is not achieved by radio waves, which would diffuse all over the place rather than specifically to the device you want to power, nor by lasers, which require a direct line of site to the target and could fry any objects that get in the way (such as the geeks sitting between the source and target above). Rather, the new technology awesomely transfers power through magnetic resonance:

"WiTricity is based on using coupled resonant objects. Two resonant objects of the same resonant frequency tend to exchange energy efficiently, while interacting weakly with extraneous off-resonant objects. A child on a swing is a good example of this. A swing is a type of mechanical resonance, so only when the child pumps her legs at the natural frequency of the swing is she able to impart substantial energy.

Another example involves acoustic resonances: Imagine a room with 100 identical wine glasses, each filled with wine up to a different level, so they all have different resonant frequencies. If an opera singer sings a sufficiently loud single note inside the room, a glass of the corresponding frequency might accumulate sufficient energy to even explode, while not influencing the other glasses. In any system of coupled resonators there often exists a so-called "strongly coupled" regime of operation. If one ensures to operate in that regime in a given system, the energy transfer can be very efficient."

Just goes to show that any idiot can have an idea for a great new technology, but it take a team of real geeks to make it happen.

I can't even imagine what this technology would mean for energy trade and availability. Imagine what it would do for power grids...peer-to-peer energy sharing? Suddenly energy technology would not have to rely on a small number of centralized, high yield sources, but rather would be all about a de-centralized network consisting of a vast number of even the lowest-yield energy generators. Call it Nanopower, or the Enerweb - free, clean energy for everyone!

Underpants science

This morning while I was perusing my drawers for a fresh pair of boxers i noticed that all my white boxers had holes, while all my black boxers were intact. Considering I bought them on the same day, I wash them together, they are the same model, why would that be? I have two theories: the color theory and the textile theory. Perhaps I wear white more often, perhaps because subconsciously they look cleaner or something like that meaning that colour influences my decision, not all that surprising considering the colour of a placebo pill influences its efficacy. Fake blue sleeping pills for example are better than red ones. The other possibility is that the textile on the white underpants was treated differently, for example in the manufacture it may have been bleached, leaving the fibers more vulnerable and weaker.

Speaking of underpants, we all know that tighty whities are bad for sperm count, but there is good research out there about the effect of textile on sperm count. So stay away from polyester, apparently the static may be harmful to your swimmers. If you're really paranoid about your underpants, you may also cook them for 30 min in the microwave to get rid of fungus, as it obliterates any candida spores. I was terrified of candida as a kid after my friend who was infected was denied any type of sweets. don't take that chance, nuke your boxers...

Finally I came across this disturbing pubmed abstract about dogs chewing on testes. So avoid to putting treats in your underpants.

Superstitious Sportsfans

The Stanley Cup finals are over and there's a sombre mood here among the Senators faithful. The Stanley Cup is steeped in history and tradition (and in my opinion is the greatest trophy in sport). Hockey players themselves have some interesting traditions, such as the playoff beard. Hockey players are also extremely superstitious and can adhere to some bizarre rituals to help tilt games in their favour. Those watching Ottawa throughout the playoffs surely noticed Ray Emery burying his head in the net before each contest. Some of these rituals are much more bizarre. Former Senators forward Bruce Gardiner used to dip his stick in the toilet before each game. Some goalies talk to their goal posts. Wayne Gretzky never go this hair cut on the road.

We in science tend to take a more evidence-based approach to things, yet we're not immune to these sort of superstition. During this year's NHL playoffs, you would still hear the majority around here talking about not watching the game at a certain location because 'they lost last time we were there', or wearing a particular t-shirt for good luck. Clearly the outcome of a sporting event is beyond the control of the viewer at home, regardless of what they're wearing (either that or the collective fan-base of Anaheim is much better at harnessing this voodoo than those of us in Ottawa), yet we still go to some lengths to set the perfect conditions. This is called illusion of control, a widespread effect and the basis for most superstitions.

Some may say this is evidence (anecdotal as it is) that men and women of science believe in some sort of higher power (you know, the Hockey Gods). In a study done a few years ago it was shown that interest in sports correlated strongly with belief in sports superstitions, but not with scores on the Paranormal Belief Scale (PBS). Not surprisingly, scores on the PBS also correlated positively with beliefs in sports superstition. I don't know if the leap can be made that the superstitious sports fans here also hold belief in the paranormal, but I don't have time to address that - I have my pre-tissue culture ritual to get to.

Fertility test for 100$

Wow, this is a cool new toy/ cheap lab instrument potentially. While it looks like a toddler's fisher price toy, Fertell's artificial cervix offers full fertility test over-the-counter. Sperm motility, hormones (FSH, LH), the whole works for under 100$.

Membrane pores aren't irreducibly complex.

Check out this somewhat odd-seeming PNAS paper (don't worry, it's open access) about diffusion across pores. Using two macroscopic models, one real and one virtual, they showed that a concentration gradient can be maintained across a membrane with leaky pores in it without the need for gating, antiporting, charges, or anything. All that's needed is a physically asymmetric pore - wider at one end.

When I first read the paper, I thought it was so obvious that I wondered why the research even had to be done in the first place. But then, I realized that it's not so intuitive; it seems to go against a lot of what we're taught about diffusion equilibria. Simply changing the geometry of the pore shifts the equilibrium to one side, without even the need for bigger particles to block one end of the pore. The reason it's relevant, the researchers suggest, is that it shows the potential for an extremely rudimentary metabolism at the very beginnings of life. It's possible to maintain a particle gradient of, say, sugars and ions, across a membrane without any of the fancy multimeric gated two-way channels that we advanced eukaryotes sport. An early ion pore could easily have evolved from a protein that already bound that ion and underwent a mutation that bound it to the membrane.

A duck designed by committee

"we would like to mention the Platypus, estranged relative of the mammal, which has a duck-bill, otter's tail, webbed feet, lays eggs, detects its aquatic prey in the same way as the electric eel, and has venomous barbs attached to its hind legs, thus combining all 'typical' Australian attributes into a single improbable creature." - Douglas Adams

As the above quote illustrates, the platypus is a bizarre beast. Belonging to the order Monotremata (literally, 'single hole'), all urinary, defecatory and reproductive systems open into a single duct, the cloaca (literally, 'sewer') and as most people know is one of the few mammals to lay eggs (the few species of echidna being the others). Platypus eggs more closely resemble those of reptiles than birds and are incubated in utero for the majority of the incubation period. The female has 2 ovaries, but only one is functional. It is also rare amongst mammals in that the male of the species has spurs on the hind legs that can produce venom toxic enough to kill a dog, or cause a great deal of pain to a human.

As if being a cross between a bird and a reptile wasn't enough, the platypus bill is packed with nerves that can be used for electrolocation, more commonly found in fish species, to aid in foraging in the riverbed.

But ultimately, the platypus is mammalian, meaning it has mammary glands, produces milk and nurses its young. Even in this aspect of its physiology, the platypus is unique. Unlike other mammals, the platypus has no nipples. Instead, the mammary glands are more like sweat glands, secreting milk directly onto the fur where it is licked off by its young.

Genetically, the platypus has other interesting features including a strange quirk in visual pigment evolution and in its sex chromosomes. The platypus has 5 pairs of sex chromosomes (making up ~15% of the genome) lacking the classic sex-determining SRY gene, which in some ways resemble the reptile/bird ZW sex determination system.

Because of its shared characteristics between mammal and reptile, some people view the platypus as an evolutionary link between the two. Because of their unique phylogenetic position, the platypus genome is currently being sequenced to answer some questions about evolutionary biology and mammalian gene organization.