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.