How cheap do they think postdocs are?

I am in the lab really late tonight, and finished everything except waiting on my MTTs to be done, so I was just doing some website searching for a few products I need for my upcoming experiments, and I came across an interesting marketing spiel.

During my PhD when I needed a lot of rapamycin for my animal studies, I found this company called LC Labs, as a result of having to shop around, and overall I think they’re pretty cool – they don’t waste money on extravagant  marketing/trade shows/brightly colored catalogs/sales reps etc to keep prices low.  When I figured out how much rapamycin I would need for even the first 2 months of the study (and I had hoped it would last even longer if the mTOR pathway was important!), it would be $40K.  Yikes!   Even though my lab in grad school was very well-funded and we never worried about money, this figure was a bit shocking, so my PI asked us to look around….LC Labs to the rescue….just as an idea 1mg at Sigma is around $279, whereas LC Labs equally pure product is $225 for 500mg!….They have a handy-dandy chart on every product page with their competitors prices based on mass and purity claim which I like again, as it demonstrates transparency.

So even now I continue to check them out for drugs/reagents that I can’t just get for free from the pharmacy here.  On the staurosporine page tonight I read this funny statement that caught my eye:

“Buy 100-300 mg from LC Labs; support a postdoc for 1-2 years with the money you save!”

LOL, but really???  Lets see, if I needed a boatload of it (since it [staurosporine] inhibits many kinases at very low nanomolar doses) and wanted to order 300mg it would cost $1590 from LC Labs.  Most of their competitors don’t sell such a large size, but biorbyt does, and they charge $2245 for the same 300mg (according to the price table)….a $655 difference. Where can I find a postdoc for $655/year or even $655/month? (I’m taking notes for my future lab

Collaboration in Science Twitter Chat Tomorrow

As the complexity of performing science increases, collaboration is becoming increasingly necessary to accomplish great things.  Collaboration may occur across disciplines, continents and type of environments, but regardless of scope, there are a number of challenges and opportunities in moving forward in this new era of collaborative science especially for young scientists lacking broad networks and experience working with diverse groups of people.

Here at MD Anderson* we’re paving the way for novel types of interactions to become mainstream – who would’ve thought multiple competing pharmaceutical companies each with drugs that would work best in combination, would work together on a clinical trial. Its happening here because we have the power!!! (ie the patients, experience and the leadership)

Other examples of new types of collaborations can include company sponsorship of academic lab activities such as preclinical studies or method validation.

Tomorrow (Wed Feb 1) on the life science twitter chat, which you can participate in by following the hashtag #ls_chat, that my friend @Comprendia and I started last year, we will be discussing collaboration in science.  Some of the topics that we will be discussing include finding opportunities for academic-corporate research collaboration, determining how to make them worthwhile to both parties, and most importantly best practices for being a successful team player in such endeavors.

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Please join us tomorrow from 10-11am PT (noon CT/1pm ET) for this (hopefully!) useful discussion between academic scientists, industry scientists and others who are interested in discussing this.  See you on the twitterz!

* note: I’m not speaking on behalf of my employer, just commenting on what’s happening here relating to the content of this post

A Cell/Molecular Biologist’s Guide to iPad Apps

I’ve had my iPad for a little over 2 months now and in spite of craziness revolving around moving across the state and settling in, and gazillions of meetings to select a lab (yes really gazillions!) I’ve had a chance to play around with my new toy a bit.  A certain friend of mine has been prodding me to write this post for a little while, and since this weekend has been relatively relaxing thought I’d go for it.  Here’s my fictional day using my iPad as much as possible.  The links are mostly to the iTunes app store pages for the mentioned apps.

Firstly, I turn on Pandora. I trust you’ve heard of this app so I’m not going to elaborate on its awesomeness.  My world is never quiet unless I’m asleep, whether I’m working on or playing. Unless I forget my headphones – then I’m not a happy camper at work.  Guess I should buy a backup pair for there.

Like most scientists (and most people in general nowadays), I start my day by checking my email on one of my iOS devices (iPhone or iPad).  Great, nothing urgent….now I move onto twitter.  I’ve tried most of the common apps, and because of my tweet consumption style of wanting to try to read everything, Hootsuite is my favorite since I can consistently scroll back the furthest, though interface-wise I much prefer the Twitter app.  Depending on time I may also check on Facebook and Google+ using these native apps.

Next I check my calendar to figure out what I need to do today…I keep my schedule in Apple’s calendar app on my iPhone, which can sync with iPad over Mobile Me. However it is not super reliable (an observation shared by some of my online buddies) so I have not turned on calendar sync lately, and rely on my phone which never really leaves my side anyway.

For my task list, I’ve tried a few apps and I’ve settled on the free-mium Remember the

Remember the Milk Icon

Milk one since its simple but flexible (eg you can designate “Waiting for” tasks, can change the dates).  Its also available for every platform, and lots of plug-ins for your computer and online activities (gmail and such) – check out the full list here. You can also organize tasks around locations to avoid making multiple trips to places that are close proximity to each other when running errands for example.  Unfortunately to sync more than 1 device with the website requires you to go “pro” for $3/month or $25/year.  The icon is not THAT cute

OK so now I know what I have to do today….so I’m likely working away either at the bench (or nowadays in the hood doing hours of cell culture!) or at my macbook pro doing these tasks.  I’m trying to get into the pattern of Mondays being a day to read – my auto Pubmed updates are set to arrive on Mondays and so now I’ll delve into reading methods. Speaking of Pubmed, Pubmed On Tap allows you to search Pubmed and read full-text of open access papers/email link to yourself for later.  Pretty useful for when you’re out and you just have to know something…

All the glamor journals (Science, Nature, Cell) have ok apps for browsing the latest tables of contents, however to get full-text its not very straightforward to use an institutional subscription currently.  But at least I can make a note of interesting sounding papers using SimpleNote, which syncs with Notational Velocity on my Mac so I can download the full-texts when I’m on the network or connected via VPN at home.  I actually have half a folder full of journal apps that include some field-specific apps (including AACR publications, my professional society and NEJM – where I aspire to publish a paper during my postdoc!)

For a quick break from work reading I might grab a coffee and check out the news on the New York Times or use Flipboard or Zite for a cool, personalized view of news in a magazine format.  But I try not to get too sucked in.

Back to reading….next I might check out my RSS feeds for my journals. On my iPhone I use Net News Wire as my RSS reader, but unfortunately the iPad version is $9.99.  I personally don’t rely on RSS that much to be worth spending that much on.  Reeder is widely thought to be the best RSS reader on the iPad (though News Rack is a worthy contender in a sizable minority), and for $5 I was willing to download it.  Not only can you read your feeds, but there are sharing options galore (including social media sites twitter and facebook, as well as Instapaper/ReadItLater/Readability and plain old email too).  Speaking of Instapaper – that is a must-buy app for me!  It allows you to save articles for later reading from your desktop/laptop or from your phone and it strips out all the distracting ads etc. and downloads for offline reading later, which for us wifi-only iPad users is great for passing the time on long flights without wifi or while cramped in coach.  As I’m reading I find an article with a useful table which I think I would like to access later, so I save it to Evernote, a great information manager app, and give it some useful tags so I can search for it later either on my computer or phone/iPad.

After all this reading I’m needing some social interaction, so I open up Words with Friends free and play some words. I’m not very good at it compared to some of my friends and my dad, but its still fun.  Then I might see if anyone is on gchat to chat using BeeJive (the iphone version, since the iPad version is $10!).  Oh bummer everyone else is working so I guilt myself back into working….

Suddenly I get a push notification that a webinar I signed up to view is starting in 10 minutes.  So I launch the GoToMeeting app, and go to my email to get the code…and soon enough I’m signed into the webinar, and maybe I eat my lunch while watching, since I gotta be always multi-tasking while eating.

After lunch I go into the lab and begin my benchwork for the day.  I open Safari and browse to my Biodata lab notebook (hopefully soon to be a real iPad app per the biodata team) and see that I have a few things to accomplish today. Firstly I have to set up some restriction digests for my latest cloning project.  But what enzymes and buffer do I need????  Promega comes to the rescue.  Out of all the science-specific apps I have downloaded, this is the most useful in my field (and no I’m not being paid by Promega to say this).  There are a variety of tools including converters, videos about lab procedures, written protocols and protocol info regarding many of their products including catalog numbers if you’re just preparing for your next experiments…..so lets say I find the perfect kit for my study, I just copy the catalog number, open my email application and shoot our lab manager a message with what I would like.  Easy peasy!  Next I realize I need to setup some PCR reactions so I get everything out to thaw, and double check my conditions using the “melting temperature for oligos” tool in Promega.  Next task accomplished.

The other useful laboratory science app I’ve found is Invitrogen’s Daily Calcs, which as it sounds is focused on calculations.  There is some overlap with the promega app here, but also there is a useful cell culture reference for newbies including useful numbers like surface areas, volume of media to use etc…(we all remember the first weeks of cell culture when we were super-anal about every detail).  There is also a useful molecular weight lookup if you know the formula of the chemical.  If only there was a way to also lookup by name.  There you go Sigma – take my idea, link it to your huge catalog and #win!

While my PCRs are running, I open the cool HHMI bulletin app to read some science outside of my field, since a too-narrowly focused scientist can miss interesting new connections.  I read an interesting epigenetics article, which discusses modifications I’m not familiar with so I open EMD Millipore’s cool Histone Map app to learn more,

Example of information from Histone Map app

and end up sucked into this fascinating world of nuclear biology for the next half-hour.  Ooops – I’m never escaping lab today at this rate!  Still, at the end of this exploration, I have a few questions ….what do I do?  I use Wikipanion to see what Wikipedia has to say….then I quickly make a post on Quora (using Social Questions) and visit EpiExperts, a cool new scientific community for epigenetics peeps (I’ll do a post on this later) in Safari to post them as discussion items.

OK back to my day.  Digests are done, PCRs are coming along. I check on my cells…everything’s good.  So I go back to my desk and start studying my flash cards I made in Evernote Peek (covered previously here) for my test on Friday.  And soon enough my collaborator from Asia is Skyping me to discuss some cool new data, since it’s the beginning of his day now. At the end of our call, he asks me to sign a form for a grant he is about to submit, so I open iAnnotate PDF and using my stylus add my signature, save and send it back to him in 2 minutes. Quite a productive day I’m having

I guess its home time soon.  I wonder what I will make for dinner?  So I browse epicurious and AllRecipes for some quick ideas, and prop my iPad up in the kitchen so I can follow along..  Once I’ve cooked my dinner, I sit down and select a movie to watch on Netflix while I eat and wind-down.  Then it’s a quick email , twitter and Words with Friends session before bed, and hopefully I remember to set my alarm (in Apple’s clock app) on my phone before falling asleep. But before sleeping I remember to check my bank account to see if I got paid so here I come Bank of America app.

That’s all peeps.  I have mentioned a lot of apps, but as you’ve probably gathered by now, I use my iPad mainly for consumption tasks, so I don’t have a personal recommendation on work software such as to create Office documents.  GoodReader seems to be a good basic choice, or if I were needing something I’d download Documents to Go. My laptop goes almost everywhere with me so right now this isn’t a huge need.

What are your favorite iOS apps fellow scientists?

My quest to learn cancer pharmacology…using my iPad and Evernote

Some of you who know me in real life, know that I’m currently writing a postdoctoral fellowship for the Department of Defense Breast Cancer Research Program that is due later this month.  Today was day 1 of actually working on it after getting my letter of intent submitted yesterday just in time, and lining up my recommendation letter writers.  Not too long to go given that our department of sponsored programs needs most of the business-y stuff a week before the deadline, but luckily I am awesome at writing under pressure (I’m modest too)!

I thought one of the important things I needed to do was getting up-to-speed on the drugs currently used in my subset of patients (my proposal is focusing on Inflammatory Breast Cancer, the rarest but most aggressive type of breast cancer). Earlier today one of my favorite tech blogs, Mashable, posted about a new (free) Evernote-based iPad app called Peek, which is basically a way to use the iPad 2′s Smart Cover combined with your evernote notebook-of-choice as an electronic flash card system.  For evernote’s blog post about it go here…Of course there are many other current flash card apps, and since I’ve not really been a flash card type during my studies I haven’t really used any of them…but tonight I decided it would be fun to try out Evernote Peek since just this morning I was thinking that my knowledge of cancer drugs should be better now that I’m going in a translational direction with my research, so flashcards would be a good way of memorizing the most common ones and their mechanisms of action.

The basics of Peek

Check out this video for how it works.

 

How to use Peek

1) Download Peek on your iPad 2, and launch the app. Sign in with your Evernote account (you do have one, right….if not go make one at evernote.com STAT!)

2) In evernote (on your phone or computer), make a new notebook and make some flashcards. The title field contains the clue (ie what will be on the bottom of your screen) and the body contains the answer or whatever you would put on the reverse side of your paper-flashcard. The body can contain text, images, you can record sound….very flexible! See my example cards below.

3) Once you’re done/want to try them out, go back to Peek and add your notebook by clicking on the add button, and change to “my notebooks” view and you should see the notebook you just made.

4) That’s it. Click on the notebook and start using Peek.

The notebook screen showing how you can add some of evernote sample flashcard packs as well as your own (mine is called Cancer Drugs in case you couldn't tell!)

Here are 2 quick examples of my flashcards:

A plain text one - you can get quite a lot of text in there!

Cool-you can include both text and a picture. Shame the picture isn't automatically scaled to the allowed size though!

 

The verdict?

This worked just as promised – fun way to memorize stuff, simple enough to setup, easy to test yourself and mark as incorrect if you got it wrong (So far I haven’t made any mistakes, but I figured out if you click anywhere on the screen, the check boxes toggle between correct and incorrect). Supposedly you can re-test yourself on only the ones you got wrong.

Some things that could be improved:

1) There seems to be lacking an auto-update.  I first made a notebook with 4 cards and added it to play around with. Then I went back and added 8 more, using my laptop to speed it up a bit since I was fact-checking in other tabs. When I went back to Peek, I expected to see the new cards, but I didn’t – the notebook didn’t auto-update. To get the latest version of the notebook, I had to delete the notebook (which you do by holding down on the notebook on the screen with all the notebooks and you get a delete notebook option) and re-add it.  When I attempted to re-add it, at first the notebook still says it only has the initial number of cards, but when selected, it flies up to the top and actually downloads the right cards. Seems like a minor programming thing that could cause some anxiety over data loss if you didn’t know.

2) Secondly I think it would be great for users to be able to share their flashcards.   Other medically-inclined trainees may be interested in my deck were I to make a comprehensive collection of well-written ones and I could see companies such as the SAT review people even selling flash card decks. This would be a nice future option….and I’d like to be able to see and add other people’s too. (I’d get scientific nerdy ones to pass the time when I’m somewhere super early, since I HATE being late for anything!).

3) The picture scaling issue I identified in the doxorubicin card above – the picture I downloaded which was from Wikipedia is really  not that large. Would have been nice to have the option of scaling or a message in Evernote that images can only be up to X by X pixels or whatever so that users would photoshop their images to fit.

But overall, I think this app has great potential both for children and adults and is a clever use of the Smart Cover. Even just the process of making the cards has taught me a bunch. Who knew it would be so simple to study up on drugs?

What flashcards will you make?  Let me know what you think of the app if you have an iPad too.

Do cell phones lead to brain tumors?

If you’ve watched the news in the past day or so, or followed any health-related twitter feeds, no doubt you’ve seen the reports that the radiofrequency electromagnetic radiation produced by cell phones has been classified as Group 2B potential carcinogen (press release) by the WHO/International Agency for Research on Cancer (IARC).  I have read that the official publication will be up in a few days on The Lancet website.

A recent CDC report found that in the US, more than a quarter of households are now wireless-only (including yours truly), and among the below 30s and renters, this percentage is closer to 50%. A natural question arising as a result of this WHO announcement might be whether you should run out and get a landline again, or is this really much ado about nothing?

What did the report actually say?

First of all, what exactly is a Group 2B carcinogen?  The WHO describes carcinogenicity of an agent by classifying into 5 groups as described below taking into account a variety of information including whether humans are exposed to it, epidemiological evidence of association with cancer risk in humans, laboratory studies in animal models supporting cancer risk and mechanistic information. The classifications are:

Group 1 – Carcinogenic to humans (eg alcohol, aflatoxin B1, benzene)
Group 2A – Probably carcinogenic to humans (eg night shift work, diesel exhaust, many chemotherapeutic drugs)
Group 2B – Possibly carcinogenic to humans (eg the pesticide DDT, gasoline exhaust, lead, and coffee!)
Group 3 – Not classifiable as to its carcinogenicity to humans (eg hydrogen peroxide, melamine, chlorinated drinking water)
Group 4 – Probably not carcinogenic to humans (the only example is caprolactam)

Probably vs Possibly?

The IARC likely classified cell phone radiation as “possibly” instead of the stronger “probably carcinogenic” since although there have been a number of conflicting epidemiological studies looking for a relationship between glioma risk and cell phone use, there remains a question about causality due to the lack of laboratory studies in model organisms, and the fact that the relative risk increase isn’t particularly large.

The largest study performed to date was the INTERPHONE study published last year, which was an international case-control study looking at 2708 cases and 2409 controls from 13 countries, which found no significant increase in either glioma or meningioma risk in cell phone users with 10 years of exposure information.  In fact, they found a slight opposite trend, which they attributed to potential sampling bias or methodological concerns with accurately determining the dose of radiation received.  The one result that may be suggestive of a negative effect was found in the highest exposure group – that is those who had reported >1640 hours (~30mins/day over 10 years) of calls without using a handsfree device — there was an odds ratio of 1.40 meaning a 40% increase in relative risk of gliomas (which at a baseline is only 4-5 per 100,000 people in the US).  Most true carcinogens however possess a dose-response such that exposure correlates with tumorigenesis over a range of values, which was not observed in this dataset.

Can we really know yet? What is the mechanism?

Cancer is a multi-step process that results from accumulation of mutations (and we’re now appreciating, epigenetic changes) in multiple genes that often takes many years.  It has been estimated that for most solid tumors, these ‘hits’ occur over a span of 10-20 years. Given that cell phone use has only been widespread about 10 years, there is significant concern that if there truly is a link, it might still be too early to detect changes in incidence of gliomas, which are not one of the tumor types we can easily detect at an early stage.  Current incidence data as shown in figure 1 (from a recent NCI report) does not support the claim that increasing cell phone use can be causally linked to gliomagenesis.

Figure 1: Glioma incidence over time

Only time will tell whether these curves remain constant or the slope changes.  Even if the epidemiological evidence demonstrates an elevated risk of gliomas, the question of mechanism is still elusive.

Radiation can be designated as either ionizing or non-ionizing based on its wavelength as depicted in figure 2.

Figure 2: Spectrum of radiation (from http://www.astrosurf.com/luxorion/qsl-em-radiation.htm)

Cell phones as you can see, give off long-wave, non-ionizing radiation which does not have enough energy to break bonds, which would be necessary for damaging DNA and inducing mutations. However, radiation at this frequency has the potential to heat tissue.  Whether this could lead to cancer development is an intriguing question.  Radiofrequency waves have been shown in a recent study in JAMA to increase brain activity as measured by an increase in glucose uptake by PET.  Any relationship between this acute response and subsequent cancer development remains tenuous.

Challenges for future research

There remain a number of challenges in future studies.  Since over three-quarters of the world’s population now uses a cell phone (and no doubt this continues to rise), finding an appropriate control group will be difficult. Even though we have historical data as a baseline, as the population ages, we would expect the incidence of age-related tumors such as gliomas to increase as well.

Secondly, as a society we are likely using cell phones differently now – many of us carry around our smartphones in our pocket all day, whereas 10 years ago when they were big and bulky and had shorter battery lives, this was less likely to be the case.  Too, the large number of different models and styles of phone might potentially affect the magnitude of radiation absorbed by the cells.  Since the product lifecycle of phones is now condensed into less than 2 years (even 6 months in the Android market is “old”), even analyzing whether there are associations due to good-or-bad performing phones will be difficult.

Determining exposure will continue to be a problem especially as awareness of this potential association increases – self-reporting of time spent on the phone may begin to suffer some of the inaccuracies seen in other surveys measuring diet or lifestyle factors.

The bottom line

So coming back to the question I raised in the introduction, should we worry about cell phones or not???  No doubt you’ve all made your mind up by now, but hopefully you’ll agree that the issue is certainly not black-and-white.  IMO the data isn’t really strong enough to personally stop me from using my cell phone for a call or 2 a day (at most), but if you like to chat for hours and hours, perhaps switching to a earpiece may be worth the potential embarassment, not to mention it would be safer if you’re driving or walking around a city. For some other practical tips on reducing your exposure, visit the Environmental Working Group’s page with 8 sensible-sounding pieces of advice.  Cumulative dose may be the key – so minimizing exposure of children may be prudent since they will likely have decades of using such devices, increasing the chance for harm, especially since it is known that children have thinner skulls than adults (by a factor of 2-4fold) which would lead to a higher penetration into the brain parenchyma. Perhaps as a public health concern, we should lobby the carriers for free text messages for all!

Figure 3: Skull thickness by age

What say you?  Will you alter your behavior as a result of this study?  Do you already use a headset while on your phone?

Recent Science Roundup 1

Its been a busy few weeks since my defense when I last blogged.  We had a nice trip to DC to receive the Cozzarelli award from the National Academy of Sciences, then the following week I had my folks in town for graduation, and in between, did thesis corrections and paperwork. Yes, they don’t tell you but the paperwork is the worst especially when you have committee members in 3 cities (5 separate buildings)…

Last week was a semi-normal lab week, and now I’m in sunny San Diego for a little break to visit my friend Mary Canady…. So I thought I’d start blogging some real science, so thought I’d try a short-summary format for a few pieces of science that have been mentioned in the media recently, not necessarily in my areas of expertise. Let me know what you think of this format.

1) Coffee consumption decreases risk of ER-negative breast cancer

This is an interesting Swedish epidemiologic study published very recently in the open access journal Breast Cancer Research. The basic design of the study, which attempted to replicate previous studies, is what is called a case-control study, where 2,818 cases (ie patients) and 3,111 controls (non-breast cancer patients, matched as closely as they could) were analyzed.  Importantly, pre-menopausal women and those who had other cancers previously (except non-melanoma skin cancer or in situ cervical cancer) were excluded so these results can only be extrapolated to the post-menopausal setting.  A detailed

Mmmm coffee!

questionnaire allowed the correlation of tumor status with coffee consumption, and factors including HRT use, educational level and alcohol consumption also taken in account.  The overall conclusion drawn was that high coffee consumption (defined as 5 cups per day) can modestly decrease the risk of ER-negative breast cancer (which is the more aggressive form that cannot be treated with anti-estrogen therapy).

My training in basic science of cancer biology leads me to postulate on some of the potential mechanisms of this protection, which are briefly proposed in the discussion section.  Coffee is known to contain hundreds of chemicals, including caffeine and polyphenols which have the potential to act both as carcinogens or as chemo-preventive agents, and dissecting out which is responsible for the protection will be a challenge. Caffeine is known to be an inhibitor of the ATM/ATR proteins which I worked on in my PhD which are involved in sensing DNA damage and inducing repair, which would be an undesirable effect of high coffee consumption, however coffee is also the largest source of anti-oxidants in the US diet, and there are weakly estrogenic compounds such as trigonelline in coffee which would only promote the growth of ER-positive breast tumor cells but have no effect on ER-negative cells.

The major downside of this study is that it’s merely a correlation – establishing causation in vivo for something as widely consumed as coffee would be a major challenge. While it’s definitely possible that this negative relationship between coffee consumption and cancer risk is merely a marker of some other factor that is indeed correlated with cancer risk, I tend to doubt this explanation given what is known about the role of coffee in cancer risk in other tumor types as well, and the vast number of chemicals found in coffee that could possibly regulate steps involved in tumorigenesis.

So while this is not medical advice, I think it’s probably safe to say enjoy your coffee in moderation and there may be a potential health benefit in some circumstances.

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OK I had thought of doing multiple articles per roundup (hence the #1 on my subtitle) but it seems maybe one is long enough. What do you think?

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References:

1. Allred KF, Yackley KM, Vanamala J, Allred CD. Trigonelline is a novel phytoestrogen in coffee beans. J Nutr. 2009;139:1833-8.

2. Arab L. Epidemiologic evidence on coffee and cancer. Nutr Cancer. 2010;62:271-83.

3. Ganmaa D, Willett WC, Li TY, Feskanich D, van Dam RM, Lopez-Garcia E, et al. Coffee, tea, caffeine and risk of breast cancer: a 22-year follow-up. Int J Cancer. 2008;122:2071-6.

4. Li J, Seibold P, Chang-Claude J, Flesch-Janys D, Liu J, Czene K, et al. Coffee consumption modifies risk of estrogen-receptor negative breast cancer. Breast Cancer Research. 2011;13:R49.

5. Tang N, Zhou B, Wang B, Yu R. Coffee consumption and risk of breast cancer: a metaanalysis. Am J Obstet Gynecol. 2009;200:290.e1-9.

6. Yu X, Bao Z, Zou J, Dong J. Coffee consumption and risk of cancers: a meta-analysis of cohort studies. BMC Cancer. 2011;11:96.

PhD Defense Day!

Those of you who either know me IRL or follow me on twitter or facebook know that I defended my PhD successfully this past Friday. Yay!  After a relaxing weekend where I attempted to think as little as possible about science (didn’t succeed to ignore completely), I’m ready to get back in the lab tomorrow, start working on some of those experiments for our paper revision, and finish up the edits on my thesis and get all my paperwork squared away for graduating and postdoc stuff etc….I have a rather long list of demands on my time for the next 2 months that I will be in my PhD lab before moving.  But my blog has to start somewhere, so I guess I’ll write some about finishing up my PhD.

D-day was rather anti-climactic to be honest.  While I had a lot to be confident about (being a quite successful student with my own funding, lots of awards and more than the average number of publications etc), the last minute nerves still got to me, mainly felt in my stomach.  Haven’t had this sort of anxiety for many years – even though as an undergrad contemplating grad school, I was scared of the candidacy exam (after all, they could ask you ANYTHING – impossible to study, right?), once it actually came up, I was pretty confident since I knew I had nailed the written proposal, that the actual presentation and questioning were rather benign.

So why was I so nervous about my defense, since intellectually I knew that in my program virtually no-one actually fails at that point, that candidacy and committee meetings are the weed-out points?  Well, it was more to do with having rushed the writing of my thesis for various reasons that had me on edge.

Earlier in March-April I had 2 back-to-back conference trips (and then an immediate day-trip to Houston), when I told myself I would make good progress on my thesis, which I had only just outlined before leaving.  Coming back from them still on chapter 1, section 1.4, wasn’t exactly what I had in mind for ‘good progress” on a thesis that was due at least in draft form less than a week later to the graduate school (which I subsequently got a short extension for by being nice).  Somehow I still got it all together in time (basically pulling 16-18 hour writing days in a few coffeeshops, including a close-by 24-hour one), and got it off to my committee a whole 5 days before my defense.  After taking a day breather with no writing and no coffee (which by then I could feel was affecting my appetite and GI system), and taking care of some life stuff, I began my presentation 2 nights before my defense….still not nervous.  I mostly finished it that night, and just left some minor polishing to do on Thursday.  Then Thursday I pretty much became a nervous wreck as can be seen by some of my tweets and facebook postings (figure 1).

Figure 1: Me freaking out the night before

It was heartwarming however to see all the great tweets of support from my “twitter friends” most of whom I still (unfortunately) don’t know IRL yet….its impossible for me to select a single special one, so figure 2 has most of them.

Figure 2: Look at all those sweet words of encouragement

Somehow I managed to get a good 4 hours of sleep on Thursday (normally if I’m that nervous I’ll stay up all night)…and in the morning, I got into one of my new favorite outfits, and I got ready to leave, with plenty time for a Starbucks tea stop (since it was also Earth Day and they had a promo for free tea/coffee if you brought in a reusable cup J ).

I arrived at the auditorium where my defense was held nice and early to setup, and test videoconference, and then I sit and chat with my friend Mary (thanks for trying to keep me calm!) on twitter until finally my PI and committee show up, and small audience, given that it was Good Friday afternoon.  PI begins and gives great introduction, and I’m still a bit nervous after her setting up all the high expectations, but once I’m a few slides into the background I settle down, and give probably one of my best talks ever…managed to slow down when going over data, and talk is perfectly timed, without any true run-throughs of this particular presentation (although large parts of it were similar to most recent student seminar in January).  So then closed grilling begins, and surprisingly it was rather mild, and my PI couldn’t even think of 1 scientific question (so she makes up some general grad student question on recruiting etc)…a total of  ~20 minutes pass before I get sent out for the committee to chat, and a minute or 2 later get called back in with the good (expected) news.  So that’s the story of my defense.  Glad it went so well, but wish I wasn’t so nervous.  PI even admitted later during champagne celebration outside the lab that it was the best thesis she’d read, and now that I’d pulled off that feat (writing the whole ~200 page masterpiece basically in 2 weeks) that I wouldn’t get to take a month off to write grants like some PIs do.

Final stats on my thesis (pre-edits, but these shouldn’t add a significant amount):

-       Pages = 200

-       Words =  34,738

-       Figures = 75

-       References = 206

Anyone else have any interesting stories about defenses? Or large writing projects?  Next time maybe I’ll delve more into how I managed to write it in that short of a time (other than writing for hours-upon-hours a day).  If anyone has any questions feel free to ask in the comments, and if the answer is long enough maybe I’ll make a special post for you.