Friday, December 25, 2009

I had a baby!

It all happened mostly Wednesday night, so that at 8:40 am on Christmas Eve, she was born! She was 7 lbs 10 oz, and all I will say for now (maybe more later about the experience) is that whoever invented epidurals and started using them in childbirth should win the Nobel Prize.

Here she is with her daddy:

Friday, December 18, 2009

Interminable

Now is when I really, REALLY wish I lived closer to where I work. I've been stuck at home for almost two weeks now (because I'm not supposed to travel further than an hour from my hospital at this point), working on grants and other computer-based things from here. The first week was GREAT, it was so nice to have the peace and quiet and comfort of being at home, I got a lot done and felt very calm. But this second week has been increasingly sucktackular. I am on edge with every weird feeling, thinking "maybe I'm going into labor now!" (but never am), trying to get work done and forcing myself to read the abstracts and fill out paperwork for the meetings I have coming up this spring. All the while there's nothing to distract me but my sleeping dog and "A Baby Story" on TLC; nobody to talk to, nowhere to get much of a change of scenery except for the mall (and I don't need to BUY any more STUFF--we've been BUYING STUFF for months for this baby!!!), wondering how my lab is doing, wondering when this baby is going to come out.

I still have some cleaning stuff I want to do, but a lot of it is vacuuming, and I need help carrying the vacuum downstairs and moving the furniture around. I might end up doing it anyway, just very, very slowly. One chair at a time.

If I just lived close to campus I could go potter around in my office there and at least get to TALK to people. I don't know anyone in our town or anywhere nearby, so I can't even go have lunch or coffee with friends or family or something. I can tell I'd make a really, really bad stay-at-home mom, given that I haven't even lasted a week before getting extremely antsy and starting to mope out with the boredom of this constant lonely scenery every day. Bleh.

Tuesday, December 15, 2009

No love for the pregnant lady

You know, I was looking forward to my Minnesotan-"Oh noh, it's okahyee, I don't want to bother anyone!"-self getting to accept some sympathetic charity door-holding, seat-offering and otherwise special treatment you are supposed to get when you're pregnant. But have I gotten any love?? NO!!! I have had none of those kindnesses from strangers, in fact, I've had people budge in front of me in lines and rush to get a seat before I do many a time. I even had one experience at 8.5 months at a gas station where *I* held the door for some other, non-pregnant lady who didn't even say thank you, and she rushed in front of me and hurried to the single-occupant bathroom before I could make it there with my waddle! We both stood there in line waiting for someone else to come out, so she could tell that was where I was headed. Beeyatch, pregnant ladies need to pee badder than you do! I scowled at her when she left.

I also had multiple experiences at 7-8 months, rushing as fast as I could manage through airports trying to make connections after my plane came in late, OBVIOUSLY struggling (a couple of times I even started to cry), and nobody helped me--I got passed from both directions by more than one non-busy-looking airport beepy truck-cart thing, and nuthin.' I was too out of breath and agitated to yell after them to come back for me, and nobody else came to my rescue, either.

Boo, world, boo! Whaaaaaa frickin' whaaaa!

Sunday, December 13, 2009

Screw you, reviewing for random journal.

Ya know, I should have known better than to get involved with reviewing for a random open access journal that I'd never heard of before and that does not have a known reputation, but I thought I would try to do my duty and help promote this, since fundamentally I like open access and think it is a good idea. Also, I recognize my responsibility to participate in peer review and actually enjoy doing it most of the time.

But the one I just worked on apparently also does fairly open-access reviewer recruitment, as well.

If you're going to ask me to review a very, very bad and badly written manuscript for your journal--telling me it must be completed within a two week time frame, and treating the communication as officially as other journals do with requests to review--and if I spend an entire evening working on this pile of crap, sifting through it and analyzing what the hell is going on so I can make a relevant critique of what the problems are with it, then you better understand that it is going to piss me off when I get an email from you telling me that:

you've received many more peer review comments than anticipated...

and so you are closing peer review within a few days. Meaning, I have to assume, that you spammed a bunch of reviewers and accepted all of their "accepts" to review and wasted everybody's time. If I knew a cast of thousands of reviewers were also laboring over this piece of junk, do you think I would have used hours of my precious time on it too??? This article was not a blog post, for me to take my time at commenting on if I felt like it and had a minute. You asked me to review it as I would for any other peer-reviewed publication.

How disrespectful is that?

Wednesday, December 9, 2009

Exams: harder for teachers than for students.

I am having so much trouble getting creative about exam questions, and I only have to do a few for my co-taught course here (and I am responsible for far less material than the course director)! I feel an obligation to come up with something interesting and challenging, but that is still within the capabilities of the best students in the class. I think stereochemistry (my main topic) might be one of the hardest chemistry topics for which to do this. For one, it is so easy to accidentally screw up your design of the question because there are so many perspectives on molecules that can lead you astray. For two, I used all my good ideas last year and for the previous exam this year, so coming up with something fresh is really wracking my brain. For three, my mental prowess has checked OUT as of about two weeks ago, and I am feeling like I have oatmeal in my head. Stereochemical creativity and late pregnancy do not go well together.

I don't want to, and absolutely refuse to, go with the 'search the internet and find something someone else has done.' Nor do I want to just slightly alter some question from before, without incorporating a substantially different challenge of some kind. So, that leaves me with no choice but to wrack my brain and meditate until I chance upon some great idea for these questions. I'm gonna have to make sure I develop this skill, because in a few years I'll be on my own for the whole course, rather than just a couple of chapters. Dang.

Tuesday, December 8, 2009

A sexist kind of cancer...

So I lol'd at myself today. I got an email announcing a call for applications to a certain cancer research foundation that said the following:

"This round of awards will focus on funding Treatment Science: studies of new ideas in man or laboratory support of a high impact clinical investigation." (emphasis mine)

and had my usual twinge of disappointment/irritation about using the term "man" for human-based research... every time I read or hear that it is like almost walking into a glass wall with a big cringe. But then I realized it's a PROSTATE cancer foundation, so yes, indeed, this is one place where it's wholly appropriate to use that term. I dunno if they realize that or not, but hey.

Saturday, December 5, 2009

ZOMG

I want to blog about something so, soooo bad but I can't because of the inevitable gradual dissolution of my pseudonymity and the potential that the wrong people would read it...


AAAAAAAAAAAHHHHHHHHHHHGGGGHHHH!!!

If anyone wants to hear my possibly profanity-laden tirade, just spot me an email and I'll indulge you (as long as you are not a secret spy out to expose my frustration on this issue). GRRAAGGGH.

Tuesday, December 1, 2009

Family leave and grants

Is this normal?:

At my institution, NIH grants cannot be used to pay the salary of someone (whether PI, postdoc or grad student) on paid family leave (such as maternity leave) for more than two weeks of that leave. As far as I can tell, you are allowed to be off on maternity leave for up to three months of the project on which you are a PI without notifying NIH and giving back your money or otherwise changing around your budget, but the institution becomes responsible for covering that leave pay on general funds. This is happening for my grant, which normally covers a major portion of my salary and is cost-shared by my department. But while I'm away for maternity leave, the department has to foot 100% of my salary bill.

I can't tell if this is an NIH policy or what--Real support (particularly for young science moms) means dollars. It looks like despite the talking of big talk, they still leave the pressure of supporting research staff and PIs who have children on the PIs (in the cases of grad students and postdocs on leave) and institutions (in the case of PIs on leave).

But then there's this policy... and this one at NIAID, which provides supplements to PIs whose postdocs go on family leave so they can hire a technician for up to two years--which would address the transitioning of the project work (that I think it was drdrA who discussed before)... I am confused.

Monday, November 23, 2009

Loss of a mentor

My PhD advisor passed away last weekend. He had been fighting with prostate cancer for about six years. When prostate cancer is caught early, it is relatively curable--unfortunately, his wasn't found until after it had already invaded his bones and lymphatic system. He pushed through all of his treatments with such enthusiasm: as a cancer researcher, he got involved in a bunch of experimental things and was so interested in all of it. Just a month ago, I was in touch with him over email and he said they'd pretty much run the gamut of options both traditional and experimental, and there wasn't much left to try. He was still upbeat about it, but the writing was pretty clearly on the wall and he was getting more and more worn out by the amount of steroids he needed to take to keep everything up and running.

Even with all of the six years of preparation, his death was sudden. He fell down at home and just didn't make it through. In a lot of ways, it is almost a good thing: it saved him the disappointment of waiting and watching more attempts at treatment fail, and for himself and his family the horrible experience of how cancer grinds people down until there is nothing left.

He did so much for me--he personally is the reason I am where I am today with the life I have now. He offered me a place in his group, an American student brought into a program in the UK and provided with full funding, even though I didn't have the 4.0 from Harvard and the fancy pedigree. The three-year PhD timing meant that I was in the right place at the right time to apply for my postdoctoral position, which ended up changing my career goals and potential immensely for the more ambitious. Even though our funding was extremely meager at the time, after he heard me joking to some labmates that I was back to eating rice and frozen vegetables halfway through the month because I had run out of money for groceries, he then magicked up an extra 60 pounds a month for me (~$100) so I could afford to do enough shopping.

I am very grateful for the path he helped me set for myself to becoming independent and ready for this job/life combination. He was traditionally British, conservative with praise and fairly reserved in general, so although I knew he was pleased with my results and he always wrote positive rec letters for me, it was difficult to read what he really thought. One of my former labmates had dinner with him and his wife a couple of weeks ago, and shared with me that he talked a good deal about how proud he was of me and how well I am doing, and that I turned out to be one of his best students in his 30+ year career. It means a lot to know that this dry, quiet Englishman thought a little bit superlatively of me after all.

Tuesday, November 17, 2009

Study Section!

Whoo, I just got my first invitation to participate in an NIH review panel. I'm super excited! It'll be happening towards the end of my so-far-scheduled maternity leave, and it will be interesting to see whether that makes it more or less stressful to focus on (compared to when I'm back in business on campus)... It's also a field I'm really interested in, and a type of grant I'm relatively (in my junior investigator inexperience) experienced with. That will make it easier to not feel like a noob, although I am sure I still will. Should be fun!

Monday, November 2, 2009

The homestretch

of pregnancy...

is making me want to chew on baking soda and eat salt crystals. I used to do this when I was a teenager: it was some form of pica, where I would just chew on then spit out spoonfuls of baking soda before they dissolved. Then I would rinse out the residue and make sure not to swallow any of it. I started craving this again now that I am at month 8. I guess it's good for my teeth? I am trying to avoid the salt eating since my ankles are already swelling enough without excessive salt. But my BP is still low so at least that's not a worry.

I am also addicted to chewing on ice--and not just any ice, it has to be certain sizes and shapes of ice cubes to be the best, approximately 1 x 0.5 x 0.5 inches, the more rock-like the better. Of course any ice will suffice but only that kind makes me truly happy.

Sunday, October 25, 2009

Culture gap: synthetic chemists and learning biology

I started responding to this comment:
Now that you have invested so long to transform in to a 'chemicalbiologist', would you mind suggesting some quick tips from your journey for the people ho want to take the same path? Are there any books or some crash courses etc?
And got so in depth that I decided to make it a post of its own. So here are my thoughts about where to start to develop better flexibility as a synthetic chemist who wants to work on bilogical problems.

The best crash course I got was weekly lab meetings in a lively, rigorous yeast genetics/molecular biology/kinase signaling lab (one of my postdoc labs). I started out so clueless that I felt like I was on Mars for the first year and a half or so. But because the people in that lab were so open and helpful, and the PI is an engaged, active teacher, they helped me learn the "language" of biology-type ways of thinking and data/information representation.

It's that language that you really need as a chemist moving into biology. And by "language," I mean more than just terminology (although that is a big part of it). It's also a change in visualization of information and getting better at logic puzzles. Imagine a multi-step synthesis with a blank at step 2, where 4-5 possibilities (which you have assumed based on either mechanism or other times people have done similar things) could fit in there to result in the product (or mixture thereof). In biology, you have to come up with ways to test *which* of those possibilities comes from the retrosynthetic direction (for which you are only postulating a route) and will result in the product(s).

In all of this you also have to accept that: a) your only measurement techniques are indirect, i.e. you usually can't just analyze the structures with some direct spectroscopic technique and figure out what they are; and b) your assumptions might be wrong. So you have to do lots of control experiments where you also assume some certain set of reagents should DEFINITELY give the products, and some other set should DEFINITELY NOT. That gives you yet another indirect way to make you feel more comfortable with your assumptions. The hardest part for many chemists is having to be okay with indirect information. The second hardest part is having to remember that if your "result" gives you something analogous to "75% yield of the product," you still have to think a lot about WHAT molecules/interactions are represented in that other 25%. You can't just purify it away and pretend it didn't exist.

Getting used to reading gel electrophoresis/Western blot (antibody detection) data, as well as biological "cartoon" format (where you mostly worry about conceptual connections, and not so much molecular mechanism and byproducts etc.), are some great ways to start. But you'll probably need a coach to guide you through it and translate how the experiments work and what the results mean. Finding friendly, sharp biologists (whether faculty, postdoc or grad student--it doesn't pay to be snobby about this, sometimes the trainees are gonna be WAY better at teaching you! Just make sure to credit them or repay them somehow!) can be the difference between this working vs. not working.

Sunday, October 18, 2009

NIH mentoring and grantwriting workshop (UPDATED 10-23-09)

I am spending the next three days at a secret location for an NIH conference grant/Program Officer-run grantwriting and mentoring workshop. Anything that is not confidential (i.e. pertaining to the specific research information shared there by proposal donators and other attendees) and might be useful to people here, I will share either as I go or after we're done! I'll just keep updating this post with info.

To discuss mentoring issues, we had multiple 'breakout' style discussion sessions where we submitted questions we had and examples we wanted to talk about, and then spent significant time digging into our own junior faculty perceptions on them and getting the more senior faculty and PO perspectives. The quality of the senior faculty "workshop mentors" was outstanding: they were all engaged and engaging, enthusiastic and contemplative. They gave us their candid but also well-considered takes on stuff from how to recruit good graduate students to how to deal with misconduct observed during the review process. They all offered their continued support, too, if we ever run into situations in the future where we don't have local senior people to help us (or just want some alternative perspectives). SO worth it.

UPDATE 10-24-09: To address a good point that CPP made but also highlight what the workshop was really about, I updated the wording about "a compelling human health relevance."

UPDATE 10-23-09: This workshop was particularly focused towards junior faculty in synthetic organic chemistry, bioorganic/bioinorganic chemistry and chemical biology. I'll give snippets of stuff about different things we learned/talked about and experiences we had as I have time. Right now I have 5 minutes, so I'll tell you about the major NIH R01 take-home message from the workshop. The key, especially for chemists and anyone who does basic synthetic research that is not necessarily easy to connect to a disease, is to establish a credible, compelling human health relevance through developing a depth of understanding and solid rationale within the biology you want to study.

If you love inventing new ways to make complex natural products, it is NOT ENOUGH to just say "this natural product is interesting because it kills a cancer cell line with a potent IC50 and came from a sponge." Nor is it quite enough to say "This methodology is interesting because it would allow access to chemical structures or information about biological function that is hard to get otherwise." You really have to craft a strong argument for WHY your particular methodology or hypothesis is fundamentally important to the study or treatment of a human health problem at whatever level your work can fit, for example:
  • tool-development for basic biological research
  • novel methodology for accessing difficult molecular architectures that can probe or affect biological function
as well as HOW it represents a new angle for approaching the problem. Once you lay that groundwork in the beginning through the specific aims page, "significance" and "innovation" sections, THEN you can get more into the details of your specialty. But no amount of beautiful chemistry or insightful methodology will get you past the hurdle of not finding a compelling connection to a disease-related biological knowledge gap.

Thursday, October 15, 2009

You know you don't get out enough when...

The Jimmy John's delivery kids know it's you by your voiceless, faceless online sandwich order and also know exactly how to find you in your labyrinthine hiding place of an office to bring you your lunch.

Wednesday, September 30, 2009

First paper accepted!

Yay!!! Our first manuscript was accepted after a re-tool and re-pitch necessitated by finding out I was wrong about us being "first."

Lessons learned:

1) READ the literature even MORE than you thought you have.

2) Be very flattering, polite and conciliatory in responses to reviewers even when you are not doing precisely what they wanted you to do in the revision (such as not performing a whole new set of control experiments that would only minimally add to the confidence in the result, and instead just thanking them very much for their insight and modifying the text to emphasize the controls you DID do).

Tuesday, September 29, 2009

Oh, blog.

I wish I had time to write in you. There are so many things to talk about, but 2nd year junior faculty life is kicking my butt. I am barely hanging in here, with days that fill with "essential" tasks that end up having little to do with getting my grants written.

Last year I made a figure that illustrated that I still have time available in the day and should be able to maintain efficiency even when busy. I now take that back.

There should be a little window of blogging opportunity here and there, especially once the semester ends and I am working from home as a 9-month pregnant lady waiting for a baby to come out.

Until then, little substance is likely from me. :(

Monday, September 14, 2009

Working from home

Ahh, what a good idea. I was completely stressed out about an impending deadline or three, arriving back last night from being at the NIH for a mini-conference last week with a blinding pregnancy headache, in other words totally dysfunctional. It's amazing how productive a day at home can be. Tasks accomplished:
  1. Dog picked up from boarding!
  2. Internal pre-proposal deadline met, including finishing project description and designing informal budget!
  3. Laundry completely taken care of!
  4. Clean dishes put away and dirty dishes put in dishwasher!
  5. Appropriate amount of calories and units of calcium/protein-containing foods consumed!
By saving myself the three hours I spend in the car every day on my commute, and the distractions of having an office right in my lab where everything and everyone catch my attention away from the work I'm supposed to be doing, I was able to actually get that work done. It is really nice to do this once in a while.

Now I need to use some of my husband-free evening to lay out my fall calendar with the other deadlines coming up, including:
  • two manuscript submissions
  • up to four proposal submissions
  • redesign of my lecture content for teaching beginning in two weeks
  • instituting a weekly journal club for my lab to start ASAP (they need it, not least for preparation for their cume exams, last two chances to pass occur over the next two months)
  • getting my lab ready for me to be gone for 2-3 months
  • getting myself and my house ready for having a freaking baby
It's gonna be one of those semesters!!! Jeebus.

Thursday, September 3, 2009

The fluuuuuueeeeewwww

I'm teaching in a big class this semester, and the other prof just told me that we've already had 2-3 students let him know they have what is very likely to be H1N1. Since I'm in a high-risk group (gestation makes you something like 6X more likely to die, based on a general death rate of 1% but a death rate in pregnant women of like 6%), and slightly OCD as it is, this totally creeps me out. Every sneeze, cough and sniff I hear in class is going to give me the heebie jeebies, and I'll be bringing my hand sanitizer to keep myself as purified as possible. Still it's extremely likely I'll get inoculated by this environment, and I can only hope it doesn't happen until AFTER I've been able to get vaccinated WHICH ISN'T UNTIL OCTOBER at the earliest!! And when we had our big institutional presentation on H1N1 to the faculty it was not clear (because nobody knows yet) what we should be doing to avoid infection ourselves in the two months of school before the vaccine is available...

Yeecchhghghg, it just weirds me out and makes me feel like everything is dirty. We already showed our class the video on Doing It In Our Sleeves and I can only hope it sunk in!

Monday, August 31, 2009

Congratulations to Dr. Jekyll and Mrs. Hyde, and apparently Becca too??!!

It sounds like we have two new blogosphere babies, with the same birthday!! Congratulations to both of you!! I want Becca to start a blog to tell us about what it is like to be a new mom in graduate school (right?)!

Wednesday, August 26, 2009

IRBs like crazy!

I am becoming a total pro at whipping up an IRB exemption application. I am now approved for three and on my way to a fourth. Once you get the hang of it it's really not so bad, and the research I am proposing is all unharmful, uses either educational data I already have access to or samples from tissue banks, from companies with pre-existing protocols, or that will otherwise be discarded.

We're working on getting one of our technologies tested out in some patient material, so we needed to get access to stuff. Since my institution does not have a medical school, that proved to be a lot trickier than I originally thought it would be. It turns out that custom patient sample collection protocols for somewhat obscure diseases COST A FRICKING BOATLOAD! You can't get samples without money, and typically cannot get money without pilot data, which requires samples of course. So we were caught in this circle of complication. Luckily, we found a company that has reasonable prices on fresh sample collection and can get us the material we need under the conditions we require. I am able to spend my start up money on things like that, and will be applying for grants to fund bigger translational projects as soon as we get some data from the pilots. But essentially, it has taken a YEAR to get to the point where we will have samples to test on. WHEW!

My other IRBs are for educational studies. I'm trying to maximize my ability to demonstrate scholarly productivity even while spending some time trying to improve my teaching and provide research opportunities to kids. As part of my CAREER award proposal (submitted this past July), I am working with two organizations, on-campus and an off-campus, to provide high school student research lab experiences in the summer. I IRB'd it up to actually do some analysis on the outcomes (perceptual confidence-wise and demonstrable career-path-wise) for the students who join the program. The other one is to try out a new technology in the class that I teach with another professor and to study whether it helps the students do better or not. For both of these, I plan on trying to get a publication out of it to get my added value and combine efforts. In our School, just being a good teacher doesn't necessarily help you much for tenure but publishing on educational research does (as long as it is only a small part of an overall well-established research program).

So after not even knowing that IRB existed a year or so ago, I am now a professional human subjects researcher. Yippee!

Thursday, August 20, 2009

What's a henweigh? About a KILOGRAM??

Ok, this story on NPR this morning about the weight of the kilogram had me thinking that analytical people just need to take some lessons from general chemistry and significant figures.

I mean, seriously, everyone's freaking out because "THE" kilogram no longer weighs exactly the same as its copies, and flapping their hands about dramatically that they don't know whether the kilogram "ITSELF" has changed in weight, or if the copies have changed.

When I was taking Gen Chem, then Organic, and then teaching these things to others in subsequent years, I came to accept that all numerical amounts in calculations (even in P-Chem) are only relevant to within certain significant figures because our means of interacting with those amounts are fundamentally limited. Limited by both technical possibility and effect on observed outcome. There may be theoretical applications in which we need to define certain constants, certain amounts, to more precise figures and sometimes those theories get tested, but even then the results are always measured in replicate and determined within a given error.

Similarly, how about if we just accept that there's a certain range of weights out to the Nth decimal place that correspond to "a kilogram" and that there is a margin of standard error, represented by its deviation among "THE" kilogram and all its certified copies? Is it really that big of a deal to know the cosmically most precise, TRUE nature of the kilogram for use in practice? Given the following:

  • a) it's something we made up

  • b) no balance in the world is capable of measuring anything to its exactitude*

  • c) no application in which someone would need to weight out some amount of something for use or characterization would likely ever need to be THAT close
and
  • d) even if the application wanted to be that precise, the readout/outcome would likely NOT be precisely enough reproducible, for the very same reasons that make "THE" kilogram so hard to measure in the first place

Can't we just accept that we mortal, biological beings cannot manifest the abstract so pedantically and with such theoretical precision? Can't we just let the kilogram be like Plato's ideal, and be comfortable with our ability to represent it as closely as we are reasonably capable? Do we seriously need to go to such lengths as working for about 12 years to get it measured on a Watt balance*, or relate a material construct of it to a physical, mathematical constant? I love NIST, but this is one enterprise that boggles my mind.

*The Watt balance at NIST is barely even stable enough to do this, and also THEY HAVE A RACCOON PROBLEM! Unless I totally misheard the radio story, raccoons get into their rafters and chew up stuff that falls into some of the rooms in the place that houses the Watt balance. I'm sure they work hard not to let their raccoon problem affect their balance, but it just highlights my point that the world, reality and our interactions with them are heterogenous things, so why can't we accept that maybe so is our ability to actually manifest a theoretical amount?

Thursday, August 13, 2009

Lab supply company corruption!

The student who does the ordering in my lab just had a really weird experience. She was outside talking on her phone and passed by one of the sales reps from whom we buy some of our supplies. He called her over and asked who she was talking to--she said she was helping someone with directions who didn't know where to park on campus. He said he would give her his temporary parking pass if she would order more stuff from him! She felt a little taken aback and said it wasn't her money, is was Dr. Arlenna's money and Dr. Arlenna knows what she likes in her products. He said something to the effect of "Sure, but you could still make some choices that would get me more orders, and then you could get this parking pass for your friend..." My student then looked at him funny, said "No thanks," and walked away.

What a strange little version of corruption! And good on my student for not caving to the attempted bribe! I don't think you should offer personal favors to lab managers to get more business--promos, better prices, that's one thing. But what's it gonna be next: dinner out? A vacation to the Bahamas (lol)? Where does he think we are, here, Illinois?

Monday, August 10, 2009

Refreshed

I just spent last week in my postdoc city helping teach a workshop that I co-organized last year with one of my bestest friends and colleagues. It was really nice--the participants were engaged, the visiting speakers were cool, it was nice to catch up with folks, and one of my students got to go for free and learn all about how to do a new kind of science for her. It was also good practice to get me reacquainted with lecturing for the upcoming semester--we start in a couple of weeks and I have my big teaching assignment again.

I don't know if it is the psuedo-"vacation," or the second trimester, but something is helping to make me feel sharp, with-it and like I have my stuff together for this fall. Even with all the more and more things piling on, I can see them all falling into their timeslots and it's feeling doable. FOR NOW that is.

Soon, in the next couple of weeks, I will finally post my follow-up to that grad recruitment survey that I did a little while ago. I got an awesome amount of response from so many people, both on the post itself and through email, and I am looking forward to summarizing things for you all who were interested.

And one more thing: I finally need new pants, because I just can't wear my normal ones anymore, and I found some decent maternity clothes! Gap Maternity actually has nice pants that FIT and aren't like potato sacks with stretchy tops. The whole Motherhood Maternity/Mimi/Pea in the Pod franchise seems to be a big scam--their fabrics are yucky (even at the expensive version) and their pants only come in three sizes, S, M and L, so you end up having to compromise on fit and feeling puffy and fat. When you could be feeling totally stylish and cute if they weren't so floppy. The only thing worth buying from that company is the maternity-adapted designer jeans. A pair of 7 for all mankind jeans that I can wear and feel hot in all fall and winter as my belly grows and grows was WORTH the huge pile of money I had to lay down for them.

Thursday, July 30, 2009

Tale of woe #356

Wow, there is nothing like a multi-year-ago-pre-scoop to fire up a blinding case of imposter syndrome even in the most confident researcher. Remember when I found out about getting scooped on one of our proof-of-concept manuscripts a little while ago? And I said oh well, "at least I guess it's better than finding a really old paper that shows you are a dumbass." Well, yeah--I'm a dumbass.

I just got a rejection email from a relatively high impact journal for a different paper we submitted on a different proof-of-concept. This proof-of-concept is the basis for my K99/R00 project (which, luckily, expands upon it dramatically, which I guess was why it was fundable). In the review, the referee said that the work was good but someone had already done it before. They gave me the reference. From 2004. 2004. In the world of technology development, that is last fricking century. I was but a baby chemist starting a postdoc and just learning what enzymes even DO at that point.

Sure, we had two potential novel and exciting aspects--but only mentioned as the next extension, not actually demonstrated yet for various reasons. One of which is that reagent I complained about before that lost 1000-fold sensitivity in the new lot, and for which there is no good replacement product. So, as I correctly stressed about, not being able to show that part of the method sufficiently was a big deal.

But the worst part is, HOW, in all my literature scouring for my K99 project, how did I miss that paper? Were the keywords just totally wacked out? Was the title somehow not close enough to what I was searching for? (It sure as hell looks like it is). I do not understand what my problem was, that I never saw this until now. I'm also weirded out that nobody else I have talked to, in the three years since conceiving of and starting to present about this project in various forums, has mentioned this pre-empt on a crucial aspect of the technology. Could it be true that nobody else knew either besides this reviewer??? No, of course not. It's in a good journal. It's from a good research group. SO WHY DIDN'T I SEE THIS BEFORE TRYING TO SUBMIT A MANUSCRIPT THAT SAYS THE SAME DAMN THING?

This is the stress of publishing in the technology development world. In chemistry, reviewers can give you trouble because they didn't understand what you did or the impact of it. In biology, reviewers will argue with you about your interpretation of your data, insisting you do 16 more controls and change the fundamental scope of your project. In technology development, people will point out to you that somebody already f'ing did what you are trying to report.

And in chemical biology, you get all f'ing THREE of those things pressing in on your impact and ability to publish. That tool who said chemical biology was easy for the "special people" can go suck it.

Tuesday, July 28, 2009

Being a hypersensitive hypochondriac is useful for something

I am super-neurotic about noticing little pains/weird feelings/bumps/whatever around my body. To the point where it irritates the heck out of my family since they are always having to listen to me talk about what new nerve pain I have going on from my herniated disc, etc.

But it's very useful when trying to start feeling baby movements: I was able to feel the first ones at about 14-15 weeks.My doctor was like "Aw, it probably isn't that...you're probably just feeling gas" but I'm now 18 weeks, and it's stronger, and I definitely know that's what it is now, and what it was before. It's pretty cool. :)

Thursday, July 23, 2009

Testing graduate students

In our department, we don't have one big prelim exam that tests our graduate students on what they've learned in their first year or two of grad school. We space it all out over the course of their first year and a half in "cume" exams, on which they need to get a certain number of points in a certain number of tries in order to pass. They also have to do an original proposal, grant application style with an oral defense. I like this way, the stress is more balanced throughout the year rather than all pinned on one day, and it fits a broader range of learning and performance styles.

I have to give my first cume this fall, and I'm totally scared. I have to come up with a current, compelling set of questions on a current research article in a certain topic area that will balance the rigor of what we expect grad students to be able to figure out against what they are capable of handling. I have a few past exams to look at, but they're pretty different from the kind of thing I was planning to do--mostly because I'm forging a slightly different research focus path than most of my colleagues have done, and also, I haven't gotten involved in teaching any of the graduate courses yet so I don't have the same frame of reference for what they are expected to know. There aren't any strict guidelines on what and how you have to write these, so I will be exercising some creative license and hopefully won't bomb it.

As with many of these first-timer responsibilities, I feel like it's more of a test for me than for them!

Monday, July 13, 2009

Women in biomedical research

Female Science Professor has a post up about this report on the status of women in the academic faculty workforce in a bunch of branches of science, including biology, chemistry, mathematics, civil engineering, electrical engineering and physics. The upshot of the report was that:
Although women are still underrepresented in the applicant pool for faculty positions in math, science, and engineering at major research universities, those who do apply are interviewed and hired at rates equal to or higher than those for men... ...women are underrepresented among those considered for tenure, but those who are considered receive tenure at the same or higher rates than men.
HOWEVER, and this is pretty interesting, those trends do not hold true for BIOLOGY. There were a number of other issues discussed in the article that apply to all the disciplines. Particularly that women are significantly less likely to be considered for tenure across all disciplines, which is problematic in itself. However, I want to focus your attention on the one that SUPPOSEDLY tends to attract more women. Despite the dogma that biology is less of a "hard science," and that there should be plenty of women in biology compared to those other STEM fields listed, the truth is that women in biological (and I think we can probably extrapolate/interpolate here biomedical) research end up with the short end of the stick, compared to men of equal rank, on a couple of key issues:
  • Staying in the pool: "while women received 45 percent of the Ph.D.s in biology awarded by research-intensive universities from 1999 to 2003, they accounted for only 26 percent of applicants to tenure-track positions at those schools." In other words, even though biology attracts more female students, it ends up losing proportionately more of them out of the pipeline.
  • Funding: "male faculty had significantly more funding than female faculty in biology; in other disciplines, the differences were not significant." As FSP suggested, maybe this is because the NIH has a bad history of unequal treatment by study sections vs. the NSF.
Both of these are pretty critical to building a bigger representation of women in the biological/biomedical sciences. You gotta feel like it is even worth APPLYING for the job in the first place, you gotta apply and get hired to one that is tenure-track, and once you're there you need to get funded to to make it past your first few years of annual review and be allowed to even submit a tenure packet. Apparently, if we can make it to that stage, then things aren't so skewed, since the report says that of those considered for tenure women are just as likely to get it as men.

So, biology, in other words, you still look like you suck pretty bad with respects to increasing the representation of women among your higher academic leadership ranks. Here you were thinking that you couldn't possibly look as bad as MATH or PHYSICS for goodness' sake, so you were fine and didn't need to worry about it. Well, guess what: you were wrong. You're now the main embarrassment on this front, and you need to get with the program.


Monday, July 6, 2009

First graduate from the lab

So, my first M.S. student successfully defended her thesis today. She worked very hard and made some major progress on her abilities in the lab and writing department, and had a nice package of results with which to complete her MS degree. Her ideas and preliminary work have set the basis for a new direction for our group that got us a one-year internal pilot grant, and could turn out to be an interesting and fruitful direction for our technology. I'm really proud of her.

I also learned a lot about my role as a committee chair before and during a defense. Apparently I CAN jump in and guide the discussion, but I wasn't aware of that and kept my mouth shut at some points where I could have clarified or reworded the questions to help her understand what she was being asked, so our discussion got a little long and drawn out on some more general issues. Fortunately my two faculty mentors were on the committee, so they were able to give me some guidance on it afterwards for next time I have to help run someone's defense (hopefully not for a few more years once my going-into-second-year Ph.D. students get to that point!).

Thursday, July 2, 2009

My cousin's story is being told.

This is a local women's news story about my cousin who I have posted about. As hard as it is to read this, I am so glad that the problems that killed her are being talked about.

Nora's story

Friday, June 26, 2009

Variability

When is a lot of variability too much? How precisely, quantitatively reproducible should biological signaling activation be? If you have different populations of the same cell line, treated all the same way, does it make sense if they still show about 20-40% variance in their response over the course of a bunch of replicates?

How do I know when it's us and our hands, or when it's just the fundamental variability of biology???

UPDATE: Thank gawd for sisters who understand ANOVA.

Thursday, June 25, 2009

Scoooooooop!!!!

During the reference cleanup for a manuscript, I hate finding brand new papers that do something extremely similar to what I am writing up!!!!! DAMMIT!

I mean, I guess it's better than finding a really old paper that shows you are a dumbass. But it still sucks majorly to find out that you can't claim to be the first people who have done something.

Wednesday, June 24, 2009

Why I couldn't drink at the winery tour...

So, about 9 weeks ago, my husband and I saw this:


At that point, even though that second pink line on the one test was pretty faint, our N of 2 was positive even though I was only at about 5 weeks along. Subsequent replicates later in the week were even more conclusive. So, now we are at a total of 14 weeks and so far so good. I have felt pretty crappy for some of the last two months, but am starting to feel a lot better. My lab is all excited and ready to pitch in for the team effort to make this work. I just told my department head today and he was very happy for me and supportive and thinks there's no doubt I'll be able to keep it together. My institution has lots of nice policies in place to make this easier for me to manage, including a one-year turning off of the tenure clock for every time it happens (whether you're the dad or the mom).

My official due date is Christmas day. I'm spending this summer and fall getting my lab all trained in and relatively independent (they are showing great signs of this already), getting a few manuscripts submitted and applying for an NSF CAREER award and an R01. Oh, and I'll be teaching my 2nd time around while ~7-9 months pregnant. LOL. I wonder what kinds of evaluation comments I'll get this year.

So, here we go! Now I'll have yet another aspect of young woman PI-hood to blog about. Let's hope I can make it work!

Tuesday, June 16, 2009

Some pros and cons of the tenure track

As many bloggers talk about a lot, the tenure track, dream job, pyramid scheme of academia is NOT all that starry-eyed grad school applicants chalk it up to be. This is a highly competitive, high-pressure, intensive and sometimes very unfair world. It can be soul-destroying to try to crack into, and only a small percentage of people who want to try it get the opportunity. It's not NECESSARILY a happy place where pottering about on what you love will result in an unassailable job for life with summers off and a four day week. If you're extremely lucky or shrewd, you can turn it into that, but a positive trajectory on the tenure track is NOT a given for ANYONE.

I got myself into this job knowing exactly what the risks and benefits were. I might not have known exactly how I would DO the job, or exactly what the daily function of a TT assistant professor would entail, but I certainly harbored no illusions about what would be expected of me. I also knew full well that it was MY RESPONSIBILITY to figure these things out, that nobody was going to hold my hand and make sure I kept up. I am expected to know what level of grants/publications/teaching excellence will be considered 'enough,' even without any documentation or policy or handbook or helper to describe it in any detail. The job description is intentionally vague: "they," the department and the university, don't want to be too specific for a number of reasons. A lot of tenured faculty resent the idea of getting bean-counted, so they don't want someone devising metrics by which to check off their productivity and progress--and if they made something like that for the TT'ers, then they themselves might have to be compared to see where they measure up. More importantly, the university doesn't want to put itself in a position where denying someone tenure can be tracked back to positive metrics and result in a lawsuit.

So, yeah--it sucks that you never quite know what is expected of you and nobody is going to tell you one way or another if you are measuring up or not. Until tenure, you are an at-will employee, which can be a precarious situation. You can get kicked off the track before you even get up for tenure through non-renewal of contract: at a lot of places (maybe all?) if your trajectory is not promising enough by year 3, your bosses can decide not to renew your contract beyond your 4th year--meaning you never even get a chance to go up against the tenure and promotion committee. It's a luxury to land in a department with high quality mentorship, colleagues who actively participate in helping you succeed from day one, and a department head who does his/her best to guide you frankly and pragmatically and/or who gives you USEFUL feedback at years 1 and 2 that helps make sure you don't get stuck in a non-renewal situation your 3rd year. (For the record, I am fully aware of how lucky I am to have this luxury! My environment is awesome!)

But on the other hand, getting a notice of non-renewal of contract in your 3rd year means you still have a whole year before your contract runs out. A whole year! You can keep doing what you've been doing, wrap things up, apply for other jobs, and all the while keep getting paid according to your original contract. How many other jobs give you that kind of leeway? Most industry jobs have at-will contracts, and when they decide to terminate your position or lay you off for whatever reason, you have about 30 minutes to clean out your desk and head home. Normally there's some severance involved, but only if you are being terminated for some reason beyond your control. Not performing up to expectations (which at least are usually bean-counted and documented a little more thoroughly in industry and government vs. academia), I am guessing, would not be considered 'beyond your control,' so you usually do not get severance etc. Also, while some benevolent companies provide mentorship and support for their employees to work their way up the system, it's certainly no MORE common than in academic departments and I'd wager a guess that it is LESS common.

So at the end of the day, tenure track assistant professors actually have it pretty good. Even if we have to get $1,000,000,000 in grants and 250 papers in 5 years all while living in our offices, eating out of vending machines and climbing uphill in the snow with no shoes on every day... we still have the sole responsibility and opportunity to control our own trajectory for success as best we can, and not many other people in the world can say that.

Saturday, June 13, 2009

Eeeek, a quandary

Hmm. What do you do when you realize (based on your own work and some deduction related to part of the molecule described) that something someone showed in a talk and published in a paper is extremely likely to be completely artifactual?

It's a minor issue, and unlikely to be field-defining or anything, so it's not like some major dogma needs to be unseated here. But the poor scientists who are working on this will likely continue to study this artifact, and it makes me sad because they are very nice people who are genuinely excited about this thing they think it novel and useful.

I mean, maybe it's not an artifact--we'd have to do the experiment to find out. But if it is...

This sucks.

Wednesday, June 10, 2009

Note to self

Winery tours are not as much fun when you can't drink. More on this later.

Monday, June 8, 2009

Conference lonely

It's amazing the confidence and comfort that a speaking slot and a sister can provide for a better conference experience. At the last conference I attended, I had such a good time and met/talked substantially to a number of great people in the society leadership, had fun giving my talk and asked lots of questions. The conference I am at right now is just feeling really lonely. Even though I know more people here than at the last one, none of them are more than relatively passing acquaintances other than a few folks from my postdoc lab (whom it has been very nice to see and talk to! but I do miss rooming with my sistah). Former postdoc PI is very famous in this field, and is here getting an award, and a bunch of his other previous postdocs/students are here too. You'd think that would feel homey, but I just don't feel like a part of that group yet. Maybe I need more CNS papers to fit in? Or just time to get to know these people? Hanging out at the bar or something? Asking more questions in talks so they wonder who I am?

However, speaker and PI wise, this is a very dudely conference. I have counted only about 10% female speakers, even though there are plenty of female grad students and postdocs around and at least a few more female PIs proportionately compared to the number they have chosen to speak. I've had some nice conversations, but it's not an environment where I can just say "Hey let's grab a beer!" to these dudes I do not know. Questions after talks are not very user-friendly, either--the whole conference is being held in this big auditorium and if you have a question you have to flag down someone who runs over to you with a microphone. It makes me an awful lot less likely to get up to ask a question if I know I will have to make a huge deal out of it, waving my arms all over the place, and then still not even get to ask it anyway because most of the mic runners are going to the older dudes in the front seats.

Is this a uniquely young-female-prof problem to have, or do the young-guy-profs have the same uncomfortable fear of having attempts at networking make you appear like some kind of groupie? Is this some kind of imposter syndrome on my part, or is it a legitimate reaction to a closed social atmosphere amongst this group? There are a bunch of events for the "elites," with award dinners etc., and events for the young'uns, with student/postdoc only parties and stuff, but nothing for us tweeners. I guess I just feel like I fall through the cracks here. Maybe I am just jealous that I don't get to give a talk.

Maybe I need to get more involved in this society and start a Women in Such-and-Such Science group, and we can have our own private beer parties with NO BOYS ALLOWED!!

Friday, June 5, 2009

Covers meme (late again!)

I wasn't tagged for this by anyone and was gonna contrarian out, but then I was reminded of these three covers that are possibly my most favorite covers of all time--and indeed three of my favorite songs in these versions. I wasn't particularly fond of any of the originals, which is what makes these even better covers to me. Y'all will probably think they are weird, but I love them! All are by the Moog Cookbook.

Basket Case/Greenday:



Buddy Holly/Weezer:



Black Hole Sun/Soundgarden:

Wednesday, June 3, 2009

First year in review (a little late)

So I missed the blogular deadline for discussing my first year of professorhood by a few weeks compared to my cohort. My excuse is that I have been very bogged down in all the things that have piled up from the completion of this year. I won't do a bullet list this time, but instead be more philosophical about where I am at (and where my lab is getting to).

On the upside, I got a very positive review from my chair, who said the primary committee doesn't have any major concerns about me so far and encourage me to go for "the big money" since it looks like my research has been fundable on a national level so far. On the downside, I am getting anxious about our pace: with the amount of money and people we have, we should be producing publishable data a lot faster than we are.

The main thing I feel now is that the log phase of growth is over. We had a banging start, flying out of the gates and getting set up, staffed and producing data within about 2.5-3 months of my start date. We quickly whirlwinded our way to functional and by the end of the first semester things were looking very optimistic. We started writing our first manuscript in about January, and supposedly only had to complete "a few more experiments" to have it submission-ready.

That's when the plateau kicked in. Plagues of variability, experimental snags, reagents that suddenly didn't work anymore (one after another after another), instrument issues, thing after thing. After all that progress, we started spinning our wheels in the dirt churning through repeated experiments that each had some little different problem, never completed all the way through, rarely with all the right controls until finally in the last month and a half. By then, it was time for my first postdoc to move on to her new lab (she was only temporary here while waiting for her future start date) and now the data-generating torch on that project needs to be passed. I'm holding it right now, and it looks like I will be wrapping this up because everyone else has their own project/trajectory/focus and the re-training time would just not be worth it.

Progress on our other projects has been medium/slow. One of them moved quickly at first, but now is suffering from the travails of interdisciplinary collaboration, where rarely is everyone on the same page and a lot of going around in circles usually needs to happen before everybody "gets" it.

So, this semester, which was supposed to be so productive since I was not teaching, has turned out to feel like treading water. Or like being stuck in one of those bad dreams where you need to run but your legs just won't work. The pressure of getting a paper submitted in 2009 and to get our novel idea out there with our name on it is really weighing on me, and we're in the phase of this process where you just have to keep pushing through the crap and struggle to wrangle it into something worthwhile.

I hope our summer is more promising.

Sunday, May 31, 2009

More lab lamenting

So we think we nailed down which of our plastics were giving us some of the background. But we still can't get any signal. So, we did some other controls and realized that the new lot of one of our reagents is about 1000X less sensitive than the old lot. A conversation with tech support later tells us that this is the only lot currently available. Hmmm. They even sent us a whole new batch (of same lot, though, since there aren't any others) and it is still only able to detect 1000X higher concentrations of the stuff we're looking for compared to our previous lot (which is all gone by now).

So, this sucks. We're stuck. This is a reagent I had already optimized as the most sensitive for what we were trying to do. We can try one other version of it, of which the company is sending a sample, but based on what I have done before I have a feeling it won't work as well. And this is all we need to publish our first paper. :(

Wednesday, May 27, 2009

Bite me LiCor!

F'ing LiCor scanner software, mysteriously throwing away my scan that took 26 minutes to complete you piece of crap! I needed to leave to go home on my 86 mile drive half an hour ago, and now I have to wait for your ass for another 26 minutes!

F YOU!!

Update 26 minutes later again: Oh, and now my dye is dead. Thanks a lot. Now I have to start all over from the beginning.

Monday, May 18, 2009

Oh, plastics.

Lab plastics are the bane of our existence right now. In my postdoc lab, we had certain products from certain brands and they worked a certain way for all of these organic solvent/strong acid mixtures I used to put in them with my various types of experiments. Now, of course, we have tried to move to some different varieties and find that they leach all kinds of background-producing additives into our experiments, and nobody can make the crucial technology of the lab give them reproducible, usable data. GREAT! Who knows if my old lab even still has any of the exact type that worked for me before--so we may never know where to get more, and we'll just have to try a bazillion samples until we get something that works. All when this is the LAST THING WE NEED TO GET THE DATA ON for our paper that really needs to be submitted TWO MONTHS AGO, and meanwhile people keep wasting their precious sample, which we will need to re-run, on these non-working plastics. Sigh.

Tuesday, May 12, 2009

And she's gone.

It's so odd how, now that my cousin has gone (she died on Saturday at about 9 pm), now I can finally talk about her cancer in more than metaphors. I don't know why that was so difficult for me before. Especially since when I talked TO her about it, I could ONLY talk in science and medicine, I was crippled from talking to her about more metaphysical, personal parts. I kept holding up my analytical, informational side for her to talk through the science of what was happening to her, rather than HER.

She died from adrenocortical carcinoma. Only about 300-400 people in the USA are diagnosed with ACC a year. In Australia, there are only a few patients currently. It is such a rare, strange cancer: rather than being undifferentiated like many cancers, these tumors are often differentiated and functioning: they pump out hormones like cortisol, causing all kinds of other side effects that are really unpleasant for the patient. It's extremely lethal, but only when found past stage 3-4. If found instages 1-2 (where the tumor has not invaded other tissue and is still encapsulated), it can be removed and survival with NED is actually pretty good. Unfortunately, because it is so rare, not many doctors know how to recognize the early warning signs, they often get mistaken for other relatively innocuous hormonal/weight/skin issues and so many patients are not diagnosed until stages 3 and 4 when it has gotten so bad, and the cortisol/Cushing's symptoms are so awful, that finally they can see there is something else going on.

And herein lies the problem: our medical system is no good at looking at small numbers of things. When a given doctor may see 1-2 people in his/her lifetime with ACC, they just don't have their radar set to the right level for catching it. We just don't know what to do with small numbers. Large numbers, yes: skin cancer? Totally watched for. Breast cancer?: yup, hudreds of thousands of women mean a nice big histogram to have in mind for someone to fall in the middle of. To that perceptual bias, add the problems with funding for things that don't affect enough thousands of people (a. not enough donors! b. no company will make enough money off THAT treatment!), and we reach the limits of the abilities of our model for medical maintenance.

What's more, she did not have health insurance for the first 3-4 years (or more) that this cancer was probably growing inside her and starting to show its signs. She saw student clinics and other free care options, and was brushed off again and again. Finally the volunteer nurses at one of these free clinics (a woman's clinic in a city) decided to look more closely and figured out to test for cortisol levels. BANG. From there is was a rush to imaging and surgery. Finally the attention that was needed, but about three or more years too late. Stage 4, invading the vena cava. Removed surgically according to what is considered the "typical" protocol, but within six months little constellations of metastases were all over her lungs and liver (which, it turns out, is also extremely typical for this protocol). These cells have an incredible propensity to invade other tissues, and the tiny seeds left over from the cutting and ensuing inflammation just floated on out and germinated in whatever narrow constricted vessels they finally landed. Once that has happened, it is definitely too late to make any major headway in treating this disease.

On the physician side, treatment of this cancer is beset by inexperience, ignorance, hubris and confusion. There are a few experts in the world, and these people are truly excellent--compassionate, thoughtful, giving everything they have to understand how to do the best they can for their ACC patients. But the non-experts sometimes kill people without realizing it. The tumors are soft and easily broken, and also most likely to metastasize when that happens--yet surgeons argue and disagree and can't decide whether laparoscopy or full resection or what-have-you-their-expertise is the best way. They argue academically about adjuvant treatments, disagreeing on paper whether they should or shouldn't help. They talk about staging and survival curves. They forget that they are talking about individuals, people, human beings who are afraid and who can sense that nobody really knows what is going on and that terrifies them.

On the basic science side, because of its small sample size this cancer highlights what we all have been coming to know and accept about cancer: it is a heterogenous disease, a collection of many different diseases from person to person (and frequently even from tumor to tumor and cell to cell in the SAME person), constantly evolving under pressures to eradicate it. When a type of cancer has millions of patients, the statistical biology means that good portions of them will have extremely similar characteristics so they can be classified together, and treatments can be tested out to know roughly what characteristics will respond favorably to which treatments. When the cancer only has a few hundred patients, this process is hit or miss--like doing a blind taste test where even the testers don't know which product is which. And when that cancer is extremely aggressive, the timeframes in which you can test are only months--so it is extremely difficult to really know what is working and what isn't. By the time you finally find something that stabilizes the disease progression, you may have broken down the patient's body so much that they cannot hold on any longer to enjoy their new control over the cancer.

When every patient is their own test case, it is impossible to predict how things will turn out. And it shows the sorry state our knowledge of this biology really is in, that we still need at least thousands, if not millions, of N to be able to make decisions about what is going on and what to do about it. Until we figure out how to quickly and mechanistically understand each patient's cancer, this will just keep happening over, and over, and over and over again. A tragedy each time, that didn't need to happen this way if only we could figure it out. Isn't that our job, science?

Saturday, May 9, 2009

Grad student recruiting survey

Hello current and future grad student and postdoc readers, I have some questions for you!

We have traditionally done pretty well with recruiting, but lately things have waned a bit and we want to know why. We want to improve recruiting in our department, so we can attract more applicants and convince more of them who visit to come to us for their PhDs. We are looking at ways to do this, and I wanted to get some brainstorming feedback from you all out there who are looking, or who have recently looked, for graduate school opportunities. I even created an email address just for this! Please email me (or comment here) with any responses you're willing to share with me: chemicalbilology@gmail.com

1. Where do you look for information about a department? What venues (internet, your current school, your current mentors, conferences, etc.) have been most effective in introducing you to departments that you might not know about otherwise? How important is the department's website in your decision to apply or not apply?

2. What are your top priorities in a grad school department? For example, rank these things (and/or add your own): reputation of department/institution name itself, reputation of PIs and their science, types of grad support available (TAships vs. RAships), length of average graduate student time to PhD, attitudes of current graduate students, exposure to postdocs, friendliness of environment, stipend level, etc...

3. If you were on the fence between two equally solid offers, what kinds of things could the recruiters do or offer to change your mind?

4. On a recruitment visit, what are the most valuable and important parts of the trip? Should there be more time with PIs, or more time with students? How much do social receptions influence your feeling of a department?

5. From afar, who seems more interesting and important to talk to: junior faculty or senior faculty? Do you want to see them give talks about their research, or do you want to spend more time one-on-one?

6. Any other things that stood out as positive or negative from visits you have had, or departments you have looked at (without identifiers please)?

Thank you!! All survey respondents will get a little gold star sticker put on my wall for them! If you don't have a way to answer anonymously by email, please feel free to comment here with your answers. If you do decide to email me, your anonymity will be protected.

Wednesday, May 6, 2009

In which she goes completely off the deep end...

There's this theory in physics called string theory (I think it's currently called M-theory and has moved onto multidimensional membranes rather than loops, but whatever, this is close enough for my purposes), which says that when you get all the way down, down past molecules, down past atoms, down past electrons and to the most smallest fundamental particle that makes up our being, everything is made up of tiny loops of energy (the strings) that vibrate in different frequencies to make up the different kinds of particles.

If this is true, we could think of each of our cells as a collection of vibrating strings all playing a different tone: kind of like a big, deep, complex chord in music. All of our cells together, then, making up our bodies, make up this huge piece of perpetual music. It would also mean that rocks, trees, gas molecules in the air, stars and planets are all made up of the same vibrating strings playing their own particular songs, making us all pretty fundamentally similar.

Following along this thought experiment theory, that means that our 'selves' and the movements we make, or thoughts we have, or memories we build would all have two components: one is the strings themselves, and one is their pattern of vibration. Thoughts are essentially ion currents, in a way, and the movements of those currents would be movements of vibration patterns. Are those patterns just traveling and transposing along a fixed matrix of strings? Or are the vibrating strings picking up and moving around, displacing each other? Either way, kind of like how Plato described the "Idea" horse (the template or recipe for a horse) versus the "actual" horse (its physical manifestation), there is the song that is the pattern of vibrations that makes up "US" and there is the actual physical manifestation of that in a particular set of strings in our place and in our time. There is the sheet music of our being and there is our being.

This means that maybe we are all just songs being played on this planet right now. And our songs can be played anywhere that there are strings, and, fundamentally, a song will still exist even if it is not currently being played on strings. After all, time is just another dimension. To dimensionless things, it is just another axis on a plot to track along with occupancy points.

I know this probably sounded really whacked out and crazy, but even though I can't believe in the traditional ideas about life and death, I'm able to feel hopeful about this fantasy right now. It means my cousin's pattern could still be around forever (for whatever forever is worth to dimensioned things like us), even if her body is not.

Monday, May 4, 2009

Trudging along

I know science gears turn slowly. I have been experiencing this for 14 years (since starting research in high school). But still, it is still a grinding source of frustration to be waiting for other people to turn those gears. This is one of the most difficult aspects of my transition from data maker to PI.

The only thing that salves it is to have multiple people's irons in the fire so that at least SOMEBODY shows me SOMETHING approximately once a day. And this summer, I have to buckle down and do some work in the lab myself, so I am sure by the end of that escapade I will be extremely happy to go back to having other people bring me the data.

But MY GOD it feels slow!!!

Friday, April 24, 2009

The Fate Game II

Miracles can happen. No, not that I've seen one recently. But I heard a story on the radio this morning (from NPR's Story Corps) about a little boy whose life was saved. It was told by a man who had been the little boy, the story of a time when he leant out of his family's five-story window a little too far and lost his grip, a fall he never would have survived, except for the barber neighbor who had come home from work early that day and was at the door to the building just at that moment. In the right place at precisely the right time. He quickly ripped off his jacket, reached out, and caught the boy (who was presumably only about 5.5 ft from the ground by then). He saved the little boy's life, and it became the most important moment in his own life, as well. A miracle for both of them, this unfathomable chance of random events coming together.

This is the kind of miracle I can believe in: the wonder and amazement of the what-ifs, the literally fantastic luck of timing. When the tragic action (of a car, of a slip or fall, of a cell, of a clot) is caught by the reaction of someone with a jacket, who just happened to be there at the right time. Where there is simply an action and a reaction, and no claim of one or the other without its partner. This is the kind of miracle that isn't there for so many, all the people who wonder "Why me?" or "Why her?" So many opportunities for a different fate, missed by miles or by hairs, the extent is no comfort because the outcome is the same.

This is how I feel right now: I have been walking, trying to run, down this street towards the building, watching her fall inexorably and slowly for more than three years like time is molasses. I don't even have a jacket on, and it took so long to process what I was seeing (and denial is so powerful), and I wasn't there at the window and I wasn't there to see the hand slip and I wasn't there to grab it. And nobody else was there either: the doctors guarding the windows failed in their jobs to watch over and test the windows against this possibility (was it their hubris? ignorance? or the age-old problem of who is going to pay for it?). Why do some of these goddamn windows have so many guardians and others are barely noticed? Some very, very good people have tried in vain to reach out and catch from other windows along the way down, like her parents running from floor to floor to floor. Good people set up experimental superstrong magnets that they are trialing to see if they can use to slow the fall or even stop time. But none of these things have worked. We needed either for the windows to be better guarded or for someone to have been there with a jacket at the very first fall of the very first cells going wrong and pumping out cortisol THAT WAS THERE IN HER BLOOD FOR ALL THE WORLD TO SEE IF ANYONE HAD JUST LOOKED. There would have been the time to catch her, and change the course of history.

So here we are now, there is still room for hope. Hope that at the most, the fall is slowed enough to give her time to look around and enjoy the feeling of flying, the beautiful sunshine outside, and all the people down there reaching out their ineffectual arms wishing they could catch her with the sheer force of their love. And at the very least, hope that with the here and now, our unique position in history, that we are on the cusp of something better. We have the opportunity and are beginning to develop the understanding to create tools to be there, at the right place and the right time, when they need it and before it is too late. All we can do is hope for the miraculous: that we are there, with our jackets out, ready to catch people.

Sunday, April 19, 2009

The greatest love of all

I hereby proclaim that if I ever obtain a Howard Hughes Medical Institute Early Career Award, or something like that, I will post an audio recording of myself singing "The Greatest Love of All." Not like I am applying right now or something, I just wanted to make sure y'all will hold me to that if I do achieve somesuch importance.

Saturday, April 18, 2009

Chemical bilology research blogging

Okay, so here's a little example of the kind of chemical biology that I am not convinced has a point for biology, it seems much more self-serving for famous chemists to indulge their 'we made this complicated thing in an extremely complicated way' obsession.

On the one hand, I read this essay by Tom Muir, which is totally SPOT ON about the future of chemical biologists as functional members of the research society. He's been one of the pioneers of this new cross-branching, so it makes sense he would know what is going on.

Then there was this. Three papers came out in the recent issue of JACS, all from the same research group (very famous) and all in a row. They all seem to contain the same authors but in different orders, all full articles. They all focus on making various parts of a fully synthetic, homogenously glycosylated EPO. They use phrases like 'Our venture commenced with the preparation of' and 'Several strategies were entertained' and this doozy: 'difficultly predictable conformation' (emphasis mine to highlight the typical chemist way with words). They also spend valuable page space (and reader time) expounding on how they tried this or that method that didn't work but fortunately such and such other method did, and detailing every little aspect of every single specific reaction including rapidity of consumption of starting material, and how happy they were about that. It ends up sounding seriously medieval.

They try to lay it all out old-fashioned-style like this is some kind of hypothesis driven research into a general glycoprotein synthesis strategy that will somehow revolutionize the field of 'biologics,' rather than the ponderous, author-heavy, complex target-based total synthesis it actually is. Yes, maybe a homogenously glycosylated EPO would be useful for figuring out which glycoforms have particular biological effects. But these (not one, not two but three, count 'em) THREE papers don't clearly highlight any generality or modularity that could be used for any glycoprotein. Their side chains are covered with protecting groups. They don't demonstrate how you could easily clip on any homogenous carbohydrate modification to relevant sites. Nor do they describe some new jump in efficiency of synthesis, or a new exquisitely-selective and exciting reaction (they just use minor modifications of existing strategies). These are the kinds of things that would be necessary to address their proposed justification that these methods could revolutionize drug discovery for biologics.

They don't appear to have a biological collaborator who might be able to make sure they are pointed in a useful direction, and regardless of their repeated assertions that the biological impact of their project is so lofty, as a chemical bilologist, nascent cell physiologist and protein chemist, I'm just not seein' it. This looks more like a classic case of misguided synthetic hubris combined with author-laundering to maximize publication number. I understand that students and postdocs want to get their first-author paper on the thing they made, but it really dilutes the report of the research unnecessarily to split up a common project in this way. This could have been one paper simply and clearly showing the synthesis of the three segments and that's it. That's all that is here. Or better yet, wait until you actually MADE the full EPO and publish ONE paper on it. We don't need to hear the stream of consciousness/chronological story of your trevails. We just want to know if you did something important.

They say at the end of the final paper that they expect to be able to use their fragment condensation strategy with the understanding that "with all complex target oriented total synthesis, intervention of the unexpected is predictable. That being said, we are hopeful that the convergent nature of our synthesis and its flexibility will enable its adaptation to reach our goals." Good, I'm glad they are hopeful!! It's much better than being depressed about how your long, long, tenuously important project is not changing anything significant about protein chemistry!

This is the kind of thing that bothers me about the divide between old-school and new-school chemistry. Young chemists are being misled into thinking this kind of thing has impact. They are not looking at these problems with biologists asking them critical questions all along the way (nor asking those critical questions of themselves). Ultimately, they are wasting a lot of their time on directions that could be much better informed by understanding how and why things like this might be useful, and the real requirements for making them so. I just don't understand why people still keep doing stuff like this.

Friday, April 17, 2009

I Love Go Fug Yourself

Because only one blog can use the phrase "rampant pantlessness" in something like a relevant context.

Wednesday, April 15, 2009

Grantwriting pointers: Research Design and Methods

Hot off the internehts, fresh grantwriting help:

The long-awaited sequel to such ChemicalBiLOLogy favorites as "Specific Aims" and "Background and Significance" is now available on the Drugmonkey Channel! All hail the Physioprof Guide to writing Research Design and Methods!

If you are here about my K99/R00 guide, I strongly encourage you to use these resources for developing the scientific part of your proposal!!

Monday, April 13, 2009

The fate game

Denial carries us a long way in life. It's pretty much the only way humans maintain sanity. Destiny means nothing. It is just a construct: something we created to make us feel better about our fate, to feel like we have something to follow purposefully to reach our final destination and state. Fate is the real truth--it is the point on which the randomness drops our data dot in the histogram of variation. Lost in a sea of stochastic possibilities, hoping to cling to the middle of the road, the typical response, the average lifespan filled with average or superior experiences.

Hoping against hope that we will only win the good lotteries, like the kind you by a ticket for, or the kind where you magically grab the correct number of forks from the drawer without trying, or get a sunny day on your birthday; and not the bad ones, like being on a plane that crashes, or the kind where you end up with two exciting events happening at the same time so you have to miss out on one, or have some of your cells overcome their checkpoints and forget their jobs and take over their home and ruin it. Fear keeps us hopeful, because otherwise why and how would we go on? Being afraid prompts us to compartmentalize and keep bad possibilities separated. But reality is: some of us are the datapoints in the unfavorable side of the histogram, and no matter how much we tighten it up around the mean, there will always be randomness and always be a spread. Ultimately, no matter how hard we try, we can't control our fate. Biology wins in the end, and we don't even know how to play the game.

If you look from far enough away, the lines seem sharp and well-defined, but trying to pin down their tracks is like trying to outline a pencil drawing with an airbrush: most of it goes in the middle of your aim but countless pixels spray in all directions. How can we hope to ever describe and understand that? How can we console the outliers and explain to them that there's no way we could have known? How can we do anything other than hope for miracles, even if we don't believe in them?

Friday, April 10, 2009

On the limits to family-friendliness: Part II

All this discussion got me thinking about this. The fundamentals of what I am talking about might not be related to the other discussion from some people's perspectives, but I do think it prompts us to think about this as a bigger picture issue.

I believe that flexibility, support, making science and the family workable, needs to be a two-way street. It needs to come from the bottom up as well as the top down.

I believe that mentors/employers owe their mentees/trainees/employees the right to flexibility and support as long as their productivity is maintained, and indeed that by offering those to their people, they give them the space TO maintain that productivity.

I also believe, however, that mentees/trainees/employees owe their mentors/employers that same degree of support and flexibility. You should be ready to give the same support that you expect from others.

Discrimination and prejudice are well-documented, prohibited by law and pretty thoroughly discussed with regards to hiring, recruiting, treating your employees. University (and other) policies are in place to protect trainees from being discriminated against, and to require their employers to support them for personal issues like medical and family situations. But nobody talks about the other side: students/postdocs/trainees/applicants unconsciously or consciously discriminating against young/pregnant/female/minority mentors or employers. You as the trainee need to make sure you are going to get the best possible opportunity, right? You expect that a mentor and institution owes that to you, right? And yes: we do, because that is our job and it is why we are where we are.

But when it comes to decision time and the top candidates are choosing whether to join a lab run by an older faculty member with no family committments (no kids or grown kids), who is on the top of the ladder in their field vs. a young assistant professor (promising, but maybe she's pregnant and you worry about how much time she'll be able to devote to your needs)... ISN'T THAT THE SAME DECISION as whether or not to hire a young, pregnant woman to work for you wondering if her productivity might suffer because of her situation?

WE NEED EACH OTHER TO SUCCEED. No, of course I'm not advocating that every trainee should perform bottom-up affirmative action in this way. But young and/or pregnant and/or minority assistant profs need you excellent trainees to believe in us just as much as you need us and the old greybeard moneybags to believe in you. And we ALL have to work together to make science more open to the people who keep getting lost out of the pipeline AT ALL LEVELS.

Thursday, April 9, 2009

What are the limits of "family friendly" workplaces?

I was disturbed into posting by Damn Good Technician's reaction to her husband's PI setting aside a room for his children to spend time in after school during his work day:

DrDGT's PI is moving his labspace within his university - the lab just moved from one building to another, and they're moving again this fall. His PI had a discussion last week with the rest of the lab about blueprints & lab rooms. Evidently, his PI told the lab that one of the rooms they were promised - a room meant for some delicate equipment - is going to be used for his kids. Yeah. Seriously. His PI's wife told him that she thinks it would be "best" if he dedicated a whole room in his lab to his kids, such that when they hang out there after school a few days a week, they have their very own room in which to reside.

WHAT?? This is wrong on so many levels. First off, that a spouse could dictate to their faculty member spouse how to allocate space in their lab is fucked up - unless you're the Jans or something, this seems beyond the pale. Second, it is wholly inappropriate for a faculty to cordon off lab space for their own child care purposes. The university is not granting him space for his kids have a place to color three times a week; he's getting space to run a lab. Lastly, you're making it perfectly clear to everyone who trains under you that you are not committed to getting them the best lab space that you can - now this delicate (and might I add fucking expensive) equipment is going to be stuck out on a bench somewhere, getting dusty, abused by other labs, etc etc.

I was utterly floored when DrDGT told me. Can faculty do this? 'Cause, shit, if that's possible then I want DrDGT's lab to have a foosball room with a keg in it.
Reader, how do you react to that idea?

I don't think she or any of her commenters realize just what they are demonstrating: they ARE BEING the people whose first impression of a scientist having their family around is inappropriate.

If the PI was a woman, would they/you feel differently? A single mom without access to a good daycare? If the children were younger, still dependent for food and naps on their mom and dad? Why should the school-age children of a father have any different set of circumstances available to them? Why can't every scientist with kids have something like this available to them? Why does across-campus or far-away daycare access factor into this, when dumping your kids off in the care of someone else does not solve the problem of the struggle to balance family/work?

Having a room to set aside for your family is EXACTLY what would make science work for parents. Sometimes day care just doesn't cut it: you want to be near your children, available to them if they want to spend physical or emotional time with you. But you need them to not be right in your office, or they constantly distract you from the work you are trying to get done. This situation sounds perfect as a way to help balance family and science, and every institution should try to offer this to their PIs.

I'm sad that it provoked such outrage from the people who want to be understanding and inclusive, and I hope you guys will realize that this is a perceptual prejudice, and by holding fast to that reaction you are being the people that you think of as the enemy.

Frankly, lab member "inconvenience" regarding a piece of equipment or some yards of bench space should not trump support for scientists with families. We will only move forward and increase representation of women when this kind of thing is less appalling to everyone.

Monday, April 6, 2009

Arrrghgllbblblaarrgh

My brain feels like oatmeal: I just finished a 10-day trip to my husband's homeland for various family things, that just so unfortunately happened to coincide with the week before one of my grants was due and all the paperwork for the Concept Award is due (the date for both is tomorrow). Of course I could only get superficial work done while I was over there, both because of internet access problems and the demands of family and friends who only get to see us about once a year/every two years. We got back about four hours ago from about 17 h total of traveling and I just spent that whole four hours hammering through first some more intense science writing revision on one grant and then i-dotting and t-crossing on paperwork for the other. So much thinking, so much detail, soooooooooooooooooooo tiiiiiiiiiiirrrrreeeeeeeeeedddddd.

Whaa f'in' whaaa, right? And I couldn't even find any salt and vinegar Squares in the airport, so no snacky favorites to help me (I guess I did eat like 20 packets while I was there, so it's probably a good thing I can't get at them anymore).

Thursday, March 26, 2009

DOD Concept award

I freakin' got one!!

All my frantic submissions last fall are coming to term in the last month or so, and of the four swings, I've got one hit on this one. This is for a project on the super-cool exciting collaboration with an awesome guy next door. We've got some really nifty preliminary data in the meantime, too, so we have an inkling that it will work.

I still have a chance to make it to another base next month--a different project was selected internally to go forward for a local pilot project grant, and we have a reasonable chance of getting that one as well.

Tiny baby steps, not big money, but enough extra infusion to keep the new project directions moving towards R01 readiness! Combined with the K99, we're doing pretty well around here for our first year!!

:)

Saturday, March 21, 2009

More pretty data

Our data continues to get prettier and prettier, I just wish I had more time to be the one looking in the microscope. I think I need to spend the summer doing that.

Sunday, March 15, 2009

First batch of pottery

A while ago I talked about how I joined the local pottery club. I have my first few things all the way through the process now, and I was pretty pleased with them! The first two pieces I am not showing anybody because they suck. But the next three after that went much better--I got back on the horse, so to speak.

I like to play with glaze overlays and make cool color combinations. I'm going to end up being the "Glaze Chair" which means I'll be helping organize and manage the club's glazes. I'm very excited about that, because it's materials science and inorganic chemistry, so it will give my brain some exercise, too!

But anyway, here are my first few pieces: a small green bowl with a shiny black glaze on top; a purple/blue cylinder; and a cream/blue/brown pitcher. I'm especially excited about how the pitcher turned out looking like it was soda fired because the underglaze was thin.