Archive for: August, 2010

A ROFL link...

Aug 28 2010 Published by under [Et Al]

And because I am too busy (as usual) and exhausted to use my brain for extra thinking (which is required for semi-decent posting), here's a link to a hilarious email that Cath (from VWXYNot?) got recently.

One response so far

Dyscalculia: Arithmetical "dyslexia"

Dude... I have always felt like I had some kind of problem with math. Like a fundamental roadblock to being able to handle numbers properly in basic ways. Reading this post from Jason Goldman at Child's Play about dyscalculia is totally eerie: I am reading my own childhood (and continuing) struggles described to a t. I guess it was just my general stubborness to push through it and alternative strategies for making math work for me that helped me make it through a Chem major, a PhD and to where I am now as a TT professor...

5 responses so far

Making the K99/R00 work long-term: what should be the focus?

Through my discussions on my K99/R00 forum, I'm noticing a trend for applicants: they get mixed messages and experience a lot of confusion about what the K99 phase of the K99/R00 is REALLY supposed to be about. Some Institutes allow the K99 phase to occur during the initiation of a tenure track position (i.e. you get the award as a postdoc but start an assistant prof job at the same time as your K99 phase starts). Other Institutes absolutely do not allow this, and require a minimum amount of time to be spent as a postdoc on the K99 portion, and then require transition to the R00 phase (rather than carry-over and continuation of the K99 phase through its maximum 2-year allowance).

Program's explanations for their positions vary: from understanding that people are in the sweet spot for K99/R00 and tenure track competitiveness within the same ~2-year window in their lives, to insisting that the point of the K99/R00 is to make people competitive (results/training-wise, not just reputation-wise, which a successful K99/R00 proposal makes you) for tenure track positions (as originally conceived) and that people who are already applying for TT should be ready to just apply for R01s instead. The latter aren't comfortable with the K99/R00 being *just* a rubber stamp "gold star" for TT application packages until after the awardee has played out their postdoc stage, and presumably think that postdocs should stay in their mentor's labs until they are fully cooked to some vaguely defined stage of additional "doneness." (which, it seems, K99 reviewers largely already expect...)

Unfortunately, that's just not how it works for most postdocs. By the time you're in prime K99 application stage, you're in year 2-3-4 of a postdoc position. You may or may not have a mentor who can afford to keep spending money on you establishing your own independent directions. You may be pressured to leave the lab soon, you may be pressured by your family concerns to move on from the low salary trainee stage. You are one of 200-300 applicants for any faculty position to which you apply. Like I said before, you cannot afford to put all of your eggs in the K99 basket, and might NEED to apply for jobs, yet should success in that process preclude you from funding if you get an outstanding score on a K99/R00 proposal and the reviewers think you would benefit from the training plan you described? (especially when that training plan can essentially just be transferred and still occur while you also start a TT position)

The other part that some POs might not quite have come to terms with (even though they are the very people with these numbers...) is that getting enough R01 support to get tenure is COMPLETELY non-trivial, even for highly successful beginning investigators with the New Investigator bonus. Here are my specific concerns about this:

1. The new structure and reviewing guidelines mean that you essentially have to have all of your preliminary data published. There simply is no room for preliminary data figures in a 12 page R01 format. If reviewers are going to adequately assess the potential for your project's success on an R01 scale (budgets typically the so-called 'modular' $250K DIRECT costs per year for 5 years), they need to see you have established significant feasibility for all of your aims, and these days that means peer-reviewed publication of preliminary work.

2. R01 budgets may be proposed at $250K for 5 years, but ALMOST ALWAYS get cut upon award by as much as 25-30% or MORE in amount, and as much as 1-2 years in time (so in reality you end up looking at a spending account that gives you only $150-200K per year for as little as 3 years). In other words, right back to R00 levels of funding. For many institutions, especially the fancy-pants medical school types, you also have to cover a large portion of your own salary and benefits (which is usually >100K), plus postdoctoral staff cost a lot more in places where the cost of living is high (as much as $100K/yr in salary and benefits themselves, think about what you all are wanting to ask for as your K99 salaries!). So right there, covering your own and ONE postdoc's salaries kills nearly the entire R01 budget at most institutions (and similarly, an R00 budget if you do come in with one).

3. Many, many many institutions (especially those aforementioned fancy-pants places and medical schools on the coasts etc.) are going to expect more than one R01 in a successful tenure package. And when you look at the numbers on the ground I described in #2 above, you can see why. In order to bring in the big papers in the Glamour Mags (which those big name places basically require for tenure), you are gonna need to populate your lab with more than just one postdoc and yourself. You are gonna need at least a couple of postdocs and a tech to keep things chugging at the pace that will get you there. In these tight funding days, that most likely means more than one major grant pre-tenure.

Of course not all institutions will require this of TT faculty. But nonetheless, the reality on the ground (with R01s being what they are and requiring what they require) is that a K99/R00 award can function as ~50-75% of an R01 as you get going pre-tenure. If used judiciously and efficiently, and if the training plan goals with appropriate mentoring are actually followed through, that can mean a substantial leg up on the tenure process.

My opinion: The goals of the programs should be to help facilitate long-term success in tenure track positions, not just to get people into them. The grant has been around long enough now that they should be able to start looking at their outcomes under different conditions (K99 phase long/short, what kind of job title held for K99 phase, what type of institution for K99 and for R00, future R01 success, future tenure success) and see how things are turning out. (NIGMS Director Berg anybody...?) My hunch is that providing more practical tenure track success mentoring (workshops? other mandated, direct contact programs? additional mentoring requirement BY grantees who successfully move on to R01 funding FOR early-stage grantees?) and allowing the K99 phase to be under the control of the investigator (rather than some imagined idealized situation) will better push future R01 and tenure success.

30 responses so far

Ask a Nobel Laureate: Harry Kroto

So Nobelprize.org is running some online media activities through Youtube and Facebook where you get to ask Nobel Laureates questions and they will answer them. Pretty cool, right? The last round of questions went to David Gross, Nobel Prize in Physics, 2004, and you can find more from previous rounds at the Youtube page.

This round features Harry Kroto, one of the chemists who originally discovered the strange but fascinating Buckyball structure of carbon (C60, aka fullerene). Buckyballs have enjoyed much trendiness in the field of chemistry, because they have some weird properties that make them do interesting things with electrons and and interact with other molecules and surfaces in some unique ways. Apparently, they have also been found in space??!! I do not claim to be a C60 Buckyball expert, or even know much about them at all other than that in the early 2000's, if you wrote a grant with the terms "Buckyball" and "HIV" somewhere in the title or abstract, you were pretty much guaranteed to get funded. They were so hot right now. However, these nifty little hollow sphere-like molecules have turned out to be quite interesting and popular, evidenced by the thousands of papers in the literature exploring their physical, chemical and biological properties.

For the "Ask a Nobel Laureate" feature, you submit your questions either by uploading a video to Youtube or in text form--and although a video would be pretty fun to do, given my pseudonymity and lack of time for overly creative pursuits, I'm going to submit mine via blog post cartoon. My question is.... (drumroll..............):

Given the relative molecular scales, if the Nanokids held a World Cup tournament, would they be able to use Buckyballs to play? Or would it end up more like Big Ball Soccer?

Go to the Nobelprize.org Google Moderator or Youtube site and vote for your favorite question!! (mine, of course!)

4 responses so far

Namnezia cracks me up.

Aug 12 2010 Published by under [Education&Careers], Uncategorized

Recent lollzers from Namnezia:

Finally you are at a point where you are completely independent and a new adventure begins. But unlike being a postdoc or a graduate student in a well-funded, established lab with ample resources, starting your own lab is like becoming captain of a creaky old ship, partially sunk, with an inexperienced and somewhat dysfunctional crew and no compass. Ahoy! So while in principle you can sail in any direction you want most of your time is spent in keeping the ship afloat and the crew from killing each other.

(post here)

4 responses so far

Repost: Culture gap: synthetic chemists and learning biology

Apologies for more reposting... I'm still trying to get out from the vacation backlog of life. New thoughts to come soon!

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.

2 responses so far

Back to civilization!

Aug 09 2010 Published by under Uncategorized

Ahhhh, internet... sweet, sweet internet. I missed you, I didn't miss you. I finally recovered from your withdrawal symptoms and then fell back off the wagon as soon as I got home.

We got back tonight from a week at the family cabin that doesn't get any cellphone signal (so no Blackberry) and has no other connectivity than a landline ring-ring-ring old timey phone. It does have buttons and not one of those crank wheel dialer things, but I had forgotten how jangling the sound of a phone ringing was, now that I am so used to a gentle buzzing noise telling me politely that someone is trying to contact me.

It makes me remember how fast my brain has to work these days, and how much more capacity we must need to keep all of these little spinning, fleeting attention chunks sorted and moving.

In the meantime, my 7.5 month old child learned to pull herself up on things and can almost climb out of a pack and play... I have a feeling I am really in for it now. Yikes...

5 responses so far

Repost: My Big Picture (tongue only partly in-cheek)

Aug 02 2010 Published by under Uncategorized

Repost: Hi everybody! I'm excited to be a part of Scientopia! I'm away at a nice, quiet, internet-free location on our most exciting launch day, so I am leaving this here repost to help you get a feel for who I am.

So, I don't currently have a working drawing program on my computer so I have to make a Google Image collage to illustrate my most mostest pulled-back biggest picture, my philosophy of my world on days when I am not OCDing about something stupid that bothers me, my Zen of path through science-human-space.

We each have our little place in it, our little walk through all the possible avenues, and just like vision (and macro lenses) we can only focus on the part right in front of us. Probably it's only practical to expect to clearly see about the next year or two of plan in any great detail. I point myself in the direction I want to go, starting at the "chemistry" paradigm point and going towards the "biology" paradigm cluster. A zoom in on the detail of how I get there would probably look like this:

Except that most of the other nodes around me, and most of the path I had taken and will take would be a lot fuzzier to the eye. A good strategist will learn how to zoom their lens back just enough to see the next set of decisions to make, while keeping active on the current processes until they reach some degree of maturity. Not saying I am a good strategist yet, but I hope to learn how to be one by paying attention to what's going on around me.

So what is everyone's personal goal? Usually to make both their paths and destinations "important." But of course, importance itself has a lot of stochastic elements and the ultimate measure would be to be 'right' about it, right about how this crazy universe/space/world/us REALLY work. But what is "right?" To go really philosophical about it: how do we know it DOES work any particular way and that we're not affecting it just by trying to look? Just because I find some spit on the cat's hair I managed to tweeze out of the box with my incredible intellectual power, I still don't know if the cat is alive or dead or even if it's a cat or maybe a RASCAL that ate a cat...

SO to get back to things that don't wake me up in the night impressing the weight of the vastness of existence on my soul, what I really want to be able to do is maximize my experience at and travel between focus nodes, and not get bogged down with either the nodes themselves, nor the paths the lab ends up taking to them.

For the purposes of communicating as a human with humans, I'm calling this "STUDYING SIGNALING BIOLOGY USING CHEMICAL TOOLS" and we will work towards doing a very good job of making whatever we need to get information about cell signaling that allows us to make more emergent observations about how that stuff is REALLY interacting in there. If I can mature in my strategic abilities, we'll be able to be both thorough and flexible, and not get stuck in the mud of either our tools or our questions while still being able to make both of those things valuable to the overall enterprise of understanding how stuff works, to gradually add elements of information to the drawing until we get a picture of what the whole thing looks like.

To put it an even sillier way, I plan on rolling my chemical biology katamari through the paradigm world and picking up stuff as I go, and hopefully by the time I retire it will be so big I can even stick things like WHOLE PEOPLE and cars and stuff. Right now it is real tiny, so we can only pick up little additional methods and small observations and such, but with some luck and luck I make myself by being sufficiently strategic, it will grow fast enough.


(**you can find the sources for all my images by looking at their links with right click, thanks to the people who gave them homes on the internets for me to find**)

6 responses so far