Archive for: April, 2014

What the effome?

NSF BIO Sent around an email today that had many recipients asking "WTF?" Apparently there is a new initiative being put together that is aiming to look at the connection between genomes and the observable traits of organisms. Cool, I'm down with that. But, um, what are we calling this?

BIO seeks community input on Genomes-Phenomes research frontiers

John Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes. The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.

The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO's future research investments and activities relevant to understanding genomes-phenomes relationships.

To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link: Sign-up. Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding. Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.

Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to

"Phenomes", eh? Jonathan Eisen has already pointed out that this is just another example of Bad Omics, and there were plenty on twitter who were busting out the side-eye on this one.

But what is the point of making up terms that are hard to define and don't convey any information? Would it really have been less "paradigm shifting" to make the program about connecting the genome and phenotypic variation? People would have actually understood what that meant, so there's that....

I'm excited to see this being considered and I think there's a huge amount of potential here, but let's use real words when trying to communicate ideas, m'kay?

2 responses so far

Your talk isn't just the sum of your data

Apr 28 2014 Published by under [Education&Careers]

Think back to the last time you saw a good scientific talk. What were the features of that talk? Undoubtedly there were interesting results that you had at least a passing interest in, but is that all you remember about the seminar?

When you go to a conference you spend your day being bombarded with information that is typically at the forefront of our knowledge. It's exhausting and mind-numbing and exciting and overwhelming. The typical conference audience sits for hours each day watching one person after another talk from the stage. Whereas having a topic and data that people find interesting is really important for giving a good talk, so too is your relationship with your audience.

What often separates a good talk from a really memorable talk is keeping the audience engaged. Too many speakers try to do that entirely with their slides, but there's ALWAYS a population of an audience uninterested in the results and a much bigger human element to grab those people than many appreciate. The talks I most remember are ones that not only had interesting data, but where I felt like there was a real person explaining those data.

One of the reasons I never practice talks anymore is because I realized that when I get bored with a presentation I project that attitude to the audience. If you are going through a talk for the tenth time and are simply the vehicle for delivery of the information, you have no hope of pulling in people who are not inherently interested in the results. I see far too many talks by people at all career stages that have all the excitement of reading the congressional record out loud.

Not everyone can make a career on a deadpan delivery.

As you become more and more accustomed to speaking in front of an audience, the most critical thing to work on is using your delivery to engage your audience. A seminar is not a book report punctuated by verbal disfluencies. It's your opportunity to show your audience why what you found is really fucking awesome. You should be excited to lead them down the path and really want to tell them the result. If you can't convey a level of interest in your own work, why should they care?

Don't let stage presence be an under-appreciated part of your development as a speaker.

One response so far


Apr 23 2014 Published by under [Education&Careers]

Tis that time of year.... Both the IOS and DEB directorates of NSF are poised to notify people about their preproposals. If you get a denial letter, you're SOL until next January (unless you can submit a CAREER) and if you get invited to write a full proposal you best get started. Most of the notifications are going out this week or next, so many of my readers and their colleagues are going to be on edge for the next couple of days.

But, a word of caution: Don't jump the gun and conclude your fate too quickly. It's a process and not everything happens at once. There's going to be a roll out of notifications and just because your colleague heard it doesn't mean your proposal in in a crumpled heap on the floor at NSF.

Breathe. Let it play out.

5 responses so far

Risk Management and betting on oneself

Apr 21 2014 Published by under [Education&Careers]

One of the aspects of this job that I find the most stressful is budgeting. I have discussed why budget issues are not very straight-forward in a lab with multiple support streams and projecting years ahead is tied up into that vortex. The current funding climate only exacerbates the issue because of the volatility of funding and the fact that most budgets get cut from the start.

This leaves many PIs asking a simple question for a complex situation: When do I bet on myself?

Fact: Most grant budgets (at least IME for NSF) provide less money than the total cost of the project. A lab can make up the difference in a variety of ways, some of which include finding supplemental streams of cash (e.g. grad fellowships) and others amount to borrowing from Peter to pay Pauline.

In the latter situation, one finds oneself over-spending now to take advantage of opportunities, with the hope that there will be money down the road to make up for the shortfall being created. It's a significant risk with real consequences if there's no reinforcements coming. At the same time, it is exceptionally difficult to make the types of jumps one's research program needs to make in order to stay at the front edge, while playing it safe with the budget. There's new technology, new techniques, new findings, all of which lead you to explore your system in ways you could never have budgeted in when submitting the proposal.

With funding rates in the single digits, the decisions that involve a significant outlay of money for a potentially important piece of the research puzzle are the one that keep PIs up at night. So far, my lab has managed to not have any spectacular failings on big investments and has been able to find those financial safety nets when they were needed. But it doesn't make me feel any better about it when faced with a new costly opportunity. It's a delicate balance with a significant risk of getting burned.

4 responses so far

Officially official (sort of)

Apr 17 2014 Published by under [Education&Careers]

From Farley Katz, of the New Yorker.

After a lengthy wait I've finally been informed that my university is recommending me for tenure, which will take effect in a couple of months. I've gotten positive feedback throughout the process, but it was good to finally get the word. Amazing to think that I've been blogging almost this whole time. Thank you to all those, both commenters and other bloggers, who helped get me through the rougher times.

33 responses so far

Fulfill my dream. Make me society secretary.

Apr 15 2014 Published by under [Education&Careers]

I've been asked to run for the position of Society Secretary by a society that I have been involved with for a number of years. As part of the ballot process, they distribute a 1 page bio of those running that includes research area, recent pubs, service, etc. But, the one piece I haven't been able to get my head around is the Personal Statement. I have examples from others running for President or VP, where one might be expected to have some sort of vision. But Secretary? Exactly what might one put in a personal statement to run for the position of taking meeting minutes? Because my brain is in Satire Mode 90% of the time, this is what I would like to send:

Many years ago I was asked to take minutes in my departmental faculty meeting. It was new to me and I did my best. I spent a week crafting the prose and at the following meeting, colleagues reviewed my minutes as "decent" and "could've used a spell check". Buoyed by their unbridled enthusiasm I immediately enrolled in secretarial training. I toiled away as an assistant professor by day so that I could pursue my calling by night. I began taking on more and more service at all university levels, insisting on taking the meeting minutes to hone my craft. Being offered the chance to apply my skills at the society level would be another landmark life event. I have trained for this for years and now you hold the ability to grant my dream. Vote for me. Vote for passion!"

14 responses so far

The cool professor

Apr 14 2014 Published by under [Education&Careers], LifeTrajectories

When I started my lab I had a very distinct idea of the type of PI I wanted to be. I had experienced some different styles and observed many others. I knew what my needs were as a graduate student and a postdoc and recognized gaps in what my mentors had provided for me. Above all I thought I could navigate that line between friend and boss where all my trainees would both respect me and want to hang out with me.

Oh, and I wanted to ride a unicorn to work every day.

I'm soon to finish up my sixth year as a PI and have mentored two cohorts of students at this stage. I'm hardly a grizzled vet of the mentoring game, but I've had enough experience to change my views on my role. There's been a discussion on twitter recently about whether someone is a Mentor or a Boss. It's a false dichotomy. An effective mentor is both. Sometimes you can spend your time leading your people in the general vicinity of water and sometimes you have to hand them a cup and tell them to drink.

When I say that I often hear people tell me "Well, my advisor was totally hands off and it helped us be independent and successful!" Whereas I won't dispute that many people can do well in that environment, it's often convenient to leave out the long list of those who flounder in those conditions and spent years of their life without advancing their career goals.

There are times when certain things need to get done for the lab and trainee alike, and there are times when the fostering of independence yields tremendous results. To pretend that a PI never has to act like "a boss" to make sure the bills get paid and the science gets done is a ridiculous view of how a lab functions. If a student comes in with all their own funding, then they can be free from the lab's reporting, publishing and proposal writing needs. Otherwise, as the lab goes, so does one's opportunities.

I still care that I have a good relationship with my people. I still hope that they like me and that we can sit down over a beer and enjoy the time spent together. But I'm far less concerned about blurring the line between the personal and professional relationships. I want to put them in the position to succeed at doing whatever it is they want to do, while advancing the lab's overall agenda. If that sometimes means pushing people to get certain things done, so be it.

9 responses so far

Dear Scientist, can you help me with a project?

Apr 01 2014 Published by under [Education&Careers]

The above tweet brought up something I have been seeing a lot of recently as well. At some point during the semester I will usually receive a good number of requests to answer questions as a . Sometimes it'll be two or three and other years I'll get up to ten such requests in a concentrated burst. Some are short "feeler" emails looking to get a response and others include the whole question package.

I hit delete.

I get the idea. And I get that some people might be inclined to help out. We all make choices about our time and I made a choice to spend my outreach time on coordinated projects that are backed by resources and people engaged in reaching a wide audience. I made this choice because I am regularly inundated with minor outreach requests. I could probably spend 40hrs a week, or close, on those efforts if I accepted everything and endeavored to do them well.

Obviously, that make no sense, so I prioritize. First and foremost are the Broader Impacts goals of my NSF grants. After that I sometimes take on opportunities that might lead to even better Broader Impacts projects. Once I've taken care of that, I'm pretty much tapped out. Responding to some form letter that a high school student is spamming me with ranks really damn low on the totem pole.

However, the discussion following that tweet did bring up one solution that might be food for thought: there's an opportunity here to engage the teachers who are giving this class assignment. Whereas I'm not responding to your spam, I am MUCh more likely to visit a classroom and engage the WHOLE class in an activity. Counter-intuitively, I would spend more time on something that students might actually enjoy than the 10 minutes it would take me to answer their cookie-cutter questions so they can say they did the assignment. Maybe that starts a collaboration with the teacher that continues on? Maybe that encourages a good student to apply to my university?

If you want my feedback and answers, let's make it worth both our time.

5 responses so far