Archive for: September, 2012

Sunday chili

Sep 30 2012 Published by under Uncategorized

Fall is the time for chili and Sunday is the day to make it. There's football on and food to make for the week. Gather your ingredients!

About a pound of stew beef.
Half a pound of ground beef.
A red pepper.
A poblano pepper.
An onion.
16 ozs of diced fire roasted tomatoes.
16 ozs of crushed fire roasted tomatoes.
8 ozs of black beans.
8 ozs of kidney beans.
2 ears of corn.
6 ozs beer (I use a malty ale)
2 ozs basalmic vinegar.
Dried chipotle peppers
Dried aji panca peppers.


Dice the fresh peppers, onion and mince the garlic. Sauté over medium heat until soft.

then add the basil and oregano.


After a minute or two, add the meat. Brown over medium heat.


Transfer to a crock pot.


Add all the canned goods, the corn (cut off the cob) the vinegar, half the beer (the other half is for the chef) and chilies to taste (I add about 4 chipotle and 2 aji panca.


Mix everything and let cook on high for 4-8 hours (longer is better)


Once it cooks done, it's ready to serve. Eat up!


6 responses so far

The transfer of genes between unrelated organisms happens. All. The. Time.

Sep 28 2012 Published by under [Education&Careers]

The regulation of GMO foods is a pretty hot topic right now. Europe requires GMO foods to be marked and there are states, such as California, who are considering similar legislation.

Most people who are pushing these regulations argue that moving genes from one organism to another is "unnatural" and potentially dangerous. The problem with that stance is that it is completely at odds with the natural world. We can watch the movement of genes between unrelated prokaryotes in real time (think, the spread of antibiotic resistance) but this process is not, as often believed, relegated to the ranks of the non-eukaryotic world.

Among the many things the modern genomic age has taught us, it has become unambiguously clear that genes move between unrelated eukaryotes. Examples abound, but a review of the Choanoflagellate (Monosiga brevicollis) genome (Tucker 2012) shows that there are roughly 1000 genes of foreign affiliations encoded there. Choanoflagellates are the sister group to Metazoans (animals), so they are not some obscure and distant branch of life (unless you only think about rats or flies, then maybe they are). And much like other organisms that have been examined, the foreign genes come from a wide range of organisms, including vertebrates, plants, algae and bacteria.

And whereas the presentation of these data is a bit dubious at times(how often do you see "phylogenetic trees" with no support values and no indication of what kind of tree they are or what models were used?) the fact is that this is not a unique case. EVERY genome tells a similar story, to varying degrees.

So if you want to make a case against GMOs, fine. Just don't use the "unnatural" gene transfer angle as the main thrust of your argument. It just shows you have no appreciation for how much nature likes to mess with things.

Tucker RP (2012). Horizontal Gene Transfer in Choanoflagellates. Journal of experimental zoology. Part B, Molecular and developmental evolution, 1-9 PMID: 22997182

15 responses so far

What if NSF Bio funding rates are LOWER this round than those past?

Sep 26 2012 Published by under [Education&Careers]

As pointed out by @biochembelle today, NIAID announced their interim paylines yesterday and the news is predictably bad. 6% for Non-new/ESI applications and 10% for the N00Bs on R01s. Why so low, because congress is playing a dangerous game of chicken right now. With the senate unable to agree on a budget, we're facing the possibility of sequestration. About a week or so ago we learned what this would do to the budgets of agencies we all apply to and NSF would take it in the teeth to the tune of $551 million (almost 10% of its overall budget).

There is certainly optimism in DC that congress won't let things go that far, but the timeline to get things done post-election will be short. This means that funding agencies have to prepare for Armageddon and plan their decisions accordingly.

Where does that leave NSF? Let's get out our calendar, shall we? Decisions on the current round of IOS and DEB proposal that survived the preproposal round and were submitted for the only call for 2012 are supposed to happen in late Oct / early Nov. You know, right around election time. Once the election occurs, we'll have a sprint to a new budget to avoid sequestration by a lame-duck congress. I totally trust that everyone will be in an agreeable mood.

So say we don't have any answers by mid-Dec. Where does that leave those waiting on DEB or IOS grants? My guess is that a small percentage will be funded and a larger percentage will be told to hold tight. Of course, the next round of preproposals (assuming Bio doesn't come to its senses) in due Jan 12. We can all see where this is going, right?

Even though NSF has been saying all along that it doesn't matter if there are one or two proposal deadlines in a year because the money is either all in one chunk or split between two rounds, we may be watching a train wreck unfold that pokes that assertion right in the eye. If NSF is forced to fund at sequestration rates for the 2013 FY, the success rate is going to be very low for the whole year and we won't be able to recover until at least Jan 2014 under the current system.

Guess what pre-tenure peeps?

9 responses so far

NSF Bio Discussing submission process - your input needed

Sep 25 2012 Published by under [Education&Careers]

A call from the Society for the Study of Evolution is going around. If you want your voice heard, now is the time.

Dear SSE Members –

The NSF BIO directorate will decide immediately (possibly Tuesday 9/25) whether to modify aspects of the current preproposal submission process. Two issues have risen as common concerns across the community and may be considered:
The limited number of preproposal submission periods per year (currently 1x/year).
The limited number of preproposals that a single PI may submit simultaneously (currently 2 at the 1x/year submission).

If you have an opinion on the current preproposal process, now is the time for your voice to be heard. The most effective message is likely to be a succinct email expressing your prioritized support for changing one of the two points above sent to:
BIO Assistant Director - John Wingfield -
BIO Deputy Assistant Director - Joan Roskoski –
and copied to your program officers

for DEB – Evolutionary Processes, these include
Elizabeth Friar –
George Gilchrist –
Lori Stevens –
Leslie Rissler –
Sam Scheiner –

for Systematic Biodiversity Science, these include
Robb Brumfield –
Maureen Kearney –
Simon Malcomber –
Thomas Ranker -
Michael Whiting –

Butch Brodie
B. F. D. Runk Professor of Biology
Director, Mt Lake Biological Station
Executive Vice President, Society for the Study of Evolution

SSE Business Office
4475 Castleman Avenue | St. Louis Missouri, 63110-3201

No responses yet

Breaking up with the NFL

Sep 24 2012 Published by under [Et Al]

Professional sports teams are one of society's stranger things. Millions of people spend hours of their valuable time obsessing over the outcome of games played by grown adults. We root for teams largely based on geography or a family member's influence and cheer for people who will never know our names. For the privilege, we collectively spend billions of dollars annually on the enterprise.

Yet despite acknowledging the ridiculousness of it, an enormous number of people follow some professional sport. I used to follow three, hockey, baseball and football*. However I started to lose interest in the NHL once it decided to hold what seem like semi-annual work stoppages. Baseball kind of lost me as the relentless schedule made it more and more difficult to keep up. But there was always football. Only 16 games in the regular season and usually confined to a single day of the week. Over time, the energy that I had left for sports became focused on the NFL.

Unlike the NHL and NBA, the NFL avoided lost games in it's most recent labor dispute. The league seems to get the fact that people pay to watch the games, not listen to bickering over millions. You take away the games and people will start to fill their time with other things. That's why I walked away from hockey a few years ago, and why that league is about to relegate itself back to sports purgatory, despite the growing interest of casual fans that has begun to develop again. You take away the action and you cut your nose off to spite your face.

But even though the NFL solved the labor dispute with players, they have let a more subtle labor issue fester. The referees for the games have been locked out this season and replacement refs have been brought in. Because the refs from the big university leagues have decided to support their NFL counterparts and not become fill ins, the NFL had to pull replacement refs from small college leagues and practically off the street. And it has showed.

There have been professional standard issues, player safety concerns and just general mayhem. There's even open discussion about whether anyone would notice the difference between the incompetence and blatant game fixing. We're to the point where the refs have a massive impact on the product. And the NFL is not solving the issue.

Why not? To paraphrase Steve Young's commentary on the situation last week, because we'll watch the games whether they are poorly officiated or not. The NFL feels that it can serve us a turd sandwich and we'll eat it, even if we complain the whole time. Unfortunately, it's not a diet that fans are going to thrive on and some will be lost along the way.

Last night was my tipping point. It's not so much that the team that I root for lost, but that the game was a total shit show throughout. In fact, one could make a convincing case that my team's opponent had a bigger referee disadvantage last night, but the point is that it was the main story from the game. The announcers were openly mocking the refs in the second half of the game and I'm not sure I have ever heard the crowd chat "bullshit" at a game for as long and as lustily as the home audience did last night. The refs, as most crews have been for the last three weeks, were overwhelmed. It was impossible to watch the game and not think the refs had way to much to do with it.

So until the NFL solves the labor issue with the refs, I'm done. I'm done watching the games. I'm done caring about things like the football pool I normally enjoy. I'm done supporting a league that is more concerned with <0.1% of worth than the product is puts out. I'm done spending time on a frustrating occupation.

Goodbye NFL, I hope you get yourself right and we can see each other again sometime.

*The real kind, not the one with a round ball.

17 responses so far

H-index douchery

Sep 20 2012 Published by under [Education&Careers]

There's been a bit of increased interest in the h-index since the h-index prediction tool came out yesterday. I've never paid attention to h-index, mostly because it is not something my university uses for evaluation (at least to my knowledge). Having never been evaluated by it, I had no reason to calculate my own.

But today I decided I should at least be aware of my h-index and I was curious what the prediction would tell me. After poking the twitterverse for how one actually comes up with these numbers, I managed to figure mine out.

And so what?

It's a number that I have no reference for. If I told you your PLS-index was 2375, it would be similarly meaningless to you. So what is considered a decent h-index for someone in my field who is coming up for tenure in a year? @EcoEvoProf mentioned that the people at her previous university who got tenure were in the 12-14 range. I guess that's helpful.

So what is a good h-index in the evolutionary biology field for roughly tenure-aged folks? How much variability is there in different fields? Does anyone give a shit?

13 responses so far


Sep 19 2012 Published by under [Et Al]

If you spent time exploring today's XKCD comic, you'll be relieved that there is a full screen version to play with.

4 responses so far

Titles: fashion or function?

Sep 18 2012 Published by under [Education&Careers]

I was innocently browsing my emailed Journal contents this morning and clearly had not consumed enough coffee. I opened the latest email from Journal of Evolutionary Biology and was smacked with the following title:

Differential investment in pre- vs. post-copulatory sexual selection reinforces a cross-continental reversal of sexual size dimorphism in Sepsis punctum (Diptera: Sepsidae) [link]

I'm sure the article is very interesting if you happen to work on that particular process in that particular organism. The study may even have wide ranging consequences for numerous other systems. But all I could think was, "say wut?" So I went to my own publication list to see how often I am guilty of equal specificity.

Of course I have similarly obscure article titles in my stable, but it's a trend I've been getting away from to a certain degree. With people tight for time to catch up on the literature, a title may be your only chance to pique the interest of a reader.

So how about you, reader? Do you make attempts to generalize your title at all? Does the venue dictate to what degree you worry about the reach of your title?

14 responses so far

The methods caboose

Sep 17 2012 Published by under [Education&Careers]

It seems that more and more journals (or perhaps just more I am writing for) are migrating to a "methods last" text arrangement for their articles. Although I don't mind this as a reader, it's kind of a PITA from a writing perspective. Occasionally one has some key piece of information that belongs in the methods section, but informs data interpretation. Tossing it in the back forces either an awkward mention higher up in the text or the assumption that readers who care will flip to the back. Both seem sub-optimal.

14 responses so far

Getting away from lecture

Sep 17 2012 Published by under [Education&Careers]

For the past few years I have been responsible for 1.3 undergrad courses in the spring semester. The class I teach myself has about 25 students, whereas the course I only responsible for part of has closer to 65. I have taught them entirely as lectures in the past and focused on honing the material to what I think are the central concepts. Overall, it has been decently effective, but I remain frustrated that a decent proportion of the class still can't wrap their heads around some key information by the time the final rolls around.

Although it would be convenient to blame this on the students not studying enough... back in my day... uphill both ways... everything cost a nickel... etc., the situation is not all that different from the "that reviewer didn't understand!" refrain of the grant game. The solution is the same: change your approach to clarify so that they can't miss the point. Last year I restructured the lectures and tried to build in some reinforcement of the topics I wanted to sink in, with only a minor improvement in retention.

So, I am musing about ways to break up the lecture and get the students involved. For the bigger class I've talked about incorporating clickers before and gotten some good advice in that comment thread about dealing with the smaller class. In particular, Alyssa was a big proponent of the "think, pair, share" approach and several others supported that idea.

In playing with this concept, one of the major issues I run into is that what I teach does not really have "problem sets" that are ready made for this strategy. The same applies for the online homework that Arlenna suggested. I think my solution will have to involve using exam-like questions that take the concepts just discussed and makes students tie those back to previous material.

Of course, the other key piece of this is avoiding a full overhaul of my lectures. Whereas I'm happy to tweak and update, anyone who has built a course from the ground up knows how time consuming that process is. This spring will be the last semester before my tenure packet goes in and I'll be dedicating my time to getting papers out and proposals written, not making sure I push my teaching evals from good to great. In a cost benefit analysis, it unfortunately doesn't make sense.

And so it goes, doing the best you can with the time you can spend.

7 responses so far

Older posts »