Sometimes you predict a tripping waitress, and get drag wrestling instead.

I attended a scientific meeting last month called “The Molecular Basis of Microbial One-Carbon Metabolism”, and had a wonderful time connecting with my colleagues and friends. This was a major nerd rave. Meetings like these are where we swap ideas, forge collaborations, and present our latest research to each other. The week-long meeting was a smallish one, with about 150 attendees, ranging from

silverbackestablished leaders in the field

 

 

beakerto budding grad students

and everybody else in-between (postdoctoral researchers, junior professors).

The meeting was organized into sessions of 3-5 speakers each, chaired by a discussion leader. I was asked to chair the session on ‘Systems Biology’, which is this really cool approach to biology where, instead of our usual reductionist schtick (e.g., one reaction, one pathway, or one organism is the focus, devoid of context), we can use the wonderment of contemporary computational power to consider such a thing enmeshed in its actual context. No biochemical reaction or pathway happens by itself; they happen inside a cell with THOUSANDS of other reactions happening simultaneously.

 

E.g., not this:

isolated reaction

Rather, this:

map

Sooooo, to introduce this concept in an amusing way, to highlight the notion that context matters, I asked the 150 scientists attending the session to predict the outcome of carrying a tray with glasses on it (e.g., I presented a process without context).

 

I then hoped to show the following video to cement home the notion that predictive power increases when you consider the context:

The correct video

However, the technology froze, and the technician began to click at random to try to fix things, and this video came up instead (true story):

A gift from the universe

This actually proved my point quite well; the video of the waitress had worked quite well when I tried it out in the auditorium before everybody arrived; once everybody arrived, well, drag wrestling.

 

Systems biology, indeed.

 

 

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Riders on the storm

Wow, here’s somebody who totally nails it:

http://www.upworthy.com/this-guy-says-were-all-faking-each-other-out-and-thats-not-helping-anything-lets-stop-that?c=ufb1

Most of the time, when we are in lab or in the field taking measurements, we are running into walls and troubleshooting ways to get through/around the walls.  It isn’t the same as ‘not knowing what we are doing’–don’t get me wrong, we are quite clear that we are testing a particular hypothesis.  Being ‘in the cloud’ as described in the video is more about running into barriers because of forgetting to examine an assumption closely, or neglecting to step back and take in the larger picture.  Science *isn’t* the shortest distance between hypothesis and results; it’s construction of testable hypotheses and the subsequent attempts to test these hypotheses based on what you think you know.  Sometimes this is pretty nonlinear.  The cloud is a scary place and it’s important but hard to keep your mind open when the lightning is flashing and you are being clobbered with hail, especially when the ‘visit’ to the cloud stretches for months or years. 

Good example of being ‘in the cloud’:

I teach a genomics class each fall (except this fall;  sabbatical).  I teach the students in the class (beginning grads and advanced undergads) the basics of molecular evolution, show them cool databases and tools to make sense of the vast amounts of data contained therein, and then have them use the tools and their understanding of molecular evolution to test hypotheses.  One year, the dataset we were using was the complete sequence of a deep-sea bacterium that I study and we hypothesized that the genes encoding the enzymes that catalyze sequential steps in pathways to build cellular building blocks like amino acids would cluster together like pearls on a string on the chromosome.  This is what we see in our pal E. coli, the best-studied bacterium on the planet.  I gave each student a biochemical pathway and told them to construct a map showing the location of the genes encoding the enzymes of each pathway.  I expected each student to hand in one map showing the genes nicely adjacent to one another (pearls on a string, right?  Easy-peasy.).  We all left for the weekend and I told the students to hand their maps in on Monday.

Soooooo.  Monday comes.  Mass pandemonium!  Shouts of mutiny!  Pearls on a string?  Get serious!  Those genes were tossed around all over the place on the chromosome like a tornado had hit it.  Students came up to the front to hand in their assignment.  Instead of a single map each, they staggered under thick stacks of maps showing how gene A was on top of a tree, while gene B was over in the cow pen by the lake (tornado metaphor alert).  The students were furious.

I apologized profusely, and then paused, and realized this was way cool.  We started asking WHY the genes were so disorganized, and came up with a different way to think about why genes might not act like pearls on a string (sorry, it doesn’t involve tornadoes).  We put it into a manuscript which got published by a fancy journal, and our new idea gets cited quite a bit.

(That author line is so long because the students are on it.  That insane weekend assignment paid off in the end.)

tcru genome

If it’s scary, don’t try to control it.

when in rome

It seems that all kinds of events in my life are coalescing into a single lesson lately: if it’s scary, don’t try to control it. Not sure that’s the exact lesson but it’s a good starting draft I think.

Let me ‘splain.

Had some papers that I submitted to peer-reviewed journals get rejected (ouch, but for most of us scientists it’s a part of the job). The scary bit: revising and resubmitting the papers (OH NO THEY MIGHT GET REJECTED AGAIN AND MY PEERS WILL THINK I’M A HALF-WIT).

Also had an interesting experience on my bicycle. Took a vacation last week during which I did RAGBRAI with dear friends (it’s a huge bike ride across Iowa). There were 5000 of us who rode our bikes all the way across from Rock Valley to Guttenberg in seven days, and many others who joined for a day or two and swelled the ranks to over 20,000 riders each day. Each town welcomed the spandex-clad rolling horde with gatorade as well as treats for sale (homemade tri-berry pie made by real live Lutheran grandmothers, freshly fried donuts, et cetera) to support church groups and school groups (e.g., I think I ate enough cookies to send most of the high school aged students in Iowa to Spain, whether they were members of the Spanish Club or not; I am also figuring I will get a phone call to be a part of ribbon-cutting ceremonies for new construction on churches across Iowa to honor my commitment to purchasing and consuming homemade pie). Any-hoo, the last day we descended into the Mississippi River Valley and there were some h-u-u-u-ge hills. We just don’t have hills in Florida, so these were a new experience. Uphill ain’t a problem, because I am a spaz. Downhill….well, then there’s downhill. Down the first hill my buddy Chris clocked us at almost 31 miles per hour. It was fun. It was terrifying. I’ve never gone that fast on my bike before. The second hill was larger, but we all took the downsweep more slowly because there were rumble strips at the bottom. The third hill…holy crap, the third hill…

I learned what ‘death shimmy’ is. If you go fast enough on your bike or motorcycle, the handlebars will start to shake violently, sometimes because of hitting a rock in the road, or because a gust of air hits your bike just right, or because the Universe has a mean sense of humor sometimes. I was flying down the hill and all of the sudden my bike was possessed by Satan. Instinctively, I leaned back and tightened my grip and upper body to try to control my violently shaking front wheel, which turns out just makes it worse. Somehow I managed to bring my bike to a stop without being sent airborne.

The right thing to do with ‘death shimmy’ is to lean forward, brace the top tube of the bike frame with your thighs, and prevent your upper body/grip on the handlebars from going rigid. Supposedly it will abate. Stay loose? Lean into a front wheel that’s shaking violently? WHAT?

So my point…I can’t control what the reviewers do with my papers. I *am* a half-wit, and really there are worse things to be, so, ok. I can’t control my front wheel if ‘death shimmy’ hits, but I can lean into it and hope for the best.

Terrifying, but ok.

Sometimes science is pretty.

 

 

IMG_1576

 

I couldn’t believe how pretty this is.  I used an old technique called ‘thin layer chromatography’ because I need to separate citrate from the by-products of an enzyme reaction.  I stained the chromatography plate by spritzing it with bromocresol green, and enhancing the contrast with ammonia fumes.  The yellow spots are citric acid, succinate, malate, and oxaloacetate.

This is madness. THIS. IS. SCIENCE.

Apologies to the movie ‘300’.

The really great thing about being a scientist is that my activities are far, far from rote and I spend most of my time light years away from my comfort zone.

Take last week.

One of my students is defending her masters thesis next week and she and I are frantically editing her thesis.  She is comparing the metabolic pathways used by different types of bacteria to construct themselves from carbon dioxide.  This is a picture of how it all comes together, borrowed from the KEGG website.  It isn’t as bad as it looks.

Image

Well, OK, maybe it is.  My grad student has about 50 pages of notes, a godzilla-sized excel workbook that she used to do her calculations, and a large bottle of ibuprophen on hand at all times.  To relax, she kayaks from De Soto Park to Marathon Key.  Really.

I am also preparing for a research cruise and needed to load a ship with my science gear today.  The cruise isn’t until November, but the ship is ported nearby in St. Pete and leaves tomorrow.  I will be meeting the ship in Manzanillo, Mexico in November.  By loading gear on now, I am avoiding a whopping bill for shipping it to Mexico.

So, here’s how things went.

1. I needed to construct shipping crates for some of my gear.  I had originally intended to purchase these, but one of my pieces of equipment came in over budget (the euro gained relative to the dollar since I wrote the proposal).  I watched a youtube video (not kidding), raided the hardware store, and built them in my garage.

Image

Done.  Rock and roll.  I am a master of rough carpentry.  Don’t look too closely; they ain’t pretty, but they’ll do the job. 

2. Next, I read my student’s thesis and emailed her a bunch of edits.  Doing my best to strike a balance between encouraging her to move forward full-throttle without sending her to a bunny-in-headlights terrified paralysis.  Our deadlines, they are a-loomin’.

3. I need to figure out how to measure enzyme activities at sea, so I did a literature search and designed an assay using gel filtration columns.  Spent a week trying to get it to work.  No go.  Will try thin layer chromatography next, which involves 8″ by 8″ glass plates.  Gee, what could possibly go wrong if I bring a bunch of 8″ by 8″ glass plates onto a rocking ship? 

4. Went through another round of edits with my student.  Things are coming along but there are some problematic biochemistry calculations we will need to revisit tomorrow.  Student is understandably fried but needs to keep rollin’.  I know she can do it.  Pyruvate, baby.  It’s just three carbons.  You got this.

5. Needed to figure out how to pack a centrifuge into a box.  This is tricky since centrifuges are heavy AND delicate.  Made a custom foam insert by sealing the centrifuge into two garbage bags, placing in a larger box, and filling the larger box with spray foam.  Once the spray foam had hardened, I had, depicted below on the left, a centrifuge inside a cube of solidified spray foam.  I then had a party with my reciprocating saw to buzz off the top and split the bottom pieces, freeing the centrifuge and allowing the custom foam packaging to be opened and closed to pack the centrifuge for shipping.  I ❤ my sawzall.

ImageImage

Custom foam insert for shipping centrifuge:  done.  However, my hands got some spray foam on them that is taking a while to peel off, so I look like I have a wicked case of eczema.  Or leprosy.  I caught one of my undergrad researchers staring at my hands.  Did not explain.  Funner that way.

6. Edited grad student’s thesis again.  Things are coming together nicely.

7. Packed six crates of gear and created a detailed inventory for each.  This is necessary since once I get on the ship I will need to do my experiments with whatever I have on hand.  Several times a day I do this mental exercise where I walk through each experiment I plan to do at sea and think about what I will need:  equipment, supplies, reagents, safety gear….so I need to know exactly what I have already loaded on the ship.  Thus, the itemized packing list:

ImageI am not an anal person at all so relative to my comfort zone, detailed listmaking exists someplace in the Andromeda Galaxy.  Done.

8. Grad student has regained the ability to blink.  I was getting worried.  Thesis is ready to send to her committee.   You go, girl.

9.  Loaded all the crates onto the research vessel Atlantis today.  273 feet long, and five abovewater decks of lime green science Nirvana, which will be my home next November. 

Image

Rock and roll.

 

Terminal velocity

What most of us see of science is provided by the news; we get blurbs about recent scientific advances, or perhaps a blurb about how a new finding challenges current understanding. I think the ‘blurbs’ scrape the substance from the process, and leave us with the impression that conclusions derived from peer-reviewed scientific studies are equivalent to opinions. They’re not. Here’s why.

I submitted a paper for peer review yesterday. Wow, that was terrifying. After uploading the document to the journal’s website, and filling out all the silly crap on the journal’s webpage, my stomach was in knots when I hit the ‘submit’ button.

I posted on Facebook that this process is more terrifying than skydiving.Image

It is. To understand why, consider scientific inquiry and the peer-review process:

  1. You spend a year or two doing experiments and analyzing the results, often with the help of undergrad students, grad students, and collaborators from other institutions. This is my favorite part.  These experiments are things that have never been done before … you are flying blind … every day is a high-stakes, poor-odds gamble. It is terrifying, but in a good way, and there are multiple opportunities to kludge with duct tape. It’s creative, it’s crazy, it turns your head inside out to have your mind in the clouds with your feet on the ground; it’s a privilege.
  2. You write the clearest possible manuscript describing the context, methods, results, and what you make of them. You choose your words carefully so that they are as unambiguous as possible.   When I was a grad student, a mentor of mine had the following suggestion for writing technical manuscripts: “Imagine writing ‘Romeo and Juliet’ to submit to a peer-reviewed science journal: They met. They f*cked. They died.”   Really. It’s like that. Words are tools in this context, and the fewer, the better.
  3. You submit the manuscript to a journal.
  4. The journal editor submits the manuscript to 3-5 anonymous peer scientists who are deemed knowledgeable in the subject matter of the manuscript.
  5. The peer scientists read the manuscript carefully and critique it.
  6. The editor collects the anonymous critiques and decides on the next step:
    1. Accept as is (this never happens to me; it rarely happens to anybody).
    2. Accept with revision (this is what happens to me on a REALLY GOOD DAY).
    3. Reject, but encourage resubmission with extensive revision and/or additional experiments. This is bearable when provided sufficient ibuprophen, and maybe a few hours with a whoopee cushion. The process of revision and additional experiments can add a year of effort to the manuscript.
    4. Flat-out, no-go, reject. FAIL. Bleak, bleak, bleak. You have the hard task of facing the reality that you spent a few years of your time, your students’ time, your collaborators’ time, and a fair bit of taxpayer money on an exercise in futility. If you can’t publish it, the research is essentially useless.

If something gets published in a respected peer-reviewed journal, it’s run the gauntlet. The peer-reviews that place the manuscript in 6a – d above are anonymous, and VERY BRUTALLY FRANK.

 

My manuscript had been previously submitted, and fell into category 6c above. The first round of reviews was VERY BRUTALLY FRANK. Some comments were helpful. Some comments were misguided and indicated that I needed to write some parts of the manuscript more clearly (they met, they f*cked, they died). Some comments, frankly, hurt.

 

I spent a year doing more experiments and rewriting the paper. When I resubmitted the paper, I had to include a point-by-point list of the reviewers’ comments, and how I addressed them. My list for this paper was 54 items long. Previous papers that I have written, submitted, and published have had lists over 100 items long. If, like me, you aren’t God’s Gift to Science, this is normal.

 

To submit a paper for peer review is to throw your ego into a chipper-shredder.

 

Hopefully the above clarifies how results from scientific studies get published, and why they are not equivalent to opinions.

PS As an amusing side note, the process I’ve described explains why it’s common for scientists to have hobbies like racecar driving, rock climbing, jumping horses, skydiving, surfing, fire-breathing, and motorcycling (I have specific colleagues in mind for each of these; this is not a fictitious list). The perception that we are meek and risk-averse couldn’t be farther from the truth.