lab methods

anonymous asked:

How you stay organized with multiple experiments / notes on papers / etc? Any Grad sci organization tips? New desk area looks super cute 💕

Thank you!

I organize my lab stuff using 3 methods: 1) the kan ban board, 2) google calendars, and 3) separate project binders and a strong urge to categorize everything.

1) The Kan Ban Board - I describe it here. Basically this is the “big picture” view that lets anyone in our lab to see what projects/experiments are up and running (or, just up). 

If your lab doesn’t want to make a big one, you can make one just for you (my lab mate has his own mini kan-ban board using a bulletin board and yarn). 

2) Google calendars - This is how I schedule my hour-to-hour, day-to-day, week-to-week, etc events, be it projects, meetings, or even just to-do lists. It’s also shared with the lab, so we can always see what someone else is up to (which is helpful so we’re not all crammed in the tissue culture hood at once). Here’s a screenshot of what this week is looking like:

My shared lab schedule is in pink, and in purple is my own personal calendar that’s not shared with anyone (hence personal notes like I gotta go grocery shopping later today haha). But yeah, I can use this to schedule things weeks and months in advance, which is extremely helpful since I sometimes have multiple-month-long animal studies. And having the ability to move things around is such a nice thing to have in a field where the unexpected is the expected (which is why I prefer an electronic calendar over hardcopy). 

3) Separate project binders - I can categorize my projects into pretty much 3 different “project titles” (aka manuscripts down the line), and I have a separate binder for each which holds all related papers, brainstorming notes, data (or at least data summaries if you don’t want to print 50 million pages), outlines, etc etc. If you’re not sure if something is a separate project, create a new binder anyway, and you can always merge them later. You can also have a separate notebook for each project, along with one for general notes (like during lab meetings). 

If you prefer something less hard-copy, you can do the same with folders in your computer. 

Related, I also categorize everyyything–be it data, papers, etc. Here’s what my “Experiments” folder looks like (which has all my data, protocols, etc)

Basically everything goes into a folder. 

And to keep things neat, once a new year starts, I move all the previous year’s files into the previous year’s folder (ex. the “2016″ file under “Westerns” as shown).

Here’s what my papers folder looks like. Also all in categories:

You could also organize papers using an electronic citation manager such as EndNote or Mendeley (which I use bc it’s free). 

Another way to organize papers which I’ve been meaning to do for 5 million years: Type up summary pages to attach to the first page if organizing by hard-copy (or just to have somewhere). Sometimes I just need like a little refresher to remember “oh yeah! that’s the paper where they showed this and that”. I’m sure my PI would appreciate that more than the blank stares I give her….

Hope that helps, or gives you ideas of your own!


There is a very fine line
Between empirical and superstitious
And lab scientists tend to weave around that line
This is what happens when you work in a place
Designed to do things that probably won’t work

If you are troubleshooting a procedure
And you hit upon something that works
After three days of sweat blood and tears
You are not likely to change anything
About the one time it worked

You will have empirically demonstrated
That the procedure works
When you do X, Y, and Z in that order
However it is unlikely you will know if X, Y, or Z
Actually made the frustrating procedure work

This ambiguity can lead
Empirical testing and method development
To morph into something
Decidedly less rational looking
Than science might seem to the outside world

You might be pretty sure that
Using the thermocycler on the left
Had nothing to do with the procedure working
Because the thermocyclers are all identical
But it is not worth the risk of finding out you were wrong

When you have enough people in the lab
Doing enough of those little calculations
It is possible to end up with something that looks
Less like a rational experimental minded group of people
And more like a superstitious medieval mob

You might be laughing at that image
But try telling a lab of overworked grad students
That they will have to use a new brand of pipette tips
Because the old one has been discontinued
And see how long it takes for the pitchforks and torches to come out

I think the thing that amazes me the most
About the scientific method
Is that it manages to work so well
Even though the people doing science
Are so very human

-Notes from a Lab Tech
April 13, 2015

HOW TO BE A MYCOLOGIST (and some cool sh*t that’s happening right now)

2016 is going to be a wild ride. It’s not even February yet and so much has happened. Here’s the long and short: I’m trying to figure out where to go for my doctorate. Canada, Colorado and Hawaii are all possibilities, but it’s a complex web of factors that I have to consider. Timing and logistics are becoming very important. However, because of all of these applications and networking, I get to fly to Boulder (Colorado) and Edmonton (Alberta) in the next couple weeks to present my thesis research and meet the labs. Scary, but satisfying. Also, I’m getting married and trying to start a company. Wild times.

It occurred to me, while applying for all these positions, that there was no road map whatsoever for someone wanting to study mycology when I was just starting school. I basically fell into mycology through my love of the forest and have been stumbling along ever since, just trying to get a job running around in the woods.

So, here’s a wee how-to about becoming a mycologist. There are lots of ways to do it (my friend Christian is an amazing mycologist and he did it an entirely different way…check out his sweet blog here), but this is what happened to me.

1. Take biology classes in high school. If there are plant science courses, definitely take those. Take as much calculus and physics as you can. It actually becomes useful.

2. Run around in the woods a lot, looking at plants and fungi.*

3. Do a plant science or ecology undergraduate degree. If there had been mycology degrees anywhere, I would have done that. Forestry is different, but if you’re interested in studying the fungi that attack forests, forestry or forest pathology is for you.

4. Run around in the woods a lot, looking at plants and fungi.*

5. While you’re an undergrad, work in the greenhouses/natural history museum/molecular labs/anywhere on campus where someone will teach you about plants, collecting specimens, lab methods, field methods..etc. Also, join or start a mycology club that takes walks, looks at mushrooms, and reads the literature (yes, papers from journals like Mycologia). This is essential. Don’t fuck this part up. I volunteered in the UCSC greenhouses for years and was a member of the MycoTeam (we had sweet t-shirts and everything) and people ask me about this stuff in interviews to this day.

6. Run around in the woods a lot, looking at plants and fungi.*

7. Go to a graduate school that teaches you about plants (or fungi, if you can find a fungi-specific program. There aren’t many). It is essential to know about plants if you’re going to study fungi; they don’t exist in a vacuum. I did a plant taxonomy (i.e. classification) course and did a mycology thesis. If you’re in a plant course and you’re interested in fungi, tell all your teachers and do a thesis based on fungi. They’ll encourage you.

8. Run around in the woods a lot, looking at plants and fungi.*

9. Once you graduate from your master’s and you’ve done a research project on fungi…the world is your oyster. Look globally for Phd positions related to fungi: there are LOADS. E-mail absolutely everyone that you would be even slightly interested in working with and tell them you’re stoked about fungi and they should let you join their lab. Whether you want to stay in academia and do research (which I’m doing) or join a consulting agency/agricultural company/mushroom farm (they make more €€€ but it’s not quite as interesting…in my opinion), this is the tipping point in your future. You have education and experience, and now you can choose.

10. Continue running around in the woods a lot, looking at plants and fungi.*

*Yes, you should actually spend lots of time chilling in the woods. Buy some identification books (see my post here if you’re in North America) and start learning who everybody is. This is the best part.

PICTURE: My master’s program learning about Amanitas in Dawyck Botanic Gardens, Scotland. The guy holding the mushroom is Stephan Helfer, German mycologist and sexy old man to boot. That’s my blonde head at the bottom.

Carbon Monoxide Burning in a Blue Flame

Carbon monoxide (CO) is a colorless, odorless, and tasteless gas that is slightly less dense than air. It is toxic to hemoglobic animals. 

Carbon monoxide is produced from the partial oxidation of carbon-containing compounds; it forms when there is not enough oxygen to produce carbon dioxide (CO2), such as when operating a stove or an internal combustion engine in an enclosed space. In the presence of oxygen, including atmospheric concentrations, carbon monoxide burns with a blue flame, producing carbon dioxide.

  •                             CO + 2O2 → CO2 + O3 

There are many ways of Carbon monoxide production, such as:

The  Boudouard reaction ( Above 800 °C ):  

  •                     CO2 + C→ 2CO  (ΔH= 170 kJ/mol) 

Via the endothermic reaction of steam and carbon:            

  •                 H2O + C → H2 + CO (ΔH = +131 kJ/mol)

As a byproduct of the reduction of metal oxide ores with carbon:           

  •                           MetalO + C → Metal + CO 

By the direct oxidation of carbon in a limited supply of oxygen:        

  •                               2C(s) + O2 → 2CO(g)

A good method for lab use is heating an intimate mixture of powdered zinc metal and calcium carbonate, which releases CO and leaves behind zinc oxide and calcium oxide:

  •                        Zn + CaCO3 → ZnO + CaO + CO 

Silver nitrate and iodoform also afford carbon monoxide:

  •               CHI3 + 3AgNO3 + H2O → 3HNO3 + 3AgI + CO

More science and gifs on: rudescience
Giffed from: this video
Read more: here

Carlos Week

Monday: Science Day

Whatever science Carlos does, I can assure you right now it tends to be EXPLOSIVE. I think he experiments with samples he’s collected throughout Night Vale and tries to find out if they’re structured similarly to other everyday things. Like if they react to the same chemicals and under the same circumstances. (The answer’s usually no.) 

His scientific method and lab safety is usually a bit… flawed. He’s suffered from quite a few burns and cuts. But that’s never stopped him before! In the end, if something reacts or blows up, it’s a success.

The Executive: Aadi-dabbadie

Several reports needed to be done, followed by a drawn up plan of the expected income for the facility over the course of the next six months, followed by a weekly log of the information drawn in by field-agents working on tracking down ‘Experiment Zero-One’s’ wareabouts.
It was exhausting work, but nothing the Executive in his late sixties sitting in his quiet office infront of a single blue monitor couldn’t handle.

He wished he could be out experimenting in the labs, testing new scientific methods of producing the finest clean energy the world had ever seen, being out in the field tracking down his experiment, but somebody had to run the place. And if not him, then who?

He only trusted himself with the job. It was a tedious, strenuous, delicate job, but it was just the kind of work he was good at.

Boney fingers tapped away at incredible speeds for their age against a keyboard infront of the blue monitor. Save for that single monitor, a black wooden desk, a swivel office chair and a one way glass window on the opposite wall looking out into a blank room that looked similar to a padded jail cell, the room was devoid of furnishings.

The slender man removed one busy hand from the keyboard and hit the button of an intercom on his desk, leaning his bald head away from the
monitor to speak into the mike.

“Floor six, files on the regrowth of organ two-sixteen are needed in my office.”
The harsh light blue light illuminating his face glinted off of one congregated, hideous set of burn scars across the left hand side of his head when he turned back to continue working at the computer, his narrow, precise grey eyes scrutinizing everything that appeared on that one screen.