Category: Science

Color theory and scientific data

~ ajlucy ~ Leave a comment

Reading scientific papers is, too often, the visual equivalent of nails on a chalkboard.  One problem I see over and over again is poor color use, because scientists don’t seem to know anything about color theory.  The example figure below is particularly bad.  Here are the principles I used to revise it:

revised figure 1.jpg

First, colors have meaning.  Blue means cold and red means hot, but I often see figures like the above that use blue to mean a high value and red to mean a low value.  This makes your figure harder to understand because it works against the natural assumptions a person is trying to apply.

Second, things with high contrast stand out.  In the example figure, most of the squares are dark, saturated red or dark, saturated blue.  A few contrasting spots stand out: the white “ND” squares and the very light blue ones.  Are these the most important things in the figure?  Probably not – ND stand for not detected, a void in the data, and the pale blue is for middle values, not the highest or lowest.  This misused contrast distracts the viewer from the main point of the figure and draws their eye to unimportant information.

Third, I often notice that scientists almost always use uniform saturation for their colors.  Adding grey and reserving really bright colors for important elements of a figure can both make the meaning of the figure more clear and make the figure easier to look at.  A ton of screaming bright colors can be a real headache.

Finally, it is important to make sure that your figure is legible without color.  One, this is an accessibility issue: some scientists are color blind.  Two, your paper may be printed in black and white.  The bad example above is almost completely impossible to read when the color is removed because the red and the blue are such similar shades of grey.

revised figure 2

In my revision, I switched the colors so that a hot red meant high values, and then used a cool grey for low values.  I used a bright, saturated red so the highest values stand out the most, and made the lower values paler and grayer so they wouldn’t compete.  In black and white, the high values are the darkest and the low values are the lightest so the patterns in the data are still easy to see.

I think my revised figure is much nicer to look at, and all I did was change the color key.  Color theory: you need it, fuckers!

What happened in Florida

~ ajlucy ~ Leave a comment

There are many reasons for the 2016 election result.  Ta-nehisi Coates’s essay, “America’s First White President,” is essential reading to understand how 2016 was possible.  FiveThirtyEight, as usual, has a big list of stuff.  America’s baked-in sexism and dedication to white supremacy, GOP redistricting, Russian kleptocrats, the prosperity gospel, Clinton’s team underestimating a group of 4chan trolls who’d sharpened their teeth on GamerGate — you can find almost anything with an large enough effect to swing a few hundred thousand votes and tip the election.

One common aspect among all the hot takes: most of these reasons are difficult to quantify.  Sexism definitely had a negative impact on Hillary Clinton’s campaign, but translating that impact into a number of votes is pretty much impossible.  For every extra thirty minutes waiting in line because half the polling places in your county were closed, how many people turn away and go home?

There is, however, one place in America where a single, quantifiable phenomena can turn the state from red to blue.  Florida has a problem with voter disenfranchisement.

In Florida, 10% of adults cannot vote because of a prior felony conviction.  Florida is one of three states in the US that strips the voting rights of anyone convicted of a felony permanently.  Because our criminal justice system has a profound racial bias, this has an outsized impact on black and latino Floridians.  One in four black men in Florida has lost his voting rights.

Donald Trump won white America, but lost spectacularly with black and latino voters.  If Florida’s 1.5 million former felons, who are significantly more likely to be black or latino, were allowed to vote, would that change the outcome?

Using exit polls from CNN and prison statistics from The Sentencing Project, I crunched the numbers.

Florida projection

If these theoretical enfranchised voters showed up in numbers even vaguely similar to the turnout among the rest of Florida’s population, Clinton could have won Florida instead of losing it by more than a hundred thousand votes.  I’m not a sociologist, and I only used data that was accessible via the internet; this projection is far from perfect.  However, it’s an obvious, dramatic change caused by a single bad policy (tirelessly protected, of course, by Republicans).

In the 2016 election, Florida’s electoral college votes wouldn’t have been enough to change the overall result.  But in 2000, when Al Gore was defeated by George W. Bush, Florida was the deciding factor.  In 2000, the margin wasn’t a hundred thousand votes, it was five hundred.

There are a lot of reasons why we’re stuck in the flaming municipal waste disposal plant of 2017, but this is, undeniably, one of them.

What’s on the biologist’s bench?

~ ajlucy ~ Leave a comment

mess

It’s a mess.

Itemized list below:

messlabeled

1 – My one milliliter pipettor.  Very useful for moving small volumes of liquid around.  You can tell it’s mine because it has orange tape on it.  Orange tape means “do not steal, fellow lab assholes, property of AJ.”  Everyone has their own tape color that means the same thing.

2 – Razor blade.  Environmental Health and Radiation Safety doesn’t think we should have loose razor blades everywhere, but EHRS doesn’t know how incredibly handy it is to have a razor within arm’s reach at all times!  Cutting up some sample tissue?  Razor.  Opening a box?  Razor.  Hacking up a plastic test tube to make an impromptu strainer out of it?  Razor.

3 – Forceps.  You could call them tweezers, but then how would people know they cost fifty bucks a pop?  These used to be extremely sharp precision instruments, but I’ve been using them for five years and if you drop them even one time on the tips they bend into sad squiggles and have to be filed blunt.

4 – A precious opaque box.  This box used to hold sample mounting medium spiked with a fluorescent dye, but now it holds all of my light-sensitive samples while I process them.  Note fuck-off tape.

5 – The lid that goes to the test tube in the green rack labeled #13.

6 – Ubiquitous tube holder.  There are many sizes of tubes and tube holders in the lab, but the most common is one and a half milliliters, or about the size of half a pinkie finger.  You can shove the tips of your fingers into 1.5mL tubes and wiggle them around like you’re a witch, but that is not an efficient way of holding tubes, and afterwards you should probably throw the contaminated tubes away.

7 – My ten microliter pipettor.  Same as #1 except for smaller volumes; the most it can move at a time is a little droplet the size of, like, one quinoa (cooked).

8 – Empty beaker.  My bench collects empty glassware the way a nightstand collects coffee mugs, except instead of coffee this beaker used to hold formaldehyde fixed tissue samples floating in saline solution.

9 – A big tube of block solution.  Block solution is salty water with soap and fetal bovine serum in it.  Fetal bovine serum is baby cow blood that’s been spun down to remove the cells and boiled.  It’s not — look — it’s useful, okay?

10 – Beaker full of tiny, sticky glass spheres.  There used to be ethanol in the beaker covering the spheres, and I put  the foil over top of it to keep the ethanol from drying up but it evaporated anyway.  The glass beads are used to spread bacteria around on plates so they get a little bit of bacteria and bacteria food on them (sticky).  I should replace the alcohol so I don’t get an exciting microbe garden.

11 – Improvised cooler (small).  Made out of electrical tape, a piece of headphone cord, packing peanuts, a plastic cup, and some other lab stuff.  Very helpful for when you have to keep just one tube cold and you have to go five buildings down the street and you’re not carrying a gallon bucket of ice over there for one tube, that’s stupid.

12 – Disposable pipettor tips.  Biology means being super militant about not ever mixing your solutions, so pipers are fitted with little plastic tips that get switched out for every sample.  We buy them by the thousand.

13 – Test tubes.  For growing bacteria!  Despite studying fish, I rely on E. coli to do all my bulk DNA replication, and I still have to smell them.  E. coli cultures smell like feet marinated in the essence of a thousand gym bags.

14 – More fetal bovine serum.

15 – Loose tips.  I may have, in the throes of science, upended a hundred-count box of tips because I was trying to balance those tips on an unstable stack of lab shit.  I have cleaned up: none.

16 – Parafilm.  Have you ever wondered what it would be like if cling wrap wasn’t garbage?  That’s parafilm.  It’s stretchy.  It doesn’t stick to itself while you’re cutting a piece of it.  It does stick to itself when you’re wrapping it around the top of a tube.  It makes a genuinely watertight seal.  It stays watertight even when you freeze it.  It does start to turn to goo at around 100˚C, but like, come on.  It’s good shit, just don’t boil it.

17 – Tiny glass bar with shallow round holes molded into it.  Sometimes I work with material that can’t touch plastic and needs to be continuously submerged and is also very very tiny.  It’s fine.  I’ve learned to make adaptations.

18 – This is garbage.  Literal trash.

19 – Sharpies.  Methanol, water, a solution full of DNA-destroying enzyme and the vial of DNA that I worked for three months to synthesize are all clear liquids.  Labels.  Gotta have ‘em.

20 – Thaw box with lid.  Most of our reagents live in the freezer, and I hate waiting for ice to melt.  Chucking a frozen tube into room temperature water makes it melt faster.  I could grab a cup of water from the sink and just toss my samples into it every time I was feeling impatient, except for two things: first, as I have mentioned, unintentional liquid mixing is anathema to biologists, and second I hate having wet gloves.  Some clever application of a razor blade turned an empty tips box into a rack that will hold just the bottom of a test tube in a reservoir of lukewarm water, because I am a problem solver at heart.

21 – Phosphate buffered saline.  All kinds of biological things love a nice bath in 0.9% salt solution at a stable pH!

22 – Lab notebook.  It’s hard to make a lab-notebook-sized space in my meticulous bench mies-en-place, so I throw it on top of whatever.

23 – Fat sharpie.  For when a label needs oomph.

24 – More disposable pipettor tips.  The boxes have a hundred each and I still go through so many.  We fill a full-size trash can with just tips every week.  (Tips go in special bins because EHRS thinks that little plastic tips are too dangerous for regular trash.)

25 – Graduate cylinder.  I used it to measure water, and then I didn’t want to put it back with the clean dishes because I’d used it, but didn’t want to put it with the dirty dishes because fuck, it’s only touched distilled deionized filtered water, calling that dirty seems absurd, and now it lives on my bench.

26 – Jar of distilled deionized filtered water that has also been sterilized by going through the autoclave.  The autoclave is an angry cabinet that pressurizes and heats things inside up to 121˚C.  Do not put styrofoam into an autoclave.

27 – Non-hazardous liquid waste.  Mostly salty water and old bacteria.  I put bleach in periodically to keep it  an acceptable odor.

28 – You can never have too many plastic bags.

29 – Tips/garbage bucket.  The trash can is only three steps away, true, but at full pipetting speed I make a hundred pieces of tiny garbage, one at a time, in five minutes.  If you’d like to know why there’s still a fine coating of garbage on my bench despite having a designated garbage spot two feet away, you can shut up.

30 – Small tube holder.  If it looks a lot like a tips box, that’s because it’s upcycled.

31 – Slide mounting stage.  I made this from parafilm, tape, a piece of a box, and a foil cover for a 96-well plate.  Works great for making little coverslip and vaseline sandwiches without breaking or losing any paper-thin squares of glass.  Actual microscope slides are easier to work with, but then you can’t take pictures from both sides, so: sandwiches.

32 – Glass-bottomed dish.  For when your sample is alive and needs to be in a warm bath of buffer and nutrients instead of smashed between two thin sheets of glass and sealed up with nail polish.

33 – My solutions library.  You want some water with salt in it?  I got it, in a hundred varieties.  I also have water without salt in it, in several grades of purity, a bunch of different alcohols, several concentrated dyes, and duplicates of everything because this library is not very organized and I keep thinking I’ve run out of one molar potassium chloride despite having some in the back.

34 – Jumbo bag of 1.5mL snap-cap tubes.  I was told that these had to be sterilized before use and I did it for years before someone finally told me that was bullshit.  They’re good right out of the bag!  Amazing!  Who knew!

Why Sewing Machines Have So Many Parts

~ ajlucy ~ Leave a comment

sewingmachine

A sewing machine uses one spinning motor (or foot pedal if you’re old school) for everything.  That means there’s a lot of gears in there!  I was going to draw how a sewing machine works today, but instead I found incomprehensible technical drawings of cranks and levers and parts labeled things like “45864” and “supplied only when repairs are made at the factory.”

The lights in the sky are coming down

~ ajlucy ~ Leave a comment

Perpetually falling around the Earth is a constellation of 72 Iridium communications satellites.  There are thousands of objects orbiting our planet, but the Iridium satellites are special.  Because of a quirk in their design, every so often the Iridium satellite’s meter-wide antennae flash in the sunlight.

From the ground, a light brighter than a thousand stars appears, flares, and fades.

People’s reaction to this phenomenon gives me a special joy.  That people track these winking satellites, that small groups of friends travel to where a washing-machine sized piece of space technology will fly over head, that they point their cameras and their gaze skyward to catch a few seconds of brilliance, four hundred miles away — it fills me with inarticulate fondness for humanity.

This year, Iridium launched the first batch of next generation satellites to replace their old fleet.  The new satellites are re-designed and are not so reflective; in a few years there will be no more Iridium flashes.

The old satellites will fall out of orbit and burn up in our atmosphere, and species of strange lights in the sky will go quietly  extinct.

I am not an amateur astronomer; even given an entire lifetime I doubt I would have ventured out to see an Iridium flare with my own eyes.  And yet, I’m glad I discovered this obscure, temporary marvel before it was gone.