Author: ajlucy

Review: How eggs and sperm get started

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germ plasm figure

Above: my hand-drawn illustration of mouse, frog and fish embryos growing.  Green: starting materials for eggs and sperm.

Earlier this year I spent a few months writing up the background of my thesis work for a chapter in The Immortal Germline.  While it’s directed toward is mainly scientists who are already in my field (or are graduate students interested in entering it), I want to share the final product!  It’s available online here, free for the rest of this month: Chapter One – The vertebrate Balbiani body, germ plasm, and oocyte polarity.

(Thanks to Ruth Lehmann for editing this volume and giving me the chance to write for it!)

I’ve spent uncountable hours, now, fascinated by eggs (oocytes, in scientific parlance).  They’re life’s beginning.  Sperm swims up and says, “hey, here’s some genetic variation for the good of the species” and doesn’t contribute much else.

The egg has all the good life-goop.  It splits in half, then half again, and it doesn’t grow until that’s gone on for many doublings.  The egg made all of that; all it’s doing is getting divvied up.

Image result for human embryo development 5 days

Above: First five days of human embryonic development.  (Embryos destined for in vitro fertilization.)

Not only that, but the life-goop is organized.  It’s not like chopping up a potato where you get eight largely identical beige chunks.  More like red cabbage: Some parts have more stem, some parts more purple leaves.  The growing critter takes that initial distinction between cabbage-wedge 1 and cabbage-wedge 2 and spins it out, fractal-like, into the information needed to make a whole animal.

My thesis is about the way that organization gets going.  I want to know how eggs go from a ziplock bag full of nutritious life-soup to a ziplock bag full of life-soup with all the carrots on the left side and all the dumplings on the top right.  It’s a tricky problem, but life is incredibly good at solving it.  Someday, we’ll know how.

New Fiction: Sequestration; Vitrification

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sequestration

Sequestration; Vitrification

I have new fiction up at Strange Horizons as of Dec. 17, 2018!  A genetic engineer struggles to modify diatoms to entrap radioactive waste, under the shadow of nuclear proliferation.  It’s about burnout, queer activist community, modern art, and glass.

It’s been long-listed for a BSFA award, and I’m grateful to be listed along many authors I admire.  I also appreciate the lovely, thoughtful reviews I’ve received here, here and here.

how DNA is like a music box

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DNA is not like blueprints.  Blueprints need an architect to draw them up, and a construction crew to turn the plans into buildings.  Biology is too self-contained for contractors.

A painting isn’t of a saint until a mind looks at it and sees a halo.  Before that it’s paint spread on cloth.

In the 1950s, abstract expressionist painters were consumed by the fact that a painting is an object and an action. Frank Stella puts a black stripe on a canvas, and it’s not a picture of a lamppost, or a snake, or a shadow; it’s a picture of radiator paint on cloth, because it is radiator paint on cloth.  Richard Serra throws molten lead against the baseboards: a sculpture of throwing.

The art is the object, rather than the representation.

DNA is like abstract expressionism.  The object is the data.  A molecular machine slides down DNA, like fingers sliding across a knotted rope, and bumps the chain push and pull on microscopic levers to make living things.  Physical.  Mindless.  Analog.

DNA is stupid the way a music box is stupid.  A music box doesn’t know the song it plays, it’s just made that way.

Screen Shot 2018-05-18 at 1.15.12 PM copy

When the crank turns (1) the pegs hit the key (2), and that’s one note.  Then, as the crank turns again, the next peg (3) hits another key, and that’s another note.  Enough turns make a song.  That’s what the song is, to the music box — an object and an action — the drum and the crank.

The same way, DNA’s physical shape creates life.  Each peg of the DNA places a molecule in a thread, (instead of notes, amino acids), and the molecular chain lengthens into a chemical song that doesn’t need a musician, a composers, or an architect.

 

DIY organic, biodegradable lip treatment: agilo et olio

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Infused with sweet steamed garlic and cracked red pepper, try this home recipe for lush, smooth lips.

First, take 5-7 cloves of garlic and crush them with the flat of a knife.  Remove the peel and stem end.  Combine with a quarter cup of olive oil and heat until the garlic is just browning, releasing its essential oils into the mixture.

Put the garlic aside with a lid over it, to sweat out sulfur-containing compounds that can cause irritation.

Now you will need to boil some water and put a generous amount of sea salt into it.  Place half a pound of spaghetti pasta into the water and cook to release the starch.  You will need the starch to hold the balm together.

Once the garlic is soft, put the garlic back on the heat and add oil cracked pepper, red chili flakes, and two thirds of a cup of pasta water.  A few tablespoons of butter will make your lip treatment more creamy and luscious.  Stir mixture until the oil and water emulsify.

Since you have the cooked spaghetti already, and since this is not actually a lip treatment, it’s an Italian pasta classic, why not put that pasta into your garlic and olive oil and butter and stir until all the pasta is coated with sauce.

Add some grated parmesan, which will pull the sauce together and everything melts together into a wonderful dish.

Put it in a bowl, add a little more cracked pepper and cheese to the top, and enjoy this simple and elegant meal.

As an added benefit, the rich sauce will glide over your lips and make them super soft.  Plus, having your lips lightly coated with fat will make you feel like a fifteenth century noble who has just feasted on duck and goose and is resplendent with decadence and wealth.

Award eligibility post

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The crap in the news has spent 2017 trying, tirelessly, to steal my joy.  I have dug in my heels and done my best to not let it.  This year I got married and finished the first draft of a book and went to a lot of protests.

I have two award-eligible stories this year:

  • Watershed, Strange Horizons, September 11, 2017
    • A story about estuaries, loneliness, and deciding to care.  Also, an eight-foot-long pet eel.
  • Two Bodies in Basting Stitch, Beneath Ceaseless Skies #227, June 8, 2017
    • From officer to revolutionary to prisoner, every time Sere risks her own life she risks her wife.  She left without saying goodbye.

I am also eligible for the Campbell Award!  (My 2011 publication in Daily Science Fiction was before the market was SFWA qualifying.)

If you think of me when nominating and putting together 2017 lists, I would appreciate it!

 

 

On not being alone

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The Asch experiment is a classic, well-replicated psychological test.  A group of participants are asked to examine a series of lines and determine which two lines are the same length.

asch_conformity

The trick is that only one person is being tested — the rest of the people in the room are in on the experiment.  After a few rounds where everyone answers correctly, the plants in the room start giving wrong answers.  With the group consensus stacked against the experimental subject, often they’ll start to bow to the will of the group.  About a third of the time, the subject will give an answer that conforms with the group instead of believing the evidence in front of their eyes.

This result is disheartening in the face of our current news environment.  However, I think there’s another important takeaway from this experiment.  In videos, it’s obvious that the subjects feel super uncomfortable.  Their voices shrink, they look around, they wince.  But give them one friend, one ally, and it changes.  When one of the plants gives the right answer while the rest continue giving the wrong one, the subjects of the experiment perk up and, overwhelmingly, give the right answers again.

It is difficult to be the one that stands up against group agreement.  But it’s easy to be one of two.

This is why it’s so harmful to have only one woman in a room, only one LGBT person in a room, only one black person in a room.  The pressure of a group can make a person deny something they can look up and see is obviously true.  If it has that power, surely it’s trivial to make us deny our own invisible discomfort.  How long until it convinces us that discomfort is not there?  That complaints of harassment or discrimination are unimportant?

Facing down a hostile group consensus alone is destabilizing — is damaging — and any space that cannot guarantee safety against this dynamic cannot be a safe one.

 

 

 

Color theory and scientific data

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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!

Small, essential joys

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Some things are wonderful — harassing bugs I find on the sidewalk, taking photographs of weeds by the road, making glossy bread and all-from-scratch dinners, brightly colored vegetables.

I love watching this texan woman catching catfish:

(Angry catfish grunt like little pigs and it makes me happy.)

I patched all the holes the cats made in our wingback chair with luxury upholstery fabric we got on the cheap from a woman on etsy who sells books of discarded fabric samples.  Our floor is glittery from extra bits of imitation gold leaf that got everywhere during my last minute wedding DIY projects.  I cleaned under the couch and fished out all the cat toys that had vanished in the past month, so the foster kitten is overjoyed with new catnip smells.

On the end table beside me is a stack of books and magazines: Vogue beneath Anne Boyer beneath Ursula Le Guin.

These are all small things, but they are good, and I am grateful for them.

What happened in Florida

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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.