Biology x Classification: An instructional on species

It’s been a while since I updated, thanks to the hectic nature of moving to a new state, driving across the U.S. for a third time, and getting settled before I start work. Here’s a cross-post from a project inspired by my friend Cindy Nguyen. She runs Haptic Press, a creative arts labspace for anyone to looking to experiment with creativity. Especially those people who haven’t done something ‘creative’ in ages like *cough* me. Graduate school was an eternal summer for my mind, but it was a long, dark winter for the creative self.

This piece is in response to Cindy’s most recent theme, “Classification”, merged with what I know to become “Biology x Classification”. This is a tribute to how messy life is, despite our best attempts as scientists to classify. Hope you like it.

An instructional on species

step one: definition

Fig01-01
Figure 1: An individual

what is a species?
do you know?
Can you look up the definition?
Go ahead. Do it now.
i’ll wait here.

Fig02-01
Figure 2: A lineage




have it? Read it out loud
And clear,
for both of us to hear.
Awesome.

Fig03-01
Figure 3: Two descendants, one ancestor

now, things get fun.
imagine the definition in your mind,
like on a piece of paper.
Take it, tear it up,
And toss it into the wind.
make a mess.

Fig04-01
Figure 4: A mess

step Two: mess

The truth is, a species is messy.
it’s messy just like the scattered paper
That now makes up our definition.
you may have looked at animals and thought,
“This duck is different than a cat,
which is different than a deer or a bat.
All different species.”

Fig05-01
Figure 5: Shared ancestry

And you’re right.
we can tell very different things apart.
but what about this bat and that?
This lizard and that?

The closer the two animals get together,
The harder to say they’re a different species.

Fig06-01
Figure 6: Species complex, wherein ring species interbreed

we biologists like to say if animals don’t breed,
meaning they can’t make offspring together,
They’re different species. Separate.
but there are species of lizards that blend,
from one place to another.
Able to breed with neighbors,
And neighbors-neighbors,
but not neighbors-neighbors-neighbors,
And more distant.
so where does one species start,
And another end?

hard to say.

Fig07-01
Figure 7: Interbreeding fails at ring edges

step Three: mix

or look at bacteria,
That make offspring only by dividing.
how do you decide a species
in a thing that does not mate for offspring?
who is to say bacteria A is a species itself,
isolated and separate from bacteria B?

Fig08-01
Figure 8: Asexual reproduction

well, we tell ourselves that it’s in the DNA,
The genetic information that makes all life.
we look at two bacteria,
And if the DNA is different enough,
(we say 1%, but where does that come from?)
we say Bacteria A and B are different species.

but it gets even messier in the bacterial world,
like the pieces of our definition swirling in the wind.
because bacteria can mate,
They just don’t make offspring.
They mate across species,
Across close relatives and distant friends
not to make more of themselves,
but to swap DNA,
The very basis of our definition!

Fig09-01
Figure 9: Horizontal gene transfer

They share DNA in mating,
Copying and swapping like teenage pirates,
a gene here, sequence there.
Copy, cut, share, paste, repeat.
each action blurring lines:
is the new cell, now carrying a bit of species A
still species B, or something new?
who’s to say.

Fig10-01
Figure 10: Which species, none, or both?

step four: matrimony

And then there’s you.
The collection of cells you think you know
All descended from a first.
but beside your human cells are the others,
A collection of millions by millions of bacteria,
on your skin, in your gut,
on every open inch of body.
The unseen multitudes of multitudes,
different between each person.
They make you, become you,
Are you.
so you are what?

Fig11-01
Figure 11: Human and microbiome

And where do you come from?
who are your ancestors,
your mother’s mother’s mothers
stretching back into unconscious unmemory.
A secret, hidden in you
Thousands by millions of years ago.

Chance cast her lot,
As one cell engulfed another.
A normal act of eat to live,
but this time the infinitely unlikely,
Completely unguessable happened.

The devourer did not kill to sate its hunger
And embraced instead the cell within it
As a host would a guest in their home.
The guest, sealed and safe from the surrounding world,
gave energy for life in return.

if you seek within your cells,
you find these once-guests still today.
making, providing, trading
Their energy for a home.
The two working together,
Creating life from mice to men.
That is the strangest thing about you,
descendent of that accidental chance.
you are a marriage of not one form of life,
but two.

Fig12-01
Figure 12: Endosymbiotic theory

step five: reality

As you can see, the definition of a species
diverges between flat paper and life.
our paperbound sentence is just convenient shorthand
hiding a stout, immovable truth.
for it’s impossible to encompass the chaos of life
of even for an individual in a word.
A name, a handle, a term,
falls short.

And life’s lineage stretches long.

Fig13-01
Figure 13: The lineage of life

What I learned by starting this blog

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The endless sea of ideas beyond the bramble of writers’ block

Hey reader!

It’s been a while since a post, hasn’t it? I’ve learned a few things in starting this blog that I want to share with you below because I’d wager a lot of people face similar problems. If you’ve been stalled on your blogging/writing, I give you 100% permission to borrow this post, blame it on one the problems below, and start anew:

  1. Writing what you know well isn’t always the easiest. You get bogged down in the details and you want it to be perfect. This is compounded in academia because you worry about the balance between reaching people outside of academia and those who might read it in the academic circle. To make blogging easier, begin with subjects you know some about and you won’t be dragged down into the deep details. Yes, sometimes you’ll write things that won’t make sense later or might be wrong, but that’s FINE. We learn nothing by venturing nothing.
  2. Don’t feel beholden to a post you said you’d do, and you can always postpone a post to later. This is a hard one for me because I feel strongly about commitments and following through. It’s the same feeling that gives us anxiety when we leave an email unanswered for what we think is ‘too long’ or haven’t posted on a blog in a while. You feel like you’re letting your audience down, whether it’s one person or a million people. But you don’t owe the internet anything—you’re a free person.
  3. This is an extension of 3, but it’s important to say on its own: write what you want. The easiest way to kill a blog is by having writing ideas but putting them aside because you “said you’d do” a specific post next. Likewise if you’re writing just for likes/favorites/exposure. It’s going to feel like an awful chore if you don’t write about what you want, so write about what you’re interested in, what you want to learn about, what won’t leave your mind. Get your thoughts out into the world.

So I’m holding off on writing in-depth about my PhD work for now. But I also didn’t want to be beholden to #1, so I wrote you a six-sentence summary of what I did in my PhD. Is it perfect? No. But it is:

As I described in the previous post, if we want to use living systems (organisms, cells) as technology, we want them to work as expected because we can’t rely on them if they don’t. One of the biggest problems is that most of life uses the same genetic code, so engineered cells can pick up genetic information from the environment that messes with their intended function. It’s as if we were all running the same version of Windows; you could install a program on any of our systems and it would run–including viruses and malicious code. To solve this problem, my PhD showed that changing the genetic code of an engineered cell makes it harder for genetic information in the environment to mess with the cell’s function, making it more stable. It was like we modified the “operating system” in our engineered cells, making it harder for malicious pieces of genetic information such as viruses to infect. In the future, we can change the genetic code in living systems to ensure they work as expected, bringing applications of biotechnology and synthetic biology closer to realization.

What will I write about next? We’ll see what I feel like, although posts will probably remain infrequent while we travel around the world (more on that here). One of the big projects I want to do over the next year is learn the physics of aerodynamics and orbital mechanics, partly because both of these are really important for space travel and partly to dispel the persistent myth that you can’t transition from “softer sciences” to “harder sciences” later in life. Anyone should be able to learn anything regardless of their background.