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

Science Oddity: The USDA doesn’t regulate sand from ocean beaches

IMG_7245
A sandy beach in New Zealand

Moving soil between countries is hard. Back when I worked in a soil microbe lab, my colleagues lamented the effort and paperwork required to import soil samples. If they wanted just the soil, they had to ask the sender to sterilize it using USDA-approved methods to kill any potential nasties that might invade the US and cause trouble. And if they wanted unsterilized soil to study the live soil microbes, they needed to apply for two different USDA permits. That meant taking precious time to submit paperwork justifying why you want the soil, how you’ll use it, and how you’ll keep any microbes in the soil from escaping.

This might sound like an unnecessary burden, but these regulatory hurdles are a vital part of keeping the US safe. Soil harbors microbes, insects, and plant seeds, including those of pests that if introduced could do serious economic and environmental damage. One study found that introduced pests and invasive species cost us nearly $120 billion annually. These include the citrus greening disease, responsible for stunting and killing citrus fruit trees in Florida and costing the state’s iconic industry $4.5 billion between 2007 and 2011. They also include pests like the soybean cyst nematode, which cost soybean growers $500 million a year and originally arrived in the U.S. via imported soil. Then there are the Zika and West Nile viruses, recently introduced diseases transmitted by people and now established on the US mainland. With any pest, it can take as little as one accidental release to unleash destruction. The stakes are high.

So it floored me when during a marine biology project, I learned that mailing ocean beach sand was essentially unregulated by the USDA. At the time, I was researching the effect of agricultural waste on reef health on the Society Islands and spent hours a day snorkeling in a fetid part of Cook’s Bay just below a goat farm. Near the project’s end, I asked our graduate student advisor how to prepare samples to ship back to the U.S. She told me to just seal them in an airtight container and they were good to go. “Do I need to sterilize it?” I asked. “Nope,” she replied, “the USDA doesn’t require it.” I ended up not shipping sand back to the U.S. for analysis, but if I had it would have carried the microbes from the goat farm runoff, potential pests and biohazards and all. Then again, I had just spent six weeks swimming around in diluted goat feces—I was probably a biohazard.

IMG_7434
Rocks on a beach in Japan; according to USDA regulations, you can bring these back to the U.S. as long as they’re free of organic matter, though they may still harbor microbes.

To this day, that USDA still technically does not regulate the import of ocean beach sand, so under this loophole you can ship the uncleaned “sediment of saltwater oceans” (i.e. sand) without any permit. Note that this doesn’t apply to the sand/sediment of inland saltwater seas or freshwater lakes. But how could the customs procedures be so different for soil versus ocean beach sand, or beach sand from the Mediterranean Sea vs the Black Sea, separated only by the thin Bosphorous Strait? Ostensibly, the reason is because all of the saltwater oceans in the world are connected, so they already share the same pests and importing beach sand won’t introduce new ones. But this logic ignores the possibility that beaches might harbor different microbes (and potential pests) due to influence from microbes in nearby land soil or human activity (like a goat farm). And while the Customs and Border Patrol (CBP) have tried to discourage people from bringing potentially contaminated sand back to the US, they also acknowledge that due to the USDA’s loophole, you’re free to bring uncleaned ocean sand back with you as long as it doesn’t have visible chunks of organic matter (like twigs or dirt).

But should you? I’m not so sure.

IMG_9543
Customs and the USDA won’t allow you to import organic matter, like this dried piece of algae. But they don’t have rules against importing the sand around it.